@article{GluecklerGengGrimmetal.2022,
  author    = {Gl{\"u}ckler, Ramesh and Geng, Rongwei and Grimm, Lennart and Baisheva, Izabella and Herzschuh, Ulrike and Stoof-Leichsenring, Kathleen R. and Kruse, Stefan and Andreev, Andrej Aleksandrovic and Pestryakova, Luidmila and Dietze, Elisabeth},
  title     = {Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies},
  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.2022.962906},
  pages     = {19},
  year      = {2022},
  abstract  = {Wildfires play an essential role in the ecology of boreal forests. In eastern Siberia, fire activity has been increasing in recent years, challenging the livelihoods of local communities. Intensifying fire regimes also increase disturbance pressure on the boreal forests, which currently protect the permafrost beneath from accelerated degradation. However, long-term relationships between changes in fire regime and forest structure remain largely unknown. We assess past fire-vegetation feedbacks using sedimentary proxy records from Lake Satagay, Central Yakutia, Siberia, covering the past c. 10,800 years. Results from macroscopic and microscopic charcoal analyses indicate high amounts of burnt biomass during the Early Holocene, and that the present-day, low-severity surface fire regime has been in place since c. 4,500 years before present. A pollen-based quantitative reconstruction of vegetation cover and a terrestrial plant record based on sedimentary ancient DNA metabarcoding suggest a pronounced shift in forest structure toward the Late Holocene. Whereas the Early Holocene was characterized by postglacial open larch-birch woodlands, forest structure changed toward the modern, mixed larch-dominated closed-canopy forest during the Mid-Holocene. We propose a potential relationship between open woodlands and high amounts of burnt biomass, as well as a mediating effect of dense larch forest on the climate-driven intensification of fire regimes. Considering the anticipated increase in forest disturbances (droughts, insect invasions, and wildfires), higher tree mortality may force the modern state of the forest to shift toward an open woodland state comparable to the Early Holocene. Such a shift in forest structure may result in a positive feedback on currently intensifying wildfires. These new long-term data improve our understanding of millennial-scale fire regime changes and their relationships to changes of vegetation in Central Yakutia, where the local population is already being confronted with intensifying wildfire seasons.},
  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{BarlowHartmannGonzalezetal.2020,
  author    = {Barlow, Axel and Hartmann, Stefanie and Gonzalez, Javier and Hofreiter, Michael and Paijmans, Johanna L. A.},
  title     = {Consensify},
  series = {Genes / Molecular Diversity Preservation International},
  volume    = {11},
  journal   = {Genes / Molecular Diversity Preservation International},
  number    = {1},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes11010050},
  pages     = {22},
  year      = {2020},
  abstract  = {A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.},
  language  = {en}
}
@article{YuanShengPreicketal.2020,
  author    = {Yuan, Junxia and Sheng, Guilian and Preick, Michaela and Sun, Boyang and Hou, Xindong and Chen, Shungang and Taron, Ulrike Helene and Barlow, Axel and Wang, Linying and Hu, Jiaming and Deng, Tao and Lai, Xulong and Hofreiter, Michael},
  title     = {Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade},
  series = {Quaternary science reviews : the international multidisciplinary research and review journal},
  volume    = {250},
  journal   = {Quaternary science reviews : the international multidisciplinary research and review journal},
  publisher = {Elsevier},
  address   = {Amsterdam [u.a.]},
  issn      = {0277-3791},
  doi       = {10.1016/j.quascirev.2020.106691},
  pages     = {8},
  year      = {2020},
  abstract  = {There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95\% CI: 0.86-1.24 Ma), and the two Old World lineages (I \& II) split at 0.88 Ma (95\% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95\% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species.},
  language  = {en}
}
@article{ChenLiZhangetal.2019,
  author    = {Chen, Shun-Gang and Li, Ji and Zhang, Fan and Xiao, Bo and Hu, Jia-Ming and Cui, Yin-Qiu and Hofreiter, Michael and Hou, Xin-Dong and Sheng, Gui-Lian and Lai, Xu-Long and Yuan, Jun-Xia},
  title     = {Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China},
  series = {Mitochondrial DNA Part A},
  volume    = {30},
  journal   = {Mitochondrial DNA Part A},
  number    = {7},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {2470-1394},
  doi       = {10.1080/24701394.2019.1659250},
  pages     = {786 -- 793},
  year      = {2019},
  abstract  = {Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95\% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.},
  language  = {en}
}
@article{SignorePaijmansHofreiteretal.2019,
  author    = {Signore, Anthony V. and Paijmans, Johanna L. A. and Hofreiter, Michael and Fago, Angela and Weber, Roy E. and Springer, Mark S. and Campbell, Kevin L.},
  title     = {Emergence of a chimeric globin pseudogene and increased Hemoglobin Oxygen Affinity Underlie the evolution of aquatic specializations in Sirenia},
  series = {Molecular biology and evolution},
  volume    = {36},
  journal   = {Molecular biology and evolution},
  number    = {6},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msz044},
  pages     = {1134 -- 1147},
  year      = {2019},
  abstract  = {As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller's sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb-O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb-O2 affinity in (sub)Arctic Steller's sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.},
  language  = {en}
}
@article{TaronLellBarlowetal.2018,
  author    = {Taron, Ulrike H. and Lell, Moritz and Barlow, Axel and Paijmans, Johanna L. A.},
  title     = {Testing of Alignment Parameters for Ancient Samples},
  series = {Genes},
  volume    = {9},
  journal   = {Genes},
  number    = {3},
