2024 |
Vasileiadou, Katerina; Chatzinikolaou, Eva; Klayn, Stefania; Pavloudi, Christina; Reizopoulou, Sofia Editorial: Marine biodiversity hotspots – challenges and resilience Journal Article Frontiers in Marine Science, 11 , pp. 1338242, 2024, ISSN: 2296-7745. @article{vasileiadou_editorial_2024, title = {Editorial: Marine biodiversity hotspots – challenges and resilience}, author = {Katerina Vasileiadou and Eva Chatzinikolaou and Stefania Klayn and Christina Pavloudi and Sofia Reizopoulou}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2024/01/2024-Vasileiadou-fmars-3.pdf https://www.frontiersin.org/articles/10.3389/fmars.2024.1338242/full}, doi = {10.3389/fmars.2024.1338242}, issn = {2296-7745}, year = {2024}, date = {2024-01-17}, urldate = {2024-01-22}, journal = {Frontiers in Marine Science}, volume = {11}, pages = {1338242}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2021 |
Keklikoglou, Kleoniki; Arvanitidis, Christos; Chatzigeorgiou, Georgios; Chatzinikolaou, Eva; Karagiannidis, Efstratios; Koletsa, Triantafyllia; Magoulas, Antonios; Makris, Konstantinos; Mavrothalassitis, George; Papanagnou, Eleni-Dimitra; Papazoglou, Andreas S; Pavloudi, Christina; Trougakos, Ioannis P; Vasileiadou, Katerina; Vogiatzi, Angeliki Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques Journal Article 7 (9), pp. 172, 2021, ISSN: 2313-433X. @article{keklikoglou_micro-ct_2021, title = {Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques}, author = {Kleoniki Keklikoglou and Christos Arvanitidis and Georgios Chatzigeorgiou and Eva Chatzinikolaou and Efstratios Karagiannidis and Triantafyllia Koletsa and Antonios Magoulas and Konstantinos Makris and George Mavrothalassitis and Eleni-Dimitra Papanagnou and Andreas S Papazoglou and Christina Pavloudi and Ioannis P Trougakos and Katerina Vasileiadou and Angeliki Vogiatzi}, url = {https://imbbc.hcmr.gr/wp-content/uploads/2021/09/2021-Keklikoglou-jimaging-66-1.pdf https://www.mdpi.com/2313-433X/7/9/172}, doi = {10.3390/jimaging7090172}, issn = {2313-433X}, year = {2021}, date = {2021-09-01}, urldate = {2021-09-22}, volume = {7}, number = {9}, pages = {172}, abstract = {Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised. |
Chatzinikolaou, Eva; Damianidis, Panagiotis; Pavloudi, Christina; Vasileiadou, Aikaterini; Faulwetter, Sarah; Keklikoglou, Kleoniki; Plaitis, Wanda; Mavraki, Dimitra; Nikolopoulou, Stamatina; Arvanitidis, Christos Benthic communities in three Mediterranean touristic ports: MAPMED project Journal Article Biodiversity Data Journal, 9 , pp. e66420, 2021, ISSN: 1314-2828. @article{chatzinikolaou_benthic_2021, title = {Benthic communities in three Mediterranean touristic ports: MAPMED project}, author = {Eva Chatzinikolaou and Panagiotis Damianidis and Christina Pavloudi and Aikaterini Vasileiadou and Sarah Faulwetter and Kleoniki Keklikoglou and Wanda Plaitis and Dimitra Mavraki and Stamatina Nikolopoulou and Christos Arvanitidis}, url = {https://bdj.pensoft.net/article/66420/ https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Chatzinikolaou-DioDiv-Data-J-32.pdf}, doi = {10.3897/BDJ.9.e66420}, issn = {1314-2828}, year = {2021}, date = {2021-04-01}, urldate = {2021-04-27}, journal = {Biodiversity Data Journal}, volume = {9}, pages = {e66420}, abstract = {Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Macrobenthic communities are an important component of the port biota and have been used as environmental quality indicators.Macrobenthic assemblages were recorded in three Mediterranean touristic ports under the framework of the ENPI CBC MED project MAPMED. Samples were collected from Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia) ports during February, May and September 2012. The sampling stations were selected according to the different sectors within each port (i.e. leisure, fishing, passenger/cargo vessels, shipyard). A total number of 277 taxa belonging to 12 phyla were found, of which the 96 taxa were found in all three ports. El Kantaoui port hosted the highest number of macrobenthic taxa. Mollusca were the most abundant group (34%) in all ports. The highest percentage of opportunistic taxa per station was found before the touristic period in the shipyard of Heraklion port (89.3%).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mediterranean ports are sources of significant economic activity and at the same time they act as recipients of considerable anthropogenic disturbance and pollution. Macrobenthic communities are an important component of the port biota and have been used as environmental quality indicators.Macrobenthic assemblages were recorded in three Mediterranean touristic ports under the framework of the ENPI CBC MED project MAPMED. Samples were collected from Cagliari (Sardinia, Italy), Heraklion (Crete, Greece) and El Kantaoui (Tunisia) ports during February, May and September 2012. The sampling stations were selected according to the different sectors within each port (i.e. leisure, fishing, passenger/cargo vessels, shipyard). A total number of 277 taxa belonging to 12 phyla were found, of which the 96 taxa were found in all three ports. El Kantaoui port hosted the highest number of macrobenthic taxa. Mollusca were the most abundant group (34%) in all ports. The highest percentage of opportunistic taxa per station was found before the touristic period in the shipyard of Heraklion port (89.3%). |
Kousteni, Vasiliki; Mazzoleni, Sofia; Vasileiadou, Katerina; Rovatsos, Michail Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs Journal Article Genes, 12 (3), pp. 324, 2021, ISSN: 2073-4425. @article{kousteni_complete_2021, title = {Complete Mitochondrial DNA Genome of Nine Species of Sharks and Rays and Their Phylogenetic Placement among Modern Elasmobranchs}, author = {Vasiliki Kousteni and Sofia Mazzoleni and Katerina Vasileiadou and Michail Rovatsos}, url = {https://www.mdpi.com/2073-4425/12/3/324 https://imbbc.hcmr.gr/wp-content/uploads/2021/03/Kousteni-2021-GENES-20.pdf}, doi = {10.3390/genes12030324}, issn = {2073-4425}, year = {2021}, date = {2021-02-01}, urldate = {2021-03-17}, journal = {Genes}, volume = {12}, number = {3}, pages = {324}, abstract = {Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chondrichthyes occupy a key position in the phylogeny of vertebrates. The complete sequence of the mitochondrial genome (mitogenome) of four species of sharks and five species of rays was obtained by whole genome sequencing (DNA-seq) in the Illumina HiSeq2500 platform. The arrangement and features of the genes in the assembled mitogenomes were identical to those found in vertebrates. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships among 172 species (including 163 mitogenomes retrieved from GenBank) based on the concatenated dataset of 13 individual protein coding genes. Both ML and BI analyses did not support the “Hypnosqualea” hypothesis and confirmed the monophyly of sharks and rays. The broad notion in shark phylogeny, namely the division of sharks into Galeomorphii and Squalomorphii and the monophyly of the eight shark orders, was also supported. The phylogenetic placement of all nine species sequenced in this study produced high statistical support values. The present study expands our knowledge on the systematics, genetic differentiation, and conservation genetics of the species studied, and contributes to our understanding of the evolutionary history of Chondrichthyes. |
Digenis, Markos; Ragkousis, Michail; Vasileiadou, Katerina; Gerovasileiou, Vasilis; Katsanevakis, Stelios New records of the Indo-Pacific shrimp Urocaridella pulchella Yokeş & Galil, 2006 from the Eastern Mediterranean Sea Journal Article BIR, 10 (2), pp. 295–303, 2021, ISSN: 22421300. @article{digenis_new_2021, title = {New records of the Indo-Pacific shrimp Urocaridella pulchella Yokeş & Galil, 2006 from the Eastern Mediterranean Sea}, author = {Markos Digenis and Michail Ragkousis and Katerina Vasileiadou and Vasilis Gerovasileiou and Stelios Katsanevakis}, url = {https://www.reabic.net/journals/bir/2021/Issue2.aspx https://imbbc.hcmr.gr/wp-content/uploads/2021/05/2021-Digenis-BioInvasions-Records-35.pdf}, doi = {10.3391/bir.2021.10.2.07}, issn = {22421300}, year = {2021}, date = {2021-01-01}, urldate = {2021-05-10}, journal = {BIR}, volume = {10}, number = {2}, pages = {295--303}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2020 |
