The role of standing variation in geographic convergent adaptation

The role of standing variation in geographic convergent adaptation
Peter L. Ralph, Graham Coop
doi: http://dx.doi.org/10.1101/009803

The extent to which populations experiencing shared selective pressures adapt through a shared genetic response is relevant to many questions in evolutionary biology. In a number of well studied traits and species, it appears that convergent evolution within species is common. In this paper, we explore how standing, deleterious genetic variation contributes to convergent genetic responses in a geographically spread population, extending our previous work on the topic. Geographically limited dispersal slows the spread of each selected allele, hence allowing other alleles — newly arisen mutants or present as standing variation — to spread before any one comes to dominate the population. When such alleles meet, their progress is substantially slowed — if the alleles are selectively equivalent, they mix slowly, dividing the species range into a random tessellation, which can be well understood by analogy to a Poisson process model of crystallization. In this framework, we derive the geographic scale over which a typical allele is expected to dominate, the time it takes the species to adapt as a whole, and the proportion of adaptive alleles that arise from standing variation. Finally, we explore how negative pleiotropic effects of alleles before an environment change can bias the subset of alleles that get to contribute to a species adaptive response. We apply the results to the many geographically localized G6PD deficiency alleles thought to confer resistance to malaria, whose large mutational target size and deleterious effects make them likely candidates to have been present as deleterious standing variation. We find the numbers and geographic spread of these alleles matches our predictions reasonably well, which suggest that these arose both from standing variation and new mutations since the advent of malaria. Our results suggest that much of adaptation may be geographically local even when selection pressures are wide-spread. We close by discussing the implications of these results for arguments of species coherence and the nature of divergence between species.

Thinking too positive? Revisiting current methods of population-genetic selection inference

Thinking too positive? Revisiting current methods of population-genetic selection inference
Claudia Bank, Gregory B Ewing, Anna Ferrer-Admettla, Matthieu Foll, Jeffrey D Jensen
doi: http://dx.doi.org/10.1101/009654

In the age of next-generation sequencing, the availability of increasing amounts and quality of data at decreasing cost ought to allow for a better understanding of how natural selection is shaping the genome than ever before. Yet, alternative forces such as demography and background selection obscure the footprints of positive selection that we would like to identify. Here, we illustrate recent developments in this area, and outline a roadmap for improved selection inference. We argue (1) that the development and obligatory use of advanced simulation tools is necessary for improved identification of selected loci, (2) that genomic information from multiple- time points will enhance the power of inference, and (3) that results from experimental evolution should be utilized to better inform population-genomic studies.

On the prospect of identifying adaptive loci in recently bottlenecked populations

On the prospect of identifying adaptive loci in recently bottlenecked populations
Yu-Ping Poh, Vera S Domingues, Hopi Hoekstra, Jeffrey Jensen
doi: http://dx.doi.org/10.1101/009456

Identifying adaptively important loci in recently bottlenecked populations—be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed—remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.

On the unfounded enthusiasm for soft selective sweeps

On the unfounded enthusiasm for soft selective sweeps
Jeffrey D. Jensen
doi: http://dx.doi.org/10.1101/009563

Underlying any understanding of the mode, tempo, and relative importance of the adaptive process in the evolution of natural populations is the notion of whether adaptation is mutation-limited. Two very different population genetic models have recently been proposed in which the rate of adaptation is not strongly limited by the rate at which newly arising beneficial mutations enter the population. This review discusses the theoretical underpinnings and requirements of these models, as well as the experimental insights on the parameters of relevance. Importantly, empirical and experimental evidence to date challenges the recent enthusiasm for invoking these models to explain observed patterns of variation in humans and Drosophila.

Origins and impacts of new exons

Origins and impacts of new exons
Jason Merkin*, Ping Chen*, Sampsa Hautaniemi, Christopher Burge
doi: http://dx.doi.org/10.1101/009282

Mammalian genes are typically broken into several protein-coding and non-coding exons, but the evolutionary origins and functions of new exons are not well understood. Here, we analyzed patterns of exon gain using deep cDNA sequencing data from several mammals and one bird, identifying thousands of species- and lineage-specific exons. While exons conserved across mammals are mostly protein-coding and constitutively spliced, species-specific exons were mostly located in 5′ untranslated regions and alternatively spliced. New exons most often derived from unique intronic sequence rather than repetitive elements, and were associated with upstream intronic deletions, increased nucleosome occupancy and RNA polymerase II pausing. Surprisingly, exon gain was associated with increased gene expression, but only in tissues where the exon was included, suggesting that splicing enhances steady-state mRNA levels and that changes in splicing represent a major contributor to the evolution of gene expression.

Different tastes for different individuals

Different tastes for different individuals
Kohei Fujikura
doi: http://dx.doi.org/10.1101/009357

Individual taste differences were first reported in the first half of the 20th century, but the primary reasons for these differences have remained uncertain. Much of the taste variation among different mammalian species can be explained by pseudogenization of taste receptors. In this study, by analyzing 14 ethnically diverse populations, we investigated whether the most recent disruptions of taste receptor genes segregate with their intact forms. Our results revealed an unprecedented prevalence of segregating loss-of-function (LoF) taste receptor variants, identifying one of the most pronounced cases of functional population diversity in the human genome. LoF variant frequency was considerably higher than the overall mutation rate, and many humans harbored varying numbers of critical mutations. In particular, molecular evolutionary rates of sour and bitter receptors were far higher in humans than those of sweet, salty, and umami receptors compared with other carnivorous mammals although not all of the taste receptors genes were identified. Many LoF variants are population-specific, some of which arose even after the population differentiation, but not before divergence of the modern and archaic (Neanderthal and Denisovan) human. Based on these findings, we conclude that modern humans might have been losing their taste receptor genes because of high-frequency LoF taste receptor variants. Finally I actually demonstrated the genetic testing of taste receptors from personal exome sequence.

The genetic ancestry of African, Latino, and European Americans across the United States.

The genetic ancestry of African, Latino, and European Americans across the United States.
Katarzyna Bryc, Eric Durand, J Michael Macpherson, David Reich, Joanna Mountain
doi: http://dx.doi.org/10.1101/009340

Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans brought largely by the Trans-Atlantic slave trade, shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relocation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States, and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry.