TY - JOUR A1 - Gamba, Cristina A1 - Jones, Eppie R. A1 - Teasdale, Matthew D. A1 - McLaughlin, Russell L. A1 - González-Fortes, Gloria M. A1 - Mattiangeli, Valeria A1 - Domboroczki, Laszlo A1 - Kovari, Ivett A1 - Pap, Ildiko A1 - Anders, Alexandra A1 - Whittle, Alasdair A1 - Dani, Janos A1 - Raczky, Pal A1 - Higham, Thomas F. G. A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Pinhasi, Ron T1 - Genome flux and stasis in a five millennium transect of European prehistory JF - Nature Communications N2 - The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence. Y1 - 2014 U6 - https://doi.org/10.1038/ncomms6257 SN - 2041-1723 VL - 5 PB - Nature Publ. Group CY - London ER - TY - GEN A1 - Gamba, Cristina A1 - Jones, Eppie R. A1 - Teasdale, Matthew D. A1 - McLaughlin, Russell L. A1 - González-Fortes, Gloria M. A1 - Mattiangeli, Valeria A1 - Domboróczki, László A1 - Kővári, Ivett A1 - Pap, Ildikó A1 - Anders, Alexandra A1 - Whittle, Alasdair A1 - Dani, János A1 - Raczky, Pál A1 - Higham, Thomas F. G. A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Pinhasi, Ron T1 - Genome flux and stasis in a five millennium transect of European prehistory T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1332 KW - ancient DNA KW - lactase-persistence KW - positive selection KW - patterns KW - sequence KW - farmers KW - pigmentation KW - homozygosity KW - ancestry KW - skin Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-437999 SN - 1866-8372 VL - 5 IS - 1332 ER - TY - JOUR A1 - Horn, Susanne A1 - Prost, Stefan A1 - Stiller, Mathias A1 - Makowiecki, Daniel A1 - Kuznetsova, Tatiana A1 - Benecke, Norbert A1 - Pucher, Erich A1 - Hufthammer, Anne K. A1 - Schouwenburg, Charles A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe JF - Molecular ecology N2 - After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction. KW - Conservation Biology KW - Phylogeography KW - Conservation Genetics KW - Population Genetics - Empirical Y1 - 2014 U6 - https://doi.org/10.1111/mec.12691 SN - 0962-1083 SN - 1365-294X VL - 23 IS - 7 SP - 1717 EP - 1729 PB - Wiley-Blackwell CY - Hoboken ER - TY - GEN A1 - Huynen, Leon A1 - Suzuki, Takayuki A1 - Ogura, Toshihiko A1 - Watanabe, Yusuke A1 - Millar, Craig D. A1 - Hofreiter, Michael A1 - Smith, Craig A1 - Mirmoeini, Sara A1 - Lambert, David M. T1 - Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya. Conclusions The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1117 KW - tbx5 KW - Moa KW - gene expression KW - ancient DNA KW - development KW - forelimb Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431599 SN - 1866-8372 IS - 1117 ER - TY - JOUR A1 - Huynen, Leon A1 - Suzuki, Takayuki A1 - Ogura, Toshihiko A1 - Watanabe, Yusuke A1 - Millar, Craig D. A1 - Hofreiter, Michael A1 - Smith, Craig A1 - Mirmoeini, Sara A1 - Lambert, David M. T1 - Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes) JF - BMC evolutionary biology N2 - Background: The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results: To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya. KW - tbx5 KW - Moa KW - Gene expression KW - Ancient DNA KW - Development KW - Forelimb Y1 - 2014 U6 - https://doi.org/10.1186/1471-2148-14-75 SN - 1471-2148 VL - 14 PB - BioMed Central CY - London ER - TY - JOUR A1 - King, Turi E. A1 - Gonzalez-Fortes, Gloria M. A1 - Balaresque, Patricia A1 - Thomas, Mark G. A1 - Balding, David A1 - Delser, Pierpaolo Maisano A1 - Neumann, Rita A1 - Parson, Walther A1 - Knapp, Michael A1 - Walsh, Susan A1 - Tonasso, Laure A1 - Holt, John A1 - Kayser, Manfred A1 - Appleby, Jo A1 - Forster, Peter A1 - Ekserdjian, David A1 - Hofreiter, Michael A1 - Schuerer, Kevin T1 - Identification of the remains of King Richard III JF - Nature Communications Y1 - 2014 U6 - https://doi.org/10.1038/ncomms6631 SN - 2041-1723 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Rainford, James L. A1 - Hofreiter, Michael A1 - Nicholson, David B. A1 - Mayhew, Peter J. T1 - Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects JF - PLoS one N2 - Insects and their six-legged