Zafeiropoulos, Haris; Viet, Ha Quoc; Vasileiadou, Katerina; Potirakis, Antonis; Arvanitidis, Christos; Topalis, Pantelis; Pavloudi, Christina; Pafilis, Evangelos PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes Journal Article GigaScience, 9 (3), 2020, ISSN: 2047-217X, (_eprint: https://academic.oup.com/gigascience/article-pdf/9/3/giaa022/32894405/giaa022.pdf). @article{zafeiropoulos_pema_2020, title = {PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes}, author = {Haris Zafeiropoulos and Ha Quoc Viet and Katerina Vasileiadou and Antonis Potirakis and Christos Arvanitidis and Pantelis Topalis and Christina Pavloudi and Evangelos Pafilis}, url = {https://doi.org/10.1093/gigascience/giaa022}, doi = {10.1093/gigascience/giaa022}, issn = {2047-217X}, year = {2020}, date = {2020-01-01}, journal = {GigaScience}, volume = {9}, number = {3}, abstract = {Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution.PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers’ needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality.A high-performance computing–based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies.}, note = {_eprint: https://academic.oup.com/gigascience/article-pdf/9/3/giaa022/32894405/giaa022.pdf}, keywords = {}, pubstate = {published}, tppubtype = {article} } Environmental DNA and metabarcoding allow the identification of a mixture of species and launch a new era in bio- and eco-assessment. Many steps are required to obtain taxonomically assigned matrices from raw data. For most of these, a plethora of tools are available; each tool's execution parameters need to be tailored to reflect each experiment's idiosyncrasy. Adding to this complexity, the computation capacity of high-performance computing systems is frequently required for such analyses. To address the difficulties, bioinformatic pipelines need to combine state-of-the art technologies and algorithms with an easy to get-set-use framework, allowing researchers to tune each study. Software containerization technologies ease the sharing and running of software packages across operating systems; thus, they strongly facilitate pipeline development and usage. Likewise programming languages specialized for big data pipelines incorporate features like roll-back checkpoints and on-demand partial pipeline execution.PEMA is a containerized assembly of key metabarcoding analysis tools that requires low effort in setting up, running, and customizing to researchers’ needs. Based on third-party tools, PEMA performs read pre-processing, (molecular) operational taxonomic unit clustering, amplicon sequence variant inference, and taxonomy assignment for 16S and 18S ribosomal RNA, as well as ITS and COI marker gene data. Owing to its simplified parameterization and checkpoint support, PEMA allows users to explore alternative algorithms for specific steps of the pipeline without the need of a complete re-execution. PEMA was evaluated against both mock communities and previously published datasets and achieved results of comparable quality.A high-performance computing–based approach was used to develop PEMA; however, it can be used in personal computers as well. PEMA's time-efficient performance and good results will allow it to be used for accurate environmental DNA metabarcoding analysis, thus enhancing the applicability of next-generation biodiversity assessment studies. |
Blakeslee, April M H; Manousaki, Tereza; Vasileiadou, Katerina; Tepolt, Carolyn K An evolutionary perspective on marine invasions Journal Article Evolutionary Applications, 13 (3), pp. 479–485, 2020, (_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12906). @article{blakeslee_evolutionary_2020, title = {An evolutionary perspective on marine invasions}, author = {April M H Blakeslee and Tereza Manousaki and Katerina Vasileiadou and Carolyn K Tepolt}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12906}, doi = {10.1111/eva.12906}, year = {2020}, date = {2020-01-01}, journal = {Evolutionary Applications}, volume = {13}, number = {3}, pages = {479--485}, abstract = {Abstract Species distributions are rapidly changing as human globalization increasingly moves organisms to novel environments. In marine systems, species introductions are the result of a number of anthropogenic mechanisms, notably shipping, aquaculture/mariculture, the pet and bait trades, and the creation of canals. Marine invasions are a global threat to human and non-human populations alike and are often listed as one of the top conservation concerns worldwide, having ecological, evolutionary, and social ramifications. Evolutionary investigations of marine invasions can provide crucial insight into an introduced species’ potential impacts in its new range, including: physiological adaptation and behavioral changes to exploit new environments; changes in resident populations, community interactions, and ecosystems; and severe reductions in genetic diversity that may limit evolutionary potential in the introduced range. This special issue focuses on current research advances in the evolutionary biology of marine invasions and can be broadly classified into a few major avenues of research: the evolutionary history of invasive populations, post-invasion reproductive changes, and the role of evolution in parasite introductions. Together, they demonstrate the value of investigating marine invasions from an evolutionary perspective, with benefits to both fundamental and applied evolutionary biology at local and broad scales.}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12906}, keywords = {}, pubstate = {published}, tppubtype = {article} } Abstract Species distributions are rapidly changing as human globalization increasingly moves organisms to novel environments. In marine systems, species introductions are the result of a number of anthropogenic mechanisms, notably shipping, aquaculture/mariculture, the pet and bait trades, and the creation of canals. Marine invasions are a global threat to human and non-human populations alike and are often listed as one of the top conservation concerns worldwide, having ecological, evolutionary, and social ramifications. Evolutionary investigations of marine invasions can provide crucial insight into an introduced species’ potential impacts in its new range, including: physiological adaptation and behavioral changes to exploit new environments; changes in resident populations, community interactions, and ecosystems; and severe reductions in genetic diversity that may limit evolutionary potential in the introduced range. This special issue focuses on current research advances in the evolutionary biology of marine invasions and can be broadly classified into a few major avenues of research: the evolutionary history of invasive populations, post-invasion reproductive changes, and the role of evolution in parasite introductions. Together, they demonstrate the value of investigating marine invasions from an evolutionary perspective, with benefits to both fundamental and applied evolutionary biology at local and broad scales. |
2018 |
Vasileiadou, K; Pavloudi, C; Camisa, F; Tsikopoulou, I; Fragopoulou, N; Kotoulas, G; Arvanitidis, C Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem Journal Article Journal of the Marine Biological Association of the United Kingdom, 98 (4), pp. 777–789, 2018, ISSN: 00253154, (Publisher: Cambridge University Press). @article{vasileiadou_genetic_2018, title = {Genetic diversity of Nephtys hombergii (Phyllodocida, Polychaeta) associated with environmental factors in a highly fluctuating ecosystem}, author = {K Vasileiadou and C Pavloudi and F Camisa and I Tsikopoulou and N Fragopoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009786126&doi=10.1017%2fS0025315416001910&partnerID=40&md5=8e7cb2651bd57afe644615018866185a}, doi = {10.1017/S0025315416001910}, issn = {00253154}, year = {2018}, date = {2018-01-01}, journal = {Journal of the Marine Biological Association of the United Kingdom}, volume = {98}, number = {4}, pages = {777--789}, abstract = {Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats. © Copyright Marine Biological Association of the United Kingdom 2017.}, note = {Publisher: Cambridge University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Genetic diversity and population distribution are influenced by environmental factors, yet information is scarce on the interrelations that define dispersal of populations. Transitional water ecosystems are hosting habitats with temporally and spatially variable conditions, which make them very useful in understanding the mechanisms affecting population establishment. For the study, seasonal samples were collected from four lagoons in the lagoonal complex of Amvrakikos Gulf (W Greece). The mitochondrial DNA (COI gene) was analysed from polychaetes of Nephtys hombergii, as it is considered an important component of these assemblages and shows great dispersal ability. The results of the genetic analysis showed intraspecific variability in all the lagoons, with genetic structuring tending to follow a seasonal pattern rather than a spatial one. The results of BIOENV analysis indicated correlation of the observed pattern with the water pH levels, the redox potential and the concentration of phosphate in the sediment. The complexity of the network suggested the enhancement of the local population with more recently established haplotypes. The findings of the study support the necessity of designing management strategies by taking into account genetic diversity and population demography approaches in addition to those based on species and habitats. © Copyright Marine Biological Association of the United Kingdom 2017. |
