Adaptation by introgression

Arnold, Michael L.; Martin, Noland H.

doi:10.1186/jbiol176

Cited by 106 publications

(79 citation statements)

References 14 publications

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“…Additional candidate hearing and/or echolocation genes must be studied for a more thorough assessment of whether there are differences in levels of introgression between hearing genes and other genes in these bats. Indeed, tests for selection for this region of Prestin were not significant, suggesting that the possible occurrence of introgression in Prestin-4 may in fact be due to neutral gene flow although we cannot reject the alternative possibility of linkage to beneficial genes [27,72,73]. It was noteworthy that the scenario of incomplete lineage sorting could not be ruled out completely, and it is possible that the parapyhly pattern at this locus might have been shaped by a combination of both introgression and incomplete lineage sorting.…”

Section: Discussionmentioning

confidence: 99%

Differential introgression among loci across a hybrid zone of the intermediate horseshoe bat (Rhinolophus affinis)

Mao

Zhu

Zhang³

et al. 2014

BMC Evol Biol

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BackgroundHybrid zones formed by the secondary contact of divergent lineages represent natural laboratories for studying the genetic basis of speciation. Here we tested for patterns of differential introgression among three X-linked and 11 autosomal regions to identify candidate loci related to either reproductive isolation or adaptive introgression across a hybrid zone between two Chinese mainland subspecies of the intermediate horseshoe bat Rhinolophus affinis: R. a. himalayanus and R. a. macrurus.ResultsOur results support the previous suggestion that macrurus formed when a third subspecies (R. a. hainanus) recolonized the mainland from Hainan Island, and that himalayanus is the ancestral taxon. However, this overall evolutionary history was not reflected in all loci examined, with considerable locus-wise heterogeneity seen in gene tree topologies, levels of polymorphism, genetic differentiation and rates of introgression. Coalescent simulations suggested levels of lineage mixing seen at some nuclear loci might result from incomplete lineage sorting. Isolation with migration models supported evidence of gene flow across the hybrid zone at one intronic marker of the hearing gene Prestin.ConclusionsWe suggest that phylogenetic discordance with respect to the species tree seen here is likely to arise via a combination of incomplete lineage sorting and a low incidence of introgression although we cannot rule out other explanations such as selection and recombination. Two X-linked loci and one autosomal locus were identified as candidate regions related to reproductive isolation across the hybrid zone. Our work highlights the importance of including multiple genomic regions in characterizing patterns of divergence and gene flow across a hybrid zone.

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Section: Discussionmentioning

confidence: 99%

Differential introgression among loci across a hybrid zone of the intermediate horseshoe bat (Rhinolophus affinis)

Mao

Zhu

Zhang³

et al. 2014

BMC Evol Biol

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“…In closely related plant species, introgression can occur asymmetrically by favoring gene flow from widespread, abundant species to rare, narrowly distributed species (Burgess et al 2005;Lepais et al 2009; Thompson et al 2010). The evolutionary consequences of introgression can be the fusion of taxa that do not reveal strong reproductive isolation or adaptive trait introgression between naturally hybridizing species linking to natural selection (Seehausen 2004;Arnold 2006;Arnold and Martin 2009).…”

Section: Introductionmentioning

confidence: 97%

Disentangling the effects of isolation-by-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi

Huang

Chen

Chang

et al. 2016

Tree Genetics & Genomes

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Ecological speciation has long been noted as a central topic in the field of evolutionary biology, and investigation into the relative importance of ecological and geographical factors is becoming increasingly emphasized. We surveyed genetic variation of 277 samples from 25 populations of nine Rhododendron species within Tsutsusi subgenus in Taiwan using simple sequence repeats of expressed sequence tags. Bayesian clustering revealed four genetic lineages: (1) the Rhododendron simsii, Rhododendron kanehirai, and Rhododendron nakaharae lineage (lineage 1); (2) the R h o d o d e n d ro n l o n g i p e r u l a t u m , R h o d o d e n d ro n breviperulatum, and Rhododendron noriakianum lineage (lineage 2); (3) the Rhododendron rubropilosum lineage (lineage 3); and (4) the Rhododendron oldhamii lineage (lineage 4).Asymmetric introgressions were found from lineage 3 into lineages 1 and 2 (introgressed lineages). Genetic admixture of non-R. oldhamii species was also revealed by a neighborjoining tree. Variation partitioning showed that environment explained much larger portions of genetic variation than geography between non-introgressed lineages (i.e., between R. oldhamii and other lineages). However, the Mantel and partial Mantel tests and the multiple matrix regression with randomization found that isolation-by-distance played a more important role than isolation-by-environment (IBE) in contributing to genetic variation in most between lineage comparisons. Nevertheless, strong IBE was found when compared between non-introgressed lineages of R. oldhamii and R. rubropilosum, suggesting post-speciation ecological divergence. Several environmental variables, including annual mean temperature, aspect, isothermality, seasonal precipitation, slope, and soil pH, could be important ecological drivers involved in reproductive isolation between R. oldhamii and non-R. oldhamii species within the Tsutsusi subgenus.

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“…Cases of introgression enabling adaptation in animals and plants have been extensively documented (for reviews, see Arnold and Martin 2009 17 , Rieseberg 2009 18 and Hedrick 2013 19 ), although surprisingly little attention has been devoted to adaptive introgression in humans 20, 21 .…”

Section: Introductionmentioning

confidence: 99%

Evidence for archaic adaptive introgression in humans

et al. 2015

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As modern and ancient DNA sequence data from diverse human populations accumulate1–4, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments — a process, known as adaptive introgression (AI). Within the past couple of years, a series of studies5–8 have identified genomic regions showing strong evidence for archaic adaptive introgression. In this Review, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans, and to determine whether positive selection has acted on these fragments. We discuss recently reported examples of adaptive introgression and consider the level of supporting evidence for each, grouped by selection pressure. We discuss challenges and recommendations for inferring selection on introgressed regions.

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Adaptation by introgression

Cited by 106 publications

References 14 publications

Differential introgression among loci across a hybrid zone of the intermediate horseshoe bat (Rhinolophus affinis)

Differential introgression among loci across a hybrid zone of the intermediate horseshoe bat (Rhinolophus affinis)

Disentangling the effects of isolation-by-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi

Evidence for archaic adaptive introgression in humans

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