relatives (Hexapoda) comprise more than half of all described species and dominate terrestrial and freshwater ecosystems. Understanding the macroevolutionary processes generating this richness requires a historical perspective, but the fossil record of hexapods is patchy and incomplete. Dated molecular phylogenies provide an alternative perspective on divergence times and have been combined with birth-death models to infer patterns of diversification across a range of taxonomic groups. Here we generate a dated phylogeny of hexapod families, based on previously published sequence data and literature derived constraints, in order to identify the broad pattern of macroevolutionary changes responsible for the composition of the extant hexapod fauna. The most prominent increase in diversification identified is associated with the origin of complete metamorphosis, confirming this as a key innovation in promoting insect diversity. Subsequent reductions are recovered for several groups previously identified as having a higher fossil diversity during the Mesozoic. In addition, a number of recently derived taxa are found to have radiated following the development of flowering plant (angiosperm) floras during the mid-Cretaceous. These results reveal that the composition of the modern hexapod fauna is a product of a key developmental innovation, combined with multiple and varied evolutionary responses to environmental changes from the mid Cretaceous floral transition onward. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pone.0109085 SN - 1932-6203 VL - 9 IS - 10 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Schubert, Mikkel A1 - Jonsson, Hakon A1 - Chang, Dan A1 - Sarkissian, Clio Der A1 - Ermini, Luca A1 - Ginolhac, Aurelien A1 - Albrechtsen, Anders A1 - Dupanloup, Isabelle A1 - Foucal, Adrien A1 - Petersen, Bent Larsen A1 - Fumagalli, Matteo A1 - Raghavan, Maanasa A1 - Seguin-Orlando, Andaine A1 - Korneliussen, Thorfinn S. A1 - Velazquez, Amhed M. V. A1 - Stenderup, Jesper A1 - Hoover, Cindi A. A1 - Rubin, Carl-Johan A1 - Alfarhan, Ahmed H. A1 - Alquraishi, Saleh A. A1 - Al-Rasheid, Khaled A. S. A1 - MacHugh, David E. A1 - Kalbfleisch, Ted A1 - MacLeod, James N. A1 - Rubin, Edward M. A1 - Sicheritz-Ponten, Thomas A1 - Andersson, Leif A1 - Hofreiter, Michael A1 - Marques-Bonet, Tomas A1 - Gilbert, M. Thomas P. A1 - Nielsen, Rasmus A1 - Excoffier, Laurent A1 - Willerslev, Eske A1 - Shapiro, Beth A1 - Orlando, Ludovic T1 - Prehistoric genomes reveal the genetic foundation and cost of horse domestication JF - Proceedings of the National Academy of Sciences of the United States of America Y1 - 2014 U6 - https://doi.org/10.1073/pnas.1416991111 SN - 0027-8424 VL - 111 IS - 52 SP - E5661 EP - E5669 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Shapiro, B. A1 - Hofreiter, Michael T1 - A paleogenomic perspective on evolution and gene function: new insights from ancient DNA JF - Science N2 - The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events. Y1 - 2014 U6 - https://doi.org/10.1126/science.1236573 SN - 0036-8075 SN - 1095-9203 VL - 343 IS - 6169 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Xiang, Hai A1 - Gao, Jianqiang A1 - Yu, Baoquan A1 - Zhou, Hui A1 - Cai, Dawei A1 - Zhang, Youwen A1 - Chen, Xiaoyong A1 - Wang, Xi A1 - Hofreiter, Michael A1 - Zhao, Xingbo T1 - Early Holocene chicken domestication in northern China JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to similar to 10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus, rather than any other related genus, such as Phasianus. Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratii contributed to the gene pool of the modern domestic chicken. Our results provide further support for the growing evidence of an early mixed agricultural complex in northern China. KW - ancient DNA KW - chicken KW - domestication KW - species origin Y1 - 2014 U6 - https://doi.org/10.1073/pnas.1411882111 SN - 0027-8424 VL - 111 IS - 49 SP - 17564 EP - 17569 PB - National Acad. of Sciences CY - Washington ER -