2017 |
Pavloudi, C; Oulas, A; Vasileiadou, K; Kotoulas, G; Troch, De M; Friedrich, M W; Arvanitidis, C Aquatic Microbial Ecology, 79 (3), pp. 209–219, 2017, ISSN: 09483055, (Publisher: Inter-Research). @article{pavloudi_diversity_2017, title = {Diversity and abundance of sulfate-reducing microorganisms in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) derived from dsrB gene}, author = {C Pavloudi and A Oulas and K Vasileiadou and G Kotoulas and M De Troch and M W Friedrich and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021092263&doi=10.3354%2fame01829&partnerID=40&md5=8be345d2d8f932cc9b640cf2072c2bb0}, doi = {10.3354/ame01829}, issn = {09483055}, year = {2017}, date = {2017-01-01}, journal = {Aquatic Microbial Ecology}, volume = {79}, number = {3}, pages = {209--219}, abstract = {Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities. © Inter-Research 2017.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sulfate-reducing microorganisms (SRMs) are a phylogenetically and physiologically diverse group of microorganisms, responsible for the dissimilatory reduction of sulfate. SRMs thrive under anaerobic conditions with high availability of organic matter. Such conditions characterize lagoonal ecosystems which experience regular dystrophic crises. The aim of the present study was to explore the biodiversity patterns of SRMs and to examine the extent to which these patterns are associated with biogeographic and environmental factors. Sediment samples were collected from 5 lagoons in the Amvrakikos Gulf (Ionian Sea, western Greece). DNA was extracted from the sediment and was further processed through pyrosequencing of a region of the dissimilatory sulfite reductase β-subunit (dsrB). The results of this exploratory study show that the majority of the observed operational taxonomic units (OTUs) belong to the Deltaproteobacteria supercluster and more specifically, to the Desulfobacteraceae family. Salinity and ammonium ions are the environmental factors that best correlated with the SRM community pattern. Furthermore, the SRM community of the brackish lagoons is differentiated from that of the brackish-marine lagoons and the studied lagoons have distinct SRM communities. © Inter-Research 2017. |
2016 |
Vasileiadou, K; Pavloudi, C; Kalantzi, I; Apostolaki, E T; Chatzigeorgiou, G; Chatzinikolaou, E; Pafilis, E; Papageorgiou, N; Fanini, L; Konstas, S; Fragopoulou, N; Arvanitidis, C Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece) Journal Article Biodiversity Data Journal, 4 (1), 2016, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{vasileiadou_environmental_2016, title = {Environmental variability and heavy metal concentrations from five lagoons in the Ionian Sea (Amvrakikos Gulf, W Greece)}, author = {K Vasileiadou and C Pavloudi and I Kalantzi and E T Apostolaki and G Chatzigeorgiou and E Chatzinikolaou and E Pafilis and N Papageorgiou and L Fanini and S Konstas and N Fragopoulou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018621471&doi=10.3897%2fBDJ.4.e8233&partnerID=40&md5=91104fbd24f94063ee946df8c2486376}, doi = {10.3897/BDJ.4.e8233}, issn = {13142828}, year = {2016}, date = {2016-01-01}, journal = {Biodiversity Data Journal}, volume = {4}, number = {1}, abstract = {Background Coastal lagoons are ecosystems of major importance as they host a number of species tolerant to disturbances and they are highly productive. Therefore, these ecosystems should be protected to ensure stability and resilience. The lagoons of Amvrakikos Gulf form one of the most important lagoonal complexes in Greece. The optimal ecological status of these lagoons is crucial for the well-being of the biodiversity and the economic prosperity of the local communities. Thus, monitoring of the area is necessary to detect possible sources of disturbance and restore stability. New information The environmental variables and heavy metals concentrations, from five lagoons of Amvrakikos Gulf were measured from seasonal samplings and compared to the findings of previous studies in the area, in order to check for possible sources of disturbance. The analysis, showed that i) the values of the abiotic parameters vary with time (season), space (lagoon) and with space over time; ii) the variability of the environmental factors and enrichment in certain elements is naturally induced and no source of contamination is detected in the lagoons. © Vasileiadou K et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } Background Coastal lagoons are ecosystems of major importance as they host a number of species tolerant to disturbances and they are highly productive. Therefore, these ecosystems should be protected to ensure stability and resilience. The lagoons of Amvrakikos Gulf form one of the most important lagoonal complexes in Greece. The optimal ecological status of these lagoons is crucial for the well-being of the biodiversity and the economic prosperity of the local communities. Thus, monitoring of the area is necessary to detect possible sources of disturbance and restore stability. New information The environmental variables and heavy metals concentrations, from five lagoons of Amvrakikos Gulf were measured from seasonal samplings and compared to the findings of previous studies in the area, in order to check for possible sources of disturbance. The analysis, showed that i) the values of the abiotic parameters vary with time (season), space (lagoon) and with space over time; ii) the variability of the environmental factors and enrichment in certain elements is naturally induced and no source of contamination is detected in the lagoons. © Vasileiadou K et al. |
Pavloudi, C; Oulas, A; Vasileiadou, K; Sarropoulou, E; Kotoulas, G; Arvanitidis, C Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) Journal Article Marine Genomics, 28 , pp. 71–81, 2016, ISSN: 18747787, (Publisher: Elsevier B.V.). @article{pavloudi_salinity_2016, title = {Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea)}, author = {C Pavloudi and A Oulas and K Vasileiadou and E Sarropoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955611416&doi=10.1016%2fj.margen.2016.01.005&partnerID=40&md5=a226c6872c0a3044831db4a1b5f65ca3}, doi = {10.1016/j.margen.2016.01.005}, issn = {18747787}, year = {2016}, date = {2016-01-01}, journal = {Marine Genomics}, volume = {28}, pages = {71--81}, abstract = {Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities. © 2016 Elsevier B.V.}, note = {Publisher: Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities. © 2016 Elsevier B.V. |
