2024 |
Katirtzoglou, Aikaterini; Tsaparis, Dimitris; Kolios, Evangelos; Magoulas, Antonios; Mylonas, Constantinos C; Fakriadis, Ioannis; Manousaki, Tereza; Tsigenopoulos, Costas S Frontiers in Fish Science, 2 , pp. 1356313, 2024, ISSN: 2813-9097. @article{katirtzoglou_population_2024, title = {Population genomic analysis of the greater amberjack (\textit{Seriola dumerili}) in the Mediterranean and the Northeast Atlantic, based on SNPs, microsatellites, and mitochondrial DNA sequences}, author = {Aikaterini Katirtzoglou and Dimitris Tsaparis and Evangelos Kolios and Antonios Magoulas and Constantinos C Mylonas and Ioannis Fakriadis and Tereza Manousaki and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/03/2024-Kaitirtzoglou-frish-14.pdf https://www.frontiersin.org/articles/10.3389/frish.2024.1356313/full}, doi = {10.3389/frish.2024.1356313}, issn = {2813-9097}, year = {2024}, date = {2024-03-14}, urldate = {2024-03-14}, journal = {Frontiers in Fish Science}, volume = {2}, pages = {1356313}, abstract = {The greater amberjack ( Seriola dumerili ) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of S. dumerili in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the tead1a /TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The greater amberjack ( Seriola dumerili ) has attracted considerable economic interest since the 1990s because it possesses traits that distinguish it as a promising candidate in aquaculture. However, the challenges of its successful rearing, combined with the need to develop proper management practices, underline the importance of research into the genetic diversity of both wild and farmed stocks. We aimed to decipher the genetic structure of S. dumerili in the Eastern Mediterranean and the Northeast Atlantic using three types of genetic markers (mitochondrial control region sequences, microsatellites, and single nucleotide polymorphisms, or SNPs) to evaluate the population genetic structure of the species. The results were compared to those of previous studies of the species focusing on the Central Mediterranean and confirmed the presence of two divergent mtDNA haplogroups distributed without any detectable geographical structuring within the Mediterranean and the Atlantic. However, population analyses of the genetic structure of the species using either 10 microsatellites or a set of 1,051 SNP markers suggest that the species forms three genetically distinct groups, one in the Mediterranean and two in the Atlantic. The latter has so far not been reported in the Northeast Atlantic, and that this differentiation refers to samples from the Canary Islands is surprising. Fifteen candidate outlier SNP loci were identified in the data set, one located within the tead1a /TEF-1A gene, which has been associated with temperature acclimation of the medaka. This work enriches our knowledge of the genetic diversity of wild populations of the greater amberjack in the Mediterranean and the Northeast Atlantic and attempts to investigate signs of local adaptation toward a better understanding of the species distribution patterns. Future studies should be conducted to investigate the genomic regions associated with temperature acclimation in marine organisms that have to adapt to the ongoing climate change pressures, such as sea temperature rise, in order to survive. |
2023 |
Sarafidou, Georgia; Tsaparis, Dimitris; Issaris, Yiannis; Chatzigeorgiou, Giorgos; Grigoriou, Panos; Chatzinikolaou, Eva; Pavloudi, Christina Insights on Pinna nobilis population genetic structure in the Aegean and Ionian Sea Journal Article PeerJ, 11 , pp. e16491, 2023, ISSN: 2167-8359. @article{sarafidou_insights_2023, title = {Insights on \textit{Pinna nobilis} population genetic structure in the Aegean and Ionian Sea}, author = {Georgia Sarafidou and Dimitris Tsaparis and Yiannis Issaris and Giorgos Chatzigeorgiou and Panos Grigoriou and Eva Chatzinikolaou and Christina Pavloudi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2023/12/2023-Sarafidou-peerj-61.pdf https://peerj.com/articles/16491}, doi = {10.7717/peerj.16491}, issn = {2167-8359}, year = {2023}, date = {2023-12-01}, urldate = {2023-12-01}, journal = {PeerJ}, volume = {11}, pages = {e16491}, abstract = {The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e. , by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species’ most suitable conservation management.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e. , by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species’ most suitable conservation management. |
Xirouchakis, S M; Botsidou, P; Baxevani, K; Andreou, G; Tsaparis, D Brood sex ratio variation in a colonial raptor, the Eleonora's falcon, Falco eleonorae Journal Article Animal Behaviour, 195 , pp. 93–106, 2023, ISSN: 00033472. @article{xirouchakis_brood_2023, title = {Brood sex ratio variation in a colonial raptor, the Eleonora's falcon, Falco eleonorae}, author = {S M Xirouchakis and P Botsidou and K Baxevani and G Andreou and D Tsaparis}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0003347222002986 https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2023-Xirouchakis-AniBeh-pre-print-20.pdf}, doi = {10.1016/j.anbehav.2022.11.001}, issn = {00033472}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-23}, journal = {Animal Behaviour}, volume = {195}, pages = {93--106}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Plis, Kamila; Niedziałkowska, Magdalena; Borowik, Tomasz; Lang, Johannes; Heddergott, Mike; Tiainen, Juha; Bunevich, Aleksey; Šprem, Nikica; Paule, Ladislav; Danilkin, Aleksey; Kholodova, Marina; Zvychaynaya, Elena; Kashinina, Nadezhda; Pokorny, Boštjan; Flajšman, Katarina; Paulauskas, Algimantas; Djan, Mihajla; Ristić, Zoran; Novák, Luboš; Kusza, Szilvia; Miller, Christine; Tsaparis, Dimitris; Stoyanov, Stoyan; Shkvyria, Maryna; Suchentrunk, Franz; Kutal, Miroslav; Lavadinović, Vukan; Šnjegota, Dragana; Krapal, Ana-Maria; Dănilă, Gabriel; Veeroja, Rauno; Dulko, Elżbieta; Jędrzejewska, Bogumiła Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe