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Jody Hey

Publications and source records attributed to Jody Hey.

At least 19 recordsLinked to original sources
PubMed2006

Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation.

The population genetic history of a 10.1-kbp noncoding region of the human X chromosome was studied using the males of the HGDP-CEPH Human Genome Diversity Panel (672 individuals from 52 populations). The geographic distribution of patterns of variation was roughly consistent with previous studies, with the major exception that 1 highly divergent haplotype (haplotype X, hX) was observed at low frequency in widely scattered non-African populations and not at all observed in sub-Saharan African populations. Microsatellite (short tandem repeat) variation within the sequenced region was low among copies of hX, even though the estimated time of ancestry of hX and other sequences was 1.44 Myr. The estimated age of the common ancestor of all hX copies was 5,230 years (95% consistency index: 2,000-75,480 years). To further address the presence of hX in Africa, additional samples from Chad and Tanzania were screened. Five additional copies of hX were observed, consistent with a history in which hX was present in Africa prior to the migration of modern humans out of Africa and with eastern Africa being the source of non-African modern human populations. Taken together, these features of hX-that it is much older than other haplotypes and uncommon and patchily distributed throughout Africa, Europe, and Asia-present a cautionary tale for interpretations of human history.

Chromosomes, Human, X↗
PubMed2006

Recent advances in assessing gene flow between diverging populations and species.

The evolutionary process of divergence, which ultimately leads to the generation of new species, is thought to occur usually without any gene exchange between the diverging populations. However, until the recent growth of multi-locus datasets, and the development of new population genetic methods, it has been very difficult to assess whether or not closely related species have, or have not, exchanged genes during their divergence. Several recent studies have found significant signals of gene flow during species formation, calling into question the conventional wisdom that gene flow is absent during speciation.

Animals↗
PubMed2006

On the failure of modern species concepts.

The modern age of species concepts began in 1942, when Ernst Mayr gave concept names to several different approaches to species identification. A long list of species concepts then followed, as well as a complex literature on their merits, motivations and uses. Some of these complexities arose as a consequence of the semantic shift that Mayr introduced, in which procedures for identifying species were elevated to concepts. Much of the debate in recent decades over concepts, and over pluralism versus monism, can be seen as an unnecessary consequence of treating species identification criteria as if they were more fundamental concepts. Recently, biologists have begun to recognize both the shortcomings of a lexicon of multiple species concepts and a common evolutionary idea that underlies them.

Animals↗
PubMed2006

Nuclear gene variation and molecular dating of the cichlid species flock of Lake Malawi.

The cichlid fishes of Lake Malawi are famously diverse. However, evolutionary studies have been difficult because of their recent and uncertain phylogenetic history. Portions of 12 nuclear loci were sequenced in nine rock-dwelling species (mbuna) and three representatives of pelagic nonmbuna species. In contrast to the pattern of variation at mitochondrial genes, which do provide phylogenetic resolution at the level of mbuna versus nonmbuna, and among some genera, the nuclear loci were virtually devoid of phylogenetic signal. Only a small minority of variable positions were phylogenetically informative, and no phylogenetic branches are supported by more than one site. From the nuclear gene perspective the Malawian radiation appears to be a star phylogeny, as if the founding of the lake was accompanied by a partial bottleneck. The pattern is different from that found in Lake Victoria, in which nuclear loci share large amounts of ancestral variation. In the case of nuclear genes of Lake Malawi, the absence of phylogenetically informative variation suggests a relative absence of ancestral variation. Nuclear genes also differed from the mitochondria in having nearly twice the amount of divergence from Oreochromis (tilapia). An approximate splitting time between mbuna and nonmbuna lineages was estimated as 0.7 Myr. Oreochromis is estimated to have diverged from the cichlids in Lake Malawi and Lake Tanganyika about 18 MYA.

Animals↗
PubMed2005

Sampling from natural populations with RNAI reveals high outcrossing and population structure in Caenorhabditis elegans.