Vasileiadou, K; Pavloudi, C; Sarropoulou, E; Fragopoulou, N; Kotoulas, G; Arvanitidis, C Unique COI haplotypes in hediste diversicolor populations in lagoons adjoining the Ionian Sea Journal Article Aquatic Biology, 25 , pp. 7–15, 2016, ISSN: 18647782, (Publisher: Inter-Research). @article{vasileiadou_unique_2016, title = {Unique COI haplotypes in hediste diversicolor populations in lagoons adjoining the Ionian Sea}, author = {K Vasileiadou and C Pavloudi and E Sarropoulou and N Fragopoulou and G Kotoulas and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84971596901&doi=10.3354%2fab00654&partnerID=40&md5=4039a8b37d89de3fef4adb17862554df}, doi = {10.3354/ab00654}, issn = {18647782}, year = {2016}, date = {2016-01-01}, journal = {Aquatic Biology}, volume = {25}, pages = {7--15}, abstract = {The present study examines the genetic diversity (using cytochrome c oxidase subunit I [COI] haplotypes) of polychaete Hediste diversicolor populations in the Amvrakikos Gulf (western Greece) in order to test Cognetti’s hypothesis on the formation of distinct isolated populations of species living in stressed transitional water habitats. To this purpose, the intraspecific diversity of H. diversicolor and the similarities among its populations in the brackish water habitats of the Eastern Mediterranean were investigated. Samples were collected from the lagoonal complex of Am - vrakikos Gulf in 2010 and 2011. Analysis showed that populations in the Amvrakikos Gulf share unique haplotypes which are distinct from the haplotypes hitherto reported, suggesting that these populations are highly isolated. This evidence partially supports Cognetti’s hypothesis. The results indicate that the genetic differentiation in the studied populations was probably caused by the complete isolation of the gulf and periodic hypoxic conditions during its formation history. The occurrence of unique haplotypes in the gulf underlines the importance of considering genetic diversity in the design of long-term biodiversity management and conservation plans. © The authors 2016.}, note = {Publisher: Inter-Research}, keywords = {}, pubstate = {published}, tppubtype = {article} } The present study examines the genetic diversity (using cytochrome c oxidase subunit I [COI] haplotypes) of polychaete Hediste diversicolor populations in the Amvrakikos Gulf (western Greece) in order to test Cognetti’s hypothesis on the formation of distinct isolated populations of species living in stressed transitional water habitats. To this purpose, the intraspecific diversity of H. diversicolor and the similarities among its populations in the brackish water habitats of the Eastern Mediterranean were investigated. Samples were collected from the lagoonal complex of Am - vrakikos Gulf in 2010 and 2011. Analysis showed that populations in the Amvrakikos Gulf share unique haplotypes which are distinct from the haplotypes hitherto reported, suggesting that these populations are highly isolated. This evidence partially supports Cognetti’s hypothesis. The results indicate that the genetic differentiation in the studied populations was probably caused by the complete isolation of the gulf and periodic hypoxic conditions during its formation history. The occurrence of unique haplotypes in the gulf underlines the importance of considering genetic diversity in the design of long-term biodiversity management and conservation plans. © The authors 2016. |
2015 |
Pafilis, E; Frankild, S P; Schnetzer, J; Fanini, L; Faulwetter, S; Pavloudi, C; Vasileiadou, K; Leary, P; Hammock, J; Schulz, K; Parr, C S; Arvanitidis, C; Jensen, L J ENVIRONMENTS and EOL: Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life Journal Article Bioinformatics, 31 (11), pp. 1872–1874, 2015, ISSN: 13674803, (Publisher: Oxford University Press). @article{pafilis_environments_2015, title = {ENVIRONMENTS and EOL: Identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life}, author = {E Pafilis and S P Frankild and J Schnetzer and L Fanini and S Faulwetter and C Pavloudi and K Vasileiadou and P Leary and J Hammock and K Schulz and C S Parr and C Arvanitidis and L J Jensen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941662911&doi=10.1093%2fbioinformatics%2fbtv045&partnerID=40&md5=521c1035d81d477752f37d09c638a7c0}, doi = {10.1093/bioinformatics/btv045}, issn = {13674803}, year = {2015}, date = {2015-01-01}, journal = {Bioinformatics}, volume = {31}, number = {11}, pages = {1872--1874}, abstract = {Summary: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary- based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. Availability and implementation: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr. © The Author 2015. Published by Oxford University Press. All rights reserved.}, note = {Publisher: Oxford University Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } Summary: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary- based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users. Availability and implementation: The software and the corpus are available under the open-source BSD and the CC-BY-NC-SA 3.0 licenses, respectively, at http://environments.hcmr.gr. © The Author 2015. Published by Oxford University Press. All rights reserved. |
Faulwetter, S; Papageorgiou, N; Koulouri, P; Fanini, L; Chatzinikolaou, E; Markantonatou, V; Pavloudi, C; Chatzigeorgiou, G; Keklikoglou, K; Vasileiadou, K; Basset, A; Pinna, M; Rosati, I; Reizopoulou, S; Nicolaidou, A; Arvanitidis, C Resistance of polychaete species and trait patterns to simulated species loss in coastal lagoons Journal Article Journal of Sea Research, 98 , pp. 73–82, 2015, ISSN: 13851101, (Publisher: Elsevier). @article{faulwetter_resistance_2015, title = {Resistance of polychaete species and trait patterns to simulated species loss in coastal lagoons}, author = {S Faulwetter and N Papageorgiou and P Koulouri and L Fanini and E Chatzinikolaou and V Markantonatou and C Pavloudi and G Chatzigeorgiou and K Keklikoglou and K Vasileiadou and A Basset and M Pinna and I Rosati and S Reizopoulou and A Nicolaidou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930278022&doi=10.1016%2fj.seares.2014.09.003&partnerID=40&md5=4f1ebcb9d504ea078f66a78cf0199509}, doi = {10.1016/j.seares.2014.09.003}, issn = {13851101}, year = {2015}, date = {2015-01-01}, journal = {Journal of Sea Research}, volume = {98}, pages = {73--82}, abstract = {The loss of species is known to have negative impacts on the integrity of ecosystems, but the details of this relationship are still far from being fully understood. This study investigates how the distribution patterns of polychaete species and their associated biological trait patterns in six Mediterranean coastal lagoons change under computationally simulated scenarios of random species loss. Species were progressively removed from the full polychaete assemblage and the similarity between the full assemblage and the reduced matrices of both species and trait patterns was calculated. The results indicate the magnitude of changes that might follow species loss in the real world, and allow consideration of the resistance of the system's functional capacity to loss of species, expressed through the species' biological traits as an approximation to functioning. Comparisons were made between the changes in the distribution of species and of traits, as well as between the six different lagoons. While the change of species and trait patterns was strongly correlated within most lagoons, different lagoons showed distinctly different patterns. In disturbed lagoons, the dominance of one or few species was the major driver for the observed patterns and the loss of these species caused extreme changes. Less disturbed lagoons were less susceptible to extreme changes and had a greater resistance towards species loss. Species richness appears to be less important for the ability of the lagoons to buffer changes, instead the initial composition of the assemblage and the identity of the lost species determine the response of the system and our ability to predict changes of the assemblage's functional potential. © 2014 Elsevier B.V.}, note = {Publisher: Elsevier}, keywords = {}, pubstate = {published}, tppubtype = {article} } The loss of species is known to have negative impacts on the integrity of ecosystems, but the details of this relationship are still far from being fully understood. This study investigates how the distribution patterns of polychaete species and their associated biological trait patterns in six Mediterranean coastal lagoons change under computationally simulated scenarios of random species loss. Species were progressively removed from the full polychaete assemblage and the similarity between the full assemblage and the reduced matrices of both species and trait patterns was calculated. The results indicate the magnitude of changes that might follow species loss in the real world, and allow consideration of the resistance of the system's functional capacity to loss of species, expressed through the species' biological traits as an approximation to functioning. Comparisons were made between the changes in the distribution of species and of traits, as well as between the six different lagoons. While the change of species and trait patterns was strongly correlated within most lagoons, different lagoons showed distinctly different patterns. In disturbed lagoons, the dominance of one or few species was the major driver for the observed patterns and the loss of these species caused extreme changes. Less disturbed lagoons were less susceptible to extreme changes and had a greater resistance towards species loss. Species richness appears to be less important for the ability of the lagoons to buffer changes, instead the initial composition of the assemblage and the identity of the lost species determine the response of the system and our ability to predict changes of the assemblage's functional potential. © 2014 Elsevier B.V. |