Journal Article 102 (5), pp. 1743–1754, 2023, ISSN: 1616-5047, 1618-1476. @article{plis_mitochondrial_2022, title = {Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe}, author = {Kamila Plis and Magdalena Niedziałkowska and Tomasz Borowik and Johannes Lang and Mike Heddergott and Juha Tiainen and Aleksey Bunevich and Nikica Šprem and Ladislav Paule and Aleksey Danilkin and Marina Kholodova and Elena Zvychaynaya and Nadezhda Kashinina and Boštjan Pokorny and Katarina Flajšman and Algimantas Paulauskas and Mihajla Djan and Zoran Ristić and Luboš Novák and Szilvia Kusza and Christine Miller and Dimitris Tsaparis and Stoyan Stoyanov and Maryna Shkvyria and Franz Suchentrunk and Miroslav Kutal and Vukan Lavadinović and Dragana Šnjegota and Ana-Maria Krapal and Gabriel Dănilă and Rauno Veeroja and Elżbieta Dulko and Bogumiła Jędrzejewska}, url = {https://link.springer.com/10.1007/s42991-022-00274-y https://imbbc.hcmr.gr/wp-content/uploads/2023/05/2022-Plis-MAMBIO-pre-print-83.pdf}, doi = {10.1007/s42991-022-00274-y}, issn = {1616-5047, 1618-1476}, year = {2023}, date = {2023-05-23}, urldate = {2023-05-24}, volume = {102}, number = {5}, pages = {1743--1754}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2022 |
Sarropoulou, Xenia; Tsaparis, Dimitris; Tsagarakis, Konstantinos; Badouvas, Nicholas; Tsigenopoulos, Costas S Different patterns of population structure and genetic diversity of three mesopelagic fishes in the Greek Seas Journal Article Mediterranean Marine Science, 23 (3), pp. 536–545, 2022, ISSN: 1791-6763. @article{sarropoulou_different_2022, title = {Different patterns of population structure and genetic diversity of three mesopelagic fishes in the Greek Seas}, author = {Xenia Sarropoulou and Dimitris Tsaparis and Konstantinos Tsagarakis and Nicholas Badouvas and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Sarropoulou-MMS-49.pdf https://ejournals.epublishing.ekt.gr/index.php/hcmr-med-mar-sc/article/view/28567}, doi = {10.12681/mms.28567}, issn = {1791-6763}, year = {2022}, date = {2022-06-01}, urldate = {2022-07-29}, journal = {Mediterranean Marine Science}, volume = {23}, number = {3}, pages = {536--545}, abstract = {Mesopelagic fishes are among the most abundant groups of vertebrates on Earth. Despite their unique biological and ecological traits, research in this group has been particularly scarce. The present study investigates the intraspecific genetic diversity of three mesopelagic fishes (Hygophum benoiti, Maurolicus muelleri, and Benthosema glaciale) in the Greek Seas. Analyses of three mitochondrial DNA genes (COI, 12S, and 16S) from a total of 168 samples revealed a lack of genetic structure for M. muelleri and B. glaciale across the studied area. However, H. benoiti specimens from the Corinthian Gulf were differentiated from the rest of the populations, suggesting that the limited connection between the Corinthian and neighboring seas may act as a barrier to gene flow. Furthermore, the COI data of this study were co-analyzed with publicly available sequences, demonstrating lack of phylogeographic structure for all three species through their distribution range. Therefore, even though indications of genetic differentiation were observed, the three mesopelagic fishes are generally characterized by genetic homogeneity, which may be the result of their recent evolutionary history.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mesopelagic fishes are among the most abundant groups of vertebrates on Earth. Despite their unique biological and ecological traits, research in this group has been particularly scarce. The present study investigates the intraspecific genetic diversity of three mesopelagic fishes (Hygophum benoiti, Maurolicus muelleri, and Benthosema glaciale) in the Greek Seas. Analyses of three mitochondrial DNA genes (COI, 12S, and 16S) from a total of 168 samples revealed a lack of genetic structure for M. muelleri and B. glaciale across the studied area. However, H. benoiti specimens from the Corinthian Gulf were differentiated from the rest of the populations, suggesting that the limited connection between the Corinthian and neighboring seas may act as a barrier to gene flow. Furthermore, the COI data of this study were co-analyzed with publicly available sequences, demonstrating lack of phylogeographic structure for all three species through their distribution range. Therefore, even though indications of genetic differentiation were observed, the three mesopelagic fishes are generally characterized by genetic homogeneity, which may be the result of their recent evolutionary history. |
Plis, Kamila; Niedziałkowska, Magdalena; Borowik, Tomasz; Lang, Johannes; Heddergott, Mike; Tiainen, Juha; Bunevich, Aleksey; Šprem, Nikica; Paule, Ladislav; Danilkin, Aleksey; Kholodova, Marina; Zvychaynaya, Elena; Kashinina, Nadezhda; Pokorny, Boštjan; Flajšman, Katarina; Paulauskas, Algimantas; Djan, Mihajla; Ristić, Zoran; Novák, Luboš; Kusza, Szilvia; Miller, Christine; Tsaparis, Dimitris; Stoyanov, Stoyan; Shkvyria, Maryna; Suchentrunk, Franz; Kutal, Miroslav; Lavadinović, Vukan; Šnjegota, Dragana; Krapal, Ana‐Maria; Dănilă, Gabriel; Veeroja, Rauno; Dulko, Elżbieta; Jędrzejewska, Bogumiła Pan‐European phylogeography of the European roe deer ( textitCapreolus capreolus ) Journal Article Ecology and Evolution, 12 (5), 2022, ISSN: 2045-7758, 2045-7758. @article{plis_paneuropean_2022, title = {Pan‐European phylogeography of the European roe deer ( textitCapreolus capreolus )}, author = {Kamila Plis and Magdalena Niedziałkowska and Tomasz Borowik and Johannes Lang and Mike Heddergott and Juha Tiainen and Aleksey Bunevich and Nikica Šprem and Ladislav Paule and Aleksey Danilkin and