Despite a nearly worldwide distribution in nature, Caenorhabditis elegans exhibits low levels of genetic polymorphism, possibly as an indirect consequence of low levels of outcrossing. In the laboratory, Caenorhabditis elegans males are produced at low rates and are steadily eliminated from cultures, so that reproduction happens largely through self-fertilization in hermaphrodites. C. elegans is increasingly the focus of evolutionary research; however, natural outcrossing rates are difficult to measure because mating tests with laboratory strains are usually required to identify C. elegans. We sampled natural populations of C. elegans with an RNA interference (RNAi) assay. Heterozygosities and polymorphism patterns revealed surprisingly high levels of population structure and outcrossing (approximately 22% of individuals are estimated to be the result of outcrossing and not self-fertilization). The finding of strong local population structure, together with low levels of diversity on local and global scales, suggests a metapopulation model of frequent extinction and recolonization of local populations. The occurrence of substantial outcrossing suggests that the extinction of local populations is probably not driven by the accumulation of harmful mutations.

Adenosine Triphosphatases↗
PubMed2005

On the number of New World founders: a population genetic portrait of the peopling of the Americas.

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

Asia↗
PubMed2005

On the origin of Lake Malawi cichlid species: a population genetic analysis of divergence.

The cichlid fishes of Lake Malawi are famously diverse. However, phylogenetic and population genetic studies of their history have been difficult because of the great amount of genetic variation that is shared between species. We apply a recently developed method for fitting the "isolation with migration" divergence model to a data set of specially designed compound loci to develop portraits of cichlid species divergence. Outgroup sequences from a cichlid from Lake Tanganyika permit model parameter estimates in units of years and effective population sizes. Estimated speciation times range from 1,000 to 17,000 years for species in the genus Tropheops. These exceptionally recent dates suggest that Malawi cichlids as a group experience a very active and dynamic diversification process. Current effective population size estimates range form 2,000 to near 40,000, and to >120,000 for estimates of ancestral population sizes. It appears that very recent speciation and gene flow are among the reasons why it has been difficult to discern the phylogenetic history of Malawi cichlids.

Animals↗
PubMed2004

Divergence population genetics of chimpanzees.

The divergence of two subspecies of common chimpanzees (Pan troglodytes troglodytes and P. t. verus) and the bonobo (P. paniscus) was studied using a recently developed method for analyzing population divergence. Under the isolation with migration model, the posterior probability distributions of divergence time, migration rates, and effective population sizes were estimated for large multilocus DNA sequence data sets drawn from the literature. The bonobo and the common chimpanzee are estimated to have diverged approximately 0.86 to 0.89 MYA, and the divergence of the two common chimpanzee subspecies is estimated to have occurred 0.42 MYA. P. t. troglodytes appears to have had a larger effective population size (22,400 to 27,900) compared with P. paniscus, P. t. verus, and the ancestral populations of these species. No evidence of gene flow was found in the comparisons involving P. paniscus; however a clear signal of unidirectional gene flow was found from P. t. verus to P. t. troglodytes (2Nm = 0.51).

Animals↗
PubMed2004

Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species.

When populations or species have recently separated they often share genetic variation. However, it can be difficult to determine whether shared polymorphisms are the result of gene flow, the result of the persistence of variation in both populations since the time of common ancestry, or both of these factors. We have developed an empirical protocol for using loci that include unique nuclear DNA sequence haplotypes together with linked microsatellites or short tandem repeats (STRs). These 'HapSTRs' offer the potentially high resolution associated with the high mutation rate of STRs, together with the advantages of low homoplasy of unique sequence DNA. We also describe a new procedure for estimating the likelihood of HapSTR data under an Isolation with Migration model. An example using Cichlid fishes from Lake Malawi is described. The analysis suggests that the species have been exchanging genes since the time they began to diverge.

Animals↗
PubMed2004

Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.

