Positive selection in the SLC11A1 gene in the family Equidae.
Immunogenetics 68(5):353 (2016)
Immunity-related genes are a suitable model for studying effects of selection at the genomic level. Some of them are highly conserved due to functional constraints and purifying selection, while others are variable and change quickly to cope with the variation of pathogens. The SLC11A1 gene enco...
Accurate continuous geographic assignment from low- to high-density SNP data.
Large-scale genotype datasets can help track the dispersal patterns of epidemiological outbreaks and predict the geographic origins of individuals. Such genetically-based geographic assignments also show a range of possible applications in forensics for profiling both victims and criminals, and ...
Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.
Molecular Ecology Resources 16(2):459 (2016)
The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of...
Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses.
Nature Genetics 48(2):152 (2016)
Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of th...
AdapterRemoval v2: rapid adapter trimming, identification, and read merging.
BMC Research Notes 9(1):88 (2016)
As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the ...
Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.
PNAS 112(50):E6889 (2015)
Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformatio...
New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA.
BioTechniques 59(6):368 (2015)
An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventi...
Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.
Cell 163(3):571 (2015)
The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from As...
Current Biology 25(20):R973 (2015)
Alongside domestic horses and donkeys, the horse family, also known as equids, comprises six extant wild species of asses and zebras (Figure 1). Equids are extremely well represented in the fossil record, comprising a 55 million-year evolutionary history, punctuated by many episodes of innovatio...
Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.
Current Biology 25(19):2577 (2015)
Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is stil...
The ancestry and affiliations of Kennewick Man.
Nature 523(7561):455 (2015)
Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and l...
Reconstructing ancient genomes and epigenomes.
Nature Reviews: Genetics 16(7):395 (2015)
Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information...
Population genomics of Bronze Age Eurasia.
Nature 522(7555):167 (2015)
The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We in...
Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.
Nature 522(7554):81 (2015)
No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much ...
Planning tiger recovery: Understanding intraspecific variation for effective conservation.
Science advances 1(5):e1400175 (2015)
Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global appro...
Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean.
PNAS 112(12):3669 (2015)
Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three e...
Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids.
Biology Letters 11(3) (2015)
Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hi...
Ancient DNA and human evolution.
Journal of Human Evolution 79:1 (2015)
Major transitions in human evolution revisited: a tribute to ancient DNA.
Journal of Human Evolution 79:4 (2015)
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this info...
Philosophical Transactions of the Royal Society... 370(1660):20130387 (2015)
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive seque...