Marina Kholodova and Elena Zvychaynaya and Nadezhda Kashinina and Boštjan Pokorny and Katarina Flajšman and Algimantas Paulauskas and Mihajla Djan and Zoran Ristić and Luboš Novák and Szilvia Kusza and Christine Miller and Dimitris Tsaparis and Stoyan Stoyanov and Maryna Shkvyria and Franz Suchentrunk and Miroslav Kutal and Vukan Lavadinović and Dragana Šnjegota and Ana‐Maria Krapal and Gabriel Dănilă and Rauno Veeroja and Elżbieta Dulko and Bogumiła Jędrzejewska}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/07/2022-Pils-Ecology-and-Evolution-43.pdf https://onlinelibrary.wiley.com/doi/10.1002/ece3.8931}, doi = {10.1002/ece3.8931}, issn = {2045-7758, 2045-7758}, year = {2022}, date = {2022-05-01}, urldate = {2022-07-29}, journal = {Ecology and Evolution}, volume = {12}, number = {5}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Nousias, O; Oikonomou, S; Manousaki, T; Papadogiannis, V; Angelova, N; Tsaparis, D; Tsakogiannis, A; Duncan, N; Estevez, A; Tzokas, K; Pavlidis, M; Chatziplis, D; Tsigenopoulos, C S Scientific Reports, 12 (1), pp. 5301, 2022, ISSN: 2045-2322. @article{nousias_linkage_2022, title = {Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing}, author = {O Nousias and S Oikonomou and T Manousaki and V Papadogiannis and N Angelova and D Tsaparis and A Tsakogiannis and N Duncan and A Estevez and K Tzokas and M Pavlidis and D Chatziplis and C S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Nousias-Sci-Report-27.pdf https://www.nature.com/articles/s41598-022-09289-4}, doi = {10.1038/s41598-022-09289-4}, issn = {2045-2322}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Scientific Reports}, volume = {12}, number = {1}, pages = {5301}, abstract = {Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Meagre ( Argyrosomus regius ), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax , traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production. |
Tsaparis, Dimitrios; Lecocq, Thomas; Kyriakis, Dimitrios; Oikonomaki, Katerina; Fontaine, Pascal; Tsigenopoulos, Costas S Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming Journal Article Animals, 12 (9), pp. 1178, 2022, ISSN: 2076-2615. @article{tsaparis_assessing_2022, title = {Assessing Genetic Variation in Wild and Domesticated Pikeperch Populations: Implications for Conservation and Fish Farming}, author = {Dimitrios Tsaparis and Thomas Lecocq and Dimitrios Kyriakis and Katerina Oikonomaki and Pascal Fontaine and Costas S Tsigenopoulos}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2022/05/2022-Tsaparis-Animals-36.pdf https://www.mdpi.com/2076-2615/12/9/1178}, doi = {10.3390/ani12091178}, issn = {2076-2615}, year = {2022}, date = {2022-01-01}, urldate = {2022-05-09}, journal = {Animals}, volume = {12}, number = {9}, pages = {1178}, abstract = {The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The pikeperch is a freshwater/brackish water fish species with growing interest for European aquaculture. Wild populations show signs of decline in many areas of the species natural range due to human activities. The comparative evaluation of genetic status in wild and domesticated populations is extremely useful for the future establishment of genetic breeding programs. The main objective of the present study was to assess and compare the genetic variability of 13 domesticated populations from commercial farms and 8 wild populations, developing an efficient microsatellite multiplex tool for genotyping. Partial cytochrome b gene sequences were also used to infer phylogeographic relationships. Results show that on average, the domesticated populations do not exhibit significantly lower levels of genetic diversity compared to the wild ones and do not suffer from inbreeding. Nuclear data provide evidence that pikeperch populations in Europe belong to at least two genetically differentiated groups: the first one is predominantly present in Northern Europe and around the Baltic Sea, while the second one comprises populations from Central Europe. In this second group, Hungarian origin populations constitute a differentiated stock that needs special consideration. Aquaculture broodstocks analyzed appear to contain fish of a single origin with only a few exceptions. |
2021 |
Tsaparis, Dimitris; Konstantinidis, Ioannis; Palandacic, Anja; Kalogianni, Eleni; Stoumboudi, Maria Th.; Barbieri, Roberta; Vardakas, Leonidas; Koutsikos, Nicholas; Tsigenopoulos, Costas S Hydrobiologia, 848 (5), pp. 1163–1176, 2021, ISSN: 0018-8158, 1573-5117. @article{tsaparis_dna_2021, title = {DNA barcoding provides new insights on the distribution, systematics and conservation of the freshwater genus Pelasgus (Cypriniformes: Cyprinidae) in Greece}, author = {Dimitris Tsaparis and Ioannis Konstantinidis and Anja Palandacic and Eleni Kalogianni and Maria Th. Stoumboudi and Roberta Barbieri and Leonidas Vardakas and Nicholas Koutsikos and Costas S Tsigenopoulos}, url = {http://link.springer.com/10.1007/s10750-021-04526-9}, doi = {10.1007/s10750-021-04526-9}, issn = {0018-8158, 1573-5117}, year = {2021}, date = {2021-03-01}, urldate = {2021-02-24}, journal = {Hydrobiologia}, volume = {848}, number = {5}, pages = {1163--1176}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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 |
