Joachim Burger | Search bioRxiv

bioRxiv2016

Ancient European dog genomes reveal continuity since the early Neolithic

Europe has played a major role in dog evolution, harbouring the oldest uncontested Paleolithic remains and having been the centre of modern dog breed creation. We sequenced the whole genomes of an Early and End Neolithic dog from Germany, including a sample associated with one of Europes earliest farming communities. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. Furthermore, we find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication. By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000-40,000 years ago. Interestingly, we do not observe the extreme copy number expansion of the AMY2B gene that is characteristic of modern dogs and has previously been proposed as an adaptation to a starch-rich diet driven by the widespread adoption of agriculture in the Neolithic.

Genomics↗

bioRxiv2016

Inferring heterozygosity from ancient and low coverage genomes

While genetic diversity can be quantified accurately from high coverage sequencing, it is often desirable to obtain such estimates from low coverage data, either to save costs or because of low DNA quality as observed for ancient samples. Here we introduce a method to accurately infer heterozygosity probabilistically from very low coverage sequences of a single individual. The method relaxes the infinite sites assumption of previous methods, does not require a reference sequence and takes into account both variable sequencing errors and potential post-mortem damage. It is thus also applicable to non-model organisms and ancient genomes. Since error rates as reported by sequencing machines are generally distorted and require recalibration, we also introduce a method to infer accurately recalibration parameter in the presence of post-mortem damage. This method does also not require knowledge about the underlying genome sequence, but instead works from haploid data (e.g. from the X-chromosome from mammalian males) and integrates over the unknown genotypes. Using extensive simulations we show that a few Mb of haploid data is sufficient for accurate recalibration even at average coverages as low as 1-3x. At similar coverages, out method also produces very accurate estimates of heterozygosity down to 10-4 within windows of about 1Mb. We further illustrate the usefulness of our approach by inferring genome-wide patterns of diversity for several ancient human samples and found that 3,000-5,000 samples showed diversity patterns comparable to modern humans. In contrast, two European hunter-gatherer samples exhibited not only considerably lower levels of diversity than modern samples, but also highly distinct distributions of diversity along their genomes. Interestingly, these distributions were also very differently between the two samples, supporting earlier conclusions of a highly diverse and structured population in Europe prior to the arrival of farming.

Genomics↗