Biology subjects

Krishna Veeramah

Publications and source records attributed to Krishna Veeramah.

4 recordsLinked to original sources

bioRxiv2015

Early farmers from across Europe directly descended from Neolithic Aegeans

Farming and sedentism first appear in southwest Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion and admixture with local foragers in the early Neolithisation of Europe. Here we present paleogenomic data for five Neolithic individuals from northwestern Turkey and northern Greece - spanning the time and region of the earliest spread of farming into Europe. We observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

Genomics↗

bioRxiv2015

Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data

1The inference of biological relatedness from DNA sequence data has a wide array of applications, such as in the study of human disease, anthropology and ecology. One of the most common analytical frameworks for performing this inference is to genotype individuals for large numbers of independent genomewide markers and use population allele frequencies to infer the probability of identity-by-descent (IBD) given observed genotypes. Current implementations of this class of methods assume genotypes are known without error. However, with the advent of 2nd generation sequencing data there are now an increasing number of situations where the confidence attached to a particular genotype may be poor because of low coverage. Such scenarios may lead to biased estimates of the kinship coefficient,{varepsilon} We describe an approach that utilizes genotype likelihoods rather than a single observed best genotype to estimate{phi} and demonstrate that we can accurately infer relatedness in both simulated and real 2nd generation sequencing data from a wide variety of human populations down to at least the third degree when coverage is as low as 2x for both individuals, while other commonly used methods such as PLINK exhibit large biases in such situations. In addition the method appears to be robust when the assumed population allele frequencies are diverged from the true frequencies for realistic levels of genetic drift. This approach has been implemented in the C++ software lcMLkin.

Genetics↗

bioRxiv2014

An Approximate Bayesian Computation Approach to Examining the Phylogenetic Relationships among the Four Gibbon Genera using Whole Genome Sequence Data

Gibbons are believed to have diverged from the larger great apes [~]16.8 Mya and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mtDNA, the Y chromosome, and short autosomal sequences have been inconclusive. To examine the relationships among gibbon genera in more depth, we performed 2nd generation whole genome sequencing to a mean of [~]15X coverage in two individuals from each genus. We developed a coalescent-based Approximate Bayesian Computation method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Our combined results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1x10-9/site/year this speciation process occurred [~]5 Mya during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.

Genomics↗

bioRxiv2014

Inference of Gorilla demographic and selective history from whole genome sequence data

While population-level genomic sequence data have been gathered extensively for humans, similar data from our closest living relatives are just beginning to emerge. Examination of genomic variation within great apes offers many opportunities to increase our understanding of the forces that have differentially shaped the evolutionary history of hominid taxa. Here, we expand upon the work of the Great Ape Genome Project by analyzing medium to high coverage whole genome sequences from 14 western lowland gorillas (Gorilla gorilla gorilla), 2 eastern lowland gorillas (G. beringei graueri), and a single Cross River individual (G. gorilla diehli). We infer that the ancestors of western and eastern lowland gorillas diverged from a common ancestor [~]261 thousand years ago (kya), and that the ancestors of the Cross River population diverged from the western lowland gorilla lineage [~]68 kya. Using a diffusion approximation approach to model the genome-wide site frequency spectrum, we infer a history of western lowland gorillas that includes an ancestral population expansion of [~]1.4-fold around [~]970 kya and a recent [~]5.6-fold contraction in population size [~]23 kya. The latter may correspond to a major reduction in African equatorial forests around the Last Glacial Maximum. We also analyze patterns of variation among western lowland gorillas to identify several genomic regions with strong signatures of recent selective sweeps. We find that processes related to taste, pancreatic and saliva secretion, sodium ion transmembrane transport, and cardiac muscle function are overrepresented in genomic regions predicted to have experienced recent positive selection.

Genomics↗