Dataset Information

Global adaptation complicates the interpretation of genome scans for local adaptation.

ABSTRACT: Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome-wide distribution of summary statistics measuring genetic differentiation, such as F_ST , are often interpreted as evidence for alleles that contribute to local adaptation. However, theoretical studies have shown that in spatially structured populations the spread of beneficial mutations with spatially uniform fitness effects can also induce transient genetic differentiation. In recent years, numerous empirical studies have suggested that such species-wide, or global, adaptation makes a substantial contribution to molecular evolution. In this perspective, we discuss how commonly such global adaptation may influence the genome-wide distribution of F_ST and generate genetic differentiation patterns, which could be mistaken for local adaptation. To illustrate this, we use forward-in-time population genetic simulations assuming parameters for the rate and strength of beneficial mutations consistent with estimates from natural populations. We demonstrate that the spread of globally beneficial mutations in parapatric populations may frequently generate F_ST outliers, which could be misinterpreted as evidence for local adaptation. The spread of beneficial mutations causes selective sweeps at flanking sites, so in some cases, the effects of global versus local adaptation may be distinguished by examining patterns of nucleotide diversity within and between populations in addition to F_ST . However, when local adaptation has been only recently established, it may be much more difficult to distinguish from global adaptation, due to less accumulation of linkage disequilibrium at flanking sites. Through our discussion, we conclude that a large fraction of F_ST outliers that are presumed to arise from local adaptation may instead be due to global adaptation.

SUBMITTER: Booker TR

PROVIDER: S-EPMC7857299 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Global adaptation complicates the interpretation of genome scans for local adaptation.

Booker Tom R TR Yeaman Sam S Whitlock Michael C MC

Evolution letters 20201215 1

Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome-wide distribution of summary statistics measuring genetic differentiation, such as <i>F<sub>ST</sub></i> , are often interpreted as evidence for alleles that contribute to local adaptation. However, theoretical studies have shown that in spatially structured populations the spread of beneficial mutations with spatia ...[more]

PMID: 33552532

Similar Datasets

Project description:Prolonged exposure to an oriented line shifts the perceived orientation of a subsequently observed line in the opposite direction, a phenomenon known as the tilt aftereffect (TAE). Here we consider whether the TAE for line stimuli is mediated by a mechanism that integrates the local parts of the line into a single global entity prior to the site of adaptation, or the result of the sum of local TAEs acting separately on the parts of the line. To test between these two alternatives we used the fact the TAE transfers almost completely across luminance contrast polarity [1]. We measured the TAE using adaptor and test lines that (1) either alternated in luminance polarity or were of a single polarity, and (2) either alternated in local orientation or were of a single orientation. We reasoned that if the TAE was agnostic to luminance polarity and was parts-based, we should obtain large TAEs using alternating-polarity adaptors with single-polarity tests. However we found that (i) TAEs using one-alternating-polarity adaptors with all-white tests were relatively small, increased slightly for two-alternating-polarity adaptors, and were largest with all-white or all-black adaptors. (ii) however TAEs were relatively large when the test was one-alternating polarity, irrespective of the adaptor type. (iii) The results with orientation closely mirrored those obtained with polarity with the difference that the TAE transfer across orthogonal orientations was weak. Taken together, our results demonstrate that the TAE for lines is mediated by a global shape mechanism that integrates the parts of lines into whole prior to the site of orientation adaptation. The asymmetry in the magnitude of TAE depending on whether the alternating-polarity lines was the adaptor or test can be explained by an imbalance in the population of neurons sensitive to 1(st)-and 2(nd)-order lines, with the 2(nd)-order lines being encoded by a subset of the mechanisms sensitive to 1(st)-order lines.

Project description:Smallholder farming systems are vulnerable to a number of challenges, including continued population growth, urbanization, income disparities, land degradation, decreasing farm size and productivity, all of which are compounded by uncertainty of climatic patterns. Understanding determinants of smallholder farming practices is critical for designing and implementing successful interventions, including climate change adaptation programs. We examine two dimensions wherein smallholder farmers may adapt agricultural practices; through intensification (i.e., adopt more practices) or diversification (i.e. adopt different practices). We use data on 5314 randomly sampled households located in 38 sites in 15 countries across four regions (East and West Africa, South Asia, and Central America). We estimate empirical models designed to assess determinants of both intensification and diversification of adaptation activities at global scales. Aspects of adaptive capacity that are found to increase intensification of adaptation globally include variables associated with access to information and human capital, financial considerations, assets, household infrastructure and experience. In contrast, there are few global drivers of adaptive diversification, with a notable exception being access to weather information, which also increases adaptive intensification. Investigating reasons for adaptation indicate that conditions present in underdeveloped markets provide the primary impetus for adaptation, even in the context of climate change. We also compare determinants across spatial scales, which reveals a variety of local avenues through which policy interventions can relax economic constraints and boost agricultural adaptation for both intensification and diversification. For example, access to weather information does not affect intensification adaptation in Africa, but is significant at several sites in Bangladesh and India. Moreover, this information leads to diversification of adaptive activities on some sites in South Asia and Central America, but increases specialization in West and East Africa.

Dataset Information

Global adaptation complicates the interpretation of genome scans for local adaptation.

Publications

Global adaptation complicates the interpretation of genome scans for local adaptation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets