@article{SchedinaGrothSchluppetal.2018, author = {Schedina, Ina Maria and Groth, Detlef and Schlupp, Ingo and Tiedemann, Ralph}, title = {The gonadal transcriptome of the unisexual Amazon molly Poecilia formosa in comparison to its sexual ancestors, Poecilia mexicana and Poecilia latipinna}, series = {BMC Genomics}, volume = {19}, journal = {BMC Genomics}, number = {12}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/s12864-017-4382-2}, pages = {1 -- 18}, year = {2018}, abstract = {Background The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna. Results We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40\% of the transcripts for each species were functionally annotated and about 70\% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR. Conclusions We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species.}, language = {en} } @article{EppKruseKathetal.2018, author = {Epp, Laura Saskia and Kruse, Stefan and Kath, Nadja J. and Stoof-Leichsenring, Kathleen Rosemarie and Tiedemann, Ralph and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike}, title = {Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling}, series = {Scientific reports}, volume = {8}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-35550-w}, pages = {9}, year = {2018}, abstract = {Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.}, language = {en} } @article{SchnitzlerReckendorfPinzoneetal.2018, author = {Schnitzler, Joseph G. and Reckendorf, Anja and Pinzone, Marianna and Autenrieth, Marijke and Tiedemann, Ralph and Covaci, Adrian and Malarvannan, Govindan and Ruser, Andreas and Das, Krishna and Siebert, Ursula}, title = {Supporting evidence for PCB pollution threatening global killer whale population}, series = {Aquatic Toxicology}, volume = {206}, journal = {Aquatic Toxicology}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0166-445X}, doi = {10.1016/j.aquatox.2018.11.008}, pages = {102 -- 104}, year = {2018}, abstract = {A recent Science report predicted the global killer whale population to collapse due to PCB pollution. Here we present empirical evidence, which supports and extends the reports' statement. In 2016, a neonate male killer whale stranded on the German island of Sylt. Neonatal attributes indicated an age of at least 3 days. The stomach contained ∼20 mL milk residue and no pathologies explaining the cause of death could be detected. Blubber samples presenting low lipid concentrations were analysed for persistent organic pollutants. Skin samples were collected for genotyping of the mitochondrial control region. The blubber PCB concentrations were very high [SPCBs, 225 mg/kg lipid weight (lw)], largely exceeding the PCB toxicity thresholds reported for the onset of immunosuppression [9 mg/kg lw ∑PCB] and for severe reproductive impairment [41 mg/kg lw ∑PCB] reported for marine mammals. Additionally, this individual showed equally high concentrations in p,p'-DDE [226 mg/kg lw], PBDEs [5 mg/kg lw] and liver mercury levels [1.1 μg/g dry weight dw]. These results suggest a high placental transfer of pollutants from mother to foetus. Consequently, blubber and plasma PCB concentrations and calf mortality rates are both high in primiparous females. With such high pollutant levels, this neonate had poor prerequisites for survival. The neonate belonged to Ecotype I (generalist feeder) and carried the mitochondrial haplotype 35 present in about 16\% of the North Atlantic killer whale from or close to the North Sea. The relevance of this data becomes apparent in the UK West Coast Community, the UK's only residentorca population, which is currently composed of only eight individuals (each four males and females) and no calves have been reported over the last 19 years.Despite worldwide regulations, PCBs persist in the environment and remain a severe concern for killer whale populations, placing calves at high risk due to the mother-offspring PCB-transfer resulting in a high toxicological burden of the neonates.}, language = {en} } @article{SenczukHavensteinMilanaetal.2018, author = {Senczuk, Gabriele and Havenstein, Katja and Milana, Valentina and Ripa, Chiara and De Simone, Emanuela and Tiedemann, Ralph and Castiglia, Riccardo}, title = {Spotlight on islands}, series = {Scientific reports}, volume = {8}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-33326-w}, pages = {12}, year = {2018}, abstract = {Groups of proximate continental islands may conceal more tangled phylogeographic patterns than oceanic archipelagos as a consequence of repeated sea level changes, which allow populations to experience gene flow during periods of low sea level stands and isolation by vicariant mechanisms during periods of high sea level stands. Here, we describe for the first time an ancient and diverging lineage of the Italian wall lizard Podarcis siculus from the western Pontine Islands. We used nuclear and mitochondrial DNA sequences of 156 individuals with the aim of unraveling their phylogenetic position, while microsatellite loci