Demography and selection shape transcriptomic divergence in field crickets

Blankers, Thomas; Vilaça, Sibelle Torres; Waurick, Isabelle; Gray, David A.; Hennig, R. Matthias; Mazzoni, Camila J.; Mayer, Frieder; Berdan, Emma L.

doi:10.1111/evo.13435

Cited by 9 publications

(7 citation statements)

References 98 publications

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“…2008; Blankers et al. 2018). Some signatures of sexual antagonism may be associated with genomic signatures of selective sweeps or balancing selection (Cheng and Kirkpatrick 2016; Wright et al.…”

Section: Discussionmentioning

confidence: 99%

Experimental evolution supports signatures of sexual selection in genomic divergence

et al. 2021

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Comparative genomics has contributed to the growing evidence that sexual selection is an important component of evolutionary divergence and speciation. Divergence by sexual selection is implicated in faster rates of divergence of the X chromosome and of genes thought to underlie sexually selected traits, including genes that are sex biased in expression. However, accurately inferring the relative importance of complex and interacting forms of natural selection, demography, and neutral processes that occurred in the evolutionary past is challenging. Experimental evolution provides an opportunity to apply controlled treatments for multiple generations and examine the consequent genomic divergence. Here, we altered sexual selection intensity, elevating sexual selection in polyandrous lines and eliminating it in monogamous lines, and examined patterns of allele frequency divergence in the genome of Drosophila pseudoobscura after more than 160 generations of experimental evolution. Divergence is not uniform across the genome but concentrated in “islands,” many of which contain candidate genes implicated in mating behaviors and other sexually selected phenotypes. These are more often seen on the X chromosome, which also shows greater divergence in FST than neutral expectations. There are characteristic signatures of selection seen in these regions, with lower diversity on the X chromosome than the autosomes, and differences in diversity on the autosomes between selection regimes. Reduced Tajima's D within some of the divergent regions may imply that selective sweeps have occurred, despite considerable recombination. These changes are associated with both differential gene expression between the lines and sex‐biased gene expression within the lines. Our results are very similar to those thought to implicate sexual selection in divergence between species and natural populations, and hence provide experimental support for the likely role of sexual selection in driving such types of genetic divergence, but also illustrate how variable outcomes can be for different genomic regions.

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Section: Discussionmentioning

confidence: 99%

Experimental evolution supports signatures of sexual selection in genomic divergence

et al. 2021

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“…Sex-biased gene expression, especially male-bias, evolves quickly and is related to phenotypic sexual dimorphism (Wright et al, 2019). Outliers in genome scans often implicate sexual selection as a diversifying force (Andres et al, 2008;Blankers et al, 2018). Sexual antagonism may be associated with genomic signatures of selective sweeps or balancing selection (Cheng & Kirkpatrick, 2016;Wright et al, 2019) and may be promoted by strong sexual selection (Connallon & Clark, 2012;2013;Dutoit et al, 2018;Ruzicka et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Experimental evolution supports signatures of sexual selection in genomic divergence

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et al. 2020

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Comparative genomics has contributed to the growing evidence that sexual selection is an important component of evolutionary divergence and speciation. Divergence by sexual selection is implicated in faster rates of divergence of the X chromosome and of genes thought to underlie sexually selected traits, including genes that are sex-biased in expression. However, accurately inferring the relative importance of complex and interacting forms of natural selection, demography and neutral processes which occurred in the evolutionary past is challenging. Experimental evolution provides an opportunity to apply controlled treatments for multiple generations and examine the consequences for genomic divergence. Here we altered sexual selection intensity, elevating sexual selection in polyandrous lines and eliminating it in monogamous lines, and examined patterns of divergence in the genome of Drosophila pseudoobscura after more than 160 generations of experimental evolution. Divergence is not uniform across the genome but concentrated in "islands", many of which contain candidate genes implicated in mating behaviours and other sexually selected phenotypes. These are more often seen on the X chromosome, which overall shows divergence above neutral expectations. There are also characteristic signatures of selection seen in these regions, with lower diversity and greater Fst on the X chromosome than the autosomes, and differences in diversity on the autosomes between selection regimes. Reduced Tajima's D implies that selective sweeps have occurred within the divergent regions, despite considerable recombination. These changes are associated with both differential gene expression between the lines and sex-biased gene expression within the lines. Our results are very similar to those thought to implicate sexual selection in divergence in natural populations, and hence provide experimental confirmation of the likely role of sexual selection in driving such types of genetic divergence, but also illustrate how variable outcomes can be for different genomic regions.

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“…To test more complex models incorporating multiple demographic events, we took an iterative approach (Blankers et al., 2018; Nater et al., 2015; Pelletier & Carstens, 2014). After ordering all of the simple models by AIC, we combined the two best‐performing models and optimized the new two‐event model.…”

Section: Methodsmentioning

confidence: 99%

Evidence for the Pleistocene Arc Hypothesis from genome‐wide SNPs in a Neotropical dry forest specialist, the Rufous‐fronted Thornbird (Furnariidae: Phacellodomus rufifrons)

et al. 2020

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South American dry forests have a complex and poorly understood biogeographic history. Based on the fragmented distribution of many Neotropical dry forest species, it has been suggested that this biome was more widely distributed and contiguous under drier climate conditions in the Pleistocene. To test this scenario, known as the Pleistocene Arc Hypothesis, we studied the phylogeography of the Rufous‐fronted Thornbird (Phacellodomus rufifrons), a widespread dry forest bird with a disjunct distribution closely matching that of the biome itself. We sequenced mtDNA and used ddRADseq to sample 7,167 genome‐wide single‐nucleotide polymorphisms from 74 P. rufifrons individuals across its range. We found low genetic differentiation over two prominent geographic breaks — particularly across a 1,000 km gap between populations in Bolivia and Northern Peru. Using demographic analyses of the joint site frequency spectrum, we found evidence of recent divergence without subsequent gene flow across those breaks. By contrast, parapatric morphologically distinct populations in northeastern Brazil show high genetic divergence with evidence of recent gene flow. These results, in combination with our paleoclimate species distribution modelling, support the idea that currently disjunct patches of dry forest were more connected in the recent past, probably during the Middle and Late Pleistocene. This notion fits the major predictions of the Pleistocene Arc Hypothesis and illustrates the importance of comprehensive genomic and geographic sampling for examining biogeographic and evolutionary questions in complex ecosystems like Neotropical dry forests.

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Demography and selection shape transcriptomic divergence in field crickets

Cited by 9 publications

References 98 publications

Experimental evolution supports signatures of sexual selection in genomic divergence

Experimental evolution supports signatures of sexual selection in genomic divergence

Experimental evolution supports signatures of sexual selection in genomic divergence

Evidence for the Pleistocene Arc Hypothesis from genome‐wide SNPs in a Neotropical dry forest specialist, the Rufous‐fronted Thornbird (Furnariidae: Phacellodomus rufifrons)

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