@article{JonesGonzalezFortesConnelletal.2015, author = {Jones, Eppie R. and Gonz{\´a}lez-Fortes, Gloria M. and Connell, Sarah and Siska, Veronika and Eriksson, Anders and Martiniano, Rui and McLaughlin, Russell L. and Llorente, Marcos Gallego and Cassidy, Lara M. and Gamba, Cristina and Meshveliani, Tengiz and Bar-Yosef, Ofer and Mueller, Werner and Belfer-Cohen, Anna and Matskevich, Zinovi and Jakeli, Nino and Higham, Thomas F. G. and Currat, Mathias and Lordkipanidze, David and Hofreiter, Michael and Manica, Andrea and Pinhasi, Ron and Bradley, Daniel G.}, title = {Upper Palaeolithic genomes reveal deep roots of modern Eurasians}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms9912}, pages = {8}, year = {2015}, abstract = {We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.}, language = {en} } @article{LudwigReissmannBeneckeetal.2015, author = {Ludwig, Arne and Reissmann, Monika and Benecke, Norbert and Bellone, Rebecca and Sandoval-Castellanos, Edson and Cieslak, Michael and Gonz{\´a}lez-Fortes, Gloria M. and Morales-Muniz, Arturo and Hofreiter, Michael and Pruvost, Melanie}, title = {Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses}, series = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, volume = {370}, journal = {Philosophical transactions of the Royal Society of London : B, Biological sciences}, number = {1660}, publisher = {Royal Society}, address = {London}, issn = {0962-8436}, doi = {10.1098/rstb.2013.0386}, pages = {7}, year = {2015}, abstract = {Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.}, language = {en} } @article{KehlmaierBarlowHastingsetal.2017, author = {Kehlmaier, Christian and Barlow, Axel and Hastings, Alexander K. and Vamberger, Melita and Paijmans, Johanna L. A. and Steadman, David W. and Albury, Nancy A. and Franz, Richard and Hofreiter, Michael and Fritz, Uwe}, title = {Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum}, series = {Proceedings of the Royal Society of London : Series B, Biological sciences}, volume = {284}, journal = {Proceedings of the Royal Society of London : Series B, Biological sciences}, publisher = {The Royal Society}, address = {London}, issn = {0962-8452}, doi = {10.1098/rspb.2016.2235}, pages = {8}, year = {2017}, abstract = {Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.}, language = {en} } @article{FagesHanghojKhanetal.2019, author = {Fages, Antoine and Hanghoj, Kristian and Khan, Naveed and Gaunitz, Charleen and Seguin-Orlando, Andaine and Leonardi, Michela and Constantz, Christian McCrory and Gamba, Cristina and Al-Rasheid, Khaled A. S. and Albizuri, Silvia and Alfarhan, Ahmed H. and Allentoft, Morten and Alquraishi, Saleh and Anthony, David and Baimukhanov, Nurbol and Barrett, James H. and Bayarsaikhan, Jamsranjav and Benecke, Norbert and Bernaldez-Sanchez, Eloisa and Berrocal-Rangel, Luis and Biglari, Fereidoun and Boessenkool, Sanne and Boldgiv, Bazartseren and Brem, Gottfried and Brown, Dorcas and Burger, Joachim and Crubezy, Eric and Daugnora, Linas and Davoudi, Hossein and Damgaard, Peter de Barros and de Chorro y de Villa-Ceballos, Maria de los Angeles and Deschler-Erb, Sabine and Detry, Cleia and Dill, Nadine and Oom, Maria do Mar and Dohr, Anna and Ellingvag, Sturla and Erdenebaatar, Diimaajav and Fathi, Homa and Felkel, Sabine and Fernandez-Rodriguez, Carlos and Garcia-Vinas, Esteban and Germonpre, Mietje and Granado, Jose D. and Hallsson, Jon H. and Hemmer, Helmut and Hofreiter, Michael and Kasparov, Aleksei and Khasanov, Mutalib and Khazaeli, Roya and Kosintsev, Pavel and Kristiansen, Kristian and Kubatbek, Tabaldiev and Kuderna, Lukas and Kuznetsov, Pavel and Laleh, Haeedeh and Leonard, Jennifer A. and Lhuillier, Johanna and von Lettow-Vorbeck, Corina Liesau and Logvin, Andrey and Lougas, Lembi and Ludwig, Arne and Luis, Cristina and Arruda, Ana Margarida and Marques-Bonet, Tomas and Silva, Raquel Matoso and Merz, Victor and Mijiddorj, Enkhbayar and Miller, Bryan K. and Monchalov, Oleg and Mohaseb, Fatemeh