@article{DolgenerSchroederSchneeweissetal.2012, author = {Dolgener, Nicola and Schr{\"o}der, Christiane and Schneeweiss, N. and Tiedemann, Ralph}, title = {Genetic population structure of the Fire-bellied toad Bombina bombina in an area of high population density implications for conservation}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {689}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-012-1016-1}, pages = {111 -- 120}, year = {2012}, abstract = {In this study, we report the genetic population structure of the Fire-bellied toad Bombina bombina in Brandenburg (East Germany) in the context of conservation. We analysed 298 samples originating from 11 populations in Brandenburg using mitochondrial control region sequences and six polymorphic microsatellite loci. For comparison, we included one population each from Poland and Ukraine into our analysis. Within Brandenburg, we detected a moderate variability in the mitochondrial control region (19 different haplotypes) and at microsatellite loci (9-12 alleles per locus). These polymorphisms revealed a clear population structure among toads in Brandenburg, despite a relatively high overall population density and the moderate size of single populations (100-2000 individuals). The overall genetic population structure is consistent with a postglacial colonization from South East-Europe and a subsequent population expansion. Based on genetic connectivity, we infer Management Units (MUs) as targets for conservation. Our genetic survey identified MUs, within which human infrastructure is currently preventing any genetic exchange. We also detect an unintentional translocation from South East to North West Brandenburg, presumably in the course of fish stocking activities. Provided suitable conservation measures are taken, Brandenburg should continue to harbor large populations of this critically endangered species.}, language = {en} } @article{GirndtRieschSchroederetal.2012, author = {Girndt, Antje and Riesch, R{\"u}diger and Schr{\"o}der, Christiane and Sehlupp, Ingo and Plath, Martin and Tiedemann, Ralph}, title = {Multiple paternity in different populations of the sailfin molly, Poecilia latipinna}, series = {Animal biology}, volume = {62}, journal = {Animal biology}, number = {3}, publisher = {Brill}, address = {Leiden}, issn = {1570-7555}, doi = {10.1163/157075611X618192}, pages = {245 -- 262}, year = {2012}, abstract = {Rates of multiple paternities were investigated in the sailfin molly (Poecilia latipinna), using eight microsatellite loci. Genotyping was performed for offspring and mothers in 40 broods from four allopatric populations from the south-eastern U.S.A. along a geographic stretch of 1200 km in west-east direction and approximately 200 km from north to south. No significant differences regarding rates of multiple paternities were found between populations despite sample populations stemming from ecologically divergent habitats. Even the most conservative statistical approach revealed a minimum of 70\% of the broods being sired by at least two males, with an average of 1.80-2.95 putative fathers per brood. Within broods, one male typically sired far more offspring than would be expected under an assumed equal probability of all detected males siring offspring.}, language = {en} } @article{HartmannHelmNickeletal.2012, author = {Hartmann, Stefanie and Helm, Conrad and Nickel, Birgit and Meyer, Matthias and Struck, Torsten H. and Tiedemann, Ralph and Selbig, Joachim and Bleidorn, Christoph}, title = {Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data}, series = {PLoS one}, volume = {7}, journal = {PLoS one}, number = {1}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0029843}, pages = {8}, year = {2012}, abstract = {Background: In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic ( or parasitic) protostomes that are either placed with annelids or flatworms. Methodology: Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. Conclusions: Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.}, language = {en} } @article{KetmaierMarroneAlfonsoetal.2012, author = {Ketmaier, Valerio and Marrone, Federico and Alfonso, Giuseppe and Paulus, Kirsten B. and Wiemann, Annika and Tiedemann, Ralph and Mura, Graziella}, title = {Mitochondrial DNA regionalism and historical demography in the extant populations of chirocephalus kerkyrensis (Branchiopoda: Anostraca)}, series = {PLoS one}, volume = {7}, journal = {PLoS one}, number = {2}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0030082}, pages = {11}, year = {2012}, abstract = {Background: Mediterranean temporary water bodies are important reservoirs of biodiversity and host a unique assemblage of diapausing aquatic invertebrates. These environments are currently vanishing because of increasing human pressure. Chirocephalus kerkyrensis is a fairy shrimp typical of temporary water bodies in Mediterranean plain forests and has undergone a substantial decline in number of populations in recent years due to habitat loss. We assessed patterns of genetic connectivity and phylogeographic history in the seven extant populations of the species from Albania, Corfu Is. (Greece), Southern and Central Italy. Methodology/Principal Findings: