2024 |
Hartle-Mougiou, Katherine; Gubili, Chrysoula; Xanthopoulou, Panagiota; Kasapidis, Panagiotis; Valiadi, Martha; Gizeli, Electra Frontiers in Marine Science, 11 , pp. 1358793, 2024, ISSN: 2296-7745. @article{hartle-mougiou_development_2024, title = {Development of a quantitative colorimetric LAMP assay for fast and targeted molecular detection of the invasive lionfish Pterois miles from environmental DNA}, author = {Katherine Hartle-Mougiou and Chrysoula Gubili and Panagiota Xanthopoulou and Panagiotis Kasapidis and Martha Valiadi and Electra Gizeli}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/07/2024-Hartle-Mougiou-fmars-32.pdf https://www.frontiersin.org/articles/10.3389/fmars.2024.1358793/full}, doi = {10.3389/fmars.2024.1358793}, issn = {2296-7745}, year = {2024}, date = {2024-07-08}, urldate = {2024-07-08}, journal = {Frontiers in Marine Science}, volume = {11}, pages = {1358793}, abstract = {The Mediterranean basin has faced an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species, Pterois miles , has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantify P. miles environmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete where P. miles had been sighted. P. miles was indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggests that populations are still at a low density. We also demonstrate the feasibility of P. miles eDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together, with the quantitative real-time colorimetric detection approach, open new possibilities for monitoring invasive P. miles in the field.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Mediterranean basin has faced an increased influx of invasive species since the Suez Canal expansion in 2015. The invasive lionfish species, Pterois miles , has rapidly established new populations in the Eastern Mediterranean Sea, impacting local fish biodiversity. Here, we have developed a new, fast (< 35 min) molecular approach to detect and quantify P. miles environmental DNA (eDNA) in combination with a portable device for field-based analysis. Using a species-specific real-time colorimetric loop-mediated isothermal amplification (qcLAMP) for the cytochrome oxidase subunit 1 (COI) gene, we demonstrate a high sensitivity with a limit of detection of 0.002 ng DNA per reaction, equivalent to only 50 copies of the COI gene. The assay is specific to the target in the presence of closely related and co-occurring species, and it is quantitative over five orders of magnitude. We validated the assay using aquarium water samples and further demonstrated its utility on natural eDNA samples collected from locations around the island of Crete where P. miles had been sighted. P. miles was indeed detected in three out of nine locations, two nature reserves and a closed bay. Lack of detection in the remaining locations suggests that populations are still at a low density. We also demonstrate the feasibility of P. miles eDNA qualitative detection directly from the filter used to collect eDNA-containing particles, completely omitting DNA extraction. Overall, we present a new approach for fast and targeted eDNA quantification. The developed LAMP assay together, with the quantitative real-time colorimetric detection approach, open new possibilities for monitoring invasive P. miles in the field. |
2023 |
Teixeira, Marcos A L; Langeneck, Joachim; Vieira, Pedro E; Hernández, José Carlos; Sampieri, Bruno R; Kasapidis, Panagiotis; Mucciolo, Serena; Bakken, Torkild; Ravara, Ascensão; Nygren, Arne; Costa, Filipe O Reappraisal of the hyperdiverse Journal Article Invertebrate Systematics, 36 (11), pp. 1017–1061, 2023, ISSN: 1445-5226, 1447-2600. @article{teixeira_reappraisal_2022b, title = {Reappraisal of the hyperdiverse}, author = {Marcos A L Teixeira and Joachim Langeneck and Pedro E Vieira and José Carlos Hernández and Bruno R Sampieri and Panagiotis Kasapidis and Serena Mucciolo and Torkild Bakken and Ascensão Ravara and Arne Nygren and Filipe O Costa}, editor = {Greg Rouse}, url = {https://www.publish.csiro.au/IS/IS21084}, doi = {10.1071/IS21084}, issn = {1445-5226, 1447-2600}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-25}, journal = {Invertebrate Systematics}, volume = {36}, number = {11}, pages = {1017--1061}, abstract = {Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D}, keywords = {}, pubstate = {published}, tppubtype = {article} } Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D |
Teixeira, Marcos A L; Bakken, Torkild; Vieira, Pedro E; Langeneck, Joachim; Sampieri, Bruno R; Kasapidis, Panagiotis; Ravara, AscensÃO; Nygren, Arne; Costa, Filipe O Systematics and Biodiversity, 20 (1), pp. 1–39, 2023, ISSN: 1477-2000, 1478-0933. @article{teixeira_curious_2022, title = {The curious and intricate case of the European textitHediste diversicolor (Annelida, Nereididae) species complex, with description of two new species}, author = {Marcos A L Teixeira and Torkild Bakken and Pedro E Vieira and Joachim Langeneck and Bruno R Sampieri and Panagiotis Kasapidis and AscensÃO Ravara and Arne Nygren and Filipe O Costa}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2022-Teixeira-Syst-Biodiv-85.pdf https://www.tandfonline.com/doi/full/10.1080/14772000.2022.2116124}, doi = {10.1080/14772000.2022.2116124}, issn = {1477-2000, 1478-0933}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-30}, journal = {Systematics and Biodiversity}, volume = {20}, number = {1}, pages = {1--39}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kondylatos, Gerasimos; Mavrouleas, Dimitrios; Gratsia, Eirini; Kasapidis, Panagiotis; Corsini-Foka, Maria; Klaoudatos, Dimitris BioInvasions Records, 12 (1), pp. 234–244, 2023, ISSN: 22421300. @article{kondylatos_first_2023, title = {First record of Arcania brevifrons Chen, 1989 (Decapoda; Leucosiidae) and further record of Macrophthalmus (Macrophthalmus) indicus Davie, 2012 (Decapoda; Macrophthalmidae) in Hellenic waters}, author = {Gerasimos Kondylatos and Dimitrios Mavrouleas and Eirini Gratsia and Panagiotis Kasapidis and Maria Corsini-Foka and Dimitris Klaoudatos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/06/2023-Kondylatos-Bioinvasions-21.pdf https://www.reabic.net/journals/bir/2023/1/BIR_2023_Kondylatos_etal.pdf}, doi = {10.3391/bir.2023.12.1.19}, issn = {22421300}, year = {2023}, date = {2023-05-23}, urldate = {2023-06-01}, journal = {BioInvasions Records}, volume = {12}, number = {1}, pages = {234--244}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Antoniou, Aglaia; Manousaki, Tereza; Ramírez, Francisco; Cariani, Alessia; Cannas, Rita; Kasapidis, Panagiotis; Magoulas, Antonios; Albo‐Puigserver, Marta; Lloret‐Lloret, Elena; Bellido, Jose Maria; Pennino, Maria Grazia; Follesa, Maria Cristina; Esteban, Antonio; Saraux, Claire; Sbrana, Mario; Spedicato, Maria Teresa; Coll, Marta; Tsigenopoulos, Costas S Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style= Journal Article Molecular Ecology, pp. mec.16840, 2023, ISSN: 0962-1083, 1365-294X. @article{antoniou_sardines_2023, title = {Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the textlessspan style=}, author = {Aglaia Antoniou and Tereza Manousaki and Francisco Ramírez and Alessia Cariani and Rita Cannas and Panagiotis Kasapidis and Antonios Magoulas and Marta Albo‐Puigserver and Elena Lloret‐Lloret and Jose Maria Bellido and Maria Grazia Pennino and Maria Cristina Follesa and Antonio Esteban and Claire Saraux and Mario Sbrana and Maria Teresa Spedicato and Marta Coll and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/02/2023-Antoniou-Mol-Eco-9-1.pdf https://onlinelibrary.wiley.com/doi/10.1111/mec.16840}, doi = {10.1111/mec.16840}, issn = {0962-1083, 1365-294X}, year = {2023}, date = {2023-02-06}, urldate = {2023-02-06}, journal = {Molecular Ecology}, pages = {mec.16840}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2022 |
Mancinelli, Giorgio; Dailianis, Thanos; Dounas, Costas; Kasapidis, Panagiotis; Koulouri, Panayota; Skouradakis, Grigorios; Bardelli, Roberta; Muri, Cristina Di; Guerra, Maria Teresa; Vizzini, Salvatrice Sustainability, 14 (22), pp. 15202, 2022, ISSN: 2071-1050. @article{mancinelli_isotopic_2022, title = {Isotopic Niche and Trophic Position of the Invasive Portunid Portunus segnis Forskål, (1775) in Elounda Bay (Crete Island, Eastern Mediterranean)}, author = {Giorgio Mancinelli and Thanos Dailianis and Costas Dounas and Panagiotis Kasapidis and Panayota Koulouri and Grigorios Skouradakis and Roberta Bardelli and Cristina Di Muri and Maria Teresa Guerra and Salvatrice Vizzini}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/11/2022-Mancinelli-Sustain-77.pdf https://www.mdpi.com/2071-1050/14/22/15202}, doi = {10.3390/su142215202}, issn = {2071-1050}, year = {2022}, date = {2022-11-21}, urldate = {2022-11-21}, journal = {Sustainability}, volume = {14}, number = {22}, pages = {15202}, abstract = {There is a growing recognition that an advanced understanding of the trophic characteristics of an invasive consumer can provide important information on its ecological impact. In recent years, the blue swimming crab Portunus segnis, one of the earliest Lessepsian invaders, has considerably expanded its distribution range in the Mediterranean Sea, yet, its trophic habits in invaded areas remain scarcely investigated. In this study, we used carbon and nitrogen stable isotopes analysis (SIA) to determine the trophic position and isotopic niche of the crab compared with other representatives of the flora and fauna occurring in Elounda Bay (Crete). P. segnis showed a trophic position of 3.9, higher than the values determined by SIA or conventional gut content analysis in other areas of the Mediterranean Sea or in the native range. Crab specimens showed a high inter-individual variability in both δ13C and δ15N values; further analysis indicated negligible differences in the isotopic niche of adult males and females. Conversely, δ15N values were significantly related to the size of the specimens, ultimately suggesting an ontogenetic dietary shift. This study represents the first attempt to characterize the trophic habits of the blue swimming crab in the context of an invaded food web and may contribute to the implementation of long-term management strategies of control and mitigation of its ecological impact.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There is a growing recognition that an advanced understanding of the trophic characteristics of an invasive consumer can provide important information on its ecological impact. In recent years, the blue swimming crab Portunus segnis, one of the earliest Lessepsian invaders, has considerably expanded its distribution range in the Mediterranean Sea, yet, its trophic habits in invaded areas remain scarcely investigated. In this study, we used carbon and nitrogen stable isotopes analysis (SIA) to determine the trophic position and isotopic niche of the crab compared with other representatives of the flora and fauna occurring in Elounda Bay (Crete). P. segnis showed a trophic position of 3.9, higher than the values determined by SIA or conventional gut content analysis in other areas of the Mediterranean Sea or in the native range. Crab specimens showed a high inter-individual variability in both δ13C and δ15N values; further analysis indicated negligible differences in the isotopic niche of adult males and females. Conversely, δ15N values were significantly related to the size of the specimens, ultimately suggesting an ontogenetic dietary shift. This study represents the first attempt to characterize the trophic habits of the blue swimming crab in the context of an invaded food web and may contribute to the implementation of long-term management strategies of control and mitigation of its ecological impact. |
Teixeira, Marcos A L; Langeneck, Joachim; Vieira, Pedro E; Hernández, José Carlos; Sampieri, Bruno R; Kasapidis, Panagiotis; Mucciolo, Serena; Bakken, Torkild; Ravara, Ascensão; Nygren, Arne; Costa, Filipe O Reappraisal of the hyperdiverse Journal Article Invertebrate Systematics, 36 (11), pp. 1017–1061, 2022, ISSN: 1445-5226, 1447-2600. @article{teixeira_reappraisal_2022, title = {Reappraisal of the hyperdiverse}, author = {Marcos A L Teixeira and Joachim Langeneck and Pedro E Vieira and José Carlos Hernández and Bruno R Sampieri and Panagiotis Kasapidis and Serena Mucciolo and Torkild Bakken and Ascensão Ravara and Arne Nygren and Filipe O Costa}, editor = {Greg Rouse}, url = {https://www.publish.csiro.au/IS/IS21084}, doi = {10.1071/IS21084}, issn = {1445-5226, 1447-2600}, year = {2022}, date = {2022-01-01}, urldate = {2023-05-25}, journal = {Invertebrate Systematics}, volume = {36}, number = {11}, pages = {1017--1061}, abstract = {Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D}, keywords = {}, pubstate = {published}, tppubtype = {article} } Morphologically similar species are often overlooked but molecular techniques have been effective in signalling potential hidden diversity, boosting the documentation of unique evolutionary lineages and ecological diversity. Platynereis dumerilii and Platynereis massiliensis are part of a recognised species complex, where differences in the reproductive biology have mainly been highlighted to date. Analyses of DNA sequence data (COI, 16S rDNA and D2 region of the 28S rDNA) of populations of the apparent morphotype of P. dumerilii obtained from a broader sampling area along European marine waters, including the Azores and Webbnesia islands (Madeira and Canaries), provided compelling evidence for the existence of at least 10 divergent evolutionary lineages. Complementing the genetic data, morphological observations of the better represented lineages revealed two major groups with distinctive paragnath patterns. Two new Platynereis species were erected: P. nunezi sp. nov., widespread in the Azores and Webbnesia islands, and P. jourdei sp. nov., restricted to the western Mediterranean. The new combination P. agilis is also proposed for Nereis agilis, previously unaccepted for one of the lineages present both in the Northeast Atlantic and western Mediterranean. Platynereis dumerilii is redescribed based on topotypic material. However, uncertainty in the identity of P. massiliensis due to the original brief description and the absence of type and topotypic material prevents the unequivocal assignment to the lineage assumed in this and previous studies. The remaining five lineages are represented by only a few small specimens with morphological features poorly preserved and were therefore not described in this study. ZooBank: urn:lsid:zoobank.org:pub:50079615-85E5-447E-BDD7-21E81C2A6F4D |
