@misc{WestburyBalekaBarlowetal.2017, author = {Westbury, Michael V. and Baleka, Sina Isabelle and Barlow, Axel and Hartmann, Stefanie and Paijmans, Johanna L. A. and Kramarz, Alejandro and Forasiepi, Anal{\´i}a M. and Bond, Mariano and Gelfo, Javier N. and Reguero, Marcelo A. and L{\´o}pez-Mendoza, Patricio and Taglioretti, Matias and Scaglia, Fernando and Rinderknecht, Andr{\´e}s and Jones, Washington and Mena, Francisco and Billet, Guillaume and de Muizon, Christian and Aguilar, Jos{\´e} Luis and MacPhee, Ross D.E. and Hofreiter, Michael}, title = {A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {793}, issn = {1866-8372}, doi = {10.25932/publishup-44080}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-440801}, pages = {8}, year = {2017}, abstract = {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.}, language = {en} } @article{WestburyBalekaBarlowetal.2017, author = {Westbury, Michael V. and Baleka, Sina Isabelle and Barlow, Axel and Hartmann, Stefanie and Paijmans, Johanna L. A. and Kramarz, Alejandro and Forasiepi, Analia M. and Bond, Mariano and Gelfo, Javier N. and Reguero, Marcelo A. and Lopez-Mendoza, Patricio and Taglioretti, Matias and Scaglia, Fernando and Rinderknecht, Andres and Jones, Washington and Mena, Francisco and Billet, Guillaume and de Muizon, Christian and Luis Aguilar, Jose and MacPhee, Ross D. E. and Hofreiter, Michael}, title = {A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica}, series = {Nature Communications}, volume = {8}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms15951}, pages = {8}, year = {2017}, abstract = {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.}, language = {en} } @misc{PaijmansBarlowHennebergeretal.2020, author = {Paijmans, Johanna L. A. and Barlow, Axel and Henneberger, Kirstin and Fickel, J{\"o}rns and Hofreiter, Michael and Foerste, Daniel W. G.}, title = {Ancestral mitogenome capture of the Southeast Asian banded linsang}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {972}, issn = {1866-8372}, doi = {10.25932/publishup-47444}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-474441}, pages = {14}, year = {2020}, abstract = {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.}, language = {en} } @article{PaijmansBarlowHennebergeretal.2020, author = {Paijmans, Johanna L. A. and Barlow, Axel and Henneberger, Kirstin and Fickel, J{\"o}rns and Hofreiter, Michael and Foerste, Daniel W. G.}, title = {Ancestral mitogenome capture of the Southeast Asian banded linsang}, series = {PLoS ONE}, volume = {15}, journal = {PLoS ONE}, number = {6}, publisher = {PLOS}, address = {San Francisco, California, US}, issn = {1932-6203}, doi = {10.1371/journal.pone.0234385}, pages = {12}, year = {2020}, abstract = {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.}, language = {en} } @article{GonzalezFortesKolbeFernandesetal.2016, author = {Gonz{\´a}lez-Fortes, Gloria M. and Kolbe, Ben and Fernandes, Daniel and Meleg, Ioana N. and Garcia-Vazquez, Ana and Pinto-Llona, Ana C. and Constantin, Silviu and de Torres, Trino J. and Ortiz, Jose E. and Frischauf, Christine and Rabeder, Gernot and Hofreiter, Michael and Barlow, Axel}, title = {Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears}, series = {Molecular ecology}, volume = {25}, journal = {Molecular ecology}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.13800}, pages = {4907 -- 4918}, year = {2016}, abstract = {Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago.}, language = {en} } @misc{XenikoudakisAhmedHarrisetal.2020, author = {Xenikoudakis, Georgios and Ahmed, Mayeesha and Harris, Jacob Colt and Wadleigh, Rachel and Paijmans, Johanna L. A. and Hartmann, Stefanie and Barlow, Axel and Lerner, Heather and Hofreiter, Michael}, title = {Ancient DNA reveals twenty million years of aquatic life in beavers}, series = {Current biology : CB}, volume = {30}, journal = {Current biology : CB}, number = {3}, publisher = {Current Biology Ltd.}, address = {London}, issn = {0960-9822}, doi = {10.1016/j.cub.2019.12.041}, pages = {R110 -- R111}, year = {2020}, abstract = {Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.}, language = {en} } @misc{BarlowHartmannGonzalezetal.2020, author = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.}, title = {Consensify}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1033}, issn = {1866-8372}, doi = {10.25932/publishup-47252}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-472521}, pages = {24}, year = {2020}, abstract = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.}, language = {en} } @article{BarlowHartmannGonzalezetal.2020, author = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.}, title = {Consensify}, series = {Genes / Molecular Diversity Preservation International}, volume = {11}, journal = {Genes / Molecular Diversity Preservation International}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes11010050}, pages = {22}, year = {2020}, abstract = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.}, language = {en} } @article{PaijmansBarnettGilbertetal.2017, author = {Paijmans, Johanna L. A. and Barnett, Ross and Gilbert, M. Thomas P. and Zepeda-Mendoza, M. Lisandra and Reumer, Jelle W. F. and de Vos, John and Zazula, Grant and Nagel, Doris and Baryshnikov, Gennady F. and Leonard, Jennifer A. and Rohland, Nadin and Westbury, Michael V. and Barlow, Axel and Hofreiter, Michael}, title = {Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics}, series = {Current biology}, volume = {27}, journal = {Current biology}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2017.09.033}, pages = {3330 -- +}, year = {2017}, abstract = {Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (similar to 18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6].}, language = {en} } @misc{WestburyHartmannBarlowetal.2018, author = {Westbury, Michael V. and Hartmann, Stefanie and Barlow, Axel and Wiesel, Ingrid and Leo, Viyanna and Welch, Rebecca and Parker, Daniel M. and Sicks, Florian and Ludwig, Arne and Dalen, Love and Hofreiter, Michael}, title = {Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {589}, issn = {1866-8372}, doi = {10.25932/publishup-41413}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414132}, pages = {13}, year = {2018}, abstract = {Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species.}, language = {en} }