Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits. Citation: Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, et al. (2007) A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 3(1): e3.
SummaryWe describe the genetic structure and affinities of five Dravidian-speaking tribal populations inhabiting the Nilgiri hills of Tamil Nadu, in south India, using 24 autosomal DNA markers. Our goals were: (i) to examine what evolutionary forces have most significantly impacted south Indian tribal genetic variation, and (ii) to test whether the phenotypic similarities of some south Indian tribal groups to Africans represent a signature of close relationship to Africans or are due to convergence. All loci were polymorphic and average heterozygosities were substantial (range: 0.347-0.423). Genetic differentiation was high (G st = 6.7%) and genetic distances were not significantly correlated with geographic distances. Genetic drift therefore probably played a significant role in shaping the patterns of genetic variation observed in southern Indian tribal populations. Otherwise, analyses of population relationships showed that Indian populations are closely related to one another, regardless of phenotypic characteristics, and do not show particular affinities to Africans. We conclude that the phenotypic similarities of some Indian groups to Africans do not reflect a close relationship between these groups, but are better explained by convergence.
The process by which agriculture diffused from the Fertile Crescent within the past 10,000 years has been widely discussed, but as yet there is no consensus: Was it mostly a demic diffusion (with massive spread of people) or rather a cultural diffusion (without substantial migration of people)? The demic diffusion model (1) predicts a substantial genetic input from migrating agriculturalists, whereas the cultural diffusion model (2) predicts no major changes at the genetic level. Hence, a way to test these competing hypotheses would be to compare genetic variation in traditional agriculturalists, traditional huntergatherers, and recent agriculturalists (i.e., former hunter-gatherers who recently shifted to agriculture). Under the demic diffusion model, recent agriculturalists are expected to show closer genetic affinities to traditional agriculturalists than do hunter-gatherers; whereas under the cultural diffusion model, recent agriculturalists should resemble hunter-gatherers genetically.Genetic studies of Europeans have led to conflicting conclusions, partly because the genetic composition of pre-agricultural European populations is unknown. However, there still exist in India both nonagricultural groups and groups that recently adopted agriculture (3, 4), allowing a formal test of the demic versus cultural diffusion models of the spread of agriculture. Caste groups can be considered as traditional agriculturalists in this context, because they introduced key innovations (such as iron technology) that facilitated the expansion of agriculture toward south India (4). There are also tribal groups in south India who are generally considered to be the aboriginal inhabitants of the region and who have traditionally been hunter-gatherers (3, 4). Some of them still survive through hunting and gathering or unskilled labor, whereas others have shifted to an agriculturalist subsistence strategy within the past 3000 years (4).Genetic affinities were deduced from the frequencies of 14 Y-chromosome haplogroups analyzed in 583 males, including 71 tribal south Indian hunter-gatherers, 60 tribal south Indian recent agriculturalists, and 283 south Indian and 169 north Indian traditional agriculturalists (5). Pairwise genetic (Fst) distances separating the different categories of individuals indicate that south Indian recent agriculturalists are signifi-cantly more closely related to traditional agriculturalists than are traditional hunter-gatherers (Fig. 1A) (t test on jackknifed Fst values, P Ͻ 0.01). This conclusion is supported by a multidimensional scaling analysis that simultaneously compared all four categories; it also reveals that recent south Indian agriculturalists are overall genetically more similar to traditional agriculturalists than to traditional hunter-gatherers (Fig. 1B).Genetic affinities were also deduced from sequences of the mitochondrial DNA (mtDNA) control region analyzed in 632 individuals, including 229 tribal south Indian hunter-gatherers, 201 tribal south Indian recent agriculturalists, and 140 sout...
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