A. and Morales, Arturo and Nieto-Espinet, Ariadna and Nistelberger, Heidi and Onar, Vedat and Palsdottir, Albina H. and Pitulko, Vladimir and Pitskhelauri, Konstantin and Pruvost, Melanie and Sikanjic, Petra Rajic and Papesa, Anita Rapan and Roslyakova, Natalia and Sardari, Alireza and Sauer, Eberhard and Schafberg, Renate and Scheu, Amelie and Schibler, Jorg and Schlumbaum, Angela and Serrand, Nathalie and Serres-Armero, Aitor and Shapiro, Beth and Seno, Shiva Sheikhi and Shevnina, Irina and Shidrang, Sonia and Southon, John and Star, Bastiaan and Sykes, Naomi and Taheri, Kamal and Taylor, William and Teegen, Wolf-Rudiger and Vukicevic, Tajana Trbojevic and Trixl, Simon and Tumen, Dashzeveg and Undrakhbold, Sainbileg and Usmanova, Emma and Vahdati, Ali and Valenzuela-Lamas, Silvia and Viegas, Catarina and Wallner, Barbara and Weinstock, Jaco and Zaibert, Victor and Clavel, Benoit and Lepetz, Sebastien and Mashkour, Marjan and Helgason, Agnar and Stefansson, Kari and Barrey, Eric and Willerslev, Eske and Outram, Alan K. and Librado, Pablo and Orlando, Ludovic}, title = {Tracking five millennia of horse management with extensive ancient genome time series}, series = {Cell}, volume = {177}, journal = {Cell}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.03.049}, pages = {1419 -- 1435}, year = {2019}, abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management.}, language = {en} } @article{HofreiterPaijmansGoodchildetal.2015, author = {Hofreiter, Michael and Paijmans, Johanna L. A. and Goodchild, Helen and Speller, Camilla F. and Barlow, Axel and Gonz{\´a}lez-Fortes, Gloria M. and Thomas, Jessica A. and Ludwig, Arne and Collins, Matthew J.}, title = {The future of ancient DNA: Technical advances and conceptual shifts}, series = {Bioessays : ideas that push the boundaries}, volume = {37}, journal = {Bioessays : ideas that push the boundaries}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0265-9247}, doi = {10.1002/bies.201400160}, pages = {284 -- 293}, year = {2015}, abstract = {Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.}, language = {en} } @article{ChangKnappEnketal.2017, author = {Chang, Dan and Knapp, Michael and Enk, Jacob and Lippold, Sebastian and Kircher, Martin and Lister, Adrian M. and MacPhee, Ross D. E. and Widga, Christopher and Czechowski, Paul and Sommer, Robert and Hodges, Emily and St{\"u}mpel, Nikolaus and Barnes, Ian and Dal{\´e}n, Love and Derevianko, Anatoly and Germonpr{\´e}, Mietje and Hillebrand-Voiculescu, Alexandra and Constantin, Silviu and Kuznetsova, Tatyana and Mol, Dick and Rathgeber, Thomas and Rosendahl, Wilfried and Tikhonov, Alexey N. and Willerslev, Eske and Hannon, Greg and Lalueza i Fox, Carles and Joger, Ulrich and Poinar, Hendrik N. and Hofreiter, Michael and Shapiro, Beth}, title = {The evolutionary and phylogeographic history of woolly mammoths}, series = {Scientific reports}, volume = {7}, journal = {Scientific reports}, publisher = {Nature Publishing Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep44585}, pages = {10}, year = {2017}, abstract = {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.}, language = {en} } @article{FolkertsmaWestburyEccardetal.2018, author = {Folkertsma, Remco and Westbury, Michael V. and Eccard, Jana and Hofreiter, Michael}, title = {The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)}, series = {Mitochondrial DNA Part B}, volume = {3}, journal = {Mitochondrial DNA Part B}, number = {1}, issn = {2380-2359}, doi = {10.1080/23802359.2018.1457994}, pages = {446 -- 447}, year = {2018}, abstract = {The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.