Rapid adaptation with gene flow via a reservoir of chromosomal inversion variation?

AbstractThe increased recognition of frequent divergence with gene flow has renewed interest in chromosomal inversions as a source for promoting adaptive divergence. Inversions can suppress recombination between heterokaryotypes so that local adapted inversions will be protected from introgression with the migrants. However, we do not have a clear understanding of the conditions for which adaptive divergence is more or less likely to be promoted by inversions when the availability of inversion variation is considered. Standing genetic variation, as opposed to new mutations, could offer a quick way to respond to sudden environmental changes, making it a likely avenue for rapid adaptation. For a scenario of secondary contact between locally-adapted populations, we might intuit that standing inversion variation would predominate over new inversion mutations in maintaining local divergence. Our results show that this is not always the case. Maladaptive gene flow, as both a demographic parameter and the cause for selection that favors locally-adapted inversions, differentiates the dynamics of standing inversion variation from that of segregating point mutations. Counterintuitively, in general, standing inversion variation will be less important to the adaptation than new inversions under the demographic and genetic conditions that are more conducive to adaptive divergence via inversions.

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Rapid, ultra-local adaptation facilitated by phenotypic plasticity

10.1101/598292 ◽

2019 ◽

Author(s):

Syuan-Jyun Sun ◽

Andrew M. Catherall ◽

Sonia Pascoal ◽

Benjamin J. M. Jarrett ◽

Sara E. Miller ◽

...

Keyword(s):

Gene Flow ◽

Rapid Evolution ◽

Reaction Norm ◽

Ancestral Population ◽

Adaptive Divergence ◽

Wild Populations ◽

Rapid Adaptation ◽

Burying Beetles ◽

Genetic Accommodation ◽

Nicrophorus Vespilloides

AbstractModels of ‘plasticity-first’ evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can still facilitate rapid evolution when diverging populations are connected by gene flow. Here we show how plasticity has generated adaptive divergence in fecundity in wild populations of burying beetlesNicrophorus vespilloides, which are still connected by gene flow, which occupy distinct Cambridgeshire woodlands that are just 2.5km apart and which diverged from a common ancestral population c. 1000-4000 years ago. We show that adaptive divergence is duetothe coupling of an evolved increase in the elevation of the reaction norm linking clutch size to carrion size (i.e. genetic accommodation) with plastic secondary elimination of surplus offspring. Working in combination, these two processes have facilitated rapid adaptation to fine-scale environmental differences, despite ongoing gene flow.

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Faster-X adaptive differentiation under divergence-with-gene-flow in diploids and haplodiploids

10.1101/2021.04.09.439183 ◽

2021 ◽

Author(s):

Emily E. Bendall ◽

Robin Bagley ◽

Catherine R. Linnen ◽

Vitor C. Sousa

Keyword(s):

Gene Flow ◽

Meta Analysis ◽

Stochastic Simulations ◽

Adaptive Divergence ◽

Effective Population ◽

Isolation With Migration ◽

Demographic Modeling ◽

Novel Approach ◽

Divergence With Gene Flow ◽

Adaptive Differentiation

AbstractEmpirical data from diverse taxa indicate that the hemizygous portions of the genome (X/Z chromosomes) evolve more rapidly than their diploid counterparts. Faster-X theory predicts increased rates of adaptive substitutions between isolated species, yet little is known about species experiencing gene flow. Here we investigate how hemizygosity impacts genome-wide patterns of differentiation during adaptive divergence with gene flow, combining simulations under isolation-with-migration models, a meta-analysis of autosomes and sex-chromosomes from diverse taxa, and analysis of haplodiploid species. First, using deterministic and stochastic simulations, we show that elevated differentiation at hemizygous loci occurs when there is gene flow, irrespective of dominance. This faster-X adaptive differentiation stems from more efficient selection resulting in reduced probability of losing the beneficial allele, greater migration-selection threshold, greater allele frequency differences at equilibrium, and a faster time to equilibrium. Second, by simulating neutral variation linked to selected loci, we show that faster-X differentiation affects linked variation due to reduced opportunities for recombination between locally adaptive and maladaptive immigrant haplotypes. Third, after correcting for expected differences in effective population size, we find that most taxon pairs (24 out of 28) exhibit faster-X differentiation in the meta-analysis. Finally, using a novel approach combining demographic modeling and simulations, we found evidence for faster-X differentiation in haplodiploid pine-feeding hymenopteran species adapted to different host plants. Together, our results indicate that divergent selection with gene flow can lead to higher differentiation at selected and linked variation in hemizygous loci (i.e., faster-X adaptive differentiation), both in X/Z-chromosomes and haplodiploid species.

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Adaptive divergence with gene flow in incipient speciation ofMiscanthus floridulus/sinensiscomplex (Poaceae)

The Plant Journal ◽

10.1111/tpj.12676 ◽

2014 ◽

Vol 80 (5) ◽

pp. 834-847 ◽

Cited By ~ 10

Author(s):

Chao-Li Huang ◽

Chuan-Wen Ho ◽

Yu-Chung Chiang ◽

Yasumasa Shigemoto ◽

Tsai-Wen Hsu ◽

...