2014 |
Faulwetter, Sarah; Dailianis, Thanos; Vasileiadou, Katerina; Kouratoras, Michail; Arvanitidis, Christos Can micro-CT become an essential tool for the 21st century taxonomist? – an evaluation using marine polychaetes Journal Article Microscopy and Analysis, 28 , pp. 10–13, 2014. @article{faulwetter_can_2014, title = {Can micro-CT become an essential tool for the 21st century taxonomist? – an evaluation using marine polychaetes}, author = {Sarah Faulwetter and Thanos Dailianis and Katerina Vasileiadou and Michail Kouratoras and Christos Arvanitidis}, year = {2014}, date = {2014-02-01}, journal = {Microscopy and Analysis}, volume = {28}, pages = {10--13}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Chatzigeorgiou, G; Sarropoulou, E; Vasileiadou, K; Brown, C; Faulwetter, S; Kotoulas, G; Arvanitidis, C D Community structure and population genetics of Eastern Mediterranean polychaetes Journal Article Frontiers in Marine Science, 1 (OCT), 2014, ISSN: 22967745, (Publisher: Frontiers Media S. A). @article{chatzigeorgiou_community_2014, title = {Community structure and population genetics of Eastern Mediterranean polychaetes}, author = {G Chatzigeorgiou and E Sarropoulou and K Vasileiadou and C Brown and S Faulwetter and G Kotoulas and C D Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85008950428&doi=10.3389%2ffmars.2014.00047&partnerID=40&md5=594f48af64289b71d3a629d8968248df}, doi = {10.3389/fmars.2014.00047}, issn = {22967745}, year = {2014}, date = {2014-01-01}, journal = {Frontiers in Marine Science}, volume = {1}, number = {OCT}, abstract = {Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1766) during two successive years at two locations in northern Crete (Aegean Sea) and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity) at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community. © 2014 Chatzigeorgiou, Sarropoulou, Vasileiadou, Brown, Faulwetter, Kotoulas and Arvanitidis.}, note = {Publisher: Frontiers Media S. A}, keywords = {}, pubstate = {published}, tppubtype = {article} } Species and genetic diversity are often found to co-vary since they are influenced by external factors in similar ways. In this paper, we analyse the genetic differences of the abundant polychaete Hermodice carunculata (Pallas, 1766) during two successive years at two locations in northern Crete (Aegean Sea) and compare them to other populations in the Mediterranean Sea and the Atlantic Ocean. The genetic analysis is combined with an analysis of ecological divergence of the total polychaete community structure (beta diversity) at these locations. The phylogenetic analysis of all included H. carunculata populations revealed two main clades, one exclusively found in the Mediterranean and a second occurring in both the Mediterranean and the Atlantic. Genetic diversity indices reveal unexpectedly high differences between the two Cretan populations, despite the absence of apparent oceanographic barriers. A similarly high divergence, represented by a high beta diversity index, was observed between the polychaete communities at the two locations. This comparatively high divergence of the genetic structure of a dominant species and the total polychaete community might be explained by the strong influence of local environmental factors as well as inter-specific interactions between the dominance of a single species and the members of the community. © 2014 Chatzigeorgiou, Sarropoulou, Vasileiadou, Brown, Faulwetter, Kotoulas and Arvanitidis. |
Faulwetter, S; Markantonatou, V; Pavloudi, C; Papageorgiou, N; Keklikoglou, K; Chatzinikolaou, E; Pafilis, E; Chatzigeorgiou, G; Vasileiadou, K; Dailianis, T; Fanini, L; Koulouri, P; Arvanitidis, C Polytraits: A database on biological traits of marine polychaetes Journal Article Biodiversity Data Journal, 2 (1), 2014, ISSN: 13142828, (Publisher: Pensoft Publishers). @article{faulwetter_polytraits_2014, title = {Polytraits: A database on biological traits of marine polychaetes}, author = {S Faulwetter and V Markantonatou and C Pavloudi and N Papageorgiou and K Keklikoglou and E Chatzinikolaou and E Pafilis and G Chatzigeorgiou and K Vasileiadou and T Dailianis and L Fanini and P Koulouri and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018193846&doi=10.3897%2fBDJ.2.e1024&partnerID=40&md5=621b076567d09921bf9b5146a7f8844e}, doi = {10.3897/BDJ.2.e1024}, issn = {13142828}, year = {2014}, date = {2014-01-01}, journal = {Biodiversity Data Journal}, volume = {2}, number = {1}, abstract = {The study of ecosystem functioning - the role which organisms play in an ecosystem - is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http:// polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources. © Faulwetter S et al.}, note = {Publisher: Pensoft Publishers}, keywords = {}, pubstate = {published}, tppubtype = {article} } The study of ecosystem functioning - the role which organisms play in an ecosystem - is becoming increasingly important in marine ecological research. The functional structure of a community can be represented by a set of functional traits assigned to behavioural, reproductive and morphological characteristics. The collection of these traits from the literature is however a laborious and time-consuming process, and gaps of knowledge and restricted availability of literature are a common problem. Trait data are not yet readily being shared by research communities, and even if they are, a lack of trait data repositories and standards for data formats leads to the publication of trait information in forms which cannot be processed by computers. This paper describes Polytraits (http:// polytraits.lifewatchgreece.eu), a database on biological traits of marine polychaetes (bristle worms, Polychaeta: Annelida). At present, the database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 marine polychaete species, all referenced by literature sources. All data can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable, and have been submitted to the Encyclopedia of Life for archival and integration with trait information from other sources. © Faulwetter S et al. |
Prentiss, N K; Vasileiadou, K; Faulwetter, S; Arvanitidis, C; Hove, Ten H A A new genus and species of Serpulidae (Annelida, Polychaeta, Sabellida) from the Caribbean Sea Journal Article Zootaxa, 3900 (2), pp. 204–222, 2014, ISSN: 11755326, (Publisher: Magnolia Press). @article{prentiss_new_2014, title = {A new genus and species of Serpulidae (Annelida, Polychaeta, Sabellida) from the Caribbean Sea}, author = {N K Prentiss and K Vasileiadou and S Faulwetter and C Arvanitidis and H A Ten Hove}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84919628735&doi=10.11646%2fzootaxa.3900.2.2&partnerID=40&md5=c759f115417f237ae2f185ed2fd4198c}, doi = {10.11646/zootaxa.3900.2.2}, issn = {11755326}, year = {2014}, date = {2014-01-01}, journal = {Zootaxa}, volume = {3900}, number = {2}, pages = {204--222}, abstract = {A new genus and species of Serpulidae (Annelida, Polychaeta) from the Caribbean Sea. Turbocavus secretus (gen. nov. and sp. nov.) is described from shallow hard substrates (0.5-3 m) in wind-sheltered bays of St. John, U.S. Virgin Islands and Curaçao, as well as from diving depths (46-49 m) around Bonaire (Leeward Antilles), Caribbean Sea. The new taxon, which has from 7 to 19 thoracic chaetigers and up to 335 abdominal chaetigers, bears a unique type of thoracic chaeta which is multifolded at the base and continues with a groove tapering to the capillary tip. The new serpulid has unique 18S rRNA sequences and genetic analysis of the 18S rRNA gene situates the new genus at the basis of the serpulid cladogram, well separated from other genera, and close to Filograna/Salmacina and Protula. Copyright © 2014 Magnolia Press.}, note = {Publisher: Magnolia Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new genus and species of Serpulidae (Annelida, Polychaeta) from the Caribbean Sea. Turbocavus secretus (gen. nov. and sp. nov.) is described from shallow hard substrates (0.5-3 m) in wind-sheltered bays of St. John, U.S. Virgin Islands and Curaçao, as well as from diving depths (46-49 m) around Bonaire (Leeward Antilles), Caribbean Sea. The new taxon, which has from 7 to 19 thoracic chaetigers and up to 335 abdominal chaetigers, bears a unique type of thoracic chaeta which is multifolded at the base and continues with a groove tapering to the capillary tip. The new serpulid has unique 18S rRNA sequences and genetic analysis of the 18S rRNA gene situates the new genus at the basis of the serpulid cladogram, well separated from other genera, and close to Filograna/Salmacina and Protula. Copyright © 2014 Magnolia Press. |