2021 |
Karamanlidis, Alexandros A; Skrbinšek, Tomaž; Amato, George; Dendrinos, Panagiotis; Gaughran, Stephen; Kasapidis, Panagiotis; Kopatz, Alexander; Stronen, Astrid Vik Sci Rep, 11 (1), pp. 373, 2021, ISSN: 2045-2322. @article{karamanlidis_genetic_2021, title = {Genetic and demographic history define a conservation strategy for earth’s most endangered pinniped, the Mediterranean monk seal Monachus monachus}, author = {Alexandros A Karamanlidis and Tomaž Skrbinšek and George Amato and Panagiotis Dendrinos and Stephen Gaughran and Panagiotis Kasapidis and Alexander Kopatz and Astrid Vik Stronen}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/02/2021-Karamanlidis-SciRep-3.pdf http://www.nature.com/articles/s41598-020-79712-1}, doi = {10.1038/s41598-020-79712-1}, issn = {2045-2322}, year = {2021}, date = {2021-12-01}, urldate = {2021-02-02}, journal = {Sci Rep}, volume = {11}, number = {1}, pages = {373}, abstract = {Abstract The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival. |
Santi, Ioulia; Kasapidis, Panagiotis; Karakassis, Ioannis; Pitta, Paraskevi A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes Journal Article Diversity, 13 (5), pp. 180, 2021. @article{santi_comparison_2021, title = {A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes}, author = {Ioulia Santi and Panagiotis Kasapidis and Ioannis Karakassis and Paraskevi Pitta}, url = {https://www.mdpi.com/1424-2818/13/5/180 https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Santi-DIVERSITY-33.pdf}, doi = {10.3390/d13050180}, year = {2021}, date = {2021-01-01}, urldate = {2021-05-10}, journal = {Diversity}, volume = {13}, number = {5}, pages = {180}, abstract = {The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes. |
Zafeiropoulos, Haris; Gioti, Anastasia; Ninidakis, Stelios; Potirakis, Antonis; Paragkamian, Savvas; Angelova, Nelina; Antoniou, Aglaia; Danis, Theodoros; Kaitetzidou, Eliza; Kasapidis, Panagiotis; Kristoffersen, Jon Bent; Papadogiannis, Vasileios; Pavloudi, Christina; Ha, Quoc Viet; Lagnel, Jacques; Pattakos, Nikos; Perantinos, Giorgos; Sidirokastritis, Dimitris; Vavilis, Panagiotis; Kotoulas, Georgios; Manousaki, Tereza; Sarropoulou, Elena; Tsigenopoulos, Costas S; Arvanitidis, Christos; Magoulas, Antonios; Pafilis, Evangelos 0s and 1s in marine molecular research: a regional HPC perspective Journal Article GigaScience, 10 (8), pp. giab053, 2021, ISSN: 2047-217X. @article{zafeiropoulos_0s_2021, title = {0s and 1s in marine molecular research: a regional HPC perspective}, author = {Haris Zafeiropoulos and Anastasia Gioti and Stelios Ninidakis and Antonis Potirakis and Savvas Paragkamian and Nelina Angelova and Aglaia Antoniou and Theodoros Danis and Eliza Kaitetzidou and Panagiotis Kasapidis and Jon Bent Kristoffersen and Vasileios Papadogiannis and Christina Pavloudi and Quoc Viet Ha and Jacques Lagnel and Nikos Pattakos and Giorgos Perantinos and Dimitris Sidirokastritis and Panagiotis Vavilis and Georgios Kotoulas and Tereza Manousaki and Elena Sarropoulou and Costas S Tsigenopoulos and Christos Arvanitidis and Antonios Magoulas and Evangelos Pafilis}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/08/2021-Zafeiropoulos-GiGa-63.pdf https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giab053/6353916}, doi = {10.1093/gigascience/giab053}, issn = {2047-217X}, year = {2021}, date = {2021-01-01}, urldate = {2021-08-23}, journal = {GigaScience}, volume = {10}, number = {8}, pages = {giab053}, abstract = {Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned. |
Danis, Theodoros; Papadogiannis, Vasileios; Tsakogiannis, Alexandros; Kristoffersen, Jon B; Golani, Daniel; Tsaparis, Dimitris; Sterioti, Aspasia; Kasapidis, Panagiotis; Kotoulas, Georgios; Magoulas, Antonios; Tsigenopoulos, Costas S; Manousaki, Tereza Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader Journal Article Frontiers in Genetics, 12 , pp. 2481, 2021, ISSN: 1664-8021. @article{danis_genome_2021, title = {Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader}, author = {Theodoros Danis and Vasileios Papadogiannis and Alexandros Tsakogiannis and Jon B Kristoffersen and Daniel Golani and Dimitris Tsaparis and Aspasia Sterioti and Panagiotis Kasapidis and Georgios Kotoulas and Antonios Magoulas and Costas S Tsigenopoulos and Tereza Manousaki}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/01/2021-Danis-FrontGen-84.pdf https://www.frontiersin.org/article/10.3389/fgene.2021.790850}, doi = {10.3389/fgene.2021.790850}, issn = {1664-8021}, year = {2021}, date = {2021-01-01}, urldate = {2022-01-12}, journal = {Frontiers in Genetics}, volume = {12}, pages = {2481}, abstract = {The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology. |
2020 |
Santi, I; Kasapidis, P; Psarra, S; Assimakopoulou, G; Pavlidou, A; Protopapa, M; Tsiola, A; Zeri, C; Pitta, P Composition and distribution patterns of eukaryotic microbial plankton in the ultra-oligotrophic Eastern Mediterranean Sea Journal Article Aquatic Microbial Ecology, 84 , pp. 155–173, 2020, ISSN: 0948-3055, (Publisher: Inter-Research Science Center). @article{santi_composition_2020, title = {Composition and distribution patterns of eukaryotic microbial plankton in the ultra-oligotrophic Eastern Mediterranean Sea}, author = {I Santi and P Kasapidis and S Psarra and G Assimakopoulou and A Pavlidou and M Protopapa and A Tsiola and C Zeri and P Pitta}, url = {https://www.int-res.com/abstracts/ame/v84/p155-173/}, doi = {10.3354/ame01933}, issn = {0948-3055}, year = {2020}, date = {2020-06-01}, journal = {Aquatic Microbial Ecology}, volume = {84}, pages = {155--173}, abstract = {Marine microbial eukaryotes play crucial roles in water-column ecosystems; however, there are regional gaps in the investigation of natural microbial eukaryote communities, and uncertainties concerning their distribution persevere. This study combined 18S rRNA metabarcoding, biomass measurements and statistical analyses of multiple environmental variables to examine the distribution of planktonic microbial eukaryotes at different sites and water layers in the ultra-oligotrophic Eastern Mediterranean Sea (Western Levantine Basin). Our results showed that microbial eukaryotic communities were structured by depth. In surface waters, different sites shared high percentages of molecular operational taxonomic units (MOTUs), but this was not the case for deep-sea communities (≥1000 m). Plankton biomass was significantly different among sites, implying that communities of a similar composition may not support the same activity or population size. The deep-sea communities showed high percentages of unassigned MOTUs, highlighting the sparsity of the existing information on deep-sea plankton eukaryotes. Water temperature and dissolved organic matter significantly affected community distribution. Micro-eukaryotic distribution was additionally affected by the nitrogen to phosphorus ratio and viral abundance, while nano- and pico-communities were affected by zooplankton. The present study explores microbial plankton eukaryotes in their natural oligotrophic environment and highlights that, even within restricted oceanic areas, marine plankton may follow distribution patterns that are largely controlled by environmental variables.}, note = {Publisher: Inter-Research Science Center}, keywords = {}, pubstate = {published}, tppubtype = {article} } Marine microbial eukaryotes play crucial roles in water-column ecosystems; however, there are regional gaps in the investigation of natural microbial eukaryote communities, and uncertainties concerning their distribution persevere. This study combined 18S rRNA metabarcoding, biomass measurements and statistical analyses of multiple environmental variables to examine the distribution of planktonic microbial eukaryotes at different sites and water layers in the ultra-oligotrophic Eastern Mediterranean Sea (Western Levantine Basin). Our results showed that microbial eukaryotic communities were structured by depth. In surface waters, different sites shared high percentages of molecular operational taxonomic units (MOTUs), but this was not the case for deep-sea communities (≥1000 m). Plankton biomass was significantly different among sites, implying that communities of a similar composition may not support the same activity or population size. The deep-sea communities showed high percentages of unassigned MOTUs, highlighting the sparsity of the existing information on deep-sea plankton eukaryotes. Water temperature and dissolved organic matter significantly affected community distribution. Micro-eukaryotic distribution was additionally affected by the nitrogen to phosphorus ratio and viral abundance, while nano- and pico-communities were affected by zooplankton. The present study explores microbial plankton eukaryotes in their natural oligotrophic environment and highlights that, even within restricted oceanic areas, marine plankton may follow distribution patterns that are largely controlled by environmental variables. |
2019 |
Santi, Ioulia; Tsiola, Anastasia; Dimitriou, Panagiotis D; Fodelianakis, Stilianos; Kasapidis, Panagiotis; Papageorgiou, Nafsika; Daffonchio, Daniele; Pitta, Paraskevi; Karakassis, Ioannis Marine Environmental Research, 150 , pp. 104752, 2019, ISSN: 18790291, (Publisher: Elsevier). @article{santi_prokaryotic_2019, title = {Prokaryotic and eukaryotic microbial community responses to N and P nutrient addition in oligotrophic Mediterranean coastal waters: Novel insights from DNA metabarcoding and network analysis}, author = {Ioulia Santi and Anastasia Tsiola and Panagiotis D Dimitriou and Stilianos Fodelianakis and Panagiotis Kasapidis and Nafsika Papageorgiou and Daniele Daffonchio and Paraskevi Pitta and Ioannis Karakassis}, url = {https://www.sciencedirect.com/science/article/pii/S0141113619302090?dgcid=coauthor https://linkinghub.elsevier.com/retrieve/pii/S0141113619302090}, doi = {10.1016/j.marenvres.2019.104752}, issn = {18790291}, year = {2019}, date = {2019-09-01}, journal = {Marine Environmental Research}, volume = {150}, pages = {104752}, abstract = {The effects of the abrupt input of high quantities of dissolved inorganic nitrogen and phosphorus on prokaryotic and eukaryotic microbial plankton were investigated in an attempt to simulate the nutrient disturbances caused by eutrophication and climate change. Two nutrient levels were created through the addition of different quantities of dissolved nutrients in a mesocosm experiment. During the developed blooms, compositional differences were found within bacteria and microbial eukaryotes, and communities progressed towards species of faster metabolisms. Regarding the different nutrient concentrations, different microbial species were associated with each nutrient treatment and community changes spanned from the phylum to the operational taxonomic unit (OTU) level. Network analyses revealed important differences in the biotic connections developed: more competitive relationships were established in the more intense nutrient disturbance and networks of contrasting complexity were formed around species of different ecological strategies. This work highlights that sudden disturbances in water column chemistry lead to the development of entirely different microbial food webs with distinct ecological characteristics.}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effects of the abrupt input of high quantities of dissolved inorganic nitrogen and phosphorus on prokaryotic and eukaryotic microbial plankton were investigated in an attempt to simulate the nutrient disturbances caused by eutrophication and climate change. Two nutrient levels were created through the addition of different quantities of dissolved nutrients in a mesocosm experiment. During the developed blooms, compositional differences were found within bacteria and microbial eukaryotes, and communities progressed towards species of faster metabolisms. Regarding the different nutrient concentrations, different microbial species were associated with each nutrient treatment and community changes spanned from the phylum to the operational taxonomic unit (OTU) level. Network analyses revealed important differences in the biotic connections developed: more competitive relationships were established in the more intense nutrient disturbance and networks of contrasting complexity were formed around species of different ecological strategies. This work highlights that sudden disturbances in water column chemistry lead to the development of entirely different microbial food webs with distinct ecological characteristics. |
Tsaparis, Dimitris; Sotiropoulos, Konstantinos; Legakis, Anastasios; Kotoulas, Georgios; Kasapidis, Panagiotis New phylogeographic insights support the distinctiveness and conservation value of the little-known Greek roe deer populations Journal Article Mammalian Biology, 96 , pp. 23–27, 2019, ISSN: 16165047. @article{tsaparis_new_2019, title = {New phylogeographic insights support the distinctiveness and conservation value of the little-known Greek roe deer populations}, author = {Dimitris Tsaparis and Konstantinos Sotiropoulos and Anastasios Legakis and Georgios Kotoulas and Panagiotis Kasapidis}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1616504718302581}, doi = {10.1016/j.mambio.2019.03.010}, issn = {16165047}, year = {2019}, date = {2019-05-01}, urldate = {2020-08-26}, journal = {Mammalian Biology}, volume = {96}, pages = {23--27}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2018 |
