Impacts of genetic correlation on the independent evolution of body mass and skeletal size in mammals

Marchini, Marta; Sparrow, Leah M.; Cosman, Miranda N; Dowhanik, Alexandra; Krueger, Carsten; Hallgrímsson, Benedikt; Rolian, Campbell

doi:10.1186/preaccept-8844566431425109

Cited by 6 publications

(7 citation statements)

References 52 publications

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“…To test this concept, we performed haplotagging on 245 "Longshanks" mice from a 20-generation selective-breeding experiment for long tibia length (12,13). We sequenced these mice to an average depth of 0.24× and phased the data using STITCH.…”

Section: Resultsmentioning

confidence: 99%

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

Meier

Salazar

Kučka

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present “haplotagging,” a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.

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Section: Resultsmentioning

confidence: 99%

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

Meier

Salazar

Kučka

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…Next, we reanalyzed the Longshanks selection experiment, which selected for longer tibiae length relative to body size in mice, leading to a response to selection of about 5 standard deviations over the course of twenty generations (Castro et al 2019;Marchini et al 2014). This study includes two independent selection lines, Longshanks 1 and 2 (LS1 and LS2), and an unselected control line (Ctrl) where parents were randomly selected.…”

Section: Resultsmentioning

confidence: 99%

Estimating the genome-wide contribution of selection to temporal allele frequency change

Buffalo

Coop

2020

Proc. Natl. Acad. Sci. U.S.A.

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Rapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data (e.g., evolve-and-resequence studies). These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one time point to be predictive of the changes at later time points, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time points and across replicates. We estimate that at least 17 to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances, we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.

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“…The G matrix has received much attention on the grounds that it constrains adaptation. However, artificial selection has proved successful even when deliberately applied to trait combinations that show minimal variance (see, for example, Weber et al, 1999;Hill and Kirkpatrick, 2010;Marchini et al, 2014): as long as there is some additive variance in the direction of selection, selection can change the mean. Of course, the G matrix has very high dimension, and some directions may have zero variance (that is, there may be some zero eigenvalues).…”

Section: Directional Selectionmentioning

confidence: 99%

How does epistasis influence the response to selection?

Barton

2016

Heredity

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Much of quantitative genetics is based on the 'infinitesimal model', under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited tõ 4N e by the 'drift load', and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large N e s, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.

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Impacts of genetic correlation on the independent evolution of body mass and skeletal size in mammals

Cited by 6 publications

References 52 publications

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

Estimating the genome-wide contribution of selection to temporal allele frequency change

How does epistasis influence the response to selection?

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