LocalizingFSToutliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow

2012 ◽  
Vol 21 (22) ◽  
pp. 5546-5560 ◽  
Author(s):  
Sara Via ◽  
Gina Conte ◽  
Casey Mason-Foley ◽  
Kelly Mills
Keyword(s):  
Gene Flow ◽  
Gene Exchange ◽  
Qtl Map ◽  
Genomic Regions

Review Lecture Disruptive selection

1972 ◽  
Vol 182 (1067) ◽  
pp. 109-143 ◽  
Keyword(s):  
Gene Flow ◽  
Genetic Variance ◽  
Natural Populations ◽  
Disruptive Selection ◽  
Ecological Niches ◽  
Gene Exchange ◽  
Bisexual Species ◽  
Frequency Dependent ◽  
Ecological Conditions ◽  
Intermediate Phenotypes

A population is exposed to disruptive selection if more than one phenotype has optimal fitness and intermediate phenotypes have lower fitnesses. Maintenance of the two or more optima may depend upon their relative fitnesses being frequency dependent. Such selection may be expected in two contrasting types of situation. First the two or more optimal phenotypes may depend on one another as do the two sexes in a bisexual species. Secondly the optima may be set by heterogeneity of the environment. Then we may think in terms of a mosaic of ecological niches or a clinal situation, and may expect that gene flow will tend to promote convergence of the sub-populations while disruptive selection tends to promote their divergence. Disruptive selection may therefore be relevant both to the evolution and maintenance of polymorphisms and to the divergence of parts of populations one from another, under the influence of variation of ecological conditions within the range of gametic and/or zygotic dispersal. Disruptive selection has been shown to be capable of increasing phenotypic and genetic variance, of producing and maintaining polymorphisms, of causing divergence of sub-populations between which substantial gene exchange occurs, and of splitting a population into two which are genetically isolated from one another. These results are reviewed and their relevance to natural populations discussed.

scholarly journals Living on the edge: how philopatry maintains adaptive potential

2013 ◽  
Vol 280 (1763) ◽  
pp. 20130305 ◽  
Author(s):  
Victor A. Stiebens ◽  
Sonia E. Merino ◽  
Christian Roder ◽  
Frédéric J. J. Chain ◽  
Patricia L. M. Lee ◽  
...  
Keyword(s):  
Gene Flow ◽  
Positive Association ◽  
Sea Turtle ◽  
Genetic Connectivity ◽  
Small Scale ◽  
Adaptive Potential ◽  
Loggerhead Sea Turtle ◽  
Local Adaptations ◽  
Population Sizes ◽  
Genomic Regions

Without genetic variation, species cannot cope with changing environments, and evolution does not proceed. In endangered species, adaptive potential may be eroded by decreased population sizes and processes that further reduce gene flow such as philopatry and local adaptations. Here, we focused on the philopatric and endangered loggerhead sea turtle ( Caretta caretta ) nesting in Cape Verde as a model system to investigate the link between adaptive potential and philopatry. We produced a dataset of three complementary genomic regions to investigate female philopatric behaviour (mitochondrial DNA), male-mediated gene flow (microsatellites) and adaptive potential (major histocompatibility complex, MHC). Results revealed genetically distinct nesting colonies, indicating remarkably small-scale philopatric behaviour of females. Furthermore, these colonies also harboured local pools of MHC alleles, especially at the margins of the population's distribution, which are therefore important reserves of additional diversity for the population. Meanwhile, directional male-mediated gene flow from the margins of distribution sustains the adaptive potential for the entire rookery. We therefore present the first evidence for a positive association between philopatry and locally adapted genomic regions. Contrary to expectation, we propose that philopatry conserves a high adaptive potential at the margins of a distribution, while asymmetric gene flow maintains genetic connectivity with the rest of the population.

scholarly journals Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia

2017 ◽  
Author(s):  
Daniel R. Schrider ◽  
Julien Ayroles ◽  
Daniel R. Matute ◽  
Andrew D. Kern
Keyword(s):  
Machine Learning ◽  
Gene Flow ◽  
Drosophila Simulans ◽  
Supervised Machine Learning ◽  
Data Set ◽  
Learning Framework ◽  
Drosophila Sechellia ◽  
Taxonomic Groups ◽  
Genomic Regions ◽  
New Statistics

ABSTRACTHybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia.AUTHOR SUMMARYUnderstanding the extent to which species or diverged populations hybridize in nature is crucially important if we are to understand the speciation process. Accordingly numerous research groups have developed methodology for finding the genetic evidence of such introgression. In this report we develop a supervised machine learning approach for uncovering loci which have introgressed across species boundaries. We show that our method, FILET, has greater accuracy and power than competing methods in discovering introgression, and in addition can detect the directionality associated with the gene flow between species. Using whole genome sequences from Drosophila simulans and Drosophila sechellia we show that FILET discovers quite extensive introgression between these species that has occurred mostly from D. simulans to D. sechellia. Our work highlights the complex process of speciation even within a well-studied system and points to the growing importance of supervised machine learning in population genetics.

scholarly journals Chromosomal rearrangements represent modular cassettes for local adaptation across different geographic scales