Kasapidis, P; Siokou, I; Khelifi-Touhami, M; Mazzocchi, M G; Matthaiaki, M; Christou, E; Puelles, Fernandez De M L; Gubanova, A; Capua, Di I; Batziakas, S; Frangoulis, C Journal of Plankton Research, 40 (5), pp. 595–605, 2018, ISSN: 01427873, (Publisher: Oxford University Press). @article{kasapidis_revising_2018, title = {Revising the taxonomic status and distribution of the Paracalanus parvus species complex (Copepoda, Calanoida) in the Mediterranean and Black Seas through an integrated analysis of morphology and molecular taxonomy}, author = {P Kasapidis and I Siokou and M Khelifi-Touhami and M G Mazzocchi and M Matthaiaki and E Christou and M L Fernandez De Puelles and A Gubanova and I Di Capua and S Batziakas and C Frangoulis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054296437&doi=10.1093%2fplankt%2ffby036&partnerID=40&md5=fa0270ee121028658499fd157ce9398b}, doi = {10.1093/plankt/fby036}, issn = {01427873}, year = {2018}, date = {2018-01-01}, journal = {Journal of Plankton Research}, volume = {40}, number = {5}, pages = {595--605}, abstract = {The marine copepod Paracalanus parvus has long been considered the most abundant representative of the genus and one of the main components of coastal zooplankton in the Mediterranean and Black Seas. However, subtle morphological differences between P. parvus, P. indicus and P. quasimodo hamper correct taxonomic identification. To clarify the taxonomic status and distribution of this species complex in the Mediterranean and Black Seas, DNA barcoding as well as an integrated morphological and molecular analysis was conducted on samples collected across these two basins. DNA barcoding confirmed the presence of P. parvus s.s. in the Black Sea and revealed four Paracalanus species in the Mediterranean Sea, including the morphologically undescribed Paracalanus sp. F. The most abundant species in all coastal areas was P. quasimodo, while P. parvus s.s. was confined to areas of the northern Mediterranean Sea. The phylogeographic analysis indicated that the boreal species P. parvus s.s. has a relic distribution in the Mediterranean and may have been displaced by the subtropical P. quasimodo during the last interglacial period. The integrated analysis revealed inconsistencies between morphological and molecular taxonomic identification and indicated that the taxonomic characters traditionally used are not adequate to discriminate between these species. © © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } The marine copepod Paracalanus parvus has long been considered the most abundant representative of the genus and one of the main components of coastal zooplankton in the Mediterranean and Black Seas. However, subtle morphological differences between P. parvus, P. indicus and P. quasimodo hamper correct taxonomic identification. To clarify the taxonomic status and distribution of this species complex in the Mediterranean and Black Seas, DNA barcoding as well as an integrated morphological and molecular analysis was conducted on samples collected across these two basins. DNA barcoding confirmed the presence of P. parvus s.s. in the Black Sea and revealed four Paracalanus species in the Mediterranean Sea, including the morphologically undescribed Paracalanus sp. F. The most abundant species in all coastal areas was P. quasimodo, while P. parvus s.s. was confined to areas of the northern Mediterranean Sea. The phylogeographic analysis indicated that the boreal species P. parvus s.s. has a relic distribution in the Mediterranean and may have been displaced by the subtropical P. quasimodo during the last interglacial period. The integrated analysis revealed inconsistencies between morphological and molecular taxonomic identification and indicated that the taxonomic characters traditionally used are not adequate to discriminate between these species. © © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. |
Kotsakiozi, P; Jablonski, D; Ilgaz, Ç; Kumlutaş, Y; Avcı, A; Meiri, S; Itescu, Y; Kukushkin, O; Gvoždík, V; Scillitani, G; Roussos, S A; Jandzik, D; Kasapidis, P; Lymberakis, P; Poulakakis, N Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species Journal Article Molecular Phylogenetics and Evolution, 125 , pp. 177–187, 2018, ISSN: 10557903, (Publisher: Academic Press Inc.). @article{kotsakiozi_multilocus_2018, title = {Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species}, author = {P Kotsakiozi and D Jablonski and Ç Ilgaz and Y Kumlutaş and A Avcı and S Meiri and Y Itescu and O Kukushkin and V Gvoždík and G Scillitani and S A Roussos and D Jandzik and P Kasapidis and P Lymberakis and N Poulakakis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85049356084&doi=10.1016%2fj.ympev.2018.03.022&partnerID=40&md5=24c03370163140f077b1861b6eaf9ea1}, doi = {10.1016/j.ympev.2018.03.022}, issn = {10557903}, year = {2018}, date = {2018-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {125}, pages = {177--187}, abstract = {Kotschy's Gecko, Mediodactylus kotschyi, is a small gecko native to southeastern Europe and the Levant. It displays great morphological variation with a large number of morphologically recognized subspecies. However, it has been suggested that it constitutes a species complex of several yet unrecognized species. In this study, we used multilocus sequence data (three mitochondrial and three nuclear gene fragments) to estimate the phylogenetic relationships of 174 specimens from 129 sampling localities, covering a substantial part of the distribution range of the species. Our results revealed high genetic diversity of M. kotschyi populations and contributed to our knowledge about the phylogenetic relationships and the estimation of the divergence times between them. Diversification within M. kotschyi began approximately 15 million years ago (Mya) in the Middle Miocene, whereas the diversification within most of the major clades have been occurred in the last 5 Mya. Species delimitation analysis suggests there exists five species within the complex, and we propose to tentatively recognize the following taxa as full species: M. kotschyi (mainland Balkans, most of Aegean islands, and Italy), M. orientalis (Levant, Cyprus, southern Anatolia, and south-eastern Aegean islands), M. danilewskii (Black Sea region and south-western Anatolia), M. bartoni (Crete), and M. oertzeni (southern Dodecanese Islands). This newly recognized diversity underlines the complex biogeographical history of the Eastern Mediterranean region. © 2018 Elsevier Inc.}, note = {Publisher: Academic Press Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Kotschy's Gecko, Mediodactylus kotschyi, is a small gecko native to southeastern Europe and the Levant. It displays great morphological variation with a large number of morphologically recognized subspecies. However, it has been suggested that it constitutes a species complex of several yet unrecognized species. In this study, we used multilocus sequence data (three mitochondrial and three nuclear gene fragments) to estimate the phylogenetic relationships of 174 specimens from 129 sampling localities, covering a substantial part of the distribution range of the species. Our results revealed high genetic diversity of M. kotschyi populations and contributed to our knowledge about the phylogenetic relationships and the estimation of the divergence times between them. Diversification within M. kotschyi began approximately 15 million years ago (Mya) in the Middle Miocene, whereas the diversification within most of the major clades have been occurred in the last 5 Mya. Species delimitation analysis suggests there exists five species within the complex, and we propose to tentatively recognize the following taxa as full species: M. kotschyi (mainland Balkans, most of Aegean islands, and Italy), M. orientalis (Levant, Cyprus, southern Anatolia, and south-eastern Aegean islands), M. danilewskii (Black Sea region and south-western Anatolia), M. bartoni (Crete), and M. oertzeni (southern Dodecanese Islands). This newly recognized diversity underlines the complex biogeographical history of the Eastern Mediterranean region. © 2018 Elsevier Inc. |
2017 |
Antoniou, A; Kasapidis, P; Kotoulas, G; Mylonas, C C; Magoulas, A Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: Insights from genome-wide SNPs and microsatellites Journal Article Journal of Biological Research-Thessaloniki, 24 (1), pp. 3, 2017. @article{antoniou_genetic_2017, title = {Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: Insights from genome-wide SNPs and microsatellites}, author = {A Antoniou and P Kasapidis and G Kotoulas and C C Mylonas and A Magoulas}, doi = {10.1186/s40709-017-0062-2}, year = {2017}, date = {2017-01-01}, journal = {Journal of Biological Research-Thessaloniki}, volume = {24}, number = {1}, pages = {3}, abstract = {© The Author(s) 2017. Background: Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species' reproduction. Results: Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study's sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions: Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } © The Author(s) 2017. Background: Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species' reproduction. Results: Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study's sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions: Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation. |
Xirouchakis, S M; Kasapidis, P; Christidis, A; Andreou, G; Kontogeorgos, I; Lymberakis, P Marine Ornithology, 45 (1), pp. 1–9, 2017, ISSN: 10183337, (Publisher: Marine Ornithology). @article{xirouchakis_status_2017, title = {Status and diet of the European Shag (Mediterranean subspecies) Phalacrocorax aristotelis desmarestii in the Libyan Sea (south Crete) during the breeding season}, author = {S M Xirouchakis and P Kasapidis and A Christidis and G Andreou and I Kontogeorgos and P Lymberakis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019046432&partnerID=40&md5=db3869943c7ccd1495baad40eeec06e1}, issn = {10183337}, year = {2017}, date = {2017-01-01}, journal = {Marine Ornithology}, volume = {45}, number = {1}, pages = {1--9}, abstract = {During 2010–2012 we collected data on the population status and ecology of the European Shag (Mediterranean subspecies) Phalacrocorax aristotelis desmarestii on Gavdos Island (south Crete), conducting boat-based surveys, nest monitoring, and diet analysis. The species’ population was estimated at 80–110 pairs, with 59% breeding success and 1.6 fledglings per successful nest. Pellet morphological and genetic analysis of otoliths and fish bones, respectively, showed that the shags’ diet consisted of 31 species. A total of 4 223 otoliths were identified to species level; 47.2% belonged to sand smelts Atherina boyeri, 14.2% to bogues Boops boops, 11.3% to picarels Spicara smaris, and 10.5% to damselfishes Chromis chromis. Our results revealed that, during the breeding season, the European Shag feeds mainly on small demersal species that are of low commercial value, posing no significant threat to the conduct of local fisheries. © 2017, Marine Ornithology. All rights reserved.}, note = {Publisher: Marine Ornithology}, keywords = {}, pubstate = {published}, tppubtype = {article} } During 2010–2012 we collected data on the population status and ecology of the European Shag (Mediterranean subspecies) Phalacrocorax aristotelis desmarestii on Gavdos Island (south Crete), conducting boat-based surveys, nest monitoring, and diet analysis. The species’ population was estimated at 80–110 pairs, with 59% breeding success and 1.6 fledglings per successful nest. Pellet morphological and genetic analysis of otoliths and fish bones, respectively, showed that the shags’ diet consisted of 31 species. A total of 4 223 otoliths were identified to species level; 47.2% belonged to sand smelts Atherina boyeri, 14.2% to bogues Boops boops, 11.3% to picarels Spicara smaris, and 10.5% to damselfishes Chromis chromis. Our results revealed that, during the breeding season, the European Shag feeds mainly on small demersal species that are of low commercial value, posing no significant threat to the conduct of local fisheries. © 2017, Marine Ornithology. All rights reserved. |
2016 |
Kousteni, V; Kasapidis, P; Kotoulas, G; Megalofonou, P Evidence of high genetic connectivity for the longnose spurdog Squalus blainville in the Mediterranean Sea Journal Article Mediterranean Marine Science, 17 (2), pp. 371–383, 2016, ISSN: 1108393X, (Publisher: Hellenic Centre for Marine Research). @article{kousteni_evidence_2016, title = {Evidence of high genetic connectivity for the longnose spurdog Squalus blainville in the Mediterranean Sea}, author = {V Kousteni and P Kasapidis and G Kotoulas and P Megalofonou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019545144&doi=10.12681%2fmms.1222&partnerID=40&md5=2e93879e948e1d3748c29224910104e5}, doi = {10.12681/mms.1222}, issn = {1108393X}, year = {2016}, date = {2016-01-01}, journal = {Mediterranean Marine Science}, volume = {17}, number = {2}, pages = {371--383}, abstract = {Squalus blainville is one of the least studied Mediterranean shark species. Despite being intensively fished in several locations, biological knowledge is limited and no genetic structure information is available. This is the first study to examine the genetic structure of S. blainville in the Mediterranean Sea. Considering the high dispersal potential inferred for other squalid sharks, the hypothesis of panmixia was tested based on a 585 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I gene from 107 individuals and six nuclear microsatellite loci from 577 individuals. Samples were collected across the Ionian, Aegean and Libyan Seas and off the Balearic Islands. Twenty three additional sequences of Mediterranean and South African origin were retrieved from GenBank and included in the mitochondrial DNA analysis. The overall haplotype diversity was high, in contrast to the low nucleotide diversity. Low and non-significant pairwise FST and FST values along with a Bayesian cluster analysis suggested high connectivity with subsequent genetic homogeneity among the populations studied, and thus a high dispersal potential for S. blainville similar to other squalids. The historical demography of the species was also assessed, revealing a pattern of population expansion since the middle Pleistocene. These findings could be considered in species-specific conservation plans, although sampling over a larger spatial scale and more genetic markers are required to fully elucidate the genetic structure and dispersal potential of S. blainville.}, note = {Publisher: Hellenic Centre for Marine Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } Squalus blainville is one of the least studied Mediterranean shark species. Despite being intensively fished in several locations, biological knowledge is limited and no genetic structure information is available. This is the first study to examine the genetic structure of S. blainville in the Mediterranean Sea. Considering the high dispersal potential inferred for other squalid sharks, the hypothesis of panmixia was tested based on a 585 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I gene from 107 individuals and six nuclear microsatellite loci from 577 individuals. Samples were collected across the Ionian, Aegean and Libyan Seas and off the Balearic Islands. Twenty three additional sequences of Mediterranean and South African origin were retrieved from GenBank and included in the mitochondrial DNA analysis. The overall haplotype diversity was high, in contrast to the low nucleotide diversity. Low and non-significant pairwise FST and FST values along with a Bayesian cluster analysis suggested high connectivity with subsequent genetic homogeneity among the populations studied, and thus a high dispersal potential for S. blainville similar to other squalids. The historical demography of the species was also assessed, revealing a pattern of population expansion since the middle Pleistocene. These findings could be considered in species-specific conservation plans, although sampling over a larger spatial scale and more genetic markers are required to fully elucidate the genetic structure and dispersal potential of S. blainville. |
