TY  - JOUR
A1  - Westbury, Michael V.
A1  - Hartmann, Stefanie
A1  - Barlow, Axel
A1  - Wiesel, Ingrid
A1  - Leo, Viyanna
A1  - Welch, Rebecca
A1  - Parker, Daniel M.
A1  - Sicks, Florian
A1  - Ludwig, Arne
A1  - Dalen, Love
A1  - Hofreiter, Michael
T1  - Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena
JF  - Molecular biology and evolution
N2  - 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.
KW  - evolution
KW  - hyena
KW  - genomics
KW  - population genomics
KW  - diversity
Y1  - 2018
U6  - https://doi.org/10.1093/molbev/msy037
SN  - 0737-4038
SN  - 1537-1719
VL  - 35
IS  - 5
SP  - 1225
EP  - 1237
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Tassi, Francesca
A1  - Vai, Stefania
A1  - Ghirotto, Silvia
A1  - Lari, Martina
A1  - Modi, Alessandra
A1  - Pilli, Elena
A1  - Brunelli, Andrea
A1  - Susca, Roberta Rosa
A1  - Budnik, Alicja
A1  - Labuda, Damian
A1  - Alberti, Federica
A1  - Lalueza-Fox, Carles
A1  - Reich, David
A1  - Caramelli, David
A1  - Barbujani, Guido
T1  - Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages
JF  - Proceedings of the Royal Society of London : B, Biological sciences
N2  - 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.
KW  - population genomics
KW  - ancient DNA
KW  - migration
KW  - Neolithic
KW  - Indo-European
KW  - approximate Bayesian computation
Y1  - 2017
U6  - https://doi.org/10.1098/rspb.2017.1540
SN  - 0962-8452
SN  - 1471-2954
VL  - 284
PB  - Royal Society
CY  - London
ER  - 
TY  - JOUR
A1  - Hofreiter, Michael
A1  - Paijmans, Johanna L. A.
A1  - Goodchild, Helen
A1  - Speller, Camilla F.
A1  - Barlow, Axel
A1  - González-Fortes, Gloria M.
A1  - Thomas, Jessica A.
A1  - Ludwig, Arne
A1  - Collins, Matthew J.
T1  - The future of ancient DNA: Technical advances and conceptual shifts
JF  - Bioessays : ideas that push the boundaries
N2  - 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.
KW  - ancient DNA
KW  - hybridisation capture
KW  - multi-locus data
KW  - next generation sequencing (NGS)
KW  - palaeogenomics
KW  - population genomics
Y1  - 2015
U6  - https://doi.org/10.1002/bies.201400160
SN  - 0265-9247
SN  - 1521-1878
VL  - 37
IS  - 3
SP  - 284
EP  - 293
PB  - Wiley-Blackwell
CY  - Hoboken
ER  -