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

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.

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.

scholarly journals Shallow evolutionary divergence between two Andean hummingbirds: Speciation with gene flow?

2018 ◽  
Author(s):  
Catalina Palacios ◽  
Silvana García-R ◽  
Juan Luis Parra ◽  
Andrés M. Cuervo ◽  
F. Gary Stiles ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Basis ◽  
Flow Model ◽  
Evolutionary Divergence ◽  
Phenotypic Differences ◽  
Adaptive Mechanisms ◽  
The Face ◽  
Divergence With Gene Flow ◽  
Neutral Markers

AbstractEcological speciation can proceed despite genetic interchange when selection counteracts homogeneizing effects of migration. We tested predictions of this divergence-with-gene-flow model in Coeligena helianthea and C. bonapartei, two parapatric Andean hummigbirds with marked plumage divergence. We sequenced neutral markers (mtDNA and nuclear ultra conserved elements) 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 Glogers’ rule that darker forms occur in more humid environments, and compared ecomorphological variables to assess adaptive mechanisms potentially promoting divergence. Genetic differentiation between species was very low and coalescent estimates of migration were consistent with divergence with gene flow. MC1R variation was unrelated to phenotypic differences. Species did not differ in macroclimatic niches but were distinct in ecomorphology. Although we reject adaptation to variation in humidity as the cause of divergence, we hypothesize that speciation likely 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.

scholarly journals Divergence in the face of gene flow in two Charadrius plovers along the Chinese coast

2018 ◽  
Author(s):  
Xuejing Wang ◽  
Pinjia Que ◽  
Gerald Heckel ◽  
Junhua Hu ◽  
Xuecong Zhang ◽  
...  
Keyword(s):  
Gene Flow ◽  
Southern China ◽  
Character Displacement ◽  
Niche Differentiation ◽  
Secondary Contact ◽  
Sea Level Changes ◽  
Charadrius Alexandrinus ◽  
Chinese Coast ◽  
The Face ◽  
Underlying Mechanisms

AbstractSpeciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient species, the Kentish (Charadrius alexandrinus) and the white-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches. These analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamical isolation and secondary contact due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow. These findings imply that the ecology can indeed counter gene flow through divergent selection and thus contribute to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and underlying mechanisms of speciation.

scholarly journals Genomic impacts of chromosomal inversions in parapatric Drosophila species

2012 ◽  
Vol 367 (1587) ◽  
pp. 422-429 ◽  
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.

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 Divergence with gene flow as facilitated by ecological differences: within-island variation in Darwin's finches

2010 ◽  
Vol 365 (1543) ◽  
pp. 1041-1052 ◽  
Author(s):  
Luis Fernando de León ◽  
Eldredge Bermingham ◽  
Jeffrey Podos ◽  
Andrew P. Hendry
Keyword(s):  
Gene Flow ◽  
Allelic Variation ◽  
Genetic Differences ◽  
Darwin's Finches ◽  
Darwin’S Finches ◽  
The Face ◽  
Beak Size ◽  
Additional Support ◽  
Divergence With Gene Flow ◽  
Ecological Differences

Divergence and speciation can sometimes proceed in the face of, and even be enhanced by, ongoing gene flow. We here study divergence with gene flow in Darwin's finches, focusing on the role of ecological/adaptive differences in maintaining/promoting divergence and reproductive isolation. To this end, we survey allelic variation at 10 microsatellite loci for 989 medium ground finches ( Geospiza fortis ) on Santa Cruz Island, Galápagos. We find only small genetic differences among G. fortis from different sites. We instead find noteworthy genetic differences associated with beak. Moreover, G. fortis at the site with the greatest divergence in beak size also showed the greatest divergence at neutral markers; i.e. the lowest gene flow. Finally, morphological and genetic differentiation between the G. fortis beak-size morphs was intermediate to that between G. fortis and its smaller ( Geospiza fuliginosa ) and larger ( Geospiza magnirostris ) congeners. We conclude that ecological differences associated with beak size (i.e. foraging) influence patterns of gene flow within G. fortis on a single island, providing additional support for ecological speciation in the face of gene flow. Patterns of genetic similarity within and between species also suggest that interspecific hybridization might contribute to the formation of beak-size morphs within G. fortis .

Introgression between non-sister species of honeyeaters (Aves: Meliphagidae) several million years after speciation

2019 ◽  
Vol 128 (3) ◽  
pp. 583-591
Author(s):  
Leo Joseph ◽  
Alex Drew ◽  
Ian J Mason ◽  
Jeffrey L Peters
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sex Chromosomes ◽  
Common Ancestor ◽  
Sister Species ◽  
Species Boundaries ◽  
North Eastern ◽  
The City

Abstract We reassessed whether two parapatric non-sister Australian honeyeater species (Aves: Meliphagidae), varied and mangrove honeyeaters (Gavicalis versicolor and G. fasciogularis, respectively), that diverged from a common ancestor c. 2.5 Mya intergrade in the Townsville area of north-eastern Queensland. Consistent with a previous specimen-based study, by using genomics methods we show one-way gene flow for autosomal but not Z-linked markers from varied into mangrove honeyeaters. Introgression barely extends south of the area of parapatry in and around the city of Townsville. While demonstrating the long-term porosity of species boundaries over several million years, our data also suggest a clear role of sex chromosomes in maintaining reproductive isolation.

scholarly journals Genomic evidence for divergence with gene flow in host races of the larch budmoth

2004 ◽  
Vol 271 (1534) ◽  
pp. 97-105 ◽  
Author(s):  
Igor Emelianov ◽  
Frantiŝek Marec ◽  
James Mallet
Keyword(s):  
Gene Flow ◽  
Host Races ◽  
Divergence With Gene Flow
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