Bounas, Anastasios; Keroglidou, Maria; Toli, Elisavet‐Aspasia; Chousidis, Ieremias; Tsaparis, Dimitris; Leonardos, Ioannis; Sotiropoulos, Konstantinos Constrained by aliens, shifting landscape, or poor water quality? Factors affecting the persistence of amphibians in an urban pond network Journal Article Aquatic Conservation: Marine and Freshwater Ecosystems, 30 (5), pp. 1037–1049, 2020, ISSN: 1052-7613, 1099-0755. @article{bounas_constrained_2020, title = {Constrained by aliens, shifting landscape, or poor water quality? Factors affecting the persistence of amphibians in an urban pond network}, author = {Anastasios Bounas and Maria Keroglidou and Elisavet‐Aspasia Toli and Ieremias Chousidis and Dimitris Tsaparis and Ioannis Leonardos and Konstantinos Sotiropoulos}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aqc.3309}, doi = {10.1002/aqc.3309}, issn = {1052-7613, 1099-0755}, year = {2020}, date = {2020-05-01}, urldate = {2020-08-26}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, volume = {30}, number = {5}, pages = {1037--1049}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kiparissis, Sotiris; Tsaparis, Dimitris; Peristeraki, Panagiota; Giannakaki, Amalia; Kosoglou, Giannis; Metaxakis, Manolis; Tserpes, George BioInvasions Records, 9 (4), pp. 814–826, 2020, ISSN: 22421300. @article{kiparissis_yellowstripe_2020, title = {The yellowstripe barracuda Sphyraena chrysotaenia (Kluzinger, 1884) in Crete (GSA 23, eastern Mediterranean): first genetically verified records and highlighted issues on the lessepsian barracudas nomenclature ambiguities}, author = {Sotiris Kiparissis and Dimitris Tsaparis and Panagiota Peristeraki and Amalia Giannakaki and Giannis Kosoglou and Manolis Metaxakis and George Tserpes}, url = {https://www.reabic.net/journals/bir/2020/Issue4.aspx}, doi = {10.3391/bir.2020.9.4.15}, issn = {22421300}, year = {2020}, date = {2020-01-01}, urldate = {2020-12-08}, journal = {BioInvasions Records}, volume = {9}, number = {4}, pages = {814--826}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2019 |
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} } |
Katsanevakis, Stelios; Tsirintanis, Konstantinos; Tsaparis, Dimitris; Doukas, Dimitrios; Sini, Maria; Athanassopoulou, F; Kolygas, Markos Nikolaos; Tontis, Dimitrios; Koutsoubas, Drosos; Bakopoulos, Vasileios The cryptogenic parasite Haplosporidium pinnae invades the Aegean Sea and causes the collapse of Pinna nobilis populations Journal Article Aquatic Invasions, 14 (2), pp. 150–164, 2019, ISSN: 18185487. @article{katsanevakis_cryptogenic_2019, title = {The cryptogenic parasite Haplosporidium pinnae invades the Aegean Sea and causes the collapse of Pinna nobilis populations}, author = {Stelios Katsanevakis and Konstantinos Tsirintanis and Dimitris Tsaparis and Dimitrios Doukas and Maria Sini and F Athanassopoulou and Markos Nikolaos Kolygas and Dimitrios Tontis and Drosos Koutsoubas and Vasileios Bakopoulos}, url = {http://www.aquaticinvasions.net/2019/issue2.html}, doi = {10.3391/ai.2019.14.2.01}, issn = {18185487}, year = {2019}, date = {2019-01-01}, urldate = {2020-08-26}, journal = {Aquatic Invasions}, volume = {14}, number = {2}, pages = {150--164}, abstract = {The cryptogenic parasite Haplosporidium pinnae has caused mass mortality of the protected endemic Mediterranean bivalve Pinna nobilis in the western Mediterranean, since the autumn of 2016. Herein, we confirm the spread of the parasite in the eastern Mediterranean, and report a mass mortality event, with textgreater 93% average mortalities, in the coastal waters of Lesvos Island (Greece, Aegean Sea). Histopathological study of collected specimens revealed the presence of a haplosporian-like protozoon in different life cycle stages, mainly within the digestive gland of the infected Pinna nobilis, with many uni- and bi-nucleate parasite cells, plasmodia and sporocysts in the wide lumen of digestive tubules causing the collapse of epithelial cells, and apparently low host haemocyte reaction. The parasite was identified as H. pinnae by molecular methods (PCR amplification and sequencing of a part of small subunit ribosomal DNA gene, and comparison with available records in Genbank). In many sites, 100% mortality was recorded, whereas in a single site (among 13 surveyed sites) mortality was relatively low (36%), successful recruitment was observed and the parasite was not detected. The latter observation stresses the importance of possible parasite-free refugia sites. We call for continuous monitoring of the spread of the parasite and its impacts, and for urgent targeted research and actions to identify the factors affecting the parasite’s virulence, investigate biotic and abiotic conditions that characterize refugia sites, and strictly protect the remaining P. nobilis populations to increase the chances for the survival of the species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The cryptogenic parasite Haplosporidium pinnae has caused mass mortality of the protected endemic Mediterranean bivalve Pinna nobilis in the western Mediterranean, since the autumn of 2016. Herein, we confirm the spread of the parasite in the eastern Mediterranean, and report a mass mortality event, with textgreater 93% average mortalities, in the coastal waters of Lesvos Island (Greece, Aegean Sea). Histopathological study of collected specimens revealed the presence of a haplosporian-like protozoon in different life cycle stages, mainly within the digestive gland of the infected Pinna nobilis, with many uni- and bi-nucleate parasite cells, plasmodia and sporocysts in the wide lumen of digestive tubules causing the collapse of epithelial cells, and apparently low host haemocyte reaction. The parasite was identified as H. pinnae by molecular methods (PCR amplification and sequencing of a part of small subunit ribosomal DNA gene, and comparison with available records in Genbank). In many sites, 100% mortality was recorded, whereas in a single site (among 13 surveyed sites) mortality was relatively low (36%), successful recruitment was observed and the parasite was not detected. The latter observation stresses the importance of possible parasite-free refugia sites. We call for continuous monitoring of the spread of the parasite and its impacts, and for urgent targeted research and actions to identify the factors affecting the parasite’s virulence, investigate biotic and abiotic conditions that characterize refugia sites, and strictly protect the remaining P. nobilis populations to increase the chances for the survival of the species. |