2020 ◽  
Author(s):  
Claire Mérot ◽  
Emma Berdan ◽  
Hugo Cayuela ◽  
Haig Djambazian ◽  
Anne-Laure Ferchaud ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Environmental Heterogeneity ◽  
Salinity Gradient ◽  
Chromosomal Rearrangements ◽  
Fine Grained ◽  
Varying Environments ◽  
Genomic Regions ◽  
Spatially Varying ◽  
Low Coverage

AbstractAcross a species range, spatially-varying environments can drive the evolution of local adaptation. Multiples sources of environmental heterogeneity, at small and large scales, draw complex landscapes of selection which may challenge adaptation, particularly when gene flow is high. Because linkage opposes gene flow but also limits the efficiency of natural selection by contrasting pressures, the key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants like chromosomal inversions are important recombination modifiers that form massive co-segregating genomic blocks linking together alleles at numerous genes. In this study, we investigate the influence of chromosomal rearrangements on genetic variation to ask how their contribution to adaptation with gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient of 10° of latitude, a salinity gradient and across a range of heterogeneous, patchy habitats. We assembled a high-quality genome to analyse 1,446 low-coverage whole-genome sequences, and we found large non-recombining genomic regions, including putative inversions. In contrast to the collinear regions depicting extensive gene flow, inversions and low-recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. Those genomic regions were disproportionately involved in associations with environmental factors and adaptive phenotypes, albeit with contrasting patterns between the different recombination modifiers. Altogether, our results highlight the importance of recombination in shaping the selection-migration balance and show that a set of several inversions behave as modular cassettes facilitating adaptation to environmental heterogeneity at local and large scales.

scholarly journals Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence

2019 ◽  
Vol 37 (3) ◽  
pp. 668-682 ◽  
Author(s):  
Fanny E Hartmann ◽  
Ricardo C Rodríguez de la Vega ◽  
Pierre Gladieux ◽  
Wen-Juan Ma ◽  
Michael E Hood ◽  
...  
Keyword(s):  
Gene Flow ◽  
Mating Type ◽  
Sex Chromosomes ◽  
Smut Fungi ◽  
Effective Population ◽  
Closely Related Species ◽  
Fungal Mating ◽  
Anther Smut ◽  
Genomic Regions

Abstract Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.

scholarly journals Genetic boundary and gene flow between 2 parapatric subspecies of brown rats

2020 ◽  
Vol 66 (6) ◽  
pp. 677-688 ◽  
Author(s):  
Lei Zhao ◽  
Jian-Xu Zhang ◽  
Yao-Hua Zhang
Keyword(s):  
Gene Flow ◽  
Northeast China ◽  
Principal Component ◽  
Inbreeding Coefficient ◽  
Dispersal Ability ◽  
Biological Processes ◽  
Gene Exchange ◽  
Morphological Divergence ◽  
Genetic Characteristics ◽  
Genetic Boundary

Abstract Two parapatric Rattus norvegicus subspecies, R. n. humiliatus (RNH) and R. n. caraco (RNC), are classified according to morphological divergence and are mainly distributed in North and Northeast China. Here, we aimed to explore the population genetic structure, genetic boundary, and gene flow in these rats using 16 microsatellite loci. Structure analysis and principal component analysis revealed 3 ancestral clusters. We found that the intermediate cluster exhibited higher genetic diversity and a lower inbreeding coefficient than the other 2 clusters. The genetic differentiation between the 3 clusters was significant but weak, with a higher FST value being observed between the clusters on both sides. The subspecies boundary inferred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning, Inner Mongolia, and Jilin Provinces, rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin. The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern, with higher gene flow from the RNH subspecies to the RNC subspecies, constraining speciation. Such genetic characteristics might be explained by biological processes such as dispersal ability, mate choice, and dynamic lineage boundaries.

scholarly journals Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex

2017 ◽  
Vol 115 (2) ◽  
pp. E236-E243 ◽  
Author(s):  
Tao Ma ◽  
Kun Wang ◽  
Quanjun Hu ◽  
Zhenxiang Xi ◽  
Dongshi Wan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Species Complex ◽  
Populus Euphratica ◽  
Genomic Islands ◽  
Ecological Selection ◽  
Poplar Trees ◽  
Genomic Divergence ◽  
Genome Divergence ◽  
Genomic Regions ◽  
Time Of Divergence

How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

scholarly journals Selection on a pleiotropic color gene block underpins early differentiation between two warbler species

2019 ◽  
Author(s):  
Silu Wang ◽  
Sievert Rohwer ◽  
Devin R. de Zwaan ◽  
David P. L Toews ◽  
Irby J. Lovette ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Basis ◽  
Early Stage ◽  
Population Substructure ◽  
Carotenoid Pigment ◽  
Single Nucleotide ◽  
Gene Block ◽  
Genome Wide ◽  
Genomic Regions ◽  
Divergence With Gene Flow

