TY - GEN A1 - Gallego-Llorente, Marcos A1 - Sarah, Connell A1 - Jones, Eppie R. A1 - Merrett, Deborah C. A1 - Jeon, Y. A1 - Eriksson, Anders A1 - Siska, Veronika A1 - Gamba, Cristina A1 - Meiklejohn, Christopher A1 - Beyer, Robert A1 - Jeon, Sungwon A1 - Cho, Yun Sung A1 - Hofreiter, Michael A1 - Bhak, Jong A1 - Manica, Andrea A1 - Pinhasi, Ron T1 - The genetics of an early Neolithic pastoralist from the Zagros, Iran T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 952 KW - whole-genome association KW - ancient KW - domestication KW - agriculture KW - mountains KW - diffusion KW - migration KW - admixture KW - patterns KW - sequence KW - archaeology KW - biological anthropology Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439355 SN - 1866-8372 IS - 952 ER - TY - JOUR A1 - Paijmans, Johanna L. A. A1 - Fickel, Jörns A1 - Courtiol, Alexandre A1 - Hofreiter, Michael A1 - Foerster, Daniel W. T1 - Impact of enrichment conditions on cross-species capture of fresh and degraded DNA JF - Molecular ecology resources N2 - Abstract By combining high-throughput sequencing with target enrichment (‘hybridization capture’), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter – hybridization temperature – on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on-target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments. KW - degraded DNA KW - Felidae KW - hybridization capture KW - mitogenomes KW - next-generation sequencing KW - sequence enrichment Y1 - 2016 U6 - https://doi.org/10.1111/1755-0998.12420 SN - 1755-098X SN - 1755-0998 VL - 16 SP - 42 EP - 55 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Rainford, James L. A1 - Hofreiter, Michael A1 - Mayhew, Peter J. T1 - Phylogenetic analyses suggest that diversification and body size evolution are independent in insects JF - BMC evolutionary biology N2 - 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. KW - Body size KW - Diversification KW - Hexapoda KW - Insects KW - Phylogeny Y1 - 2016 U6 - https://doi.org/10.1186/s12862-015-0570-3 SN - 1471-2148 VL - 16 SP - 47 EP - 55 PB - BioMed Central CY - London ER - TY - JOUR A1 - Almathen, Faisal A1 - Charruau, Pauline A1 - Mohandesan, Elmira A1 - Mwacharo, Joram M. A1 - Orozco-terWengel, Pablo A1 - Pitt, Daniel A1 - Abdussamad, Abdussamad M. A1 - Uerpmann, Margarethe A1 - Uerpmann, Hans-Peter A1 - De Cupere, Bea A1 - Magee, Peter A1 - Alnaqeeb, Majed A. A1 - Salim, Bashir A1 - Raziq, Abdul A1 - Dessie, Tadelle A1 - Abdelhadi, Omer M. A1 - Banabazi, Mohammad H. A1 - Al-Eknah, Marzook A1 - Walzer, Chris A1 - Fayer, Bernard A1 - Hofreiter, Michael A1 - Peters, Joris A1 - Hanotte, Olivier A1 - Burger, Pamela A. T1 - Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments. KW - anthropogenic admixture KW - Camelus dromedarius KW - demographic history KW - paleogenetics KW - wild dromedary Y1 - 2016 U6 - https://doi.org/10.1073/pnas.1519508113 SN - 0027-8424 VL - 113 SP - 6707 EP - 6712 PB - National Acad. of Sciences CY - Washington ER - TY - GEN A1 - Wutke, Saskia A1 - Andersson, Leif A1 - Benecke, Norbert A1 - Sandoval-Castellanos, Edson A1 - Gonzalez, Javier A1 - Hallsson, Jon Hallsteinn A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Palsdottir, Albina Hulda A1 - Reissmann, Monika A1 - Munoz-Rodriguez, Mariana B. A1 - Ruttkay, Matej A1 - Trinks, Alexandra A1 - Hofreiter, Michael A1 - Ludwig, Arne T1 - The origin of ambling horses T2 - Current biology N2 - Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called ‘gaited’ horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9th–11th century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date. Y1 - 2016 U6 - https://doi.org/10.1016/j.cub.2016.07.001 SN - 0960-9822 SN - 1879-0445 VL - 26 SP - R697 EP - R699 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Speller, Camilla A1 - van den Hurk, Youri A1 - Charpentier, Anne A1 - Rodrigues, Ana A1 - Gardeisen, Armelle A1 - Wilkens, Barbara A1 - McGrath, Krista A1 - Rowsell, Keri A1 - Spindler, Luke A1 - Collins, Matthew J. A1 - Hofreiter, Michael T1 - Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans JF - Philosophical transactions of the Royal Society of London : B, Biological sciences KW - ancient DNA