Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?

Background

While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge.

Methods

We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods.

Results

We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs).

Conclusion

Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.

     

Genetic ancestry of participants in the National Children’s Study

Background

The National Children’s Study (NCS) is a prospective epidemiological study in the USA tasked with identifying a nationally representative sample of 100,000 children, and following them from their gestation until they are 21 years of age. The objective of the study is to measure environmental and genetic influences on growth, development, and health. Determination of the ancestry of these NCS participants is important for assessing the diversity of study participants and for examining the effect of ancestry on various health outcomes.

Results

We estimated the genetic ancestry of a convenience sample of 641 parents enrolled at the 7 original NCS Vanguard sites, by analyzing 30,000 markers on exome arrays, using the 1000 Genomes Project superpopulations as reference populations, and compared this with the measures of self-reported ethnicity and race. For 99% of the individuals, self-reported ethnicity and race agreed with the predicted superpopulation. NCS individuals self-reporting as Asian had genetic ancestry of either South Asian or East Asian groups, while those reporting as either Hispanic White or Hispanic Other had similar genetic ancestry. Of the 33 individuals who self-reported as Multiracial or Non-Hispanic Other, 33% matched the South Asian or East Asian groups, while these groups represented only 4.4% of the other reported categories.

Conclusions

Our data suggest that self-reported ethnicity and race have some limitations in accurately capturing Hispanic and South Asian populations. Overall, however, our data indicate that despite the complexity of the US population, individuals know their ancestral origins, and that self-reported ethnicity and race is a reliable indicator of genetic ancestry.     

The jigsaw puzzle of our African ancestry: unsolved,or unsolvable?

A revised root for the Y chromosome phylogeny further fragments the picture of modern human origins that can be reconstructed from genetic, linguistic and archaeological data.     

Is xenodontine snake reproduction shaped by ancestry,more than by ecology?

One of the current challenges of evolutionary ecology is to understand the effects of phylogenetic history (PH) and/or ecological factors (EF) on the life‐history traits of the species. Here, the effects of environment and phylogeny are tested for the first time on the reproductive biology of South American xenodontine snakes. We studied 60% of the tribes of this endemic and most representative clade in a temperate region of South America. A comparative method (canonical phylogenetic ordination—CPO) was used to find the relative contributions of EF and PH upon life‐history aspects of snakes, comparing the reproductive mode, mean fecundity, reproductive potential, and frequency of nearly 1,000 specimens. CPO analysis showed that PH or ancestry explained most of the variation in reproduction, whereas EF explained little of this variation. The reproductive traits under study are suggested to have a strong phylogenetic signal in this clade, the ancestry playing a big role in reproduction. The EF also influenced the reproduction of South American xenodontines, although to a lesser extent. Our finding provides new evidence of how the evolutionary history is embodied in the traits of living species.     

Does Homo neanderthalensis play a role in modern human ancestry? The mandibular evidence

Data obtained from quantifying the upper part of the mandibular ramus (the coronoid process, the condylar process, and the notch between them) lead us to conclude that Neanderthals (both European and Middle Eastern) differ more from Homo sapiens (early specimens such as Tabun II, Skhul, and Qafzeh, as well as contemporary populations from as far apart as Alaska and Australia) than the latter differs from Homo erectus. The specialized Neanderthal mandibular ramus morphology emerges as yet another element constituting the derived complex of morphologies of the mandible and face that are unique to Neanderthals. These morphologies provide further support for the contention that Neanderthals do not play a role in modern human biological ancestry, either through "regional continuity" or through any other form of anagenetic progression.     

Are homologies in vertebrate sex determination due to shared ancestry or to limited options?

The same candidate genes and the same autosomes are repeatedly used as sex chromosomes in vertebrates. Are these systems identical by descent, or are some genes or chromosomes intrinsically better at triggering the first steps of sex determination?     

Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?

Glass sponges (Hexactinellida) are a group of deep-water benthicanimals that have a unique syncytial organization and possessa characteristic siliceous skeleton. Although hexactinellidsare traditionally grouped with calcareous and demosponges inthe phylum Porifera, the monophyly of sponges and the phylogeneticposition of the Hexactinellida remain contentious. We determinedand analyzed the nearly complete mitochondrial genome sequencesof the hexactinellid sponges Iphiteon panicea and Sympagellanux. Unexpectedly, our analysis revealed several mitochondrialgenomic features shared between glass sponges and bilateriananimals, including an Arg Ser change in the genetic code, acharacteristic secondary structure of one of the serine tRNAs,highly derived tRNA and rRNA genes, and the presence of a singlelarge noncoding region. At the same time, glass sponge mtDNAcontains atp9, a gene previously found only in the mtDNA ofdemosponges (among animals), and encodes a with an atypical A11–U24 pair that is alsofound in demosponges and placozoans. Most of our sequence-basedphylogenetic analyses place Hexactinellida as the sister groupto the Bilateria; however, these results are suspect given acceleratedrates of mitochondrial sequence evolution in these groups. Thus,it remains an open question whether shared mitochondrial genomicfeatures in glass sponges and bilaterian animals reflect theirclose phylogenetic affinity or provide a remarkable exampleof parallel evolution.     