2018 |
Bounas, Anastasios; Catsadorakis, Giorgos; Logotheti, Annita; Voslamber, Berend; Magoulas, Antonios; Tsaparis, Dimitris Conservation genetics of a resident population of Greylag Goose (Anser anser) at the southernmost limit of the species’ distribution in Europe Journal Article Avian Research, 9 (1), pp. 47, 2018, ISSN: 2053-7166. @article{bounas_conservation_2018, title = {Conservation genetics of a resident population of Greylag Goose (Anser anser) at the southernmost limit of the species’ distribution in Europe}, author = {Anastasios Bounas and Giorgos Catsadorakis and Annita Logotheti and Berend Voslamber and Antonios Magoulas and Dimitris Tsaparis}, url = {https://avianres.biomedcentral.com/articles/10.1186/s40657-018-0139-0}, doi = {10.1186/s40657-018-0139-0}, issn = {2053-7166}, year = {2018}, date = {2018-12-01}, urldate = {2020-08-26}, journal = {Avian Research}, volume = {9}, number = {1}, pages = {47}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bounas, A; Tsaparis, D; Efrat, R; Gradev, G; Gustin, M; Mikulic, K; Rodríguez, A; Sarà, M; Kotoulas, G; Sotiropoulos, K Genetic structure of a patchily distributed philopatric migrant: Implications for management and conservation Journal Article Biological Journal of the Linnean Society, 124 (4), pp. 633–644, 2018, ISSN: 00244066, (Publisher: Oxford University Press). @article{bounas_genetic_2018, title = {Genetic structure of a patchily distributed philopatric migrant: Implications for management and conservation}, author = {A Bounas and D Tsaparis and R Efrat and G Gradev and M Gustin and K Mikulic and A Rodríguez and M Sarà and G Kotoulas and K Sotiropoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047856934&doi=10.1093%2fbiolinnean%2fbly073&partnerID=40&md5=9d0888f5ed006f4f62c6383a965fbe40}, doi = {10.1093/biolinnean/bly073}, issn = {00244066}, year = {2018}, date = {2018-01-01}, journal = {Biological Journal of the Linnean Society}, volume = {124}, number = {4}, pages = {633--644}, abstract = {Significant demographic fluctuations can have major genetic consequences in wild populations. The lesser kestrel (Falco naumanni) has suffered both population declines and range fragmentation during the second half of the 20th century. In this study we analysed multilocus microsatellite data to assess the genetic structure of the species. Our analysis revealed significant genetic structuring of lesser kestrel populations, not only at the cross-continental scale, but also regionally within the Central and Eastern (CE) Mediterranean region. We detected signs of genetic bottlenecks in some of the peripheral populations coupled with small effective population sizes. Values of genetic differentiation among the largest populations were low, albeit significant, whereas the small peripheral CE Mediterranean populations showed higher levels of differentiation from all other populations. Gene flow levels were relatively low among the discontinuously distributed populations of the CE Mediterranean region. We argue that the observed spatial genetic structure can be attributed at some level to the past demographic decline experienced by the species. Finally, we identify management units in the region, and inform the design of conservation actions aimed at the increase of population sizes and dispersal rates among peripheral populations. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Significant demographic fluctuations can have major genetic consequences in wild populations. The lesser kestrel (Falco naumanni) has suffered both population declines and range fragmentation during the second half of the 20th century. In this study we analysed multilocus microsatellite data to assess the genetic structure of the species. Our analysis revealed significant genetic structuring of lesser kestrel populations, not only at the cross-continental scale, but also regionally within the Central and Eastern (CE) Mediterranean region. We detected signs of genetic bottlenecks in some of the peripheral populations coupled with small effective population sizes. Values of genetic differentiation among the largest populations were low, albeit significant, whereas the small peripheral CE Mediterranean populations showed higher levels of differentiation from all other populations. Gene flow levels were relatively low among the discontinuously distributed populations of the CE Mediterranean region. We argue that the observed spatial genetic structure can be attributed at some level to the past demographic decline experienced by the species. Finally, we identify management units in the region, and inform the design of conservation actions aimed at the increase of population sizes and dispersal rates among peripheral populations. © 2018 The Linnean Society of London, Biological Journal of the Linnean Society. |
Bounas, A; Tsaparis, D; Gustin, M; Mikulic, K; Sarà, M; Kotoulas, G; Sotiropoulos, K Using genetic markers to unravel the origin of birds converging towards pre-migratory sites Journal Article Scientific Reports, 8 (1), 2018, ISSN: 20452322, (Publisher: Nature Publishing Group). @article{bounas_using_2018, title = {Using genetic markers to unravel the origin of birds converging towards pre-migratory sites}, author = {A Bounas and D Tsaparis and M Gustin and K Mikulic and M Sarà and G Kotoulas and K Sotiropoulos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047852224&doi=10.1038%2fs41598-018-26669-x&partnerID=40&md5=8e2ef459ac38098f966dd8cf2ad04369}, doi = {10.1038/s41598-018-26669-x}, issn = {20452322}, year = {2018}, date = {2018-01-01}, journal = {Scientific Reports}, volume = {8}, number = {1}, abstract = {Identifying patterns of individual movements in spatial and temporal scales can provide valuable insight into the structure of populations and the