How accurate is the current picture of human genetic variation?

Abstract

Our understanding of the distribution of worldwide human genomic diversity has greatly increased over recent years thanks to the availability of large data sets derived from short tandem repeats (STRs), insertion deletion polymorphisms (indels) and single nucleotide polymorphisms (SNPs). A concern, however, is that the current picture of worldwide human genomic diversity may be inaccurate because of biases in the selection process of genetic markers (so-called 'ascertainment bias'). To evaluate this problem, we first compared the distribution of genomic diversity between these three types of genetic markers in the populations from the HGDP-CEPH panel for evidence of bias or incongruities. In a second step, using a very relaxed set of criteria to prevent the intrusion of bias, we developed a new set of unbiased STR markers and compared the results against those from available panels. Contrarily to recent claims, our results show that the STR markers suffer from no discernible bias, and can thus be used as a baseline reference for human genetic diversity and population differentiation. The bias on SNPs is moderate compared to that on the set of indels analysed, which we recommend should be avoided for work describing the distribution of human genetic diversity or making inference on human settlement history.

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

“…Our failure to detect subpopulations within vintage varieties contrasts with past studies that detected differentiation within landraces and vintage varieties (Park et al, 2004;Mazzucato et al, 2008). These differences likely reflect the germplasm and markers sampled as subpopulations are determined with respect to genotypes within the collection chosen for analysis (Chikhi, 2008;Romero et al, 2009).…”

“…An inconsistent pattern of clustering was observed when using the exon sequence markers, the SSR markers or the InDel markers alone. The instances of inconsistent clustering that we occasionally observed are most likely due to the population and marker sampling, which is referred to as ascertainment bias (Chikhi, 2008;Romero et al, 2009). Our failure to detect subpopulations within vintage varieties contrasts with past studies that detected differentiation within landraces and vintage varieties (Park et al, 2004;Mazzucato et al, 2008).…”

The contribution of subsistence to global human cranial variation

“…As there is a very strong correlation between genetic and geographic distances (Manica et al, 2005;Ramachandran et al, 2005;Romero et al, 2008), geographic distance (when measured along land migration routes) can be used as a proxy for population history (Lawson Handley et al, 2007;Hubbe et al, 2009;Betti et al, 2010).…”

Deep evolutionary roots of strepsirrhine primate labyrinthine morphology

“…Such an approach also permits a posteriori refinement of the choice of the morphological characters which are used for the purpose of phylogenetic reconstructions (Pilbeam, 1997). Studies analyzing the morphological variation in the light of the molecular evidence have already proven useful in identifying phenetic features characteristic for the human-chimpanzee clade (Gibbs et al 2002;Lockwood et al 2004;Bradley, 2008), and in the search for cranial features reflecting hominin phylogeny (Gonzá lez-Jose et al 2008) and modern human phylogeography (Harvati & Weaver, 2006;Manica et al 2007;Roseman & Weaver, 2007;Smith et al 2007;Betti et al 2009;Romero et al 2009). Furthermore, geometric morphometric methods offer new possibilities to study the phylogenetic signal contained in morphology because these methods permit comprehensive quantification of morphological features, which are traditionally described as an array of characters with discrete states.…”