The genetic study of diverging, closely related populations is required for basic questions on demography and speciation, as well as for biodiversity and conservation research. However, it is often unclear whether divergence is due simply to separation or whether populations have also experienced gene flow. These questions can be addressed with a full model of population separation with gene flow, by applying a Markov chain Monte Carlo method for estimating the posterior probability distribution of model parameters. We have generalized this method and made it applicable to data from multiple unlinked loci. These loci can vary in their modes of inheritance, and inheritance scalars can be implemented either as constants or as parameters to be estimated. By treating inheritance scalars as parameters it is also possible to address variation among loci in the impact via linkage of recurrent selective sweeps or background selection. These methods are applied to a large multilocus data set from Drosophila pseudoobscura and D. persimilis. The species are estimated to have diverged approximately 500,000 years ago. Several loci have nonzero estimates of gene flow since the initial separation of the species, with considerable variation in gene flow estimates among loci, in both directions between the species.

Animals↗
PubMed2003

The causes of phylogenetic conflict in a classic Drosophila species group.

Bifurcating phylogenies are frequently used to describe the evolutionary history of groups of related species. However, simple bifurcating models may poorly represent the evolutionary history of species that have been exchanging genes. Here, we show that the history of three well-known closely related species, Drosophila pseudoobscura, D. persimilis and D. p. bogotana, is not well represented by a bifurcating phylogenetic tree. The phylogenetic relationships among these species vary widely between different genomic regions. Much of this phylogenetic variation can be explained by the potential of different genomic regions to introgress between species, as measured in laboratory studies. We argue that the utility of multiple markers in species-level phylogenetic studies can be greatly enhanced by knowledge of genomic location and, in the case of hybridizing species, by knowledge of the functional or linkage relationships among the markers and regions of the genome that reduce hybrid fitness.

Animals↗
PubMed2003

Speciation and inversions: chimps and humans.

A new set of models has resurrected a role for chromosomal inversions in the formation of new species. Traditional models, which are generally considered to be unlikely in most cases, had imagined that inversions might aid speciation by directly causing low hybrid fitness. In contrast, the newer models focus on the effect that inversions have on local recombination rates. A test of these models found a strikingly high rate of amino-acid substitution within regions where humans and chimpanzees differ by inversions, suggesting perhaps that our ancestral species underwent a divergence process in which gene flow and inversions played a key role. However, it remains uncertain whether this interesting finding is actually consistent with the proposed model.

Animals↗
PubMed2003

Hill-Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud and Duret.

The usage of preferred codons in Drosophila melanogaster is reduced in regions of lower recombination. This is consistent with population genetics theory, whereby the effectiveness of selection on multiple targets is limited by stochastic effects caused by linkage. However, because the selectively preferred codons in D. melanogaster end in C or G, it has been argued that base-composition-biasing effects of recombination can account for the observed relationship between preferred codon usage and recombination rate (Marais et al., 2003). Here, we show that the correlation between base composition (of protein-coding and intron regions) and recombination rate holds only for lower values of the latter. This is consistent with a Hill-Robertson interference model and does not support a model whereby the entire effect of recombination on codon usage can be attributed to its potential role in generating compositional bias.

Animals↗
PubMed2003

The study of structured populations--new hope for a difficult and divided science.

Natural populations, including those of humans, have complex geographies and histories. Studying how they evolve is difficult, but it is possible with population-based DNA sequence data. However, the study of structured populations is divided by two distinct schools of thought and analysis. The phylogeographic approach is fundamentally graphical and begins with a gene-tree estimate. By contrast, the more traditional approach of using summary statistics is fundamentally mathematical. Both approaches have limitations, but there is promise in newer probabilistic methods that offer the flexibility and data exploitation of the phylogeographic approach in an explicitly model-based mathematical framework.

Animals↗
PubMed2003

Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species.

Caenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

Animals↗
PubMed2002

Interactions between natural selection, recombination and gene density in the genes of Drosophila.

In Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination--as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation. The same reasoning leads to the expectation that the efficiency of selection, and thus average codon bias, should decline with gene density. However, this prediction is not confirmed. Levels of codon bias and gene expression are highest for those genes in an intermediate range of gene density, a pattern that may be the result of a tradeoff between the advantages for gene expression of close gene spacing and disadvantages arising from regulatory conflicts among tightly packed genes. These factors appear to overlay the more subtle effect of linkage among selected sites that gives rise to the association between recombination rate and codon bias.

Animals↗