dynamics of communities and ecosystems. Especially for migrating birds, that can face a variety of unfavorable conditions along their journey, resolving movements of individuals across their annual cycle is necessary in order to design better targeted conservation strategies. Here, we studied the movements of a small migratory falcon, the Lesser Kestrel (Falco naumanni), by genetically assigning feathers from individuals of unknown origin that concentrate in large roosts during the pre-migratory period. Our findings suggest that birds from multiple breeding populations in the Central and Eastern Mediterranean region move towards two pre-migratory sites in the Balkans, some of them detouring greatly from their expected flyways, travelling more than 500 km to reach these sites and prepare for the post-nuptial migration. By identifying the origin of individuals using the pre-migratory sites, not only we provide a better understanding of the possible impact of local threats at these sites on multiple breeding populations but also inform the design of effective conservation actions for the species. © 2018 The Author(s).}, note = {Publisher: Nature Publishing Group}, keywords = {}, pubstate = {published}, tppubtype = {article} } Identifying patterns of individual movements in spatial and temporal scales can provide valuable insight into the structure of populations and the dynamics of communities and ecosystems. Especially for migrating birds, that can face a variety of unfavorable conditions along their journey, resolving movements of individuals across their annual cycle is necessary in order to design better targeted conservation strategies. Here, we studied the movements of a small migratory falcon, the Lesser Kestrel (Falco naumanni), by genetically assigning feathers from individuals of unknown origin that concentrate in large roosts during the pre-migratory period. Our findings suggest that birds from multiple breeding populations in the Central and Eastern Mediterranean region move towards two pre-migratory sites in the Balkans, some of them detouring greatly from their expected flyways, travelling more than 500 km to reach these sites and prepare for the post-nuptial migration. By identifying the origin of individuals using the pre-migratory sites, not only we provide a better understanding of the possible impact of local threats at these sites on multiple breeding populations but also inform the design of effective conservation actions for the species. © 2018 The Author(s). |
Viret, A; Tsaparis, D; Tsigenopoulos, C S; Berrebi, P; Sabatini, A; Arculeo, M; Fassatoui, C; Magoulas, A; Marengo, M; Morales-Nin, B; Caill-Milly, N; Durieux, E D H PLoS ONE, 13 (9), 2018, ISSN: 19326203, (Publisher: Public Library of Science). @article{viret_absence_2018, title = {Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers}, author = {A Viret and D Tsaparis and C S Tsigenopoulos and P Berrebi and A Sabatini and M Arculeo and C Fassatoui and A Magoulas and M Marengo and B Morales-Nin and N Caill-Milly and E D H Durieux}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053134390&doi=10.1371%2fjournal.pone.0203866&partnerID=40&md5=bc629c803f2e5c8490f76f3d27813b81}, doi = {10.1371/journal.pone.0203866}, issn = {19326203}, year = {2018}, date = {2018-01-01}, journal = {PLoS ONE}, volume = {13}, number = {9}, abstract = {The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well. © 2018 Viret et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.}, note = {Publisher: Public Library of Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well. © 2018 Viret et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
2016 |
Manousaki, Tereza; Tsakogiannis, Alexandros; Taggart, John B; Palaiokostas, Christos; Tsaparis, Dimitris; Lagnel, Jacques; Chatziplis, Dimitrios; Magoulas, Antonios; Papandroulakis, Nikos; Mylonas, Constantinos C; TSIGENOPOULOS, C S Exploring a nonmodel teleost genome through rad sequencing—linkage mapping in Common Pandora, Pagellus erythrinus and comparative genomic analysis Journal Article G3: Genes, genomes, genetics, 6 (3), pp. 509–519, 2016, (Publisher: G3: Genes, Genomes, Genetics). @article{manousaki_exploring_2016, title = {Exploring a nonmodel teleost genome through rad sequencing—linkage mapping in Common Pandora, Pagellus erythrinus and comparative genomic analysis}, author = {Tereza Manousaki and Alexandros Tsakogiannis and John B Taggart and Christos Palaiokostas and Dimitris Tsaparis and Jacques Lagnel and Dimitrios Chatziplis and Antonios Magoulas and Nikos Papandroulakis and Constantinos C Mylonas and C. S. TSIGENOPOULOS }, year = {2016}, date = {2016-01-01}, journal = {G3: Genes, genomes, genetics}, volume = {6}, number = {3}, pages = {509--519}, note = {Publisher: G3: Genes, Genomes, Genetics}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2015 |
Tsaparis, D; Kyriakis, D; Darivianakis, S; Fontaine, P; Tsigenopoulos, C S Assessing genetic diversity in domesticated pikeperch (Sander lucioperca) broodstocks Inproceedings 11th Panhellenic Symposium on Oceanography and Fisheries, pp. 261–264, Mytilene, Lesvos island, Greece, 2015, ISBN: 978-960-9798-08-2. @inproceedings{tsaparis_assessing_2015, title = {Assessing genetic diversity in domesticated pikeperch (Sander lucioperca) broodstocks}, author = {D Tsaparis and D Kyriakis and S Darivianakis and P Fontaine and C S Tsigenopoulos}, isbn = {978-960-9798-08-2}, year = {2015}, date = {2015-01-01}, booktitle = {11th Panhellenic Symposium on Oceanography and Fisheries}, pages = {261--264}, address = {Mytilene, Lesvos island, Greece}, abstract = {The pikeperch (Sander lucioperca) is a fish species with growing interest for the European aquaculture. The main objective was to develop and use highly informative multiplex panels of microsatellite loci, in order to assess the genetic variability of domesticated broodstocks in commercial farms around Europe. Two multiplexes (4plex & 7plex) were developed, optimized and finally used for genotyping of 13 populations (439 fish samples). Results indicate that most of the populations show medium to low levels of genetic diversity and some of them may be inbred. Differentiation between broodstocks was high in most cases, while lowest values were estimated for pairs of known common origin or geographic proximity.