@article{MarroneHavensteinTiedemannetal.2016, author = {Marrone, F. and Havenstein, Katja and Tiedemann, Ralph and Ketmaier, V.}, title = {Identification and characterization of five polymorphic microsatellite loci in the freshwater copepod Hemidiaptomus gurneyi (Copepoda: Calanoida: Diaptomidae)}, series = {The Italian journal of zoology}, volume = {83}, journal = {The Italian journal of zoology}, publisher = {Springer}, address = {Abingdon}, issn = {1125-0003}, doi = {10.1080/11250003.2015.1126363}, pages = {146 -- 150}, year = {2016}, abstract = {Hemidiaptomus diaptomid copepods are known to be excellent biological indicators for the highly biodiverse crustacean communities inhabiting Mediterranean temporary ponds (MTPs), an endangered inland water habitat whose conservation is considered a priority according to the "Habitat Directive" of the European Union. This study reports on the characterization of five polymorphic microsatellite loci in Hemidiaptomus gurneyi, to be used as markers for fine-scale studies on the population genetic structure and metapopulation dynamics of a typical and obligate MTP dweller. The five selected loci proved to be polymorphic in the species, with three to five polymorphic loci per studied population. Overall, mean heterozygosity scored for all loci and populations was lower than that reported for the few other diaptomid species for which microsatellite loci have been to date described; this is possibly due to the intrinsically fragmented and isolated peculiar habitat inhabited by the species. Furthermore, the presence of indels within the flanking regions of selected loci was scored. This study, albeit confirming the technical difficulties in finding proper microsatellite markers in copepods, provides for the first time a set of useful polymorphic microsatellite loci for a Hemidiaptomus species, thus allowing the realization of fine-scale phylogeographic and population genetics studies of this flagship crustacean taxon for MTPs.}, language = {en} } @article{ZhuSchluppTiedemann2016, author = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph}, title = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0156209}, pages = {19}, year = {2016}, abstract = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., ar\&\#945;/ar\&\#946;, er\&\#945;/er\&\#946;1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, er\&\#946;1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of er\&\#945; in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.}, language = {en} } @article{LamannaKirschbaumErnstetal.2016, author = {Lamanna, Francesco and Kirschbaum, Frank and Ernst, Anja R. R. and Feulner, Philine G. D. and Mamonekene, Victor and Paul, Christiane and Tiedemann, Ralph}, title = {Species delimitation and phylogenetic relationships in a genus of African weakly-electric fishes (Osteoglossiformes, Mormyridae, Campylomormyrus)}, series = {Molecular phylogenetics and evolution}, volume = {101}, journal = {Molecular phylogenetics and evolution}, publisher = {Elsevier}, address = {San Diego}, issn = {1055-7903}, doi = {10.1016/j.ympev.2016.04.035}, pages = {8 -- 18}, year = {2016}, abstract = {African weakly-electric fishes (Mormyridae) are able to communicate through species-specific electric signals; this feature might have favoured the evolutionary radiation observed in this family (over 200 species) by acting as an effective pre-zygotic isolation mechanism. In the present study we used mitochondria((cytb) and nuclear (rps7, scn4aa) markers in order to reconstruct a species-phylogeny and identify species boundaries for the genus Campylomormyrus, by applying inference methods based on the multispecies coalescent model. Additionally, we employed 16 microsatellite markers, landmark-based morphometric measurements, and electro-physiological analyses as independent lines of evidence to the results obtained from the sequence data. The results show that groups that are morphologically different are also significantly divergent at the genetic level, whereas morphologically similar groups, displaying dissimilar electric signals, do not show enough genetic diversity to be considered separate species. Furthermore, the data confirm the presence of a yet undescribed species within the genus Campylomormyrus. (C) 2016 Elsevier Inc. All rights reserved.