AbstractWhen one species gradually splits into two, divergent selection on specific traits can cause peaks of differentiation in the genomic regions encoding those traits. Whether speciation is initiated by strong selection on a few genomic regions with large effects or by more diffused selection on many regions with small effects remains controversial. Differentiated phenotypes between differentiating lineages are commonly involved in reproductive isolation, thus their genetic underpinnings are key to the genomics architecture of speciation. When two species hybridize, recombination over multiple generations can help reveal the genetic regions responsible for the differentiated phenotypes against a genomic background that has been homogenized via backcrossing and introgression. We used admixture mapping to investigate genomic differentiation and the genetic basis of differentiated plumage features (relative melanin and carotenoid pigment) between hybridizing sister species in the early stage of speciation: Townsend’s (Setophaga townsendi) and Hermit warblers (S. occidentalis). We found a few narrow and dispersed divergent regions between allopatric parental populations, consistent with the ‘divergence with gene flow’ model of speciation. One of the divergent peaks involves three genes known to affect pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). After controlling for population substructure, we found that a single nucleotide polymorphism (SNP) inside the intron of RALY displays a strong pleiotropic association with cheek, crown, and breast coloration. In addition, we detect selection on the ASIP-RALY gene block, as the geographic cline of the RALY marker of this gene block has remained narrower than the plumage cline, which remained narrower than expected under neutral diffusion over two decades. Despite extensive gene flow between these species across much of the genome, the selection on ASIP-RALY gene block maintains stable genotypic and plumage difference between species allowing further differentiation to accumulate via linkage to its flanking genetic region or linkage-disequilibrium genome-wide.

scholarly journals Recombination, variance in genetic relatedness, and selection against introgressed DNA

2019 ◽  
Author(s):  
Carl Veller ◽  
Nathaniel B. Edelman ◽  
Pavitra Muralidhar ◽  
Martin A. Nowak
Keyword(s):  
Gene Flow ◽  
Genetic Relatedness ◽  
Hybrid Vigor ◽  
Recombination Rates ◽  
Deleterious Alleles ◽  
Genome Wide ◽  
Average Proportion ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Hybrid Cross

AbstractThe genomic proportion that two relatives share identically by descent—their genetic relatedness—can vary depending on the patterns of recombination and segregation in their pedigree. Here, we calculate the precise connection between genome-wide genetic shuffling and variance in genetic relatedness. For the relationships of grandparent-grandoffspring and siblings, the variance in genetic relatedness is a simple decreasing function of , the average proportion of locus pairs that recombine in gametogenesis. These formulations explain several recent observations about variance in genetic relatedness. They further allow us to calculate the neutral variance of ancestry among F2s in a hybrid cross, enabling F2-based tests for various kinds of selection, such as Dobzhansky-Muller incompatibilities and hybrid vigor. Our calculations also allow us to characterize how recombination affects the rate at which selection eliminates deleterious introgressed DNA after hybridization—by modulating the variance of introgressed ancestry across individuals. Species with low aggregate recombination rates, like Drosophila, purge introgressed DNA more rapidly and more completely than species with high aggregate recombination rates, like humans. These conclusions also hold for different genomic regions. Within the genomes of several species, positive correlations have been observed between local recombination rate and introgressed ancestry. Our results imply that these correlations can be driven more by recombination’s effect on the purging of deleterious introgressed alleles than its effect in unlinking neutral introgressed alleles from deleterious alleles. In general, our results demonstrate that the aggregate recombination process—as quantified by and analogs—acts as a variable barrier to gene flow between species.

scholarly journals MEASURING GENE FLOW AMONG POPULATIONS HAVING HIGH LEVELS OF GENETIC FRAGMENTATION

Genetics ◽  
1984 ◽  
Vol 106 (2) ◽  
pp. 293-308
Author(s):  
Allan Larson ◽  
David B Wake ◽  
Kay P Yanev
Keyword(s):  
Gene Flow ◽  
Flow Parameter ◽  
Alternative Methods ◽  
Stabilizing Selection ◽  
Gene Exchange ◽  
Epigenetic Factors ◽  
Effective Population ◽  
Population Number ◽  
Genetic Structures ◽  
Future Work

ABSTRACT We present an analysis of the genetic structures of 22 species of salamanders, with regard to levels of gene flow among populations. We estimate the gene flow parameter, Nm (the product of the effective population number and rate of migration among populations) using two alternative methods described by Wright and Slatkin. For most species, these two methods give approximately congruent estimates of Nm; when estimates differ, the method of Wright produces values slightly larger than those derived by the method of Slatkin. We analyze these results in light of independently derived historical inferences of the fragmentation of populations. This analysis suggests that the Nm values calculated from protein polymorphisms may contain information more relevant to historical patterns of gene exchange than to the current population dynamics; moderately large values of Nm may be calculated for species containing populations known to be no longer exchanging genes. Application of a method for estimating the maximum possible rate of gene exchange among populations indicates that, for most species studied here, gene flow among populations probably is no greater than the mutation rate. We suggest that most plethodontid species cannot be viewed as units whose cohesion is maintained by continuing gene exchange. Furthermore, we suggest that phenotypic uniformity among populations is not easily explained by hypotheses of continual stabilizing selection and propose that future work concentrate upon clarification of the genetic and epigenetic factors conferring self-maintenance or autopoietic properties on living systems.

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