  publisher = {Molecular Diversity Preservation International},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes9030157},
  pages     = {1 -- 12},
  year      = {2018},
  abstract  = {High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.},
  language  = {en}
}
@article{TaronLellBarlowetal.2018,
  author    = {Taron, Ulrike H. and Lell, Moritz and Barlow, Axel and Paijmans, Johanna L. A.},
  title     = {Testing of Alignment Parameters for Ancient Samples},
  series = {Genese},
  volume    = {9},
  journal   = {Genese},
  number    = {3},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes9030157},
  pages     = {12},
  year      = {2018},
  abstract  = {High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.},
  language  = {en}
}
@article{AlbertiGonzalezPaijmansetal.2018,
  author    = {Alberti, Federica and Gonzalez, Javier and Paijmans, Johanna L. A. and Basler, Nikolas and Preick, Michaela and Henneberger, Kirstin and Trinks, Alexandra and Rabeder, Gernot and Conard, Nicholas J. and Muenzel, Susanne C. and Joger, Ulrich and Fritsch, Guido and Hildebrandt, Thomas and Hofreiter, Michael and Barlow, Axel},
  title     = {Optimized DNA sampling of ancient bones using Computed Tomography scans},
  series = {Molecular ecology resources},
  volume    = {18},
  journal   = {Molecular ecology resources},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12911},
  pages     = {1196 -- 1208},
  year      = {2018},
  abstract  = {The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99\% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.},
  language  = {en}
}
@article{ThomasCarvalhoHaileetal.2017,
  author    = {Thomas, Jessica E. and Carvalho, Gary R. and Haile, James and Martin, Michael D. and Castruita, Jose A. Samaniego and Niemann, Jonas and Sinding, Mikkel-Holger S. and Sandoval-Velasco, Marcela and Rawlence, Nicolas J. and Fuller, Errol and Fjeldsa, Jon and Hofreiter, Michael and Stewart, John R. and Gilbert, M. Thomas P. and Knapp, Michael},
  title     = {An ‛Aukward' tale},
  series = {Genes},
  volume    = {8},
  journal   = {Genes},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes8060164},
  pages     = {164},
  year      = {2017},
  abstract  = {One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller's candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars' minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.},
  language  = {en}
}
@article{MohandesanSpellerPetersetal.2017,
  author    = {Mohandesan, Elmira and Speller, Camilla F. and Peters, Joris and Uerpmann, Hans-Peter and Uerpmann, Margarethe and De Cupere, Bea and Hofreiter, Michael and Burger, Pamela A.},
  title     = {Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel},
  series = {Molecular ecology resources},
  volume    = {17},
  journal   = {Molecular ecology resources},
  number    = {2},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12551},
  pages     = {300 -- 313},
  year      = {2017},
  abstract  = {The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95\% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.},
  language  = {en}
}
@article{TassiVaiGhirottoetal.2017,
  author    = {Tassi, Francesca and Vai, Stefania and Ghirotto, Silvia and Lari, Martina and Modi, Alessandra and Pilli, Elena and Brunelli, Andrea and Susca, Roberta Rosa and Budnik, Alicja and Labuda, Damian and Alberti, Federica and Lalueza-Fox, Carles and Reich, David and Caramelli, David and Barbujani, Guido},
  title     = {Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages},
  series = {Proceedings of the Royal Society of London : B, Biological sciences},
  volume    = {284},
  journal   = {Proceedings of the Royal Society of London : B, Biological sciences},
  publisher = {Royal Society},
  address   = {London},
  issn      = {0962-8452},
  doi       = {10.1098/rspb.2017.1540},
  pages     = {9},
  year      = {2017},
  abstract  = {It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.},
  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{GonzalezFortesKolbeFernandesetal.2016,
  author    = {Gonz{\´a}lez-Fortes, Gloria M. and Kolbe, Ben and Fernandes, Daniel and Meleg, Ioana N. and Garcia-Vazquez, Ana and Pinto-Llona, Ana C. and Constantin, Silviu and de Torres, Trino J. and Ortiz, Jose E. and Frischauf, Christine and Rabeder, Gernot and Hofreiter, Michael and Barlow, Axel},
  title     = {Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears},
  series = {Molecular ecology},
  volume    = {25},
  journal   = {Molecular ecology},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0962-1083},
  doi       = {10.1111/mec.13800},
  pages     = {4907 -- 4918},
  year      = {2016},
  abstract  = {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.},
  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{AlterMeyerPostetal.2015,
  author    = {Alter, S. Elizabeth and Meyer, Matthias and Post, Klaas and Czechowski, Paul and Gravlund, Peter and Gaines, Cork and Rosenbaum, Howard C. and Kaschner, Kristin and Turvey, Samuel T. and van der Plicht, Johannes and Shapiro, Beth and Hofreiter, Michael},
  title     = {Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100},
  series = {Molecular ecology},
  volume    = {24},
  journal   = {Molecular ecology},
  number    = {7},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0962-1083},
  doi       = {10.1111/mec.13121},
  pages     = {1510 -- 1522},
  year      = {2015},
  abstract  = {Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.},
  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{TeasdalevanDoornFiddymentetal.2015,
  author    = {Teasdale, Matthew David and van Doorn, N. L. and Fiddyment, S. and Webb, C. C. and Hofreiter, Michael and Collins, Matthew J. and Bradley, Daniel G.},
  title     = {Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing},
  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.2013.0379},
  pages     = {7},
  year      = {2015},
  abstract  = {Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4\% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5\%. Over 45\% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7\% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.},
  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}
}