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

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.

scholarly journals Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Megan Phifer-Rixey ◽  
Bettina Harr ◽  
Jody Hey
Keyword(s):  
Gene Flow ◽  
Mus Musculus ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
House Mice ◽  
Mus Musculus Domesticus ◽  
Effective Population ◽  
Isolation With Migration ◽  
Mus Musculus Musculus ◽  
History Of

Abstract Background The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. Results Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, Ne, of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short. Conclusions Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.

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

2014 ◽  
Vol 80 (5) ◽  
pp. 834-847 ◽  
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

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

2017 ◽  
Author(s):  
Qixin He ◽  
L. Lacey Knowles
Keyword(s):  
Gene Flow ◽  
Environmental Changes ◽  
Point Mutations ◽  
Secondary Contact ◽  
Adaptive Divergence ◽  
Clear Understanding ◽  
Rapid Adaptation ◽  
Chromosomal Inversions ◽  
Divergence With Gene Flow ◽  
New Mutations

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.

scholarly journals Accounting for Gene Flow from Unsampled ‘Ghost’ Populations while Estimating Evolutionay History under the Isolation with Migration Model

2019 ◽  
Author(s):  
Arun Sethuraman ◽  
Melissa Lynch
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Population Genomics ◽  
Divergence Times ◽  
Effective Population ◽  
Migration Rates ◽  
Isolation With Migration ◽  
Population Sizes ◽  
And Migration ◽  
Erroneous Inferences

AbstractUnsampled or extinct ‘ghost’ populations leave signatures on the genomes of individuals from extant, sampled populations, especially if they have exchanged genes with them over evolutionary time. This gene flow from ‘ghost’ populations can introduce biases when estimating evolutionary history from genomic data, often leading to data misinterpretation and ambiguous results. Here we assess these biases while accounting, or not accounting for gene flow from ‘ghost’ populations under the Isolation with Migration (IM) model. We perform extensive simulations under five scenarios with no gene flow (Scenario A), to extensive gene flow to- and from- an unsampled ‘ghost’ population (Scenarios B, C, D, and E). Estimates of evolutionary history across all scenarios A-E (effective population sizes, divergence times, and migration rates) indicate consistent a) under-estimation of divergence times between sampled populations, (b) over-estimation of effective population sizes of sampled populations, and (c) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ‘ghost’ population. Without accounting for an unsampled ‘ghost’, summary statistics like FST are under-estimated, and π is over-estimated with increased gene flow from the‘ghost’. To show this persistent issue in empirical data, we use a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ‘ghosts’. Considering the large effects of gene flow from these ‘ghosts’, we propose a multi-pronged approach to account for the presence of unsampled ‘ghost’ populations in population genomics studies to reduce erroneous inferences.

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

Genes ◽  
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.

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

The Auk ◽  
2019 ◽  
Vol 136 (4) ◽  
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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