were used to test several a priori insular biogeographic models of migration with empirical data. Our results suggest that the western Pontine populations colonized the islands early during their Pliocene volcanic formation, while populations from the eastern Pontine Islands seem to have been introduced recently. The inter-island genetic makeup indicates an important role of historical migration, probably due to glacial land bridges connecting islands followed by a recent vicariant mechanism of isolation. Moreover, the most supported migration model predicted higher gene flow among islands which are geographically arranged in parallel. Considering the threatened status of small insular endemic populations, we suggest this new evolutionarily independent unit be given priority in conservation efforts.}, language = {en} } @article{NagelKirschbaumEngelmannetal.2018, author = {Nagel, Rebecca and Kirschbaum, Frank and Engelmann, Jacob and Hofmann, Volker and Pawelzik, Felix and Tiedemann, Ralph}, title = {Male-mediated species recognition among African weakly electric fishes}, series = {Royal Society Open Science}, volume = {5}, journal = {Royal Society Open Science}, number = {2}, publisher = {Royal Society}, address = {London}, issn = {2054-5703}, doi = {10.1098/rsos.170443}, pages = {8}, year = {2018}, abstract = {Effective communication among sympatric species is often instrumental for behavioural isolation, where the failure to successfully discriminate between potential mates could lead to less fit hybrid offspring. Discrimination between con- and heterospecifics tends to occur more often in the sex that invests more in offspring production, i.e. females, but males may also mediate reproductive isolation. In this study, we show that among two Campylomormyrus Africanweakly electric fish species, males preferentially associate with conspecific females during choice tests using live fish as stimuli, i.e. when all sensory modalities potentially used for communication were present. We then conducted playback experiments to determine whether the species-specific electric organ discharge (EOD) used for electrocommunication serves as the cue for this conspecific association preference. Interestingly, only C. compressirostris males associated significantly more with the conspecific EOD waveform when playback stimuli were provided, while no such association preference was observed in C. tamandua males. Given our results, the EOD appears to serve, in part, as a male-mediated pre-zygotic isolation mechanism among sympatric species. However, the failure of C. tamandua males to discriminate between con- and heterospecific playback discharges suggests that multiple modalities may be necessary for species recognition in some African weakly electric fish species.}, language = {en} } @article{SchererTiedemannSchlupp2018, author = {Scherer, Ulrike and Tiedemann, Ralph and Schlupp, Ingo}, title = {Male size, not female preferences influence female reproductive success in a poeciliid fish (Poecilia latipinna)}, series = {BMC Research Notes}, volume = {11}, journal = {BMC Research Notes}, number = {364}, publisher = {Biomed Central}, address = {London}, issn = {1756-0500}, doi = {10.1186/s13104-018-3487-2}, pages = {1 -- 5}, year = {2018}, abstract = {Objective We investigated the potential role of indirect benefits for female mate preferences in a highly promiscuous species of live-bearing fishes, the sailfin molly Poecilia latipinna using an integrative approach that combines methods from animal behavior, life-history evolution, and genetics. Males of this species solely contribute sperm for reproduction, and consequently females do not receive any direct benefits. Despite this, females typically show clear mate preferences. It has been suggested that females can increase their reproductive success through indirect benefits from choosing males of higher quality. Results Although preferences for large body size have been recorded as an honest signal for genetic quality, this particular study resulted in female preference being unaffected by male body size. Nonetheless, larger males did sire more offspring, but with no effect on offspring quality. This study presents a methodical innovation by combining preference testing with life history measurements—such as the determination of the dry weight of fish embryos—and paternity analyses on single fish embryos.