Leese, Florian; Altermatt, Florian; Bouchez, Agnès; Ekrem, Torbjørn; Hering, Daniel; Meissner, Kristian; Mergen, Patricia; Pawlowski, Jan; Piggott, Jeremy; Rimet, Frédéric; Steinke, Dirk; Taberlet, Pierre; Weigand, Alexander; Abarenkov, Kessy; Beja, Pedro; Bervoets, Lieven; Björnsdóttir, Snaedís; Boets, Pieter; Boggero, Angela; Bones, Atle; Borja, Ángel; Bruce, Kat; Bursić, Vojislava; Carlsson, Jens; Čiampor, Fedor; Čiamporová-Zatovičová, Zuzana; Coissac, Eric; Costa, Filipe; Costache, Marieta; Creer, Simon; Csabai, Zoltán; Deiner, Kristy; DelValls, Ángel; Drakare, Stina; Duarte, Sofia; Eleršek, Tina; Fazi, Stefano; Fišer, Cene; Flot, Jean-François; Fonseca, Vera; Fontaneto, Diego; Grabowski, Michael; Graf, Wolfram; Guðbrandsson, Jóhannes; Hellström, Micaela; Hershkovitz, Yaron; Hollingsworth, Peter; Japoshvili, Bella; Jones, John; Kahlert, Maria; Stroil, Belma Kalamujic; Kasapidis, Panagiotis; Kelly, Martyn; Kelly-Quinn, Mary; Keskin, Emre; Kõljalg, Urmas; Ljubešić, Zrinka; Maček, Irena; Mächler, Elvira; Mahon, Andrew; Marečková, Marketa; Mejdandzic, Maja; Mircheva, Georgina; Montagna, Matteo; Moritz, Christian; Mulk, Vallo; Naumoski, Andreja; Navodaru, Ion; Padisák, Judit; Pálsson, Snæbjörn; Panksep, Kristel; Penev, Lyubomir; Petrusek, Adam; Pfannkuchen, Martin; Primmer, Craig; Rinkevich, Baruch; Rotter, Ana; Schmidt-Kloiber, Astrid; Segurado, Pedro; Speksnijder, Arjen; Stoev, Pavel; Strand, Malin; Šulčius, Sigitas; Sundberg, Per; Traugott, Michael; Tsigenopoulos, Costas; Turon, Xavier; Valentini, Alice; Hoorn, Berry Van Der; Várbíró, Gábor; Hadjilyra, Marlen Vasquez; Viguri, Javier; Vitonytė, Irma; Vogler, Alfried; Vrålstad, Trude; Wägele, Wolfgang; Wenne, Roman; Winding, Anne; Woodward, Guy; Zegura, Bojana; Zimmermann, Jonas DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe Journal Article Research Ideas and Outcomes, 2 , pp. e11321, 2016, ISSN: 2367-7163. @article{leese_dnaqua-net_2016, title = {DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe}, author = {Florian Leese and Florian Altermatt and Agnès Bouchez and Torbjørn Ekrem and Daniel Hering and Kristian Meissner and Patricia Mergen and Jan Pawlowski and Jeremy Piggott and Frédéric Rimet and Dirk Steinke and Pierre Taberlet and Alexander Weigand and Kessy Abarenkov and Pedro Beja and Lieven Bervoets and Snaedís Björnsdóttir and Pieter Boets and Angela Boggero and Atle Bones and Ángel Borja and Kat Bruce and Vojislava Bursić and Jens Carlsson and Fedor Čiampor and Zuzana Čiamporová-Zatovičová and Eric Coissac and Filipe Costa and Marieta Costache and Simon Creer and Zoltán Csabai and Kristy Deiner and Ángel DelValls and Stina Drakare and Sofia Duarte and Tina Eleršek and Stefano Fazi and Cene Fišer and Jean-François Flot and Vera Fonseca and Diego Fontaneto and Michael Grabowski and Wolfram Graf and Jóhannes Guðbrandsson and Micaela Hellström and Yaron Hershkovitz and Peter Hollingsworth and Bella Japoshvili and John Jones and Maria Kahlert and Belma Kalamujic Stroil and Panagiotis Kasapidis and Martyn Kelly and Mary Kelly-Quinn and Emre Keskin and Urmas Kõljalg and Zrinka Ljubešić and Irena Maček and Elvira Mächler and Andrew Mahon and Marketa Marečková and Maja Mejdandzic and Georgina Mircheva and Matteo Montagna and Christian Moritz and Vallo Mulk and Andreja Naumoski and Ion Navodaru and Judit Padisák and Snæbjörn Pálsson and Kristel Panksep and Lyubomir Penev and Adam Petrusek and Martin Pfannkuchen and Craig Primmer and Baruch Rinkevich and Ana Rotter and Astrid Schmidt-Kloiber and Pedro Segurado and Arjen Speksnijder and Pavel Stoev and Malin Strand and Sigitas Šulčius and Per Sundberg and Michael Traugott and Costas Tsigenopoulos and Xavier Turon and Alice Valentini and Berry Van Der Hoorn and Gábor Várbíró and Marlen Vasquez Hadjilyra and Javier Viguri and Irma Vitonytė and Alfried Vogler and Trude Vrålstad and Wolfgang Wägele and Roman Wenne and Anne Winding and Guy Woodward and Bojana Zegura and Jonas Zimmermann}, url = {http://riojournal.com/articles.php?id=11321}, doi = {10.3897/rio.2.e11321}, issn = {2367-7163}, year = {2016}, date = {2016-01-01}, urldate = {2023-03-03}, journal = {Research Ideas and Outcomes}, volume = {2}, pages = {e11321}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2015 |
Radojičić, Jelena M; Krizmanić, Imre; Kasapidis, Panagiotis; Zouros, Eleftherios Extensive mitochondrial heteroplasmy in hybrid water frog (Pelophylax spp.) populations from Southeast Europe Journal Article Ecology and Evolution, 5 (20), pp. 4529–4541, 2015, ISSN: 20457758. @article{radojicic_extensive_2015, title = {Extensive mitochondrial heteroplasmy in hybrid water frog (Pelophylax spp.) populations from Southeast Europe}, author = {Jelena M Radojičić and Imre Krizmanić and Panagiotis Kasapidis and Eleftherios Zouros}, url = {http://doi.wiley.com/10.1002/ece3.1692}, doi = {10.1002/ece3.1692}, issn = {20457758}, year = {2015}, date = {2015-10-01}, urldate = {2020-11-01}, journal = {Ecology and Evolution}, volume = {5}, number = {20}, pages = {4529--4541}, abstract = {Water frogs of the genus Pelophylax (previous Rana) species have been much studied in Europe for their outstanding reproductive mechanism in which sympatric hybridization between genetically distinct parental species produces diverse genetic forms of viable hybrid animals. The most common hybrid is P. esculentus that carries the genomes of both parental species, P. ridibundus and P. lessonae, but usually transfers the whole genome of only one parent to its offsprings (hybridogenesis). The evolutionary cost of transfer of the intact genome and hence the hemiclonal reproduction is the depletion of heterozygosity in the hybrid populations. Pelophylax esculentus presents an excellent example of the long-term sustained hybridization and hemiclonal reproduction in which the effects of the low genetic diversity are balanced through the novel mutations and periodic recombinations. In this study, we analyzed the mitochondrial (mt) and microsatellites DNA variations in hybrid Pelophylax populations from southern parts of the Pannonian Basin and a north-south transect of the Balkan Peninsula, which are home for a variety of Pelophylax genetic lineages. The mtDNA haplotypes found in this study corresponded to P. ridibundus and P. epeiroticus of the Balkan - Anatolian lineage (ridibundus-bedriagae) and to P. lessonae and a divergent lessonae haplotype of the lessonae lineage. The mtDNA genomes showed considerable intraspecific variation and geographic differentiation. The Balkan wide distributed P. ridibundus was found in all studied populations and its nuclear genome, along with either the lessonae or the endemic epeiroticus genome, in all hybrids. An unexpected finding was that the hybrid populations were invariably heteroplasmic, that is, they contained the mtDNA of both parental species. We discussed the possibility that such extensive heteroplasmy is a result of hybridization and it comes from regular leakage of the paternal mtDNA from a sperm of one species that fertilizes eggs of another. In this case, the mechanisms that protect the egg from heterospecific fertilization and further from the presence of sperm mtDNA could become compromised due to their differences and divergence at both, mitochondrial and nuclear DNA. The heteroplasmy once retained in the fertilized egg could be transmitted by hybrid backcrossing to the progeny and maintained in a population over generations. The role of interspecies and heteroplasmic hybrid animals due to their genomic diversity and better fitness compare to the parental species might be of the special importance in adaptations to miscellaneous and isolated environments at the Balkan Peninsula. © 2015 The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Water frogs of the genus Pelophylax (previous Rana) species have been much studied in Europe for their outstanding reproductive mechanism in which sympatric hybridization between genetically distinct parental species produces diverse genetic forms of viable hybrid animals. The most common hybrid is P. esculentus that carries the genomes of both parental species, P. ridibundus and P. lessonae, but usually transfers the whole genome of only one parent to its offsprings (hybridogenesis). The evolutionary cost of transfer of the intact genome and hence the hemiclonal reproduction is the depletion of heterozygosity in the hybrid populations. Pelophylax esculentus presents an excellent example of the long-term sustained hybridization and hemiclonal reproduction in which the effects of the low genetic diversity are balanced through the novel mutations and periodic recombinations. In this study, we analyzed the mitochondrial (mt) and microsatellites DNA variations in hybrid Pelophylax populations from southern parts of the Pannonian Basin and a north-south transect of the Balkan Peninsula, which are home for a variety of Pelophylax genetic lineages. The mtDNA haplotypes found in this study corresponded to P. ridibundus and P. epeiroticus of the Balkan - Anatolian lineage (ridibundus-bedriagae) and to P. lessonae and a divergent lessonae haplotype of the lessonae lineage. The mtDNA genomes showed considerable intraspecific variation and geographic differentiation. The Balkan wide distributed P. ridibundus was found in all studied populations and its nuclear genome, along with either the lessonae or the endemic epeiroticus genome, in all hybrids. An unexpected finding was that the hybrid populations were invariably heteroplasmic, that is, they contained the mtDNA of both parental species. We discussed the possibility that such extensive heteroplasmy is a result of hybridization and it comes from regular leakage of the paternal mtDNA from a sperm of one species that fertilizes eggs of another. In this case, the mechanisms that protect the egg from heterospecific fertilization and further from the presence of sperm mtDNA could become compromised due to their differences and divergence at both, mitochondrial and nuclear DNA. The heteroplasmy once retained in the fertilized egg could be transmitted by hybrid backcrossing to the progeny and maintained in a population over generations. The role of interspecies and heteroplasmic hybrid animals due to their genomic diversity and better fitness compare to the parental species might be of the special importance in adaptations to miscellaneous and isolated environments at the Balkan Peninsula. © 2015 The Authors. |
Xirouchakis, S; Kasapidis, P; Andreou, G; Kontogeorgos, I; Lyberakis, P Population status, breeding biology and diet of the European Shag (Phalacrocorax aristotelis desmarestii) on Gavdos island (south Crete, Greece) Inproceedings Proceedings of the 11th Panhellenic Symposium on Oceanography and Fisheries, pp. 81–84, 2015. @inproceedings{xirouchakis_population_2015, title = {Population status, breeding biology and diet of the European Shag (Phalacrocorax aristotelis desmarestii) on Gavdos island (south Crete, Greece)}, author = {S Xirouchakis and P Kasapidis and G Andreou and I Kontogeorgos and P Lyberakis}, year = {2015}, date = {2015-01-01}, booktitle = {Proceedings of the 11th Panhellenic Symposium on Oceanography and Fisheries}, pages = {81--84}, abstract = {During 2009-2012 we collected data on the population status and the ecology of the Mediterranean shag (Phalacrocorax aristotelis desmarestii) on Gavdos Island, by applying boat-based surveys, nest monitoring and telemetry techniques. The species population was estimated at 80-110 pairs (59% breeding success and 1.6 fledglings per successful nest). Pellets were used for morphometric and genetic analysis of fish otoliths and bones respectively. Our results revealed that shags feed mainly on small benthopelagic species. The maximum depth of underwater feeding ranged from 74.8-109.2m (one dive-pursuit/ 26.5± 12 sec) whereas the mean foraging offshore distance was estimated at 425± 505m (range= 21 -1985m).}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } During 2009-2012 we collected data on the population status and the ecology of the Mediterranean shag (Phalacrocorax aristotelis desmarestii) on Gavdos Island, by applying boat-based surveys, nest monitoring and telemetry techniques. The species population was estimated at 80-110 pairs (59% breeding success and 1.6 fledglings per successful nest). Pellets were used for morphometric and genetic analysis of fish otoliths and bones respectively. Our results revealed that shags feed mainly on small benthopelagic species. The maximum depth of underwater feeding ranged from 74.8-109.2m (one dive-pursuit/ 26.5± 12 sec) whereas the mean foraging offshore distance was estimated at 425± 505m (range= 21 -1985m). |
