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.

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 Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Heredity ◽  
2021 ◽  
Author(s):  
Yael S. Rodger ◽  
Alexandra Pavlova ◽  
Steve Sinclair ◽  
Melinda Pickup ◽  
Paul Sunnucks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Evolutionary History ◽  
Livestock Grazing ◽  
Genetic Connectivity ◽  
Evolutionary Divergence ◽  
Common Component ◽  
A Genome ◽  
Eastern Australia

AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

New insights on the genetic basis of Portuguese grapevine and on grapevine domestication

Genome ◽  
2009 ◽  
Vol 52 (9) ◽  
pp. 790-800 ◽  
Author(s):  
M. S. Lopes ◽  
D. Mendonça ◽  
M. Rodrigues dos Santos ◽  
J. E. Eiras-Dias ◽  
A. da Câmara Machado
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Vitis Vinifera ◽  
Ssr Markers ◽  
Genetic Basis ◽  
Genetic Resource ◽  
Putative Parent ◽  
Last Glaciation ◽  
Wild Grapevine ◽  
Nuclear Ssr

As the ancestor of cultivated grape, Vitis vinifera subsp. sylvestris represents a unique, invaluable genetic resource for the improvement of cultivated grapevines. Recently, five populations of wild grapevines were identified in Portugal. Sixty vines were characterized with 11 nuclear SSR markers and further compared with 70 genotypes of Portuguese Vitis vinifera subsp. sativa. The obtained data demonstrate moderate genetic differentiation between wild grapevine populations and moderate to high genetic differentiation between wild and cultivated grapevines. However, the identification of high degrees of similarity between wild and cultivated grapes (up to 87%) and a putative parent–progeny relationship between wild and cultivated grapes with 17 additional SSR markers is indicative of gene flow between local wild grapevine populations and Portuguese domesticated vines. Also, the ancestry of some Azorean cultivars was ascertained. The obtained data further support the hypothesis of several domestication centres, with Portugal, Spain, and Italy playing a particular role after the last glaciation, giving rise to many of the Western European cultivars.

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 Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex

Heredity ◽  
2015 ◽  
Vol 116 (4) ◽  
pp. 351-361 ◽  
Author(s):  
F Balao ◽  
M Tannhäuser ◽  
M T Lorenzo ◽  
M Hedrén ◽  
O Paun
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Evolutionary Significance ◽  
Young Sibling ◽  
Phenotypic Divergence ◽  
Distribution Ranges ◽  
Genetic Patterns ◽  
The Alps ◽  
Distinct Distribution ◽  
Neutral Markers

Abstract Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.

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 .

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.

The Use of Protein Electrophoresis for Determining Species Boundaries in Amphipods

Crustaceana ◽  
1993 ◽  
Vol 65 (2) ◽  
pp. 265-277 ◽  
Author(s):  
Barbara A. Stewart
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Morphological Variation ◽  
Protein Electrophoresis ◽  
Species Boundaries ◽  
Allopatric Populations ◽  
A Value ◽  
Electrophoretic Data

AbstractThe use of protein electrophoretic data for determining species boundaries in amphipods is addressed. Analysis of published literature on genetic differentiation in amphipods showed that pairs of allopatric populations which have genetic identities (I) above a value of 0.85 probably represent intraspecific populations, whereas pairs of populations which have genetic identities below about 0.45 probably represent different species. It was recommended that if I values fall between 0.45 and 0.85, additional factors such as evidence of a lack of gene flow between the populations, and concordant morphological variation should be considered.

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