TY - JOUR A1 - Förster, Daniel W. A1 - Bull, James K. A1 - Lenz, Dorina A1 - Autenrieth, Marijke A1 - Paijmans, Johanna L. A. A1 - Kraus, Robert H. S. A1 - Nowak, Carsten A1 - Bayerl, Helmut A1 - Kühn, Ralph A1 - Saveljev, Alexander P. A1 - Sindicic, Magda A1 - Hofreiter, Michael A1 - Schmidt, Krzysztof A1 - Fickel, Jörns T1 - Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species JF - Molecular ecology resources N2 - Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species. KW - CDS KW - conservation genetics KW - Eurasian lynx KW - genetic monitoring KW - hybridization capture KW - single nucleotide polymorphism Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12924 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1356 EP - 1373 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Schnitzler, Joseph G. A1 - Reckendorf, Anja A1 - Pinzone, Marianna A1 - Autenrieth, Marijke A1 - Tiedemann, Ralph A1 - Covaci, Adrian A1 - Malarvannan, Govindan A1 - Ruser, Andreas A1 - Das, Krishna A1 - Siebert, Ursula T1 - Supporting evidence for PCB pollution threatening global killer whale population JF - Aquatic Toxicology N2 - 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. KW - Killer whale KW - PCB KW - DDT KW - PBDE KW - Mercury KW - North Sea Y1 - 2018 U6 - https://doi.org/10.1016/j.aquatox.2018.11.008 SN - 0166-445X SN - 1879-1514 VL - 206 SP - 102 EP - 104 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Schnitzler, Joseph G. A1 - Pinzone, Marianna A1 - Autenrieth, Marijke A1 - van Neer, Abbo A1 - IJsseldijk, Lonneke L. A1 - Barber, Jonathan L. A1 - Deaville, Rob A1 - Jepson, Paul A1 - Brownlow, Andrew A1 - Schaffeld, Tobias A1 - Thome, Jean-Pierre A1 - Tiedemann, Ralph A1 - Das, Krishna A1 - Siebert, Ursula T1 - Inter-individual differences in contamination profiles as tracer of social group association in stranded sperm whales JF - Scientific reports N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-29186-z SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Autenrieth, Marijke A1 - Hartmann, Stefanie A1 - Lah, Ljerka A1 - Roos, Anna A1 - Dennis, Alice B. A1 - Tiedemann, Ralph T1 - High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena) JF - Molecular ecology resources N2 - 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. KW - cetaceans KW - genomics/proteomics KW - mammals KW - molecular evolution Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12932 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1469 EP - 1481 PB - Wiley CY - Hoboken ER -