Kousteni, V; Kasapidis, P; Kotoulas, G; Megalofonou, P Heredity, 114 (3), pp. 333–343, 2015, ISSN: 0018067X, (Publisher: Nature Publishing Group). @article{kousteni_strong_2015, title = {Strong population genetic structure and contrasting demographic histories for the small-spotted catshark (Scyliorhinus canicula) in the Mediterranean Sea}, author = {V Kousteni and P Kasapidis and G Kotoulas and P Megalofonou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922647393&doi=10.1038%2fhdy.2014.107&partnerID=40&md5=8214d4d9474b3495446e06c1ce805396}, doi = {10.1038/hdy.2014.107}, issn = {0018067X}, year = {2015}, date = {2015-01-01}, journal = {Heredity}, volume = {114}, number = {3}, pages = {333--343}, abstract = {Coastal and demersal chondrichthyans, such as the small-spotted catshark, are expected to exhibit genetic differentiation in areas of complex geomorphology like the Mediterranean Basin because of their limited dispersal ability. To test this hypothesis, we used a fragment of the mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear microsatellite loci in order to investigate the genetic structure and historical demography of this species, and to identify potential barriers to gene flow. Samples were collected from the Balearic Islands, the Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations across the Aegean Sea. Additional sequences from the Atlantic and the Levantine Basin retrieved from GenBank were included in the mitochondrial DNA analysis. Both mitochondrial and nuclear microsatellite DNA data revealed a strong genetic subdivision, mainly between the western and eastern Mediterranean, whereas the Levantine Basin shared haplotypes with both areas. The geographic isolation of the Mediterranean basins seems to enforce the population genetic differentiation of the species, with the deep sea acting as a strong barrier to its dispersal. Contrasting historical demographic patterns were also observed in different parts of the species' distribution, most notably a population growth trend in the western Mediterranean/Atlantic area and a slight decreasing one in the Aegean Sea. The different effects of the Pleistocene glacial periods on the habitat availability may explain the contrasting demographic patterns observed. The current findings suggest that the small-spotted catshark exhibits several genetic stocks in the Mediterranean, although further study is needed. © 2015 Macmillan Publishers Limited.}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } Coastal and demersal chondrichthyans, such as the small-spotted catshark, are expected to exhibit genetic differentiation in areas of complex geomorphology like the Mediterranean Basin because of their limited dispersal ability. To test this hypothesis, we used a fragment of the mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear microsatellite loci in order to investigate the genetic structure and historical demography of this species, and to identify potential barriers to gene flow. Samples were collected from the Balearic Islands, the Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations across the Aegean Sea. Additional sequences from the Atlantic and the Levantine Basin retrieved from GenBank were included in the mitochondrial DNA analysis. Both mitochondrial and nuclear microsatellite DNA data revealed a strong genetic subdivision, mainly between the western and eastern Mediterranean, whereas the Levantine Basin shared haplotypes with both areas. The geographic isolation of the Mediterranean basins seems to enforce the population genetic differentiation of the species, with the deep sea acting as a strong barrier to its dispersal. Contrasting historical demographic patterns were also observed in different parts of the species' distribution, most notably a population growth trend in the western Mediterranean/Atlantic area and a slight decreasing one in the Aegean Sea. The different effects of the Pleistocene glacial periods on the habitat availability may explain the contrasting demographic patterns observed. The current findings suggest that the small-spotted catshark exhibits several genetic stocks in the Mediterranean, although further study is needed. © 2015 Macmillan Publishers Limited. |
2014 |
Kasapidis, Panagiotis Phylogeography and Population Genetics Incollection Ganias, Konstantinos (Ed.): Biology and Ecology of Sardines and Anchovies, pp. 43–75, CRC Press, 2014, ISBN: 978-1-4822-2854-0 978-1-4822-2856-4. @incollection{ganias_phylogeography_2014, title = {Phylogeography and Population Genetics}, author = {Panagiotis Kasapidis}, editor = {Konstantinos Ganias}, url = {http://www.crcnetbase.com/doi/abs/10.1201/b16682-4}, doi = {10.1201/b16682-4}, isbn = {978-1-4822-2854-0 978-1-4822-2856-4}, year = {2014}, date = {2014-03-01}, urldate = {2020-08-11}, booktitle = {Biology and Ecology of Sardines and Anchovies}, pages = {43--75}, publisher = {CRC Press}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Fodelianakis, S; Pitta, P; Thingstad, T F; Kasapidis, P; Karakassis, I; Ladoukakis, E D Phosphate addition has minimal short-term effects on bacterioplankton community structure of the p-starved Eastern Mediterranean Journal Article Aquatic Microbial Ecology, 72 (2), pp. 98–104, 2014, ISSN: 09483055, (Publisher: Inter-Research). @article{fodelianakis_phosphate_2014, title = {Phosphate addition has minimal short-term effects on bacterioplankton community structure of the p-starved Eastern Mediterranean}, author = {S Fodelianakis and P Pitta and T F Thingstad and P Kasapidis and I Karakassis and E D Ladoukakis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84901319508&doi=10.3354%2fame01693&partnerID=40&md5=6afcaecd3a73335f3e34bed5e91ae7e0}, doi = {10.3354/ame01693}, issn = {09483055}, year = {2014}, date = {2014-01-01}, journal = {Aquatic Microbial Ecology}, volume = {72}, number = {2}, pages = {98--104}, abstract = {The effect of the addition of a limiting nutrient to the composition and structure of bacterial communities in oligotrophic environments remains an interesting question. We conducted a mesocosm experiment to study short-term effects of phosphorus addition on bacterioplankton communities in the Eastern Mediterranean, which is a phosphorus-starved ecosystem. Inorganic phosphorus was added to 10 m deep pelagic water which was transported from offshore Crete, Greece, to mesocosms to yield a final concentration of 100 nM. Using 454 16S amplicon sequencing, we found that phosphorus addition during the first 72 h of the experiment had a minimal effect on bacterioplankton community composition and structure, affecting mostly the abundance of the 'non-unique' members of the community. © Inter-Research 2014.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } The effect of the addition of a limiting nutrient to the composition and structure of bacterial communities in oligotrophic environments remains an interesting question. We conducted a mesocosm experiment to study short-term effects of phosphorus addition on bacterioplankton communities in the Eastern Mediterranean, which is a phosphorus-starved ecosystem. Inorganic phosphorus was added to 10 m deep pelagic water which was transported from offshore Crete, Greece, to mesocosms to yield a final concentration of 100 nM. Using 454 16S amplicon sequencing, we found that phosphorus addition during the first 72 h of the experiment had a minimal effect on bacterioplankton community composition and structure, affecting mostly the abundance of the 'non-unique' members of the community. © Inter-Research 2014. |
Fodelianakis, S; Papageorgiou, N; Pitta, P; Kasapidis, P; Karakassis, I; Ladoukakis, E D The pattern of change in the abundances of specific bacterioplankton groups is consistent across different nutrient-enriched habitats in crete Journal Article Applied and Environmental Microbiology, 80 (13), pp. 3784–3792, 2014, ISSN: 00992240, (Publisher: American Society for Microbiology). @article{fodelianakis_pattern_2014, title = {The pattern of change in the abundances of specific bacterioplankton groups is consistent across different nutrient-enriched habitats in crete}, author = {S Fodelianakis and N Papageorgiou and P Pitta and P Kasapidis and I Karakassis and E D Ladoukakis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84902142722&doi=10.1128%2fAEM.00088-14&partnerID=40&md5=afa6689340ce971f86accdc4f1567bae}, doi = {10.1128/AEM.00088-14}, issn = {00992240}, year = {2014}, date = {2014-01-01}, journal = {Applied and Environmental Microbiology}, volume = {80}, number = {13}, pages = {3784--3792}, abstract = {A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. © 2014, American Society for Microbiology.}, note = {Publisher: American Society for Microbiology}, keywords = {}, pubstate = {published}, tppubtype = {article} } A common source of disturbance for coastal aquatic habitats is nutrient enrichment through anthropogenic activities. Although the water column bacterioplankton communities in these environments have been characterized in some cases, changes in α-diversity and/or the abundances of specific taxonomic groups across enriched habitats remain unclear. Here, we investigated the bacterial community changes at three different nutrient-enriched and adjacent undisturbed habitats along the north coast of Crete, Greece: a fish farm, a closed bay within a town with low water renewal rates, and a city port where the level of nutrient enrichment and the trophic status of the habitat were different. Even though changes in α-diversity were different at each site, we observed across the sites a common change pattern accounting for most of the community variation for five of the most abundant bacterial groups: a decrease in the abundance of the Pelagibacteraceae and SAR86 and an increase in the abundance of the Alteromonadaceae, Rhodobacteraceae, and Cryomorphaceae in the impacted sites. The abundances of the groups that increased and decreased in the impacted sites were significantly correlated (positively and negatively, respectively) with the total heterotrophic bacterial counts and the concentrations of dissolved organic carbon and/or dissolved nitrogen and chlorophyll α, indicating that the common change pattern was associated with nutrient enrichment. Our results provide an in situ indication concerning the association of specific bacterioplankton groups with nutrient enrichment. These groups could potentially be used as indicators for nutrient enrichment if the pattern is confirmed over a broader spatial and temporal scale by future studies. © 2014, American Society for Microbiology. |
2013 |
Kasapidis, P; Boyer, F; Christidis, A; Kristoffersen, JB; Oulas, A; Nikolioudakis, N; Fric, J Using next-generation sequencing technologies to assess the diet of the Mediterranean shag (Phalacrocorax aristotelis) and implication of these technologies for high-throughput study and monitoring of marine biodiversity. Inproceedings Kasapidis, P (Ed.): Mediterranean marine biodiversity in view of climate change and the invasion of alien species, Heraklion Crete, Greece, 2013. @inproceedings{kasapidis_using_2013, title = {Using next-generation sequencing technologies to assess the diet of the Mediterranean shag (Phalacrocorax aristotelis) and implication of these technologies for high-throughput study and monitoring of marine biodiversity.}, author = {P Kasapidis and F Boyer and A Christidis and JB Kristoffersen and A Oulas and N Nikolioudakis and J Fric}, editor = {P Kasapidis}, year = {2013}, date = {2013-10-01}, booktitle = {Mediterranean marine biodiversity in view of climate change and the invasion of alien species}, address = {Heraklion Crete, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Sotiropoulos, K; Eleftherakos, K; Tsaparis, D; Kasapidis, P; Giokas, S; Legakis, A; Kotoulas, G Fine scale spatial genetic structure of two syntopic newts across a network of ponds: Implications for conservation Journal Article Conservation Genetics, 14 (2), pp. 385–400, 2013, ISSN: 15660621. @article{sotiropoulos_fine_2013, title = {Fine scale spatial genetic structure of two syntopic newts across a network of ponds: Implications for conservation}, author = {K Sotiropoulos and K Eleftherakos and D Tsaparis and P Kasapidis and S Giokas and A Legakis and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84875694931&doi=10.1007%2fs10592-013-0452-4&partnerID=40&md5=bdc097a5f03307fe2303be30e8f62c02}, doi = {10.1007/s10592-013-0452-4}, issn = {15660621}, year = {2013}, date = {2013-01-01}, journal = {Conservation Genetics}, volume = {14}, number = {2}, pages = {385--400}, abstract = {In this study we used genetic approaches to assess the influence of landscape features on the dispersal patterns and genetic structure of two newt species (Triturus macedonicus and Lissotriton vulgaris) living syntopically in a network of ponds. Multilocus genotypes were used to detect and measure genetic variation patterns, population genetic structure and levels of gene flow. We interpret results on the basis of the different dispersal properties of the two species and explored the influence of certain landscape features, such as road and channel networks, on population connectivity. We found marked differences in the spatial genetic patterns of the respective species, which can be explained by their different dispersal properties. The road network seems to act as a barrier to dispersal in the overland dispersing L. vulgaris, while the channel network maintains connectivity in the aquatic dispersing T. macedonicus. The simultaneous and comparative consideration of species in a given area offers a much better understanding of the processes that govern population dynamics and persistence, providing valuable knowledge useful in conservation and management design. © 2013 Springer Science+Business Media Dordrecht.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this study we used genetic approaches to assess the influence of landscape features on the dispersal patterns and genetic structure of two newt species (Triturus macedonicus and Lissotriton vulgaris) living syntopically in a network of ponds. Multilocus genotypes were used to detect and measure genetic variation patterns, population genetic structure and levels of gene flow. We interpret results on the basis of the different dispersal properties of the two species and explored the influence of certain landscape features, such as road and channel networks, on population connectivity. We found marked differences in the spatial genetic patterns of the respective species, which can be explained by their different dispersal properties. The road network seems to act as a barrier to dispersal in the overland dispersing L. vulgaris, while the channel network maintains connectivity in the aquatic dispersing T. macedonicus. The simultaneous and comparative consideration of species in a given area offers a much better understanding of the processes that govern population dynamics and persistence, providing valuable knowledge useful in conservation and management design. © 2013 Springer Science+Business Media Dordrecht. |
2012 |