2013 |
Pafilis, E; Frankild, S; I, Umer; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, C; Schnetzer, J; Vasileiadou, A; Arvanitidis, C; Quince, C; Jensen, L J Identification of Environment Ontology terms in Text and Annotation of Biodiversity (ENVIRONMENTS-EOL) and Genomics (SEQenv) Information Inproceedings Pafilis, E (Ed.): Biodiversity Information Standards TDWG Conference, Florence, Italy, 2013. @inproceedings{pafilis_identification_2013, title = {Identification of Environment Ontology terms in Text and Annotation of Biodiversity (ENVIRONMENTS-EOL) and Genomics (SEQenv) Information}, author = {E Pafilis and S Frankild and Umer I and Lucia Fanini and Sarah Faulwetter and C Pavloudi and J Schnetzer and A Vasileiadou and C Arvanitidis and C Quince and L J Jensen}, editor = {E Pafilis}, year = {2013}, date = {2013-10-01}, booktitle = {Biodiversity Information Standards TDWG Conference, Florence, Italy}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Faulwetter, Sarah; Dailianis, Thanos; Vasileiadou, Aikaterini; Arvanitidis, Christos Contrast enhancing techniques for the application of micro-CT in marine biodiversity studies Journal Article Microscopy and Analysis, 27 (2), pp. S4–S7, 2013. @article{faulwetter_contrast_2013, title = {Contrast enhancing techniques for the application of micro-CT in marine biodiversity studies}, author = {Sarah Faulwetter and Thanos Dailianis and Aikaterini Vasileiadou and Christos Arvanitidis}, url = {http://www.microscopy-analysis.com/sites/default/files/2013_March_Faulwetter.pdf}, year = {2013}, date = {2013-02-01}, journal = {Microscopy and Analysis}, volume = {27}, number = {2}, pages = {S4--S7}, abstract = {X-ray micro-computed tomography holds large potential for zoology and taxonomy in particular. The scanning of soft-bodied invertebrates requires however some form of contrast enhancement to produce useful results. Here, we apply three different methods (tissue staining with iodine and with phosphotungstic acid and drying with hexamethyldisilazane) to three different invertebrates and compare their effects. The effects of each method on different organisms and their advantages and disadvantages are discussed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } X-ray micro-computed tomography holds large potential for zoology and taxonomy in particular. The scanning of soft-bodied invertebrates requires however some form of contrast enhancement to produce useful results. Here, we apply three different methods (tissue staining with iodine and with phosphotungstic acid and drying with hexamethyldisilazane) to three different invertebrates and compare their effects. The effects of each method on different organisms and their advantages and disadvantages are discussed. |
Faulwetter, S; Vasileiadou, A; Kouratoras, M; Dailianis, T; Arvanitidis, C Micro-computed tomography: Introducing new dimensions to taxonomy Journal Article ZooKeys, 263 , pp. 1–45, 2013, ISSN: 13132989. @article{faulwetter_micro-computed_2013, title = {Micro-computed tomography: Introducing new dimensions to taxonomy}, author = {S Faulwetter and A Vasileiadou and M Kouratoras and T Dailianis and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873465745&doi=10.3897%2fzookeys.263.4261&partnerID=40&md5=79eb83ef960d142fc3d30b24f193ab45}, doi = {10.3897/zookeys.263.4261}, issn = {13132989}, year = {2013}, date = {2013-01-01}, journal = {ZooKeys}, volume = {263}, pages = {1--45}, abstract = {Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called "cybertypes", and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information. © 2013 Sarah Faulwetter.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Continuous improvements in the resolution of three-dimensional imaging have led to an increased application of these techniques in conventional taxonomic research in recent years. Coupled with an ever increasing research effort in cybertaxonomy, three-dimensional imaging could give a boost to the development of virtual specimen collections, allowing rapid and simultaneous access to accurate virtual representations of type material. This paper explores the potential of micro-computed tomography (X-ray micro-tomography), a non-destructive three-dimensional imaging technique based on mapping X-ray attenuation in the scanned object, for supporting research in systematics and taxonomy. The subsequent use of these data as virtual type material, so-called "cybertypes", and the creation of virtual collections lie at the core of this potential. Sample preparation, image acquisition, data processing and presentation of results are demonstrated using polychaetes (bristle worms), a representative taxon of macro-invertebrates, as a study object. Effects of the technique on the morphological, anatomical and molecular identity of the specimens are investigated. The paper evaluates the results and discusses the potential and the limitations of the technique for creating cybertypes. It also discusses the challenges that the community might face to establish virtual collections. Potential future applications of three-dimensional information in taxonomic research are outlined, including an outlook to new ways of producing, disseminating and publishing taxonomic information. © 2013 Sarah Faulwetter. |
Pafilis, E; Frankild, S P; Fanini, L; Faulwetter, S; Pavloudi, C; Vasileiadou, A; Arvanitidis, C; Jensen, L J The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text Journal Article PLoS ONE, 8 (6), 2013, ISSN: 19326203. @article{pafilis_species_2013, title = {The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text}, author = {E Pafilis and S P Frankild and L Fanini and S Faulwetter and C Pavloudi and A Vasileiadou and C Arvanitidis and L J Jensen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879162734&doi=10.1371%2fjournal.pone.0065390&partnerID=40&md5=fee446181731231a273637d3d09c5002}, doi = {10.1371/journal.pone.0065390}, issn = {19326203}, year = {2013}, date = {2013-01-01}, journal = {PLoS ONE}, volume = {8}, number = {6}, abstract = {The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. © 2013 Pafilis et al.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. © 2013 Pafilis et al. |
Prentiss, N; Vasileiadou, A; Faulwetter, Sarah; Arvanitidis, C A new serpulid genus, (Polychaeta; Serpulidae) from the Caribbean Inproceedings Sydney, 2013, (Publication Title: 11th International Polychaete Conference Type: Abstract/Poster). @inproceedings{prentiss_new_2013, title = {A new serpulid genus, (Polychaeta; Serpulidae) from the Caribbean}, author = {N Prentiss and A Vasileiadou and Sarah Faulwetter and C Arvanitidis}, url = {https://custom.cvent.com/33FC1B6811EC461DA18796A3281D21F3/files/3f76df8999754bb1a17b584a686c1d0a.pdf}, year = {2013}, date = {2013-01-01}, address = {Sydney}, note = {Publication Title: 11th International Polychaete Conference Type: Abstract/Poster}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Vasileiadou, A; Pavloudi, C; Chatzinikolaou, E; Gonzalez-Wanguemert, M; Tsikopoulou, I; Kotoulas, G; Arvanitidis, C Genetic diversity patterns of macrobenthic populations from lagoonal ecosystems Inproceedings Lisbon (Portugal), 2013, (Publication Title: 14th Congress of European Society for Evolutionary Biology, 19-24 August 2013 Type: Poster). @inproceedings{vasileiadou_genetic_2013, title = {Genetic diversity patterns of macrobenthic populations from lagoonal ecosystems}, author = {A Vasileiadou and C Pavloudi and E Chatzinikolaou and M Gonzalez-Wanguemert and I Tsikopoulou and G Kotoulas and C Arvanitidis}, year = {2013}, date = {2013-01-01}, address = {Lisbon (Portugal)}, note = {Publication Title: 14th Congress of European Society for Evolutionary Biology, 19-24 August 2013 Type: Poster}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
2012 |
