Biology subjects

Dean Bobo

Publications and source records attributed to Dean Bobo.

3 recordsLinked to original sources

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

False Negatives Are a Significant Feature of Next Generation Sequencing Callsets

Short-read, next-generation sequencing (NGS) is now broadly used to identify rare or de novo mutations in population samples and disease cohorts. However, NGS data is known to be error-prone and post-processing pipelines have primarily focused on the removal of spurious mutations or \"false positives\" in downstream genome datasets. Less attention has been paid to characterizing the fraction of missing mutations or \"false negatives\" (FN). We design a phylogeny-aware tool to determine false negatives [PhyloFaN] and describe how read coverage and reference bias affect the FN rate. Using thousand-fold coverage NGS data from both Illumina HiSeq and Complete Genomics platforms derived from the 1000 Genomes Project, we first characterize the false negative rate in human mtDNA genomes. The false negative rate for the publically available callsets is 17-20%, even for extremely high coverage haploid data. We demonstrate that high FN rates are not limited to mtDNA by comparing autosomal data from 28 publically available full genomes to intergenic Sanger sequenced regions for each individual. We examine both low-coverage Illumina and high-coverage Complete Genomics genomes. We show that the FN rate varies between [~]6%-18% and that false-positive rates are considerably lower (<3%). The FN rate is strongly dependent on calling pipeline parameters, as well as read coverage. Our results demonstrate that missing mutations are a significant feature of genomic datasets and imply additional fine-tuning of bioinformatics pipelines is needed. We provide a tool which can be used to quantify the FN rate for haploid genomic experiments, without additional generation of validation data.\n\nData depositionData and software are freely available on the Henn Lab website: https://ecoevo.stonybrook.edu/hennlab/data-software/\n\nSoftwareGITHUB via https://ecoevo.stonybrook.edu/hennlab/data-software/

Bioinformatics↗

bioRxiv2016

Fine-scale human population structure in southern Africa reflects ecological boundaries

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until about 2,000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about population history within southern Africa. We examine new genome-wide polymorphism data and whole mitochondrial genomes for more than one hundred South Africans from the =Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking =Khomani (formerly hunter-gatherers) share recent ancestry with other Khoe-speaking forager populations that forms a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu-speakers, approximately 14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited impact from eastern African genetic diffusion.

Genetics↗