@article{WestburyHartmannBarlowetal.2018,
  author    = {Westbury, Michael V. and Hartmann, Stefanie and Barlow, Axel and Wiesel, Ingrid and Leo, Viyanna and Welch, Rebecca and Parker, Daniel M. and Sicks, Florian and Ludwig, Arne and Dalen, Love and Hofreiter, Michael},
  title     = {Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena},
  series = {Molecular biology and evolution},
  volume    = {35},
  journal   = {Molecular biology and evolution},
  number    = {5},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0737-4038},
  doi       = {10.1093/molbev/msy037},
  pages     = {1225 -- 1237},
  year      = {2018},
  abstract  = {Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species.},
  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{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}
}