KW - archaeozoology KW - cetaceans KW - collagen peptide mass fingerprinting KW - species identification KW - zooarchaeology by mass spectrometry Y1 - 2016 U6 - https://doi.org/10.1098/rstb.2015.0332 SN - 0962-8436 SN - 1471-2970 VL - 371 PB - Royal Society CY - London ER - TY - JOUR A1 - González-Fortes, Gloria M. A1 - Kolbe, Ben A1 - Fernandes, Daniel A1 - Meleg, Ioana N. A1 - Garcia-Vazquez, Ana A1 - Pinto-Llona, Ana C. A1 - Constantin, Silviu A1 - de Torres, Trino J. A1 - Ortiz, Jose E. A1 - Frischauf, Christine A1 - Rabeder, Gernot A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears JF - Molecular ecology N2 - 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. KW - ancient DNA KW - extinction KW - homing KW - sociality KW - Ursus arctos KW - Ursus spelaeus Y1 - 2016 U6 - https://doi.org/10.1111/mec.13800 SN - 0962-1083 SN - 1365-294X VL - 25 SP - 4907 EP - 4918 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Procter, Duncan S. A1 - Cottrell, Joan E. A1 - Watts, Kevin A1 - Hofreiter, Michael A1 - Robinson, Elva J. H. T1 - Does cooperation mean kinship between spatially discrete ant nests? JF - Ecology and evolution N2 - Eusociality is one of the most complex forms of social organization, characterized by cooperative and reproductive units termed colonies. Altruistic behavior of workers within colonies is explained by inclusive fitness, with indirect fitness benefits accrued by helping kin. Members of a social insect colony are expected to be more closely related to one another than they are to other conspecifics. In many social insects, the colony can extend to multiple socially connected but spatially separate nests (polydomy). Social connections, such as trails between nests, promote cooperation and resource exchange, and we predict that workers from socially connected nests will have higher internest relatedness than those from socially unconnected, and noncooperating, nests. We measure social connections, resource exchange, and internest genetic relatedness in the polydomous wood ant Formica lugubris to test whether (1) socially connected but spatially separate nests cooperate, and (2) high internest relatedness is the underlying driver of this cooperation. Our results show that socially connected nests exhibit movement of workers and resources, which suggests they do cooperate, whereas unconnected nests do not. However, we find no difference in internest genetic relatedness between socially connected and unconnected nest pairs, both show high kinship. Our results suggest that neighboring pairs of connected nests show a social and cooperative distinction, but no genetic distinction. We hypothesize that the loss of a social connection may initiate ecological divergence within colonies. Genetic divergence between neighboring nests may build up only later, as a consequence rather than a cause of colony separation. KW - colony organization KW - eusociality KW - Formica lugubris KW - kin selection KW - polydomy KW - social organization Y1 - 2016 U6 - https://doi.org/10.1002/ece3.2590 SN - 2045-7758 VL - 6 SP - 8846 EP - 8856 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Wutke, Saskia A1 - Benecke, Norbert A1 - Sandoval-Castellanos, Edson A1 - Döhle, Hans-Jürgen A1 - Friederich, Susanne A1 - Gonzalez Soto, Javier Esteban A1 - Hallsson, Jon Hallsteinn A1 - Hofreiter, Michael A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Palsdottir, Albina Hulda A1 - Reissmann, Monika A1 - Ruttkay, Matej A1 - Trinks, Alexandra A1 - Ludwig, Arne T1 - Spotted phenotypes in horses lost attractiveness in the Middle Ages JF - Scientific reports N2 - 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. Y1 - 2016 U6 - https://doi.org/10.1038/srep38548 SN - 2045-2322 VL - 6 PB - Nature Publ. Group CY - London ER - TY - GEN A1 - Rainford, James L. A1 - Hofreiter, Michael A1 - Mayhew, Peter J. T1 - Phylogenetic analyses suggest that diversification and body size evolution are independent in insects T2 - BMC evolutionary biology N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 441 KW - body size KW - diversification KW - hexapoda KW - insects KW - phylogeny Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-407328 ER -