TY  - JOUR
A1  - Springer, Mark S.
A1  - Signore, Anthony V.
A1  - Paijmans, Johanna L. A.
A1  - Velez-Juarbe, Jorge
A1  - Domning, Daryl P.
A1  - Bauer, Cameron E.
A1  - He, Kai
A1  - Crerar, Lorelei
A1  - Campos, Paula F.
A1  - Murphy, William J.
A1  - Meredith, Robert W.
A1  - Gatesy, John
A1  - Willerslev, Eske
A1  - MacPhee, Ross D. E.
A1  - Hofreiter, Michael
A1  - Campbell, Kevin L.
T1  - Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia
JF  - Molecular phylogenetics and evolution
N2  - The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30 kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean = 98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans. (C) 2015 Elsevier Inc. All rights reserved.
Y1  - 2015
U6  - https://doi.org/10.1016/j.ympev.2015.05.022
SN  - 1055-7903
SN  - 1095-9513
VL  - 91
SP  - 178
EP  - 193
PB  - Elsevier
CY  - San Diego
ER  - 
TY  - JOUR
A1  - Palkopoulou, Eleftheria
A1  - Lipson, Mark
A1  - Mallick, Swapan
A1  - Nielsen, Svend
A1  - Rohland, Nadin
A1  - Baleka, Sina Isabelle
A1  - Karpinski, Emil
A1  - Ivancevici, Atma M.
A1  - Thu-Hien To, 
A1  - Kortschak, Daniel
A1  - Raison, Joy M.
A1  - Qu, Zhipeng
A1  - Chin, Tat-Jun
A1  - Alt, Kurt W.
A1  - Claesson, Stefan
A1  - Dalen, Love
A1  - MacPhee, Ross D. E.
A1  - Meller, Harald
A1  - Rocar, Alfred L.
A1  - Ryder, Oliver A.
A1  - Heiman, David
A1  - Young, Sarah
A1  - Breen, Matthew
A1  - Williams, Christina
A1  - Aken, Bronwen L.
A1  - Ruffier, Magali
A1  - Karlsson, Elinor
A1  - Johnson, Jeremy
A1  - Di Palma, Federica
A1  - Alfoldi, Jessica
A1  - Adelsoni, David L.
A1  - Mailund, Thomas
A1  - Munch, Kasper
A1  - Lindblad-Toh, Kerstin
A1  - Hofreiter, Michael
A1  - Poinar, Hendrik
A1  - Reich, David
T1  - A comprehensive genomic history of extinct and living elephants
JF  - Proceedings of the National Academy of Sciences of the United States of America
KW  - paleogenomics
KW  - elephantid evolution
KW  - mammoth
KW  - admixture
KW  - species divergence
Y1  - 2018
U6  - https://doi.org/10.1073/pnas.1720554115
SN  - 0027-8424
VL  - 115
IS  - 11
SP  - E2566
EP  - E2574
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Chang, Dan
A1  - Knapp, Michael
A1  - Enk, Jacob
A1  - Lippold, Sebastian
A1  - Kircher, Martin
A1  - Lister, Adrian M.
A1  - MacPhee, Ross D. E.
A1  - Widga, Christopher
A1  - Czechowski, Paul
A1  - Sommer, Robert
A1  - Hodges, Emily
A1  - Stümpel, Nikolaus
A1  - Barnes, Ian
A1  - Dalén, Love
A1  - Derevianko, Anatoly
A1  - Germonpré, Mietje
A1  - Hillebrand-Voiculescu, Alexandra
A1  - Constantin, Silviu
A1  - Kuznetsova, Tatyana
A1  - Mol, Dick
A1  - Rathgeber, Thomas
A1  - Rosendahl, Wilfried
A1  - Tikhonov, Alexey N.
A1  - Willerslev, Eske
A1  - Hannon, Greg
A1  - Lalueza i Fox, Carles
A1  - Joger, Ulrich
A1  - Poinar, Hendrik N.
A1  - Hofreiter, Michael
A1  - Shapiro, Beth
T1  - The evolutionary and phylogeographic history of woolly mammoths
BT  - a comprehensive mitogenomic analysis
JF  - Scientific reports
N2  - Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
Y1  - 2017
U6  - https://doi.org/10.1038/srep44585
SN  - 2045-2322
VL  - 7
PB  - Nature Publishing Group
CY  - London
ER  - 
TY  - JOUR
A1  - Westbury, Michael V.
A1  - Baleka, Sina Isabelle
A1  - Barlow, Axel
A1  - Hartmann, Stefanie
A1  - Paijmans, Johanna L. A.
A1  - Kramarz, Alejandro
A1  - Forasiepi, Analia M.
A1  - Bond, Mariano
A1  - Gelfo, Javier N.
A1  - Reguero, Marcelo A.
A1  - Lopez-Mendoza, Patricio
A1  - Taglioretti, Matias
A1  - Scaglia, Fernando
A1  - Rinderknecht, Andres
A1  - Jones, Washington
A1  - Mena, Francisco
A1  - Billet, Guillaume
A1  - de Muizon, Christian
A1  - Luis Aguilar, Jose
A1  - MacPhee, Ross D. E.
A1  - Hofreiter, Michael
T1  - A mitogenomic timetree for Darwin’s enigmatic South American mammal  Macrauchenia patachonica
JF  - Nature Communications
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.
Y1  - 2017
U6  - https://doi.org/10.1038/ncomms15951
SN  - 2041-1723
VL  - 8
PB  - Nature Publ. Group
CY  - London
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  -