Pafilis, E; Frankild, S; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, C; Vasileiadou, A; Arvanitidis, C; Jensen, L J SPECIES: Organism Name Identification in the Scientific Literature Inproceedings Pafilis, E (Ed.): 7th conference of the Hellenic Society for Computational Biology and Bioinformatics, Heraklion, Greece, 2012. @inproceedings{pafilis_species_2012, title = {SPECIES: Organism Name Identification in the Scientific Literature}, author = {E Pafilis and S Frankild and Lucia Fanini and Sarah Faulwetter and C Pavloudi and A Vasileiadou and C Arvanitidis and L J Jensen}, editor = {E Pafilis}, year = {2012}, date = {2012-10-01}, booktitle = {7th conference of the Hellenic Society for Computational Biology and Bioinformatics, Heraklion, Greece}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Vasileiadou, A; Sarropoulou, E; Tsigenopoulos, C S; Reizopoulou, S; Nikolaidou, A; Orfanidis, S; Simboura, N; Kotoulas, G; Arvanitidis, C Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem Journal Article Transitional Waters Bulletin, 6 , pp. 20–33, 2012. @article{vasileiadou_genetic_2012, title = {Genetic vs community diversity patterns of macrobenthic species: preliminary results from the lagoonal ecosystem}, author = {A Vasileiadou and E Sarropoulou and C S Tsigenopoulos and S Reizopoulou and A Nikolaidou and S Orfanidis and N Simboura and G Kotoulas and C Arvanitidis}, url = {http://siba-ese.unisalento.it/index.php/twb/article/view/12797/11396}, doi = {10.1285/i1825229Xv6n2p20}, year = {2012}, date = {2012-01-01}, journal = {Transitional Waters Bulletin}, volume = {6}, pages = {20--33}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2011 |
Arvanitidis, C; Faulwetter, S; Chatzigeorgiou, G; Penev, L; Bánki, O; Dailianis, T; Pafilis, E; Kouratoras, M; Chatzinikolaou, E; Fanini, L; Vasileiadou, A; Pavloudi, C; Vavilis, P; Koulouri, P; Dounas, C Engaging the broader community in biodiversity research: The concept of the COMBER pilot project for divers in vibrant Journal Article ZooKeys, 150 , pp. 211–229, 2011, ISSN: 13132989. @article{arvanitidis_engaging_2011, title = {Engaging the broader community in biodiversity research: The concept of the COMBER pilot project for divers in vibrant}, author = {C Arvanitidis and S Faulwetter and G Chatzigeorgiou and L Penev and O Bánki and T Dailianis and E Pafilis and M Kouratoras and E Chatzinikolaou and L Fanini and A Vasileiadou and C Pavloudi and P Vavilis and P Koulouri and C Dounas}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856457337&doi=10.3897%2fzookeys.150.2149&partnerID=40&md5=48d27ff65c2def3588c3e0f3a8b72a92}, doi = {10.3897/zookeys.150.2149}, issn = {13132989}, year = {2011}, date = {2011-01-01}, journal = {ZooKeys}, volume = {150}, pages = {211--229}, abstract = {This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens' Network for the Observation of Marine Biodiv ERsity, http://www.comber.hcmr.gr, which has been initiated under the Vi BRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens' Network for the Observation of Marine Biodiv ERsity, http://www.comber.hcmr.gr, which has been initiated under the Vi BRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far. |
2009 |
Arvanitidis, C; Somerfield, P J; Rumohr, H; Faulwetter, S; Valavanis, V; Vasileiadou, A; Chatzigeorgiou, G; Berghe, Vanden E; Vanaverbeke, J; Labrune, C; Grémare, A; Zettler, M L; Kȩdra, M; Włodarska-Kowalczuk, M; Aleffi, I F; Amouroux, J M; Anisimova, N; Bachelet, G; Büntzow, M; Cochrane, S J; Costello, M J; Craeymeersch, J; Dahle, S; Degraer, S; Denisenko, S; Dounas, C; Duineveld, G; Emblow, C; Escavarage, V; Fabri, M C; Fleischer, D; Gray, J S; Heip, C H R; Herrmann, M; Hummel, H; Janas, U; Karakassis, I; Kendall, M A; Kingston, P; Kotwicki, L; Laudien, J; Mackie, A S Y; Nevrova, E L; Occhipinti-Ambrogi, A; Oliver, P G; Olsgard, F; Palerud, R; Petrov, A; Rachor, E; Revkov, N K; Rose, A; Sardá, R; Sistermans, W C H; Speybroeck, J; Hoey, Van G; Vincx, M; Whomersley, P; Willems, W; Zenetos, A Biological geography of the European seas: Results from the MacroBen database Journal Article Marine Ecology Progress Series, 382 , pp. 265–278, 2009, ISSN: 01718630. @article{arvanitidis_biological_2009, title = {Biological geography of the European seas: Results from the MacroBen database}, author = {C Arvanitidis and P J Somerfield and H Rumohr and S Faulwetter and V Valavanis and A Vasileiadou and G Chatzigeorgiou and E Vanden Berghe and J Vanaverbeke and C Labrune and A Grémare and M L Zettler and M Kȩdra and M Włodarska-Kowalczuk and I F Aleffi and J M Amouroux and N Anisimova and G Bachelet and M Büntzow and S J Cochrane and M J Costello and J Craeymeersch and S Dahle and S Degraer and S Denisenko and C Dounas and G Duineveld and C Emblow and V Escavarage and M C Fabri and D Fleischer and J S Gray and C H R Heip and M Herrmann and H Hummel and U Janas and I Karakassis and M A Kendall and P Kingston and L Kotwicki and J Laudien and A S Y Mackie and E L Nevrova and A Occhipinti-Ambrogi and P G Oliver and F Olsgard and R Palerud and A Petrov and E Rachor and N K Revkov and A Rose and R Sardá and W C H Sistermans and J Speybroeck and G Van Hoey and M Vincx and P Whomersley and W Willems and A Zenetos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66649133743&doi=10.3354%2fmeps07955&partnerID=40&md5=b494b7aad3e4476e31b82b871b6c26e6}, doi = {10.3354/meps07955}, issn = {01718630}, year = {2009}, date = {2009-01-01}, journal = {Marine Ecology Progress Series}, volume = {382}, pages = {265--278}, abstract = {This study examines whether or not biogeographical and/or managerial divisions across the European seas can be validated using soft-bottom macrobenthic community data. The faunal groups used were: all macrobenthos groups, polychaetes, molluscs, crustaceans, echinoderms, sipun-culans and the last 5 groups combined. In order to test the discriminating power of these groups, 3 criteria were used: (1) proximity, which refers to the expected closer faunal resemblance of adjacent areas relative to more distant ones; (2) randomness, which in the present context is a measure of the degree to which the inventories of the various sectors, provinces or regions may in each case be considered as a random sample of the inventory of the next largest province or region in a hierarchy of geographic scales; and (3) differentiation, which provides a measure of the uniqueness of the pattern. Results show that only polychaetes fulfill all 3 criteria and that the only marine biogeographic system supported by the analyses is the one proposed by Longhurst (1998). Energy fluxes and other interactions between the planktonic and benthic domains, acting over evolutionary time scales, can be associated with the multivariate pattern derived from the macrobenthos datasets. Third-stage multidimensional scaling ordination reveals that polychaetes produce a unique pattern when all systems are under consideration. Average island distance from the nearest coast, number of islands and the island surface area were the geographic variables best correlated with the community patterns produced by polychaetes. Biogeographic patterns suggest a vicariance model dominating over the founder-dispersal model except for the semi-closed regional seas, where a model substantially modified from the second option could be supported. © Inter-Research 2009.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study examines whether or not biogeographical and/or managerial divisions across the European seas can be validated using soft-bottom macrobenthic community data. The faunal groups used were: all macrobenthos groups, polychaetes, molluscs, crustaceans, echinoderms, sipun-culans and the last 5 groups combined. In order to test the discriminating power of these groups, 3 criteria were used: (1) proximity, which refers to the expected closer faunal resemblance of adjacent areas relative to more distant ones; (2) randomness, which in the present context is a measure of the degree to which the inventories of the various sectors, provinces or regions may in each case be considered as a random sample of the inventory of the next largest province or region in a hierarchy of geographic scales; and (3) differentiation, which provides a measure of the uniqueness of the pattern. Results show that only polychaetes fulfill all 3 criteria and that the only marine biogeographic system supported by the analyses is the one proposed by Longhurst (1998). Energy fluxes and other interactions between the planktonic and benthic domains, acting over evolutionary time scales, can be associated with the multivariate pattern derived from the macrobenthos datasets. Third-stage multidimensional scaling ordination reveals that polychaetes produce a unique pattern when all systems are under consideration. Average island distance from the nearest coast, number of islands and the island surface area were the geographic variables best correlated with the community patterns produced by polychaetes. Biogeographic patterns suggest a vicariance model dominating over the founder-dispersal model except for the semi-closed regional seas, where a model substantially modified from the second option could be supported. © Inter-Research 2009. |