Tsaparis, D; Fric, J; Kristoffersen, JB; Karris, G; Kasapidis, P Genetic structure and differentiation patterns of ship rat (Rattus rattus) populations in island and islet complexes of Greek Seas. [In Greek] Inproceedings Tsaparis, D (Ed.): 6th Panhellenic Ecological Congress, Athens, Greece, 2012. @inproceedings{tsaparis_genetic_2012, title = {Genetic structure and differentiation patterns of ship rat (Rattus rattus) populations in island and islet complexes of Greek Seas. [In Greek]}, author = {D Tsaparis and J Fric and JB Kristoffersen and G Karris and P Kasapidis}, editor = {D Tsaparis}, year = {2012}, date = {2012-10-01}, booktitle = {6th Panhellenic Ecological Congress, Athens, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Kasapidis, P; Silva, A; Zampicinini, G; Magoulas, A Scientia Marina, 76 (1), pp. 123–132, 2012, ISSN: 02148358. @article{kasapidis_evidence_2012, title = {Evidence for microsatellite hitchhiking selection in European sardine (Sardina pilchardus) and implications in inferring stock structure [Evidencia para selección hitchhiking de microsatélite en sardina europea (Sardina pilchardus) y las implicaciones para inferir la estructura del stock]}, author = {P Kasapidis and A Silva and G Zampicinini and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84857560434&doi=10.3989%2fscimar.03366.29B&partnerID=40&md5=e9dfcaa4674c55f68be14a06ce7e34b1}, doi = {10.3989/scimar.03366.29B}, issn = {02148358}, year = {2012}, date = {2012-01-01}, journal = {Scientia Marina}, volume = {76}, number = {1}, pages = {123--132}, abstract = {The genetic structure of the European sardine (Sardina pilchardus) was assessed throughout its geographic range using five microsatellite loci. One of the loci seemed to be under hitchhiking selection and exhibited a latitudinal cline along the eastern Atlantic, with abrupt change in allele frequencies from the Alboran Sea to the western Mediterranean and from the east Atlantic coast to the Azores and Madeira. This pattern was very similar to that previously described for the allozymic locus SOD * and these 2 loci could be linked. A Bayesian analysis of environmental factors with the genetic data indicated temperature as a potential selection factor. Selection pressure may be stronger at the southern limit of sardine distribution, because heterozygosity of the non-neutral locus was much lower there. The abrupt change in allele frequencies of the non-neutral locus in certain regions seem to be related more to strong barriers to gene flow, which were not evident for neutral loci, than to abrupt changes in selection pressure. These areas of discontinuity provide a guideline to define and delineate genetic stocks and are generally consistent with areas of phenotypic change in sardine, but they are not in concordance with the currently recognized morphological subspecies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The genetic structure of the European sardine (Sardina pilchardus) was assessed throughout its geographic range using five microsatellite loci. One of the loci seemed to be under hitchhiking selection and exhibited a latitudinal cline along the eastern Atlantic, with abrupt change in allele frequencies from the Alboran Sea to the western Mediterranean and from the east Atlantic coast to the Azores and Madeira. This pattern was very similar to that previously described for the allozymic locus SOD * and these 2 loci could be linked. A Bayesian analysis of environmental factors with the genetic data indicated temperature as a potential selection factor. Selection pressure may be stronger at the southern limit of sardine distribution, because heterozygosity of the non-neutral locus was much lower there. The abrupt change in allele frequencies of the non-neutral locus in certain regions seem to be related more to strong barriers to gene flow, which were not evident for neutral loci, than to abrupt changes in selection pressure. These areas of discontinuity provide a guideline to define and delineate genetic stocks and are generally consistent with areas of phenotypic change in sardine, but they are not in concordance with the currently recognized morphological subspecies. |
Sarropoulou, E; Galindo-Villegas, J; García-Alcázar, A; Kasapidis, P; Mulero, V Characterization of European Sea Bass Transcripts by RNA SEQ After Oral Vaccine Against V. anguillarum Journal Article Marine Biotechnology, 14 (5), pp. 634–642, 2012, ISSN: 14362228. @article{sarropoulou_characterization_2012, title = {Characterization of European Sea Bass Transcripts by RNA SEQ After Oral Vaccine Against V. anguillarum}, author = {E Sarropoulou and J Galindo-Villegas and A García-Alcázar and P Kasapidis and V Mulero}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84865444000&doi=10.1007%2fs10126-012-9466-z&partnerID=40&md5=9c0f09c470e3b9a06d0ec9930b4c3a42}, doi = {10.1007/s10126-012-9466-z}, issn = {14362228}, year = {2012}, date = {2012-01-01}, journal = {Marine Biotechnology}, volume = {14}, number = {5}, pages = {634--642}, abstract = {The European sea bass (Dicentrarchus labrax) is, along with the gilthead sea bream (Sparus aurata), one of the most extensively cultured species in European aquaculture productions. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Evaluation of the efficacy of an oral vaccine against Vibrio anguillarum (Aquavac Vibrio Oral) in sea bass revealed specific immune gene expression profiles in the gut as well as protection of fish. In the present study, we performed RNA SEQ in two different tissues: the hind gut and the head kidney. For each tissue, one control sample (where a sample presents a pool of four to five individuals) and one sample after oral vaccine against V. anguillarum were submitted to 454 next-generation sequencing. In total, 269,043 sequences were obtained, 143,007 for head kidney and 125,036 for gut. The read lengths ranged from 40 to 706 bp with an average length of 348 bp. The total number of clustered sequences for head kidney is accounting to 49,089 ( 34 %) and for gut to 71,676 ( 57 %). Differential expression was detected for 496 transcripts in head kidney and for 336 in gut. The results not only enrich the present collection of expressed sequence tag sequences including rare transcripts like leukocyte immune-type receptors, cullin, or supervillin but also show the efficacy of oral vaccination against V. anguillarum. © 2012 Springer Science+Business Media, LLC.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The European sea bass (Dicentrarchus labrax) is, along with the gilthead sea bream (Sparus aurata), one of the most extensively cultured species in European aquaculture productions. Massive mortalities may be caused by bacterial or viral infections in intensive aquaculture production. Evaluation of the efficacy of an oral vaccine against Vibrio anguillarum (Aquavac Vibrio Oral) in sea bass revealed specific immune gene expression profiles in the gut as well as protection of fish. In the present study, we performed RNA SEQ in two different tissues: the hind gut and the head kidney. For each tissue, one control sample (where a sample presents a pool of four to five individuals) and one sample after oral vaccine against V. anguillarum were submitted to 454 next-generation sequencing. In total, 269,043 sequences were obtained, 143,007 for head kidney and 125,036 for gut. The read lengths ranged from 40 to 706 bp with an average length of 348 bp. The total number of clustered sequences for head kidney is accounting to 49,089 ( 34 %) and for gut to 71,676 ( 57 %). Differential expression was detected for 496 transcripts in head kidney and for 336 in gut. The results not only enrich the present collection of expressed sequence tag sequences including rare transcripts like leukocyte immune-type receptors, cullin, or supervillin but also show the efficacy of oral vaccination against V. anguillarum. © 2012 Springer Science+Business Media, LLC. |
2011 |
Kasapidis, P; Kristoffersen, JB; Pakaki, V; Magoulas, A The puzzling phylogeographic history of the European anchovy (Engraulis encrasicolus) Inproceedings Kasapidis, P (Ed.): 5th Biennial Conference of the International Biogeography Society, Heraklion, Greece, 2011. @inproceedings{kasapidis_puzzling_2011, title = {The puzzling phylogeographic history of the European anchovy (Engraulis encrasicolus)}, author = {P Kasapidis and JB Kristoffersen and V Pakaki and A Magoulas}, editor = {P Kasapidis}, year = {2011}, date = {2011-01-01}, booktitle = {5th Biennial Conference of the International Biogeography Society}, address = {Heraklion, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
2010 |
Tsigenopoulos, C S; Kasapidis, P; Berrebi, P Phylogenetic relationships of hexaploid large-sized barbs (genus Labeobarbus, Cyprinidae) based on mtDNA data Journal Article Molecular Phylogenetics and Evolution, 56 (2), pp. 851–856, 2010, ISSN: 10557903. @article{tsigenopoulos_phylogenetic_2010, title = {Phylogenetic relationships of hexaploid large-sized barbs (genus Labeobarbus, Cyprinidae) based on mtDNA data}, author = {C S Tsigenopoulos and P Kasapidis and P Berrebi}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953126705&doi=10.1016%2fj.ympev.2010.02.006&partnerID=40&md5=3ac6c3b5564b3f5548c45c2972bc3f84}, doi = {10.1016/j.ympev.2010.02.006}, issn = {10557903}, year = {2010}, date = {2010-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {56}, number = {2}, pages = {851--856}, abstract = {The phylogenetic relationships among species of the Labeobarbus genus (Teleostei, Cyprinidae) which comprises large body-sized hexaploid taxa were inferred using complete cytochrome b mitochondrial gene sequences. Molecular data suggest two main evolutionary groups which roughly correspond to a Northern (Middle East and Northwest Africa) and a sub-Saharan lineage. The splitting of the African hexaploids from their Asian ancestors and their subsequent diversification on the African continent occurred in the Late Miocene, a period in which other cyprinins also invaded Africa and radiated in the Mediterranean region. Finally, systematic implications of these results to the taxonomic validity of genera or subgenera such as Varicorhinus, Kosswigobarbus, Carasobarbus and Capoeta are further discussed. © 2010 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The phylogenetic relationships among species of the Labeobarbus genus (Teleostei, Cyprinidae) which comprises large body-sized hexaploid taxa were inferred using complete cytochrome b mitochondrial gene sequences. Molecular data suggest two main evolutionary groups which roughly correspond to a Northern (Middle East and Northwest Africa) and a sub-Saharan lineage. The splitting of the African hexaploids from their Asian ancestors and their subsequent diversification on the African continent occurred in the Late Miocene, a period in which other cyprinins also invaded Africa and radiated in the Mediterranean region. Finally, systematic implications of these results to the taxonomic validity of genera or subgenera such as Varicorhinus, Kosswigobarbus, Carasobarbus and Capoeta are further discussed. © 2010 Elsevier Inc. All rights reserved. |
2009 |
Sotiropoulos, K; Eleftherakos, K; Tsaparis, D; Kasapidis, P; Magoulas, A; Legakis, A New polymorphic microsatellite loci for the Greek smooth newt, Lissotriton vulgaris graecus, and their utility in the nominotypical subspecies Journal Article Molecular Ecology Resources, 9 (1), pp. 292–295, 2009, ISSN: 1755098X. @article{sotiropoulos_new_2009, title = {New polymorphic microsatellite loci for the Greek smooth newt, Lissotriton vulgaris graecus, and their utility in the nominotypical subspecies}, author = {K Sotiropoulos and K Eleftherakos and D Tsaparis and P Kasapidis and A Magoulas and A Legakis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-58949099095&doi=10.1111%2fj.1755-0998.2008.02245.x&partnerID=40&md5=541bd79e38722806c070c62462f9466a}, doi = {10.1111/j.1755-0998.2008.02245.x}, issn = {1755098X}, year = {2009}, date = {2009-01-01}, journal = {Molecular Ecology Resources}, volume = {9}, number = {1}, pages = {292--295}, abstract = {Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)11 probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean number of alleles at 5.0 and mean observed heterozygosity at 0.520. The amplification success also in the nominotypical subspecies favours the use of these microsatellite loci in population genetic analyses as well as in the study of contact zones between smooth newt subspecies. © 2008 The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eight polymorphic microsatellites were isolated from the Greek smooth newt (Lissotriton vulgaris graecus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)11 probe. The loci showed different variation patterns in a single breeding population (32 individuals) with mean number of alleles at 5.0 and mean observed heterozygosity at 0.520. The amplification success also in the nominotypical subspecies favours the use of these microsatellite loci in population genetic analyses as well as in the study of contact zones between smooth newt subspecies. © 2008 The Authors. |
Kasapidis, P; Pakaki, V; Kotoulas, G; Magoulas, A Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius Journal Article Molecular Ecology Resources, 9 (5), pp. 1383–1386, 2009, ISSN: 1755098X. @article{kasapidis_isolation_2009, title = {Isolation and characterization of 18 new polymorphic microsatellite loci for the swordfish, Xiphias gladius}, author = {P Kasapidis and V Pakaki and G Kotoulas and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-68949088416&doi=10.1111%2fj.1755-0998.2009.02665.x&partnerID=40&md5=1d9054fa754b8be29bee29ef86e5c592}, doi = {10.1111/j.1755-0998.2009.02665.x}, issn = {1755098X}, year = {2009}, date = {2009-01-01}, journal = {Molecular Ecology Resources}, volume = {9}, number = {5}, pages = {1383--1386}, abstract = {Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci. © 2009 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eighteen microsatellite loci (13 di- and 5 tri-repeats) were isolated from swordfish and characterized in two populations from the Atlantic Ocean and Mediterranean Sea. The number of alleles per locus ranged from two to 29 and the observed heterozygosity from 0.302 to 0.953. All but one locus conformed to Hardy-Weinberg expectations and there was no evidence for linkage disequilibrium between loci. © 2009 Blackwell Publishing Ltd. |
