@article{GambaJonesTeasdaleetal.2014, author = {Gamba, Cristina and Jones, Eppie R. and Teasdale, Matthew D. and McLaughlin, Russell L. and Gonz{\´a}lez-Fortes, Gloria M. and Mattiangeli, Valeria and Domboroczki, Laszlo and Kovari, Ivett and Pap, Ildiko and Anders, Alexandra and Whittle, Alasdair and Dani, Janos and Raczky, Pal and Higham, Thomas F. G. and Hofreiter, Michael and Bradley, Daniel G. and Pinhasi, Ron}, title = {Genome flux and stasis in a five millennium transect of European prehistory}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms6257}, pages = {9}, year = {2014}, abstract = {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.}, language = {en} } @misc{GambaJonesTeasdaleetal.2014, author = {Gamba, Cristina and Jones, Eppie R. and Teasdale, Matthew D. and McLaughlin, Russell L. and Gonz{\´a}lez-Fortes, Gloria M. and Mattiangeli, Valeria and Dombor{\´o}czki, L{\´a}szl{\´o} and Kőv{\´a}ri, Ivett and Pap, Ildik{\´o} and Anders, Alexandra and Whittle, Alasdair and Dani, J{\´a}nos and Raczky, P{\´a}l and Higham, Thomas F. G. and Hofreiter, Michael and Bradley, Daniel G. and Pinhasi, Ron}, title = {Genome flux and stasis in a five millennium transect of European prehistory}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, volume = {5}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1332}, issn = {1866-8372}, doi = {10.25932/publishup-43799}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437999}, pages = {9}, year = {2014}, abstract = {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.}, language = {en} } @article{HornProstStilleretal.2014, author = {Horn, Susanne and Prost, Stefan and Stiller, Mathias and Makowiecki, Daniel and Kuznetsova, Tatiana and Benecke, Norbert and Pucher, Erich and Hufthammer, Anne K. and Schouwenburg, Charles and Shapiro, Beth and Hofreiter, Michael}, title = {Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe}, series = {Molecular ecology}, volume = {23}, journal = {Molecular ecology}, number = {7}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.12691}, pages = {1717 -- 1729}, year = {2014}, abstract = {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.}, language = {en} } @misc{HuynenSuzukiOguraetal.2014, author = {Huynen, Leon and Suzuki, Takayuki and Ogura, Toshihiko and Watanabe, Yusuke and Millar, Craig D. and Hofreiter, Michael and Smith, Craig and Mirmoeini, Sara and Lambert, David M.}, title = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1117}, issn = {1866-8372}, doi = {10.25932/publishup-43159}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431599}, pages = {10}, year = {2014}, abstract = {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.}, language = {en} } @article{HuynenSuzukiOguraetal.2014, author = {Huynen, Leon and Suzuki, Takayuki and Ogura, Toshihiko and Watanabe, Yusuke and Millar, Craig D. and Hofreiter, Michael and Smith, Craig and Mirmoeini, Sara and Lambert, David M.}, title = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)}, series = {BMC evolutionary biology}, volume = {14}, journal = {BMC evolutionary biology}, publisher = {BioMed Central}, address = {London}, issn = {1471-2148}, doi = {10.1186/1471-2148-14-75}, pages = {8}, year = {2014}, abstract = {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.}, language = {en} } @article{KingGonzalezFortesBalaresqueetal.2014, author = {King, Turi E. and Gonzalez-Fortes, Gloria M. and Balaresque, Patricia and Thomas, Mark G. and Balding, David and Delser, Pierpaolo Maisano and Neumann, Rita and Parson, Walther and Knapp, Michael and Walsh, Susan and Tonasso, Laure and Holt, John and Kayser, Manfred and Appleby, Jo and Forster, Peter and Ekserdjian, David and Hofreiter, Michael and Schuerer, Kevin}, title = {Identification of the remains of King Richard III}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms6631}, pages = {8}, year = {2014}, language = {en} } @article{RainfordHofreiterNicholsonetal.2014, author = {Rainford, James L. and Hofreiter, Michael and Nicholson, David B. and Mayhew, Peter J.}, title = {Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects}, series = {PLoS one}, volume = {9}, journal = {PLoS one}, number = {10}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0109085}, pages = {7}, year = {2014}, abstract = {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.}, language = {en} } @article{SchubertJonssonChangetal.2014, author = {Schubert, Mikkel and Jonsson, Hakon and Chang, Dan and Sarkissian, Clio Der and Ermini, Luca and Ginolhac, Aurelien and Albrechtsen, Anders and Dupanloup, Isabelle and Foucal, Adrien and Petersen, Bent Larsen and Fumagalli, Matteo and Raghavan, Maanasa and Seguin-Orlando, Andaine and Korneliussen, Thorfinn S. and Velazquez, Amhed M. V. and Stenderup, Jesper and Hoover, Cindi A. and Rubin, Carl-Johan and Alfarhan, Ahmed H. and Alquraishi, Saleh A. and Al-Rasheid, Khaled A. S. and MacHugh, David E. and Kalbfleisch, Ted and MacLeod, James N. and Rubin, Edward M. and Sicheritz-Ponten, Thomas and Andersson, Leif and Hofreiter, Michael and Marques-Bonet, Tomas and Gilbert, M. Thomas P. and Nielsen, Rasmus and Excoffier, Laurent and Willerslev, Eske and Shapiro, Beth and Orlando, Ludovic}, title = {Prehistoric genomes reveal the genetic foundation and cost of horse domestication}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {52}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1416991111}, pages = {E5661 -- E5669}, year = {2014}, language = {en} } @misc{ShapiroHofreiter2014, author = {Shapiro, B. and Hofreiter, Michael}, title = {A paleogenomic perspective on evolution and gene function: new insights from ancient DNA}, series = {Science}, volume = {343}, journal = {Science}, number = {6169}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.1236573}, pages = {7}, year = {2014}, abstract = {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.}, language = {en} } @article{XiangGaoYuetal.2014, author = {Xiang, Hai and Gao, Jianqiang and Yu, Baoquan and Zhou, Hui and Cai, Dawei and Zhang, Youwen and Chen, Xiaoyong and Wang, Xi and Hofreiter, Michael and Zhao, Xingbo}, title = {Early Holocene chicken domestication in northern China}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {49}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1411882111}, pages = {17564 -- 17569}, year = {2014}, abstract = {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.}, language = {en} }