}, language = {en} } @article{AgneNaylorPreicketal.2022, author = {Agne, Stefanie and Naylor, Gavin J. P. and Preick, Michaela and Yang, Lei and Thiel, Ralf and Weigmann, Simon and Paijmans, Johanna L. A. and Barlow, Axel and Hofreiter, Michael and Straube, Nicolas}, title = {Taxonomic identification of two poorly known lantern shark species based on mitochondrial DNA from wet-collection paratypes}, series = {Frontiers in Ecology and Evolution}, volume = {10}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-701X}, doi = {10.3389/fevo.2022.910009}, pages = {10}, year = {2022}, abstract = {Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites. For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence. In contrast, DNA sequence information has rarely been used. Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions. The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far. However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data. Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals. Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species. Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research.}, language = {en} } @article{FoersterBullLenzetal.2018, author = {F{\"o}rster, Daniel W. and Bull, James K. and Lenz, Dorina and Autenrieth, Marijke and Paijmans, Johanna L. A. and Kraus, Robert H. S. and Nowak, Carsten and Bayerl, Helmut and K{\"u}hn, Ralph and Saveljev, Alexander P. and Sindicic, Magda and Hofreiter, Michael and Schmidt, Krzysztof and Fickel, J{\"o}rns}, title = {Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12924}, pages = {1356 -- 1373}, year = {2018}, abstract = {Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.}, language = {en} } @article{WutkeBeneckeSandovalCastellanosetal.2016, author = {Wutke, Saskia and Benecke, Norbert and Sandoval-Castellanos, Edson and D{\"o}hle, Hans-J{\"u}rgen and Friederich, Susanne and Gonzalez Soto, Javier Esteban and Hallsson, Jon Hallsteinn and Hofreiter, Michael and Lougas, Lembi and Magnell, Ola and Morales-Muniz, Arturo and Orlando, Ludovic and Palsdottir, Albina Hulda and Reissmann, Monika and Ruttkay, Matej and Trinks, Alexandra and Ludwig, Arne}, title = {Spotted phenotypes in horses lost attractiveness in the Middle Ages}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep38548}, pages = {9}, year = {2016}, abstract = {Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.}, language = {en} } @article{CasasMarceMarmesatSorianoetal.2017, author = {Casas-Marce, Mireia and Marmesat, Elena and Soriano, Laura and Martinez-Cruz, Begona and Lucena-Perez, Maria and Nocete, Francisco and Rodriguez-Hidalgo, Antonio and Canals, Antoni and Nadal, Jordi and Detry, Cleia and Bernaldez-Sanchez, Eloisa and Fernandez-Rodriguez, Carlos and Perez-Ripoll, Manuel and Stiller, Mathias and Hofreiter, Michael and Rodriguez, Alejandro and Revilla, Eloy and Delibes, Miguel and Godoy, Jose A.}, title = {Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA}, series = {Molecular biology and evolution}, volume = {34}, journal = {Molecular biology and evolution}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msx222}, pages = {2893 -- 2907}, year = {2017}, abstract = {There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N\&\#8201;=\&\#8201;10), historical (N\&\#8201;=\&\#8201;245), and contemporary (N\&\#8201;=\&\#8201;172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.}, language = {en} } @article{AgnePreickStraubeetal.2022, author = {Agne, Stefanie and Preick, Michaela and Straube, Nicolas and Hofreiter, Michael}, title = {Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set}, series = {Frontiers in Ecology and Evolution}, volume = {10}, journal = {Frontiers in Ecology and Evolution}, publisher = {Frontiers Media S.A.}, address = {Lausanne, Schweiz}, issn = {2296-701X}, doi = {10.3389/fevo.2022.909846}, pages = {5}, year = {2022}, abstract = {A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84\% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50\% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.}, 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{HofreiterHartmann2020, author = {Hofreiter, Michael and Hartmann, Stefanie}, title = {Reconstructing protein-coding sequences from ancient DNA}, series = {Odorant binding and chemosensory proteins}, volume = {642}, journal = {Odorant binding and chemosensory proteins}, publisher = {Academic Press, an imprint of Elsevier}, address = {Cambridge, MA.