Pakaki, V; Magoulas, A; Kasapidis, P New polymorphic microsatellite loci for population studies in the European anchovy, Engraulis encrasicolus (L.) Journal Article Molecular Ecology Resources, 9 (5), pp. 1406–1409, 2009, ISSN: 1755098X. @article{pakaki_new_2009, title = {New polymorphic microsatellite loci for population studies in the European anchovy, Engraulis encrasicolus (L.)}, author = {V Pakaki and A Magoulas and P Kasapidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-68949083365&doi=10.1111%2fj.1755-0998.2009.02681.x&partnerID=40&md5=0821f16843bcdc50f7b239e6b4e4aad9}, doi = {10.1111/j.1755-0998.2009.02681.x}, issn = {1755098X}, year = {2009}, date = {2009-01-01}, journal = {Molecular Ecology Resources}, volume = {9}, number = {5}, pages = {1406--1409}, abstract = {Eleven microsatellite loci were developed in the European anchovy, Engraulis encrasicolus, and tested in samples from two geographically distant populations (Atlantic and Mediterranean Sea). Number of alleles ranged from eight to 28 and observed heterozygosity from 0.440 to 0.920. There was no evidence of linkage disequilibrium, although two loci are indeed linked. All loci were in Hardy-Weinberg equilibrium, except for one locus in the Atlantic and two loci in the Mediterranean sample. These three loci plus two more showed evidence for null alleles. © 2009 Blackwell Publishing Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eleven microsatellite loci were developed in the European anchovy, Engraulis encrasicolus, and tested in samples from two geographically distant populations (Atlantic and Mediterranean Sea). Number of alleles ranged from eight to 28 and observed heterozygosity from 0.440 to 0.920. There was no evidence of linkage disequilibrium, although two loci are indeed linked. All loci were in Hardy-Weinberg equilibrium, except for one locus in the Atlantic and two loci in the Mediterranean sample. These three loci plus two more showed evidence for null alleles. © 2009 Blackwell Publishing Ltd. |
2008 |
Sotiropoulos, K; Tsaparis, D; Eleftherakos, K; Kotoulas, G; Legakis, A; Kasapidis, P Molecular Ecology Resources, 8 (6), pp. 1402–1404, 2008, ISSN: 1755098X. @article{sotiropoulos_new_2008, title = {New polymorphic microsatellite loci for the Macedonian crested newt, Triturus macedonicus, and cross-priming testing in four other crested newt species}, author = {K Sotiropoulos and D Tsaparis and K Eleftherakos and G Kotoulas and A Legakis and P Kasapidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-55149089288&doi=10.1111%2fj.1755-0998.2008.02318.x&partnerID=40&md5=fb01beea4ddfaf49596cc574066f8b1d}, doi = {10.1111/j.1755-0998.2008.02318.x}, issn = {1755098X}, year = {2008}, date = {2008-01-01}, journal = {Molecular Ecology Resources}, volume = {8}, number = {6}, pages = {1402--1404}, abstract = {Eleven microsatellites have been characterized for Triturus macedonicus. Nine loci showed different variation patterns in a sample of 40 individuals from a single breeding pond in Zagori province (Greece), with an average number of 4.2 alleles per locus and an expected heterozygosity ranging from 0.1199 to 0.8079. Distinct cross-priming amplification rates were recovered on four additional crested newt species. Two monomorphic T. macedonicus loci were polymorphic in other Triturus species. The microsatellites developed herein could be a useful intraspecific genetic tool to undertake fine-scale population genetic analyses as well as in the study of contact zones between crested newt species. © 2008 The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Eleven microsatellites have been characterized for Triturus macedonicus. Nine loci showed different variation patterns in a sample of 40 individuals from a single breeding pond in Zagori province (Greece), with an average number of 4.2 alleles per locus and an expected heterozygosity ranging from 0.1199 to 0.8079. Distinct cross-priming amplification rates were recovered on four additional crested newt species. Two monomorphic T. macedonicus loci were polymorphic in other Triturus species. The microsatellites developed herein could be a useful intraspecific genetic tool to undertake fine-scale population genetic analyses as well as in the study of contact zones between crested newt species. © 2008 The Authors. |
Kasapidis, P; Magoulas, A Development and application of microsatellite markers to address the population structure of the horse mackerel Trachurus trachurus Journal Article Fisheries Research, 89 (2), pp. 132–135, 2008, ISSN: 01657836. @article{kasapidis_development_2008, title = {Development and application of microsatellite markers to address the population structure of the horse mackerel Trachurus trachurus}, author = {P Kasapidis and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-38749149338&doi=10.1016%2fj.fishres.2007.09.015&partnerID=40&md5=fbea467751d7c1a424f5a26938b8f88e}, doi = {10.1016/j.fishres.2007.09.015}, issn = {01657836}, year = {2008}, date = {2008-01-01}, journal = {Fisheries Research}, volume = {89}, number = {2}, pages = {132--135}, abstract = {The genetic structure of the horse mackerel Trachurus trachurus was studied over almost its entire distribution range by genotyping 16 samples for 4 microsatellite loci. No temporal or spatial genetic differentiation was detected. A few statistically significant pairwise differences were most probably of stochastic nature, since they do not reveal any specific pattern. The lack of genetic differentiation in horse mackerel probably reflects the large population size and lack of barriers to the gene flow. However, this result should be viewed with caution, given the relatively low number of loci used in this study. © 2007 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The genetic structure of the horse mackerel Trachurus trachurus was studied over almost its entire distribution range by genotyping 16 samples for 4 microsatellite loci. No temporal or spatial genetic differentiation was detected. A few statistically significant pairwise differences were most probably of stochastic nature, since they do not reveal any specific pattern. The lack of genetic differentiation in horse mackerel probably reflects the large population size and lack of barriers to the gene flow. However, this result should be viewed with caution, given the relatively low number of loci used in this study. © 2007 Elsevier B.V. All rights reserved. |
2007 |
Kotoulas, G; Mejuto, J; Antoniou, A; Kasapidis, P; Tserpes, G; Piccineti, C; Peristeraki, P; Garcia-Cortes, B; Oikonomaki, K; la Serna, De M J; Magoulas, A Global genetic structure of the swordfish Xiphias gladius, as revealed by microsatellite markers Journal Article Collect. Vol. Sci. Pap. ICCAT, 61 , pp. 79–88, 2007. @article{kotoulas_global_2007, title = {Global genetic structure of the swordfish Xiphias gladius, as revealed by microsatellite markers}, author = {G Kotoulas and J Mejuto and A Antoniou and P Kasapidis and G Tserpes and C Piccineti and P Peristeraki and B Garcia-Cortes and K Oikonomaki and M J De la Serna and A Magoulas}, year = {2007}, date = {2007-01-01}, journal = {Collect. Vol. Sci. Pap. ICCAT}, volume = {61}, pages = {79--88}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kasapidis, P; Valeiras, X; Antoniou, A; Kotoulas, Giorgios; Garcia-Cortes, B; Mejuto, J Genetic and growth profiles of three specimens of swordfish (Xiphias gladius) tagged and recaptured in the North Atlantic Journal Article Col. Vol. Sci. Pap., ICCAT SCRS-06-119, 60 (6), pp. 1964–1973, 2007. @article{kasapidis_genetic_2007, title = {Genetic and growth profiles of three specimens of swordfish (Xiphias gladius) tagged and recaptured in the North Atlantic}, author = {P Kasapidis and X Valeiras and A Antoniou and Giorgios Kotoulas and B Garcia-Cortes and J Mejuto}, year = {2007}, date = {2007-01-01}, journal = {Col. Vol. Sci. Pap., ICCAT SCRS-06-119}, volume = {60}, number = {6}, pages = {1964--1973}, abstract = {This paper presents an analysis of the genetic and growth patterns of three swordfish specimens (two males and one female) tagged with traditional tags and later recaptured over a period of time ranging from 2.7 to 5.4 years. Two of these specimens were tagged and recaptured in the NW Atlantic, while the third individual was tagged and recaptured in the NE Atlantic. These three specimens were genotyped for four micro-satellite loci and were analysed together with additional genotyped specimens from Atlantic and Mediterranean areas using a Bayesian cluster analyses. The results suggest that the three recaptured swordfish have a genetic profile that is characteristic of the Atlantic. The growth patterns were seen to differ in two of the specimens analysed (male and female): the male was assumed as a single ring pattern, while the female was assumed as a mostly double ring pattern. The age estimation of these two specimens according to these premises could be accommodated to previous growth studies. The third specimen which is known to be a male at least 6 years of age, tagged and recaptured in the NW Atlantic, was not possible to accommodate to previous growth studies. The examination of genetic data in combination with tagging-recapture information may facilitate the study of aspects related to individual and stock specific growth and elucidate the patterns of ring formation on the hard parts (spines). It would be advisable to enhance the tagging-recapture protocols of swordfish and to include the routine sampling of tissues and hard parts in all the recaptures made by the different fleets.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper presents an analysis of the genetic and growth patterns of three swordfish specimens (two males and one female) tagged with traditional tags and later recaptured over a period of time ranging from 2.7 to 5.4 years. Two of these specimens were tagged and recaptured in the NW Atlantic, while the third individual was tagged and recaptured in the NE Atlantic. These three specimens were genotyped for four micro-satellite loci and were analysed together with additional genotyped specimens from Atlantic and Mediterranean areas using a Bayesian cluster analyses. The results suggest that the three recaptured swordfish have a genetic profile that is characteristic of the Atlantic. The growth patterns were seen to differ in two of the specimens analysed (male and female): the male was assumed as a single ring pattern, while the female was assumed as a mostly double ring pattern. The age estimation of these two specimens according to these premises could be accommodated to previous growth studies. The third specimen which is known to be a male at least 6 years of age, tagged and recaptured in the NW Atlantic, was not possible to accommodate to previous growth studies. The examination of genetic data in combination with tagging-recapture information may facilitate the study of aspects related to individual and stock specific growth and elucidate the patterns of ring formation on the hard parts (spines). It would be advisable to enhance the tagging-recapture protocols of swordfish and to include the routine sampling of tissues and hard parts in all the recaptures made by the different fleets. |
Kasapidis, P; Mejuto, J; Tserpes, G; Antoniou, A; Garcia-Cortes, B; Peristeraki, P; Oikonomaki, K; Kotoulas, Giorgios; A., Magoulas Genetic structure of the swordfish (Xiphias gladius) stocks in the Atlantic using microsatellite DNA analysis Journal Article Col. Vol. Sci. Pap., ICCAT SCRS-06-035, 61 , pp. 89–98, 2007. @article{kasapidis_genetic_2007-1, title = {Genetic structure of the swordfish (Xiphias gladius) stocks in the Atlantic using microsatellite DNA analysis}, author = {P Kasapidis and J Mejuto and G Tserpes and A Antoniou and B Garcia-Cortes and P Peristeraki and K Oikonomaki and Giorgios Kotoulas and Magoulas A.}, year = {2007}, date = {2007-01-01}, journal = {Col. Vol. Sci. Pap., ICCAT SCRS-06-035}, volume = {61}, pages = {89--98}, abstract = {The genetic structure of the swordfish (Xiphias gladius) in the Atlantic Ocean was examined by genotyping 1179 individuals for 4 microsatellite loci. These individuals were collected during the years 1999-2002 from the following regions: south Atlantic (up to 5oN), mid-Atlantic (9oN to 20oN), northeast Atlantic (North of 30oN and East of 31oW), northwest Atlantic (North of 30oN and West of 31oW). Gene diversity was very high (textbackslashtextgreater0.96) for all four loci. Heterogeneity tests and pairwise Fsts showed that the South Atlantic group was significantly different from all the other groups (ptextbackslashtextless0.000).These results are in agreement with previous mitochondrial DNA data and do not support a need for changing the 5oN latitude as a boundary for fisheries. Some individuals were also genotyped for the Calmodulin intron 4 gene (CaM) to compare with an earlier dataset for this marker. Allele frequencies found for CaM were in agreement with previous observation and showed a different population structure pattern compared to that revealed by microsatellites. However, the pattern reflected in CaM should be treated with caution, since CaM is only a single diallelic locus, possibly under strong selection. The genotyping of the samples for more microsatellite loci, which is in progress, is expected to further elucidate the genetic structure of the swordfish in the Atlantic, by further increasing resolution.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The genetic structure of the swordfish (Xiphias gladius) in the Atlantic Ocean was examined by genotyping 1179 individuals for 4 microsatellite loci. These individuals were collected during the years 1999-2002 from the following regions: south Atlantic (up to 5oN), mid-Atlantic (9oN to 20oN), northeast Atlantic (North of 30oN and East of 31oW), northwest Atlantic (North of 30oN and West of 31oW). Gene diversity was very high (textbackslashtextgreater0.96) for all four loci. Heterogeneity tests and pairwise Fsts showed that the South Atlantic group was significantly different from all the other groups (ptextbackslashtextless0.000).These results are in agreement with previous mitochondrial DNA data and do not support a need for changing the 5oN latitude as a boundary for fisheries. Some individuals were also genotyped for the Calmodulin intron 4 gene (CaM) to compare with an earlier dataset for this marker. Allele frequencies found for CaM were in agreement with previous observation and showed a different population structure pattern compared to that revealed by microsatellites. However, the pattern reflected in CaM should be treated with caution, since CaM is only a single diallelic locus, possibly under strong selection. The genotyping of the samples for more microsatellite loci, which is in progress, is expected to further elucidate the genetic structure of the swordfish in the Atlantic, by further increasing resolution. |