}, language = {en} } @article{SchnitzlerPinzoneAutenriethetal.2018, author = {Schnitzler, Joseph G. and Pinzone, Marianna and Autenrieth, Marijke and van Neer, Abbo and IJsseldijk, Lonneke L. and Barber, Jonathan L. and Deaville, Rob and Jepson, Paul and Brownlow, Andrew and Schaffeld, Tobias and Thome, Jean-Pierre and Tiedemann, Ralph and Das, Krishna and Siebert, Ursula}, title = {Inter-individual differences in contamination profiles as tracer of social group association in stranded sperm whales}, series = {Scientific reports}, volume = {8}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-29186-z}, pages = {11}, year = {2018}, abstract = {Ecological and physiological factors lead to different contamination patterns in individual marine mammals. The objective of the present study was to assess whether variations in contamination profiles are indicative of social structures of young male sperm whales as they might reflect a variation in feeding preferences and/or in utilized feeding grounds. We used a total of 61 variables associated with organic compounds and trace element concentrations measured in muscle, liver, kidney and blubber gained from 24 sperm whales that stranded in the North Sea in January and February 2016. Combining contaminant and genetic data, there is evidence for at least two cohorts with different origin among these stranded sperm whales; one from the Canary Island region and one from the northern part of the Atlantic. While genetic data unravel relatedness and kinship, contamination data integrate over areas, where animals occured during their lifetime. Especially in long-lived animals with a large migratory potential, as sperm whales, contamination data may carry highly relevant information about aggregation through time and space.}, language = {en} } @article{AutenriethHartmannLahetal.2018, author = {Autenrieth, Marijke and Hartmann, Stefanie and Lah, Ljerka and Roos, Anna and Dennis, Alice B. and Tiedemann, Ralph}, title = {High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12932}, pages = {1469 -- 1481}, year = {2018}, abstract = {The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50\% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.}, language = {en} } @article{ReckendorfLudesWehrmeisterWohlseinetal.2018, author = {Reckendorf, Anja and Ludes-Wehrmeister, Eva and Wohlsein, Peter and Tiedemann, Ralph and Siebert, U. and Lehnert, Kristina}, title = {First record of Halocercus sp (Pseudaliidae) lungworm infections in two stranded neonatal orcas (Orcinus orca)}, series = {Parasitology}, volume = {145}, journal = {Parasitology}, number = {12}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {0031-1820}, doi = {10.1017/S0031182018000586}, pages = {1553 -- 1557}, year = {2018}, abstract = {Orca (Orcinus orca) strandings are rare and post-mortem examinations on fresh individuals are scarce. Thus, little is known about their parasitological fauna, prevalence of infections, associated pathology and the impact on their health. During post-mortem examinations of two male neonatal orcas stranded in Germany and Norway, lungworm infections were found within the bronchi of both individuals. The nematodes were identified as Halocercus sp. (Pseudaliidae), which have been described in the respiratory tract of multiple odontocete species, but not yet in orcas. The life cycle and transmission pathways of some pseudaliid nematodes are incompletely understood. Lungworm infections in neonatal cetaceans are an unusual finding and thus seem to be an indicator for direct mother-to-calf transmission (transplacental or transmammary) of Halocercus sp. nematodes in orcas.}, language = {en} } @article{NagelKirschbaumHofmannetal.2018, author = {Nagel, Rebecca and Kirschbaum, Frank and Hofmann, Volker and Engelmann, Jacob and Tiedemann, Ralph}, title = {Electric pulse characteristics can enable species recognition in African weakly electric fish species}, series = {Scientific Reports}, volume = {8}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-29132-z}, pages = {1 -- 12}, year = {2018}, abstract = {Communication is key to a wide variety of animal behaviours and multiple modalities are often involved in this exchange of information from sender to receiver. The communication of African weakly electric fish, however, is thought to be predominantly unimodal and is mediated by their electric sense, in which species-specific electric organ discharges (EODs) are generated in a context-dependent and thus variable sequence of pulse intervals (SPI). While the primary function of the electric sense is considered to be electrolocation, both of its components likely carry information regarding identity of the sender. However, a clear understanding of their contribution to species recognition is incomplete. We therefore analysed these two electrocommunication components (EOD waveform and SPI statistics) in two sympatric mormyrid Campylomormyrus species. In a set of five playback conditions, we further investigated which components may drive interspecific recognition and discrimination. While we found that both electrocommunication components are species-specific, the cues necessary for species recognition differ between the two species studied. While the EOD waveform and SPI were both necessary and sufficient for species recognition in C. compressirostris males, C. tamandua males apparently utilize other, non-electric modalities. Mapped onto a recent phylogeny, our results suggest that discrimination by electric cues alone may be an apomorphic trait evolved during a recent radiation in this taxon.}, language = {en} }