Keyword(s):

Gene Flow ◽

Adaptive Divergence ◽

Incipient Speciation ◽

Divergence With Gene Flow

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Genomic impacts of chromosomal inversions in parapatric Drosophila species

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0250 ◽

2012 ◽

Vol 367 (1587) ◽

pp. 422-429 ◽

Cited By ~ 92

Author(s):

Suzanne E. McGaugh ◽

Mohamed A. F. Noor

Keyword(s):

Gene Flow ◽

Secondary Contact ◽

Chromosome 2 ◽

Chromosomal Inversions ◽

The Face ◽

Flow Through ◽

Drosophila Persimilis ◽

Suppressed Recombination ◽

Or Gene ◽

Double Crossovers

Chromosomal inversions impact genetic variation and facilitate speciation in part by reducing recombination in heterokaryotypes. We generated multiple whole-genome shotgun sequences of the parapatric species pair Drosophila pseudoobscura and Drosophila persimilis and their sympatric outgroup ( Drosophila miranda ) and compared the average pairwise differences for neutral sites within, just outside and far outside of the three large inversions. Divergence between D. pseudoobscura and D. persimilis is high inside the inversions and in the suppressed recombination regions extending 2.5 Mb outside of inversions, but significantly lower in collinear regions further from the inversions. We observe little evidence of decreased divergence predicted to exist in the centre of inversions, suggesting that gene flow through double crossovers or gene conversion is limited within the inversion, or selection is acting within the inversion to maintain divergence in the face of gene flow. In combination with past studies, we provide evidence that inversions in this system maintain areas of high divergence in the face of hybridization, and have done so for a substantial period of time. The left arm of the X chromosome and chromosome 2 inversions appear to have arisen in the lineage leading to D. persimilis approximately 2 Ma, near the time of the split of D. persimilis–D. pseudoobscura–D. miranda , but likely fixed within D. persimilis much more recently, as diversity within D. persimilis is substantially reduced inside and near these two inversions. We also hypothesize that the inversions in D. persimilis may provide an empirical example of the ‘mixed geographical mode’ theory of inversion origin and fixation, whereby allopatry and secondary contact both play a role.

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Genomic signatures of isolation, hybridization, and selection during speciation of island finches

10.1101/2022.01.05.474904 ◽

2022 ◽

Author(s):

Martin Stervander ◽

Martim Melo ◽

Peter Jones ◽

Bengt Hansson

Keyword(s):

Gene Flow ◽

Introgressive Hybridization ◽

Sister Species ◽

Secondary Contact ◽

Gulf Of Guinea ◽

Island Endemic ◽

Genomic Signatures ◽

The Face ◽

Bill Morphology ◽

Divergence With Gene Flow

Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, 'giant' finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.

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Faculty Opinions recommendation of Genomic evidence for divergence with gene flow in host races of the larch budmoth.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1017881.204351 ◽

2004 ◽

Author(s):

Mohamed Noor

Keyword(s):

Gene Flow ◽

Host Races ◽

Divergence With Gene Flow

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Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species

Genes ◽

10.3390/genes12030435 ◽

2021 ◽

Vol 12 (3) ◽

pp. 435

Author(s):

Thijs M. P. Bal ◽

Alejandro Llanos-Garrido ◽

Anurag Chaturvedi ◽

Io Verdonck ◽

Bart Hellemans ◽

...

Keyword(s):

Gene Flow ◽

Brackish Water ◽

Environmental Gradient ◽

Spatial Scales ◽

Morphological Differentiation ◽

Genotyping By Sequencing ◽

Adaptive Divergence ◽

Linkage Groups ◽

Closely Related Species ◽

Genomic Patterns

There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.

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Shallow genetic divergence and distinct phenotypic differences between two Andean hummingbirds: Speciation with gene flow?

The Auk ◽

10.1093/auk/ukz046 ◽

2019 ◽

Vol 136 (4) ◽

Cited By ~ 3

Author(s):

Catalina Palacios ◽

Silvana García-R ◽

Juan Luis Parra ◽

Andrés M Cuervo ◽

F Gary Stiles ◽

...

Keyword(s):

Gene Flow ◽

Genetic Differentiation ◽

Incomplete Lineage Sorting ◽

Lineage Sorting ◽

Phenotypic Differences ◽

Adaptive Mechanisms ◽

The Face ◽

Gloger’S Rule ◽

Divergence With Gene Flow ◽

Neutral Markers

Abstract Ecological speciation can proceed despite genetic interchange when selection counteracts the homogenizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, 2 parapatric Andean hummingbirds with marked plumage divergence. We sequenced putatively neutral markers (mitochondrial DNA [mtDNA] and nuclear ultraconserved elements [UCEs]) to examine genetic structure and gene flow, and a candidate gene (MC1R) to assess its role underlying divergence in coloration. We also tested the prediction of Gloger’s rule that darker forms occur in more humid environments, and examined morphological variation to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was low in both ND2 and UCEs. Coalescent estimates of migration were consistent with divergence with gene flow, but we cannot reject incomplete lineage sorting reflecting recent speciation as an explanation for patterns of genetic variation. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in morphology. Although we reject adaptation to variation in macroclimatic conditions as a cause of divergence, speciation may have occurred in the face of gene flow driven by other ecological pressures or by sexual selection. Marked phenotypic divergence with no neutral genetic differentiation is remarkable for Neotropical birds, and makes C. helianthea and C. bonapartei an appropriate system in which to search for the genetic basis of species differences employing genomics.

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