}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } The pikeperch (Sander lucioperca) is a fish species with growing interest for the European aquaculture. The main objective was to develop and use highly informative multiplex panels of microsatellite loci, in order to assess the genetic variability of domesticated broodstocks in commercial farms around Europe. Two multiplexes (4plex & 7plex) were developed, optimized and finally used for genotyping of 13 populations (439 fish samples). Results indicate that most of the populations show medium to low levels of genetic diversity and some of them may be inbred. Differentiation between broodstocks was high in most cases, while lowest values were estimated for pairs of known common origin or geographic proximity. |
Tsaparis, D; Karaiskou, N; Mertzanis, Y; Triantafyllidis, A Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region – Greece Journal Article Journal of Natural History, 49 (5-8), pp. 393–410, 2015, ISSN: 00222933, (Publisher: Taylor and Francis Ltd.). @article{tsaparis_non-invasive_2015, title = {Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region – Greece}, author = {D Tsaparis and N Karaiskou and Y Mertzanis and A Triantafyllidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84926154371&doi=10.1080%2f00222933.2013.877992&partnerID=40&md5=2f44a8b3e9a756e52d1d203a8b322807}, doi = {10.1080/00222933.2013.877992}, issn = {00222933}, year = {2015}, date = {2015-01-01}, journal = {Journal of Natural History}, volume = {49}, number = {5-8}, pages = {393--410}, abstract = {The brown bear (Ursus arctos) in Greece is considered endangered but little is known about the genetic status and the exact size of local populations. Non-invasive genetic sampling was used in this study to investigate the genetic diversity and genetic structure of the brown bear population in the Kastoria region (northwest Macedonia, Greece) and to estimate its population size. Estimation of demographic parameters was based on innovative, well-evaluated methods that can provide estimates from a single sampling session. DNA was extracted from hairs, scat and blood samples and subsequent amplification of 10 microsatellite loci allowed the identification of a minimum number of 75 living bears in the study area while the mark–recapture-based analysis resulted in a point estimation of 219 individuals. Relatively high diversity values, lack of heterozygosity deficiency as well as estimated effective population size, support the Kastoria bear population having good conservation status. © 2014, © 2014 Taylor & Francis.}, note = {Publisher: Taylor and Francis Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The brown bear (Ursus arctos) in Greece is considered endangered but little is known about the genetic status and the exact size of local populations. Non-invasive genetic sampling was used in this study to investigate the genetic diversity and genetic structure of the brown bear population in the Kastoria region (northwest Macedonia, Greece) and to estimate its population size. Estimation of demographic parameters was based on innovative, well-evaluated methods that can provide estimates from a single sampling session. DNA was extracted from hairs, scat and blood samples and subsequent amplification of 10 microsatellite loci allowed the identification of a minimum number of 75 living bears in the study area while the mark–recapture-based analysis resulted in a point estimation of 219 individuals. Relatively high diversity values, lack of heterozygosity deficiency as well as estimated effective population size, support the Kastoria bear population having good conservation status. © 2014, © 2014 Taylor & Francis. |
2014 |
Vogiatzi, E; Kalogianni, E; Zimmerman, B; Giakoumi, S; Barbieri, R; Paschou, P; Magoulas, A; Tsaparis, D; Poulakakis, N; Tsigenopoulos, CS. Biological Journal of the Linnean Society, 111 , pp. 334–349, 2014. @article{vogiatzi_reduced_2014, title = {Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers}, author = {E Vogiatzi and E Kalogianni and B Zimmerman and S Giakoumi and R Barbieri and P Paschou and A Magoulas and D Tsaparis and N Poulakakis and CS. Tsigenopoulos}, url = {http://dx.doi.org/10.1111/bij.12206}, doi = {10.1111/bij.12206}, year = {2014}, date = {2014-01-01}, journal = {Biological Journal of the Linnean Society}, volume = {111}, pages = {334--349}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2013 |
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} } |
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. |