}, language = {en} } @article{PaulKirschbaumMamonekeneetal.2016, author = {Paul, Christiane and Kirschbaum, Frank and Mamonekene, Victor and Tiedemann, Ralph}, title = {Evidence for Non-neutral Evolution in a Sodium Channel Gene in African Weakly Electric Fish (Campylomormyrus, Mormyridae)}, series = {Journal of molecular evolution}, volume = {83}, journal = {Journal of molecular evolution}, publisher = {Springer}, address = {New York}, issn = {0022-2844}, doi = {10.1007/s00239-016-9754-8}, pages = {61 -- 77}, year = {2016}, abstract = {Voltage-gated sodium channels, Nav1, play a crucial role in the generation and propagation of action potentials and substantially contribute to the shape of their rising phase. The electric organ discharge (EOD) of African weakly electric fish (Mormyroidea) is the sum of action potentials fired from all electrocytes of the electric organ at the same time and hence voltage-gated sodium channels are one factor—together with the electrocyte's morphology and innervation pattern—that determines the properties of these EODs. Due to the fish-specific genome duplication, teleost fish possess eight copies of sodium channel genes (SCN), which encode for Nav1 channels. In mormyroids, SCN4aa is solely expressed in the electrocytes of the adult electric organ. In this study, we compared entire SCN4aa sequences of six species of the genus Campylomormyrus and identified nonsynonymous substitutions among them. SCN4aa in Campylomormyrus exhibits a much higher evolutionary rate compared to its paralog SCN4ab, whose expression is not restricted to the electric organ. We also found evidence for strong positive selection on the SCN4aa gene within Mormyridae and along the lineage ancestral to the Mormyridae. We have identified sites at which all nonelectric teleosts are monomorphic in their amino acid, but mormyrids have different amino acids. Our findings confirm the crucial role of SCN4aa in EOD evolution among mormyrid weakly electric fish. The inferred positive selection within Mormyridae makes this gene a prime candidate for further investigation of the divergent evolution of pulse-type EODs among closely related species.}, language = {en} } @article{MakowiczTiedemannSteeleetal.2016, author = {Makowicz, Amber M. and Tiedemann, Ralph and Steele, Rachel N. and Schlupp, Ingo}, title = {Kin Recognition in a Clonal Fish, Poecilia formosa}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0158442}, pages = {20}, year = {2016}, abstract = {Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50\% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity.}, language = {en} } @article{LahTrenseBenkeetal.2016, author = {Lah, Ljerka and Trense, Daronja and Benke, Harald and Berggren, Per and Gunnlaugsson, Porvaldur and Lockyer, Christina and {\"O}zt{\"u}rk, Ayaka and {\"O}zt{\"u}rk, Bayram and Pawliczka, Iwona and Roos, Anna and Siebert, Ursula and Skora, Krzysztof and Vikingsson, Gisli and Tiedemann, Ralph}, title = {Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0162792}, pages = {23}, year = {2016}, abstract = {The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymor-phisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.}, language = {en} } @misc{LahTrenseBenkeetal.2016, author = {Lah, Ljerka and Trense, Daronja and Benke, Harald and Berggren, Per and Gunnlaugsson, Þorvaldur and Lockyer, Christina and {\"O}zt{\"u}rk, Ayaka and {\"O}zt{\"u}rk, Bayram and Pawliczka, Iwona and Roos, Anna and Siebert, Ursula and Sk{\´o}ra, Krzysztof and V{\´i}kingsson, G{\´i}sli and Tiedemann, Ralph}, title = {Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise}, issn = {1866-8372}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-100813}, pages = {23 Seiten}, year = {2016}, abstract = {The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.}, language = {en} } @article{LahTrenseBenkeetal.2016, author = {Lah, Ljerka and Trense, Daronja and Benke, Harald and Berggren, Per and Gunnlaugsson, Þorvaldur and Lockyer, Christina and {\"O}zt{\"u}rk, Ayaka and {\"O}zt{\"u}rk, Bayram and Pawliczka, Iwona and Roos, Anna and Siebert, Ursula and Sk{\´o}ra, Krzysztof and V{\´i}kingsson, G{\´i}sli and Tiedemann, Ralph}, title = {Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, number = {10}, publisher = {PLoS}, address = {Lawrence, Kan.}, issn = {1932-6203}, doi = {10.1371/journal.pone.0162792}, pages = {23 Seiten}, year = {2016}, abstract = {The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.}, language = {en} } @misc{ZhuSchluppTiedemann2016, author = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph}, title = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97119}, pages = {19}, year = {2016}, abstract = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.}, language = {en} } @article{ZhuSchluppTiedemann2016, author = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph}, title = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors}, series = {PLoS one}, volume = {11}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {Lawrence, Kan.}, issn = {1932-6203}, doi = {10.1371/JOURNAL.PONE.0156209}, pages = {19}, year = {2016}, abstract = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.}, language = {en} }