TY  - JOUR
A1  - Ludwig, Arne
A1  - Reissmann, Monika
A1  - Benecke, Norbert
A1  - Bellone, Rebecca
A1  - Sandoval-Castellanos, Edson
A1  - Cieslak, Michael
A1  - González-Fortes, Gloria M.
A1  - Morales-Muniz, Arturo
A1  - Hofreiter, Michael
A1  - Pruvost, Melanie
T1  - Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses
JF  - Philosophical transactions of the Royal Society of London : B, Biological sciences
N2  - 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.
KW  - ancient DNA
KW  - coat colour
KW  - domestication
KW  - Equus
KW  - palaeogenetics
KW  - population
Y1  - 2015
U6  - https://doi.org/10.1098/rstb.2013.0386
SN  - 0962-8436
SN  - 1471-2970
VL  - 370
IS  - 1660
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  -