We analyzed sequence variation at two mitochondrial DNA genes (Cytochrome Oxidase I and 16s rRNA) in all the known populations of C. kerkyrensis. We used multiple phylogenetic, phylogeographic and coalescence-based approaches to assess connectivity and historical demography across the whole distribution range of the species. C. kerkyrensis is genetically subdivided into three main mitochondrial lineages; two of them are geographically localized (Corfu Is. and Central Italy) and one encompasses a wide geographic area (Albania and Southern Italy). Most of the detected genetic variation (approximate to 81\%) is apportioned among the aforementioned lineages. Conclusions/Significance: Multiple analyses of mismatch distributions consistently supported both past demographic and spatial expansions with the former predating the latter; demographic expansions were consistently placed during interglacial warm phases of the Pleistocene while spatial expansions were restricted to cold periods. Coalescence methods revealed a scenario of past isolation with low levels of gene flow in line with what is already known for other co-distributed fairy shrimps and suggest drift as the prevailing force in promoting local divergence. We recommend that these evolutionary trajectories should be taken in proper consideration in any effort aimed at protecting Mediterranean temporary water bodies.}, language = {en} } @article{NahavandiKetmaierTiedemann2012, author = {Nahavandi, Nahid and Ketmaier, Valerio and Tiedemann, Ralph}, title = {Intron structure of the elongation factor 1-alpha gene in the ponto-caspian amphipod pontogammarus maeoticus (Sowinsky, 1894) and its phylogeographic utility}, series = {Journal of crustacean biology}, volume = {32}, journal = {Journal of crustacean biology}, number = {3}, publisher = {Brill}, address = {San Antonio}, issn = {0278-0372}, doi = {10.1163/193724012X626584}, pages = {425 -- 433}, year = {2012}, abstract = {We tested the utility of a 230 base pair intron fragment of the highly conserved nuclear gene Elongation Factor 1-alpha (EF1-alpha) as a proper marker to reconstruct the phylogeography of the marine amphipod Pontogammarus maeoticus (Sowinsky, 1894) from the Caspian and Black Seas. As a prerequisite for further analysis, we confirmed by Southern blot analysis that EF1-alpha is encoded at a single locus in P. maeoticus. We included 15 populations and 60 individuals in the study. Both the phylogeny of the 27 unique alleles found and population genetic analyses revealed a significant differentiation between populations from the aforementioned sea basins. Our results are in remarkable agreement with recent studies on a variety of species from the same area, which invariably support a major phylogeographic break between the Caspian and Black Seas. We thus conclude that our EF1-alpha intron is an informative marker for phylogeographic studies in amphipods at the shallow population level.}, language = {en} } @article{PavesiDeidunDeMatthaeisetal.2012, author = {Pavesi, Laura and Deidun, Alan and De Matthaeis, Elvira and Tiedemann, Ralph and Ketmaier, Valerio}, title = {Mitochondrial DNA and microsatellites reveal significant divergence in the beachflea Orchestia montagui (Talitridae: Amphipoda)}, series = {Aquatic sciences : research across boundaries}, volume = {74}, journal = {Aquatic sciences : research across boundaries}, number = {3}, publisher = {Springer}, address = {Basel}, issn = {1015-1621}, doi = {10.1007/s00027-012-0250-y}, pages = {587 -- 596}, year = {2012}, abstract = {Talitrids are semiterrestrial crustacean amphipods inhabiting sandy and rocky beaches; they generally show limited active dispersal over long distances. In this study we assessed levels of population genetic structure and variability in the talitrid amphipod Orchestia montagui, a species strictly associated to stranded decaying heaps of the seagrass Posidonia oceanica. The study is based on six populations (153 individuals) and covers five basins of the Mediterranean Sea (Tyrrhenian, Ionian, Adriatic, Western and Eastern basins). Samples were screened for polymorphisms at a fragment of the mitochondrial DNA (mtDNA) coding for the cytochrome oxidase subunit I gene (COI; 571 base pairs) and at eight microsatellite loci. MtDNA revealed a relatively homogeneous haplogroup, which clustered together the populations from the Western, Tyrrhenian and Eastern basins, but not the populations from the Adriatic and Ionian ones; microsatellites detected two clusters, one including the Adriatic and Ionian populations, the second grouping all the others. We found a weak geographic pattern in the genetic structuring of the species, with a lack of isolation by distance at either class of markers. Results are discussed in terms of probability of passive dispersal over long distances through heaps of seagrass.