Kasapidis, P; Peristeraki, P; Tserpes, G; Magoulas, A First record of the Lessepsian migrant Lagocephalus sceleratus (Gmelin 1789) (Osteichthyes: Tetraodontidae) in the Cretan Sea (Aegean, Greece) Journal Article Aquatic Invasions, 2 (1), pp. 71–73, 2007, ISSN: 17986540, (Publisher: Regional Euro-Asian Biological Invasions Centre). @article{kasapidis_first_2007, title = {First record of the Lessepsian migrant Lagocephalus sceleratus (Gmelin 1789) (Osteichthyes: Tetraodontidae) in the Cretan Sea (Aegean, Greece)}, author = {P Kasapidis and P Peristeraki and G Tserpes and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-56949103595&doi=10.3391%2fai.2007.2.1.9&partnerID=40&md5=c4ba957c29ae825b2870dc9302e3daa6}, doi = {10.3391/ai.2007.2.1.9}, issn = {17986540}, year = {2007}, date = {2007-01-01}, journal = {Aquatic Invasions}, volume = {2}, number = {1}, pages = {71--73}, abstract = {The Lessepsian migrant fish Lagocephalus sceleratus was recorded for the first time in July and in December 2005 from the Cretan Sea (Aegean, Greece). The species identity was confirmed by both morphometric and genetic analyses. These records indicate that the species has established populations around the continental shelf of Crete. © 2007 The Author(s).}, note = {Publisher: Regional Euro-Asian Biological Invasions Centre}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Lessepsian migrant fish Lagocephalus sceleratus was recorded for the first time in July and in December 2005 from the Cretan Sea (Aegean, Greece). The species identity was confirmed by both morphometric and genetic analyses. These records indicate that the species has established populations around the continental shelf of Crete. © 2007 The Author(s). |
Kasapidis, P; Magoulas, A Genetic structure of fish stocks in the Hellenic Seas and the Mediterranean Incollection Papaconstantinou, C; Zenetos, A (Ed.): State of the Hellenic Fisheries, pp. 391–399, HCMR, Athens, 2007, (Backup Publisher: HCMR Section: VII.4). @incollection{kasapidis_genetic_2007-2, title = {Genetic structure of fish stocks in the Hellenic Seas and the Mediterranean}, author = {P Kasapidis and A Magoulas}, editor = {C Papaconstantinou and A Zenetos}, year = {2007}, date = {2007-01-01}, booktitle = {State of the Hellenic Fisheries}, pages = {391--399}, publisher = {HCMR}, address = {Athens}, note = {Backup Publisher: HCMR Section: VII.4}, keywords = {}, pubstate = {published}, tppubtype = {incollection} } |
Kasapidis, P; Peristeraki, P; Tserpes, G; Magoulas, A A new record of the Lessepsian invasive fish Etrumeus teres (Osteichthyes: Clupeidae) in the Mediterranean Sea (Aegean, Greece) Journal Article Aquatic Invasions, 2 (2), pp. 152–154, 2007, ISSN: 17986540, (Publisher: Regional Euro-Asian Biological Invasions Centre). @article{kasapidis_new_2007, title = {A new record of the Lessepsian invasive fish Etrumeus teres (Osteichthyes: Clupeidae) in the Mediterranean Sea (Aegean, Greece)}, author = {P Kasapidis and P Peristeraki and G Tserpes and A Magoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84892849154&doi=10.3391%2fai.2007.2.2.12&partnerID=40&md5=74a91588f31c323b30d07687778d9ce9}, doi = {10.3391/ai.2007.2.2.12}, issn = {17986540}, year = {2007}, date = {2007-01-01}, journal = {Aquatic Invasions}, volume = {2}, number = {2}, pages = {152--154}, abstract = {The Lessepsian invasive fish Etrumeus teres was recorded for the first time off Crete, Greece in July 2005. Their abundance suggests that the species may become of commercial importance in the south Aegean Sea. © 2007 The Author(s).}, note = {Publisher: Regional Euro-Asian Biological Invasions Centre}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Lessepsian invasive fish Etrumeus teres was recorded for the first time off Crete, Greece in July 2005. Their abundance suggests that the species may become of commercial importance in the south Aegean Sea. © 2007 The Author(s). |
2005 |
Kasapidis, P; Suchentrunk, F; Magoulas, A; Kotoulas, G Molecular Phylogenetics and Evolution, 34 (1), pp. 55–66, 2005, ISSN: 10557903. @article{kasapidis_shaping_2005, title = {The shaping of mitochondrial DNA phylogeographic patterns of the brown hare (Lepus europaeus) under the combined influence of Late Pleistocene climatic fluctuations and anthropogenic translocations}, author = {P Kasapidis and F Suchentrunk and A Magoulas and G Kotoulas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-9744258860&doi=10.1016%2fj.ympev.2004.09.007&partnerID=40&md5=a65c976ffbb7419b3edd624a3efbeb4d}, doi = {10.1016/j.ympev.2004.09.007}, issn = {10557903}, year = {2005}, date = {2005-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {34}, number = {1}, pages = {55--66}, abstract = {The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species. © 2004 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species. © 2004 Elsevier Inc. All rights reserved. |
Kasapidis, P; Magoulas, A; Mylonas, M; Zouros, E The phylogeography of the gecko Cyrtopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago Journal Article Molecular Phylogenetics and Evolution, 35 (3), pp. 612–623, 2005, ISSN: 10557903. @article{kasapidis_phylogeography_2005, title = {The phylogeography of the gecko Cyrtopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago}, author = {P Kasapidis and A Magoulas and M Mylonas and E Zouros}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-18144425199&doi=10.1016%2fj.ympev.2005.02.005&partnerID=40&md5=51a9fa8e77d60205ccf8124439085449}, doi = {10.1016/j.ympev.2005.02.005}, issn = {10557903}, year = {2005}, date = {2005-01-01}, journal = {Molecular Phylogenetics and Evolution}, volume = {35}, number = {3}, pages = {612--623}, abstract = {Cyrtopodion kotschyi is a small gecko, widely distributed on the islands of the Aegean archipelago and the adjacent mainland. We unveiled the phylogeography of the species by using a portion of the cytochrome oxidase I mitochondrial DNA gene from 35 insular and mainland populations. The distinct geographic distribution of the major clades of the phylogenetic tree and its topology suggest a spatial and temporal sequence of phylogenetic separations that coincide with some major paleogeographical separations during the geological history of the Aegean and support a mainly vicariant pattern of differentiation. The separation times and 95% confidence limits among the different clades were estimated according to two different paleogeographical scenarios. The very high interpopulation genetic divergence (up to 20% uncorrected pairwise distances) and the better concordance between paleogeographical and phylogenetic separations for one of the scenarios suggest that species differentiation started during Miocene (about 10 Mya) due to the fragmentation of the united landmass of "Ägäis" that was Aegean at that time. © 2005 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Cyrtopodion kotschyi is a small gecko, widely distributed on the islands of the Aegean archipelago and the adjacent mainland. We unveiled the phylogeography of the species by using a portion of the cytochrome oxidase I mitochondrial DNA gene from 35 insular and mainland populations. The distinct geographic distribution of the major clades of the phylogenetic tree and its topology suggest a spatial and temporal sequence of phylogenetic separations that coincide with some major paleogeographical separations during the geological history of the Aegean and support a mainly vicariant pattern of differentiation. The separation times and 95% confidence limits among the different clades were estimated according to two different paleogeographical scenarios. The very high interpopulation genetic divergence (up to 20% uncorrected pairwise distances) and the better concordance between paleogeographical and phylogenetic separations for one of the scenarios suggest that species differentiation started during Miocene (about 10 Mya) due to the fragmentation of the united landmass of "Ägäis" that was Aegean at that time. © 2005 Elsevier Inc. All rights reserved. |
2004 |
Kasapidis, P; Planes, S; Laurent, V; Quinta, R; Teia, A; Lenfant, R; Darivianakis, S; Terzoglou, V; Kotoulas, G; Magoulas, A Stock discrimination and temporal and spatial genetic variation of sardine (Sardina pilchardus) in northeastern Atlantic, with a combined analysis of nuclear (microsatellites and allozymes) and mitochondrial DNA markers. Inproceedings Kasapidis, P (Ed.): 2004 ICES Annual Science Conference, 2004. @inproceedings{kasapidis_stock_2004, title = {Stock discrimination and temporal and spatial genetic variation of sardine (Sardina pilchardus) in northeastern Atlantic, with a combined analysis of nuclear (microsatellites and allozymes) and mitochondrial DNA markers.}, author = {P Kasapidis and S Planes and V Laurent and R Quinta and A Teia and R Lenfant and S Darivianakis and V Terzoglou and G Kotoulas and A Magoulas}, editor = {P Kasapidis}, year = {2004}, date = {2004-09-01}, booktitle = {2004 ICES Annual Science Conference}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
1998 |
Hill, J; Hostert, P; Tsiourlis, G; Kasapidis, P; Udelhoven, T; Diemer, C Monitoring 20 years of increased grazing impact on the Greek island of Crete with earth observation satellites Journal Article Journal of Arid Environments, 39 (2), pp. 165–178, 1998, ISSN: 01401963, (Publisher: Academic Press). @article{hill_monitoring_1998, title = {Monitoring 20 years of increased grazing impact on the Greek island of Crete with earth observation satellites}, author = {J Hill and P Hostert and G Tsiourlis and P Kasapidis and T Udelhoven and C Diemer}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032103622&doi=10.1006%2fjare.1998.0392&partnerID=40&md5=5948f809f102880deb29992fcbf6ba03}, doi = {10.1006/jare.1998.0392}, issn = {01401963}, year = {1998}, date = {1998-01-01}, journal = {Journal of Arid Environments}, volume = {39}, number = {2}, pages = {165--178}, abstract = {The degradation of permanent semi-natural vegetation and the resulting acceleration of soil degradation and erosion processes constitute major elements of land degradation in the Mediterranean basin. These elements are triggered by human activities rather than climatic conditions. The Greek island of Crete represents a characteristic case of land degradation resulting from hundreds of years of intensive grazing and fires. Since Greece joined the European Communities in 1981, grazing in mountainous regions has greatly increased due to subsidies that became available through the Common Agricultural Policy. Within a European Research Project on the use of satellite remote sensing for monitoring environmental change in Mediterranean ecosystems (DeMon-2: An Integrated Approach to Assess and Monitor Desertification Processes in the Mediterranean Basin), we have initiated a study to monitor the impact of increased grazing pressure on two mountainous ecosystems in Crete. The approach is based on describing surface conditions and vegetation cover over time with a long-term series of earth observation satellites.}, note = {Publisher: Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } The degradation of permanent semi-natural vegetation and the resulting acceleration of soil degradation and erosion processes constitute major elements of land degradation in the Mediterranean basin. These elements are triggered by human activities rather than climatic conditions. The Greek island of Crete represents a characteristic case of land degradation resulting from hundreds of years of intensive grazing and fires. Since Greece joined the European Communities in 1981, grazing in mountainous regions has greatly increased due to subsidies that became available through the Common Agricultural Policy. Within a European Research Project on the use of satellite remote sensing for monitoring environmental change in Mediterranean ecosystems (DeMon-2: An Integrated Approach to Assess and Monitor Desertification Processes in the Mediterranean Basin), we have initiated a study to monitor the impact of increased grazing pressure on two mountainous ecosystems in Crete. The approach is based on describing surface conditions and vegetation cover over time with a long-term series of earth observation satellites. |
1996 |
Kasapidis, P; Provatidou, S; Maragou, P; Valakos, E D Neue Daten über die Herpetofauna von Lesbos (ägäische Inseln, Griechenland) und einige biogeographische Bemerkungen über die Inseln des nordöstlichen ägäischen Archipels Journal Article Salamandra, 32 (3), pp. 171–180, 1996. @article{kasapidis_neue_1996, title = {Neue Daten über die Herpetofauna von Lesbos (ägäische Inseln, Griechenland) und einige biogeographische Bemerkungen über die Inseln des nordöstlichen ägäischen Archipels}, author = {P Kasapidis and S Provatidou and P Maragou and E D Valakos}, year = {1996}, date = {1996-01-01}, journal = {Salamandra}, volume = {32}, number = {3}, pages = {171--180}, abstract = {New data on the herpetofauna of Lesbos ( Aegean Islands, Greece) and some biogeographical remarks on the islands of the northern Aegean Archipelago. Fourteen species of reptiles were found on Lesbos lsland. The species Ablepharus kitaibelii and Mallolon monspessulanus are recorded for the first time from the island. The localities and some morphometric characters of the caught specimens are noted. Finally, we attempt to combine our data and the bibliographical ones in a biogeographical approach to the fauna of the islands of the northeastern Aegean Archipelago.}, keywords = {}, pubstate = {published}, tppubtype = {article} } New data on the herpetofauna of Lesbos ( Aegean Islands, Greece) and some biogeographical remarks on the islands of the northern Aegean Archipelago. Fourteen species of reptiles were found on Lesbos lsland. The species Ablepharus kitaibelii and Mallolon monspessulanus are recorded for the first time from the island. The localities and some morphometric characters of the caught specimens are noted. Finally, we attempt to combine our data and the bibliographical ones in a biogeographical approach to the fauna of the islands of the northeastern Aegean Archipelago. |