TY - JOUR A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Henneberger, Kirstin A1 - Fickel, Jörns A1 - Hofreiter, Michael A1 - Foerste, Daniel W. G. T1 - Ancestral mitogenome capture of the Southeast Asian banded linsang JF - PLoS ONE N2 - Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives. KW - Shotgun sequencing KW - Mitochondria KW - Phylogenetics KW - Phylogenetic analysis KW - Paleogenetics KW - Sequence alignment KW - Genomics KW - Museum collections Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0234385 SN - 1932-6203 VL - 15 IS - 6 PB - PLOS CY - San Francisco, California, US ER - TY - GEN A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Henneberger, Kirstin A1 - Fickel, Jörns A1 - Hofreiter, Michael A1 - Foerste, Daniel W. G. T1 - Ancestral mitogenome capture of the Southeast Asian banded linsang T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 972 KW - Shotgun sequencing KW - Mitochondria KW - Phylogenetics KW - Phylogenetic analysis KW - Paleogenetics KW - Sequence alignment KW - Genomics KW - Museum collections Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-474441 SN - 1866-8372 IS - 972 ER - TY - GEN A1 - Westbury, Michael V. A1 - Baleka, Sina Isabelle A1 - Barlow, Axel A1 - Hartmann, Stefanie A1 - Paijmans, Johanna L. A. A1 - Kramarz, Alejandro A1 - Forasiepi, Analía M. A1 - Bond, Mariano A1 - Gelfo, Javier N. A1 - Reguero, Marcelo A. A1 - López-Mendoza, Patricio A1 - Taglioretti, Matias A1 - Scaglia, Fernando A1 - Rinderknecht, Andrés A1 - Jones, Washington A1 - Mena, Francisco A1 - Billet, Guillaume A1 - de Muizon, Christian A1 - Aguilar, José Luis A1 - MacPhee, Ross D.E. A1 - Hofreiter, Michael T1 - A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 793 KW - ancient DNA KW - evolutionary history KW - genome sequence KW - reveals KW - contamination KW - alignment KW - reads KW - bones Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-440801 SN - 1866-8372 IS - 793 ER -