}, language = {en} } @article{SammlerHavensteinTiedemann2012, author = {Sammler, Svenja and Havenstein, Katja and Tiedemann, Ralph}, title = {Fourteen new microsatellite markers for the Visayan tarictic hornbill (Penelopides panini) and their cross-species applicability among other endangered Philippine hornbills}, series = {Conservation genetics resources}, volume = {4}, journal = {Conservation genetics resources}, number = {2}, publisher = {Springer}, address = {Dordrecht}, issn = {1877-7252}, doi = {10.1007/s12686-011-9567-4}, pages = {435 -- 438}, year = {2012}, abstract = {Fourteen microsatellite markers were isolated and characterized for the endangered Visayan tarictic hornbill (Penelopides panini, Aves: Bucerotidae). In an analysis of 76 individuals, the number of alleles per locus varied from one to 12. Expected and observed heterozygosity ranged from 0.00 to 0.87 and from 0.00 to 0.89, respectively. All primers also amplify microsatellite loci in Luzon tarictic hornbill (Penelopides manillae), Mindanao tarictic hornbill (Penelopides affinis), the critically endangered Walden's hornbill (Aceros waldeni) and the near-threatened writhed hornbill (Aceros leucocephalus). Two loci which are monomorphic in P. panini were found polymorphic in at least one of the other species. These 14 new microsatellite markers specifically developed for two genera of Philippine hornbills, in combination with those already available for the hornbill genera Buceros and Bucorvus, comprise a reasonable number of loci to genetically analyse wild and captive populations of these and probably other related, often endangered hornbills.}, language = {en} } @phdthesis{SammlerKetmaierHavensteinetal.2012, author = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Krause, Ulrike and Curio, Eberhard and Tiedemann, Ralph}, title = {Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss}, doi = {10.1186/1471-2148-12-203}, year = {2012}, language = {en} } @article{SammlerKetmaierHavensteinetal.2012, author = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Krause, Ulrike and Curio, Eberhard and Tiedemann, Ralph}, title = {Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss}, series = {BMC evolutionary biology}, volume = {12}, journal = {BMC evolutionary biology}, number = {25}, publisher = {BioMed Central}, address = {London}, issn = {1471-2148}, doi = {10.1186/1471-2148-12-203}, pages = {14}, year = {2012}, abstract = {Background: The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in similar to 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results: Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions: We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow and population exchange across islands, saving of the remaining birds of almost extinct local populations - be it in the wild or in captivity - is particularly important to preserve the species' genetic potential.}, language = {en} } @article{SchroederPokornyDolgeneretal.2012, author = {Schr{\"o}der, Christiane and Pokorny, Ina and Dolgener, Nicola and Herden, Christoph and Drews, Hauke and Tiedemann, Ralph}, title = {Allochthonous individuals in managed populations of the fire-bellied toad Bombina bombina genetic detection and conservation implications}, series = {Limnologica : ecology and management of inland waters}, volume = {42}, journal = {Limnologica : ecology and management of inland waters}, number = {4}, publisher = {Elsevier}, address = {Jena}, issn = {0075-9511}, doi = {10.1016/j.limno.2012.08.008}, pages = {291 -- 298}, year = {2012}, abstract = {The ongoing global amphibian decline calls for an increase of habitat and population management efforts. Pond restoration and construction is more and more accompanied by breeding and translocation programs. However, the appropriateness of translocations as a tool for conservation has been widely debated, as it can cause biodiversity loss through genetic homogenization and can disrupt local adaptation, eventually leading to outbreeding depression. In this study, we investigated the genetic structure of two translocated populations of the critically endangered fire-bellied toad Bombina bombina at its north western distribution edge using supposedly neutral genetic markers (variation in the mitochondrial control region and microsatellites) as well as a marker under selection (major histocompatibility complex (MHC) genes). While one of the newly established populations showed the typical genetic composition of surrounding populations, the other was extremely diverged without clear affinity to its putative source. In this population we detected a profound impact of allochthonous individuals: 100\% of the analyzed individuals exhibited a highly divergent mitochondrial haplotype which was otherwise found in Austria. 83\% of them were also assigned to Austria by the analysis of microsatellites. Interestingly, for the adaptive marker (MHC) local alleles were predominant in this population, while only very few alleles were shared with the Austrian population. Probably Mendelian inheritance has reshuffled genotypes such that adaptive local alleles are maintained (here, MHC), while presumably neutral allochthonous alleles dominate at other loci. The release of allochthonous individuals generally increased the genetic variability of the affected population without wiping out locally adaptive genotypes. Thus, outbreeding depression might be less apparent than sometimes thought and natural selection appears strong enough to maintain locally adaptive alleles, at least in functionally important immune system genes.}, language = {en} }