Somerfield, P J; Arvanitidis, C; Faulwetter, S; Chatzigeorgiou, G; Vasileiadou, A; Amouroux, J M; Anisimova, N; Cochrane, S J; Craeymeersch, J; Dahle, S; Denisenko, S; Dounas, K; Duineveld, G; Grémare, A; Heip, C H R; Herrmann, M; Karakassis, I; Kȩdra, M; Kendall, M A; Kingston, P; Kotwicki, L; Labrune, C; Laudien, J; Nevrova, H; Nicolaidou, A; Occhipinti-Ambrogi, A; Palerud, R; Petrov, A; Rachor, E; Revkov, N; Rumohr, H; Sardá, R; Janas, U; Berghe, Vanden E; Włodarska-Kowalczuk, M Assessing evidence for random assembly of marine benthic communities from regional species pools Journal Article Marine Ecology Progress Series, 382 , pp. 279–286, 2009, ISSN: 01718630. @article{somerfield_assessing_2009, title = {Assessing evidence for random assembly of marine benthic communities from regional species pools}, author = {P J Somerfield and C Arvanitidis and S Faulwetter and G Chatzigeorgiou and A Vasileiadou and J M Amouroux and N Anisimova and S J Cochrane and J Craeymeersch and S Dahle and S Denisenko and K Dounas and G Duineveld and A Grémare and C H R Heip and M Herrmann and I Karakassis and M Kȩdra and M A Kendall and P Kingston and L Kotwicki and C Labrune and J Laudien and H Nevrova and A Nicolaidou and A Occhipinti-Ambrogi and R Palerud and A Petrov and E Rachor and N Revkov and H Rumohr and R Sardá and U Janas and E Vanden Berghe and M Włodarska-Kowalczuk}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-66649136488&doi=10.3354%2fmeps07934&partnerID=40&md5=dcce15cc6eb45417bba0ef6f162fb1df}, doi = {10.3354/meps07934}, issn = {01718630}, year = {2009}, date = {2009-01-01}, journal = {Marine Ecology Progress Series}, volume = {382}, pages = {279--286}, abstract = {Local species diversity may be determined by processes operating locally, such as disturbance, predation and competition, or by regional processes, such as environmental structuring or history. Classical theory focusing on competition predicts that the species combining to form communities will be less similar to each other than they would be if they were assembled at random from a regional species pool. Theory focusing on environmental structuring predicts that species will be more similar to each other than expected by chance. A randomisation test that determines the extent to which local species lists represent random selections from a regional list, based on the average relatedness between species, was applied to data held in the MacroBen database. Little or no evidence was found for species lists of whole faunas at any scale being random subsets of species lists at larger scales. Species tend to be more closely related to each other than would be expected if they were assembled at random. Thus marine soft-sediment macrofauna are not locally assembled at random from regional species pools and it is likely that regional processes determine the assembly of communities. Focusing on the most abundant class within the macrofauna, a different pattern emerges, in that there is a much stronger tendency for local polychaete composition to be a random subset from regional pools at all scales. Thus it is not possible to determine whether local polychaete diversity is independent of both local and regional processes, or determined by a combination of both acting antagonistically. © Inter-Research 2009.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Local species diversity may be determined by processes operating locally, such as disturbance, predation and competition, or by regional processes, such as environmental structuring or history. Classical theory focusing on competition predicts that the species combining to form communities will be less similar to each other than they would be if they were assembled at random from a regional species pool. Theory focusing on environmental structuring predicts that species will be more similar to each other than expected by chance. A randomisation test that determines the extent to which local species lists represent random selections from a regional list, based on the average relatedness between species, was applied to data held in the MacroBen database. Little or no evidence was found for species lists of whole faunas at any scale being random subsets of species lists at larger scales. Species tend to be more closely related to each other than would be expected if they were assembled at random. Thus marine soft-sediment macrofauna are not locally assembled at random from regional species pools and it is likely that regional processes determine the assembly of communities. Focusing on the most abundant class within the macrofauna, a different pattern emerges, in that there is a much stronger tendency for local polychaete composition to be a random subset from regional pools at all scales. Thus it is not possible to determine whether local polychaete diversity is independent of both local and regional processes, or determined by a combination of both acting antagonistically. © Inter-Research 2009. |
2008 |
Faulwetter, S; Vasileiadou, A; Papageorgiou, N; Arvanitidis, C Zootaxa, (1847), pp. 1–18, 2008, ISSN: 11755326. @article{faulwetter_description_2008, title = {Description of a new species of Streptosyllis (Polychaeta: Syllidae) from the Mediterranean and Canary Islands with a re-description of Streptosyllis arenae and comments on the taxonomy of Streptosyllis and some morphologically similar genera}, author = {S Faulwetter and A Vasileiadou and N Papageorgiou and C Arvanitidis}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-49949102313&partnerID=40&md5=b42a78644d6b92d3f2632c2d783a2b69}, issn = {11755326}, year = {2008}, date = {2008-01-01}, journal = {Zootaxa}, number = {1847}, pages = {1--18}, abstract = {A new Streptosyllis species, S. nunezi n. sp., is described from shallow sandy substrates in the Mediterranean and the Canary Islands. The new species is distinguished by a unique combination of characters: teeth of the shafts of the compound chaetae covered by hyaline hood; 1-2 lateral tips formed by the hyaline hood covering the blades of the compound chaetae; strongly serrated dorsal simple chaetae which appear as 2-4 robust teeth when viewed laterally. The re-description of its closest congener, the type species S. arenae Webster and Benedict, 1884, is also provided based on the type material, as well as a key to the currently valid species and table of characters for the genus. Finally, some comments are made for the characters distinguishing the genera Streptosyllis, Syllides, Anoplosyllis, Astreptosyllis and Streptospinigera, which are listed in a table and a potential key for their identification is proposed. Copyright © 2008 Magnolia Press.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new Streptosyllis species, S. nunezi n. sp., is described from shallow sandy substrates in the Mediterranean and the Canary Islands. The new species is distinguished by a unique combination of characters: teeth of the shafts of the compound chaetae covered by hyaline hood; 1-2 lateral tips formed by the hyaline hood covering the blades of the compound chaetae; strongly serrated dorsal simple chaetae which appear as 2-4 robust teeth when viewed laterally. The re-description of its closest congener, the type species S. arenae Webster and Benedict, 1884, is also provided based on the type material, as well as a key to the currently valid species and table of characters for the genus. Finally, some comments are made for the characters distinguishing the genera Streptosyllis, Syllides, Anoplosyllis, Astreptosyllis and Streptospinigera, which are listed in a table and a potential key for their identification is proposed. Copyright © 2008 Magnolia Press. |
2007 |
Vasileiadou, A; Sarropoulou, E; Tsigenopoulos, K; Reizopoulou, S; Nikolaidou, A; Orfanidis, S; Simboura, M; Kotoulas, G; Arvanitidis, C Polychaete community genetics from the northwestern Greek lagoons sampling: Preliminary results Journal Article MarBEF Newsletter, 6 , pp. 26–27, 2007. @article{vasileiadou_polychaete_2007, title = {Polychaete community genetics from the northwestern Greek lagoons sampling: Preliminary results}, author = {A Vasileiadou and E Sarropoulou and K Tsigenopoulos and S Reizopoulou and A Nikolaidou and S Orfanidis and M Simboura and G Kotoulas and C Arvanitidis}, url = {http://www.marbef.org/outreach/newsletter.php}, year = {2007}, date = {2007-01-01}, journal = {MarBEF Newsletter}, volume = {6}, pages = {26--27}, keywords = {}, pubstate = {published}, tppubtype = {article} } |