Discerning the origins of the Negritos, first Sundaland people: Deep divergence and archaic admixture

Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the “First Sundaland People.” To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People

Are Roma People Descended from the Punjab Region of Pakistan: A Y-Chromosomal Perspective

Gypsies are a separate ethnic group living in Pakistan and some other countries as well. They are mostly known as ‘Roma’ and ‘untouchables’. They have different types of lifestyles as compared to other common people, as they always keep migrating from one place to another. They do not have proper houses; they live in tent houses and most probably work on daily wages to earn their living. Gypsies cannot be specified according to the place of residence and can only be classified according to their migration route. Previous historical and linguistic research showed the north Indian origin of Roma people. The present study collected 285 unrelated Roma individuals living in Punjab and typed with the Goldeneye Y20 system. Allelic frequencies ranged between 0.0035 and 0.5266, with haplotype diversity (HD) of 0.9999 and discrimination capacity (DC) of 0.8790. Gene diversity (GD) ranged from 0.6489 (DYS391) to 0.9764 (DYS391) (DY385ab). A total of 223 unique alleles were observed. Interestingly, the haplogroup R accounted for 40.56% and J for 22.06%. In MDS analysis, Pakistani Roma formed a close cluster with Roma from Constanta, Romania. The migration pattern of the Roma population from Pakistan, India and Europe was inferred using coalescence theory in the Migrate-n program. Overlapping Y-STR data were used to test different migration models. These migration models showed us the dominant gene flow from Pakistan to India and Europe to Pakistan. The results of our study showed that Y STRs provided substantially stronger discriminatory power in the Pakistani Roma population

In silico karyotyping of chromosomally polymorphic malaria mosquitoes in the Anopheles gambiae complex

Chromosomal inversion polymorphisms play an important role in adaptation to environmental heterogeneities. For mosquito species in the Anopheles gambiae complex that are significant vectors of human malaria, paracentric inversion polymorphisms are abundant and are associated with ecologically and epidemiologically important phenotypes. Improved understanding of these traits relies on determining mosquito karyotype, which currently depends upon laborious cytogenetic methods whose application is limited both by the requirement for specialized expertise and for properly preserved adult females at specific gonotrophic stages. To overcome this limitation, we developed sets of tag single nucleotide polymorphisms (SNPs) inside inversions whose biallelic genotype is strongly correlated with inversion genotype. We leveraged 1,347 fully sequenced An. gambiae and Anopheles coluzzii genomes in the Ag1000G database of natural variation. Beginning with principal components analysis (PCA) of population samples, applied to windows of the genome containing individual chromosomal rearrangements, we classified samples into three inversion genotypes, distinguishing homozygous inverted and homozygous uninverted groups by inclusion of the small subset of specimens in Ag1000G that are associated with cytogenetic metadata. We then assessed the correlation between candidate tag SNP genotypes and PCA-based inversion genotypes in our training sets, selecting those candidates with >80% agreement. Our initial tests both in held-back validation samples from Ag1000G and in data independent of Ag1000G suggest that when used for in silico inversion genotyping of sequenced mosquitoes, these tags perform better than traditional cytogenetics, even for specimens where only a small subset of the tag SNPs can be successfully ascertained

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

The yak is remarkable for its adaptation to high altitude and occupies a central place in the economies of the mountainous regions of Asia. At lower elevations, it is common to hybridize yaks with cattle to combine the yak’s hardiness with the productivity of cattle. Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited ~1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years. The introgressed regions are enriched in genes involved in nervous system development and function, and particularly in glutamate metabolism and neurotransmission. We also identified a novel mutation associated with a polled (hornless) phenotype originating from Mongolian Turano cattle. Our results suggest that introgressive hybridization contributed to the improvement of yak management and breeding

Algorithms for genomics and genetics : compression-accelerated search and admixture analysis

Thesis (Ph. D.)--Massachusetts Institute of Technology, Department of Mathematics, 2013.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 133-139).Rapid advances in next-generation sequencing technologies are revolutionizing genomics, with data sets at the scale of thousands of human genomes fast becoming the norm. These technological leaps promise to enable corresponding advances in biology and medicine, but the deluge of raw data poses substantial mathematical, computational and statistical challenges that must first be overcome. This thesis consists of two research thrusts along these lines. First, we propose an algorithmic framework, "compressive genomics," that accelerates bioinformatic computations through analysis-aware compression. We demonstrate this methodology with proof-of-concept implementations of compression-accelerated search (CaBLAST and CaBLAT). Second, we develop new computational tools for investigating population admixture, a phenomenon of importance in understanding demographic histories of human populations and facilitating association mapping of disease genes. Our recently released ALDER and MixMapper software packages provide fast, sensitive, and robust methods for detecting and analyzing signatures of admixture created by genetic drift and recombination on genome-wide, large-sample scales.by Po-Ru Loh.Ph.D

Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis)

International audienceThe identification and delimitation of species boundaries are essential for understanding speciation and adaptation processes and for the management of biodiversity as well as development for applications. Ophiocordyceps unilateralis sensu lato is a complex of fungal pathogens parasitizing Formicine ants, inducing zombie behaviors in their hosts. Previous taxonomic works with limited numbers of samples and markers led to the "one ant-one fun-gus" paradigm, resulting in the use of ant species as a proxy for fungal identification. Here, a population genomics study with sampling on three ant species across Thailand supported the existence of host-specific species in O. unilateralis s.l. with no footprints of long term introgression despite occasional host shifts and first-generation hybrids. We further detected genetic clusters within the previously delimited fungal species, with each little footprints of recombination, suggesting high levels of inbreeding. The clusters within each of O. camponoti-leonardi and O. camponoti-saundersi were supported by differentiation throughout the genome, suggesting they may constitute further cryptic species parasitizing the same host, challenging the one ant-one fungus paradigm. These genetic clusters had different geographical ranges, supporting different biogeographic influences between the north/center and the south of Thailand, reinforcing the scenario in which Thailand endured compartmentation during the latest Pleistocene glacial cycles

Admixture and ancestry inference from ancient and modern samples through measures of population genetic drift

Methods that leverage the information about population history contained within the increasingly abundant genetic sequences of extant and extinct Hominid populations are diverse in form and versatile in application. Here, we review key methods recently developed to detect and quantify admixture and ancestry in modern human populations. We begin with an overview of the f- and D-statistics, covering their conceptual principles and important applications, as well as any extensions developed for them. We then cover a combination of more recent and more complex methods for admixture and ancestry inference, discussing tests for direct ancestry between two populations, quantification of admixture in large datasets, and determination of admixture dates. These methods have revolutionized our understanding of human population history and additionally highlighted its complexity. Therefore, we emphasize that current methods may not capture this population history in its entirety, but nonetheless provide a reasonable picture that is supported by data from multiple methods, and from the historical record