The allotypic patchwork pattern of the rabbit IGKC1 allele b5wf: genic exchange or common ancestry?

 The protein sequences of different alleles of the rabbit immunoglobulin IGKC1 gene can differ at more than 40% of the amino acid positions. This exceptional degree of allelic divergence raises questions concerning the causal underlying mechanisms. We report the DNA sequence of the coding region of an allotype which is associated with the mitochondrial lineage A (Southwestern Spain). At the serological level, this b5wf allotype presents a patchwork of antigenic determinants which in domestic breeds are characteristic of the b4, b5, and b6 allotypes. The inferred protein sequence of the b5wf allotype was found to differ from that of the b4, b5, and b6 allotypes at 25, 10, and 15% of the amino acid positions, respectively. Sequence comparisons show that the b4-specific epitopes of the b5wf allotype are probably due to a shared ThrThrGlnThr motif at Kabat positions 153–156. Similarly, the shared b5-specific determinants should relate to the motifs 161ThrSerLys163 and/or 182LysSerAspGlu185. A monoclonal antibody binding epitope shared among the b5wf, b5, and b6 sequences appeared to be correlated with the presence of Asp190. Although there is evidence of interallelic genic exchange, sequence comparisons suggest that the apparent mosaic structure of the b5wf allotype is better explained by common ancestry and point mutation. Received: 22 June 1998 / Revised: 18 August 1998     

The Longue Durée of genetic ancestry: multiple genetic marker systems and Celtic origins on the Atlantic facade of Europe

Celtic languages are now spoken only on the Atlantic facade of Europe, mainly in Britain and Ireland, but were spoken more widely in western and central Europe until the collapse of the Roman Empire in the first millennium a.d. It has been common to couple archaeological evidence for the expansion of Iron Age elites in central Europe with the dispersal of these languages and of Celtic ethnicity and to posit a central European "homeland" for the Celtic peoples. More recently, however, archaeologists have questioned this "migrationist" view of Celtic ethnogenesis. The proposition of a central European ancestry should be testable by examining the distribution of genetic markers; however, although Y-chromosome patterns in Atlantic Europe show little evidence of central European influence, there has hitherto been insufficient data to confirm this by use of mitochondrial DNA (mtDNA). Here, we present both new mtDNA data from Ireland and a novel analysis of a greatly enlarged European mtDNA database. We show that mtDNA lineages, when analyzed in sufficiently large numbers, display patterns significantly similar to a large fraction of both Y-chromosome and autosomal variation. These multiple genetic marker systems indicate a shared ancestry throughout the Atlantic zone, from northern Iberia to western Scandinavia, that dates back to the end of the last Ice Age.     

A probabilistic view on the deterministic mutation–selection equation: dynamics,equilibria, and ancestry via individual lines of descent

We reconsider the deterministic haploid mutation–selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes ancestral (random) structures inherent in this deterministic model. In a first step, we obtain a representation of the deterministic equation’s solution (and, in particular, of its equilibria) in terms of an ancestral process called the killed ancestral selection graph. This representation allows one to understand the bifurcations related to the error threshold phenomenon from a genealogical point of view. Next, we characterise the ancestral type distribution by means of the pruned lookdown ancestral selection graph and study its properties at equilibrium. We also provide an alternative characterisation in terms of a piecewise-deterministic Markov process. Throughout, emphasis is on the underlying dualities as well as on explicit results.

     

Drafting human ancestry: what does the Neanderthal genome tell us about hominid evolution? Commentary on Green et al. (2010)

Ten years after the first draft versions of the human genome were announced, technical progress in both DNA sequencing and ancient DNA analyses has allowed a research team around Ed Green and Svante P??bo to complete this task from infinitely more difficult hominid samples: a few pieces of bone originating from our closest, albeit extinct, relatives, the Neanderthals. Pulling the Neanderthal sequences out of a sea of contaminating environmental DNA impregnating the bones and at the same time avoiding the problems of contamination with modern human DNA is in itself a remarkable accomplishment. However, the crucial question in the long run is, what can we learn from such genomic data about hominid evolution?     

Genetic diversity and inferred ancestry of Asian lotus(Nelumbo nucifera) germplasms in Thailand and VietnamOA

Tropical lotus(Nelumbo) is an important and unique ecological type of lotus germplasm.Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization.Using 42 EST-SSR(expressed sequence tag-simple sequence repeats) and 30 SRAP(sequence-related amplified polymorphism) markers,we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam.In total,164 and 41 polymorphic ...