Tsaparis, D; Katsanevakis, S; Ntolka, E; Legakis, A European Journal of Wildlife Research, 55 , pp. 167–172, 2009. @article{tsaparis_estimating_2009, title = {Estimating dung decay rates of roe deer (Capreolus capreolus) in different habitat types of a Mediterranean ecosystem: an information theory approach}, author = {D Tsaparis and S Katsanevakis and E Ntolka and A Legakis}, doi = {10.1007/s10344-008-0233-4}, year = {2009}, date = {2009-01-01}, journal = {European Journal of Wildlife Research}, volume = {55}, pages = {167--172}, abstract = {For elusive species living in concealing habitats (e.g. deer in a forest habitat), indirect methods such as faecal pellet counts are considered more practical means of estimating population density and abundance. Accurate estimation of deer density using the faecal standing crop (FSC) method necessitates the reliable estimation of the mean time to decay of pellet groups present during the survey. Mean time to decay is generally habitat specific, and separate estimations should be made for each habitat type in the study area. In a confined mountainous area of Greece, the habitat-specific mean time to decay of roe deer pellet groups was estimated by locating and marking fresh pellet groups on several dates in the lead up to an FSC survey and returning to the marked signs at the time of the survey to record whether or not each pellet group had survived. Several logistic models were fitted to the data, and estimations were based on a multi-model inference (MMI) approach according to information theory. The highest mean time to decay was estimated in coniferous forests, while mid-ranged values were found in maquis shrubs, and the lowest mean time to decay was observed in open areas. MMI by model averaging, based on Akaike weights, is recommended for making robust parameter estimations and for dealing with uncertainty in model selection.}, keywords = {}, pubstate = {published}, tppubtype = {article} } For elusive species living in concealing habitats (e.g. deer in a forest habitat), indirect methods such as faecal pellet counts are considered more practical means of estimating population density and abundance. Accurate estimation of deer density using the faecal standing crop (FSC) method necessitates the reliable estimation of the mean time to decay of pellet groups present during the survey. Mean time to decay is generally habitat specific, and separate estimations should be made for each habitat type in the study area. In a confined mountainous area of Greece, the habitat-specific mean time to decay of roe deer pellet groups was estimated by locating and marking fresh pellet groups on several dates in the lead up to an FSC survey and returning to the marked signs at the time of the survey to record whether or not each pellet group had survived. Several logistic models were fitted to the data, and estimations were based on a multi-model inference (MMI) approach according to information theory. The highest mean time to decay was estimated in coniferous forests, while mid-ranged values were found in maquis shrubs, and the lowest mean time to decay was observed in open areas. MMI by model averaging, based on Akaike weights, is recommended for making robust parameter estimations and for dealing with uncertainty in model selection. |
2008 |
Tsaparis, Dimitris; Katsanevakis, Stelios; Stamouli, Christina; Legakis, Anastasios Estimation of roe deer Capreolus capreolus and mouflon Ovis aries densities, abundance and habitat use in a mountainous Mediterranean area Journal Article Acta Theriologica, 53 (1), pp. 87–94, 2008, ISSN: 0001-7051, 2190-3743. @article{tsaparis_estimation_2008, title = {Estimation of roe deer Capreolus capreolus and mouflon Ovis aries densities, abundance and habitat use in a mountainous Mediterranean area}, author = {Dimitris Tsaparis and Stelios Katsanevakis and Christina Stamouli and Anastasios Legakis}, url = {http://link.springer.com/10.1007/BF03194281}, doi = {10.1007/BF03194281}, issn = {0001-7051, 2190-3743}, year = {2008}, date = {2008-03-01}, urldate = {2020-08-18}, journal = {Acta Theriologica}, volume = {53}, number = {1}, pages = {87--94}, abstract = {The abundance, density, and habitat use of roe deer Capreolus capreolus (Linnaeus, 1758) and mouflon Ovis aries Linnaeus, 1758 were studied in a confined Mediterranean area in Greece with a dung survey based on the faecal accumulation rate (FAR) technique. Estimated density was modelled with generalized additive models using altitude, habitat type, and slope as potential covariates. Model selection among the set of candidate models was conducted based on their generalized cross-validation score. Roe deer had an estimated mean density of 13.9 ind./km2 and the best model included slope and habitat type as covariates. The mean density of mouflon in the study area was 22.1 ind./km2 and the best model used altitude and habitat type as covariates. For both species, the highest densities were encountered in abandoned cultivations and glades, followed by conifer forests, while the lowest densities were observed in maquis. However, use of open habitats by mouflon was much greater than it was for roe deer. The strong preference of mouflon (a grazer species) for open habitats that were abundant with grasses probably reflected food availability and contrasted with the more diverse habitat use by roe deer (a selective browser).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The abundance, density, and habitat use of roe deer Capreolus capreolus (Linnaeus, 1758) and mouflon Ovis aries Linnaeus, 1758 were studied in a confined Mediterranean area in Greece with a dung survey based on the faecal accumulation rate (FAR) technique. Estimated density was modelled with generalized additive models using altitude, habitat type, and slope as potential covariates. Model selection among the set of candidate models was conducted based on their generalized cross-validation score. Roe deer had an estimated mean density of 13.9 ind./km2 and the best model included slope and habitat type as covariates. The mean density of mouflon in the study area was 22.1 ind./km2 and the best model used altitude and habitat type as covariates. For both species, the highest densities were encountered in abandoned cultivations and glades, followed by conifer forests, while the lowest densities were observed in maquis. However, use of open habitats by mouflon was much greater than it was for roe deer. The strong preference of mouflon (a grazer species) for open habitats that were abundant with grasses probably reflected food availability and contrasted with the more diverse habitat use by roe deer (a selective browser). |
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. |