}, isbn = {978-0-12-821157-1}, issn = {0076-6879}, doi = {10.1016/bs.mie.2020.05.008}, pages = {21 -- 33}, year = {2020}, abstract = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.}, 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} } @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{RainfordHofreiterMayhew2016, author = {Rainford, James L. and Hofreiter, Michael and Mayhew, Peter J.}, title = {Phylogenetic analyses suggest that diversification and body size evolution are independent in insects}, series = {BMC evolutionary biology}, volume = {16}, journal = {BMC evolutionary biology}, publisher = {BioMed Central}, address = {London}, issn = {1471-2148}, doi = {10.1186/s12862-015-0570-3}, pages = {47 -- 55}, year = {2016}, abstract = {Background: Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. Results: The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. Conclusions: Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.}, language = {en} } @article{BarlowCahillHartmannetal.2018, author = {Barlow, Axel and Cahill, James A. and Hartmann, Stefanie and Theunert, Christoph and Xenikoudakis, Georgios and Gonzalez-Fortes, Gloria M. and Paijmans, Johanna L. A. and Rabeder, Gernot and Frischauf, Christine and Garcia-Vazquez, Ana and Murtskhvaladze, Marine and Saarma, Urmas and Anijalg, Peeter and Skrbinsek, Tomaz and Bertorelle, Giorgio and Gasparian, Boris and Bar-Oz, Guy and Pinhasi, Ron and Slatkin, Montgomery and Dalen, Love and Shapiro, Beth and Hofreiter, Michael}, title = {Partial genomic survival of cave bears in living brown bears}, series = {Nature Ecology \& Evolution}, volume = {2}, journal = {Nature Ecology \& Evolution}, number = {10}, publisher = {Nature Publ. Group}, address = {London}, issn = {2397-334X}, doi = {10.1038/s41559-018-0654-8}, pages = {1563 -- 1570}, year = {2018}, abstract = {Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4\% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.}, language = {en} } @article{GonzalezFortesJonesLightfootetal.2017, author = {Gonz{\´a}lez-Fortes, Gloria M. and Jones, Eppie R. and Lightfoot, Emma and Bonsall, Clive and Lazar, Catalin and Dolores Garralda, Maria and Drak, Labib and Siska, Veronika and Simalcsik, Angela and Boroneant, Adina and Vidal Romani, Juan Ramon and Vaqueiro Rodriguez, Marcos and Arias, Pablo and Pinhasi, Ron and Manica, Andrea and Hofreiter, Michael}, title = {Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin}, series = {Current biology}, volume = {27}, journal = {Current biology}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2017.05.023}, pages = {1801 -- +}, year = {2017}, abstract = {The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.13 to 4.13 coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.73- and 5.33) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stableisotope analysis of this sample suggests a mixed terrestrial/ aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization.}, language = {en} } @article{ShengBaslerJietal.2019, author = {Sheng, Gui-Lian and Basler, Nikolas and Ji, Xue-Ping and Paijmans, Johanna L. A. and Alberti, Federica and Preick, Michaela and Hartmann, Stefanie and Westbury, Michael V. and Yuan, Jun-Xia and Jablonski, Nina G. and Xenikoudakis, Georgios and Hou, Xin-Dong and Xiao, Bo and Liu, Jian-Hui and Hofreiter, Michael and Lai, Xu-Long and Barlow, Axel}, title = {Paleogenome reveals genetic contribution of extinct giant panda to extant populations}, series = {Current biology}, volume = {29}, journal = {Current biology}, number = {10}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2019.04.021}, pages = {1695 -- 1700}, year = {2019}, abstract = {Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an similar to 5,000-year-old giant panda from Jiangdongshan, Teng-chong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions.}, language = {en} }