Divergence and gene flow among Darwin's finches: A genome-wide view of adaptive radiation driven by interspecies allele sharing

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

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Population Genomic Evidence Reveals Subtle Patterns of Differentiation in the Trophically Polymorphic Cuatro Ciénegas Cichlid, Herichthys minckleyi

Journal of Heredity ◽

10.1093/jhered/esz004 ◽

2019 ◽

Vol 110 (3) ◽

pp. 361-369 ◽

Cited By ~ 1

Author(s):

Katherine L Bell ◽

Chris C Nice ◽

Darrin Hulsey

Keyword(s):

Gene Flow ◽

Biological Diversity ◽

Molecular Genetic ◽

Molecular Ecology ◽

Cichlid Fish ◽

Genome Wide ◽

A Genome ◽

The Face ◽

Or Gene ◽

Herichthys Minckleyi

Abstract In recent decades, an increased understanding of molecular ecology has led to a reinterpretation of the role of gene flow during the evolution of reproductive isolation and biological novelty. For example, even in the face of ongoing gene flow strong selection may maintain divergent polymorphisms, or gene flow may introduce novel biological diversity via hybridization and introgression from a divergent species. Herein, we elucidate the evolutionary history and genomic basis of a trophically polymorphic trait in a species of cichlid fish, Herichthys minckleyi. We explored genetic variation at 3 hierarchical levels; between H. minckleyi (n = 69) and a closely related species Herichthys cyanoguttatus (n = 10), between H. minckleyi individuals from 2 geographic locations, and finally between individuals with alternate morphotypes at both a genome-wide and locus-specific scale. We found limited support for the hypothesis that the H. minckleyi polymorphism is the result of ongoing hybridization between the 2 species. Within H. minckleyi we found evidence of geographic genetic structure, and using traditional population genetic analyses found that individuals of alternate morphotypes within a pool appear to be panmictic. However, when we used a locus-specific approach to examine the relationship between multi-locus genotype, tooth size, and geographic sampling, we found the first evidence for molecular genetic differences between the H. minckleyi morphotypes.

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The tale of the finch: adaptive radiation and behavioural flexibility

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2009.0291 ◽

2010 ◽

Vol 365 (1543) ◽

pp. 1099-1109 ◽

Cited By ~ 96

Author(s):

Sabine Tebbich ◽

Kim Sterelny ◽

Irmgard Teschke

Keyword(s):

Adaptive Radiation ◽

Darwin's Finches ◽

Genetic Accommodation ◽

Darwin’S Finches ◽

Morphological Adaptations ◽

Extra Factor ◽

Extraordinary Means ◽

Flexible Stem ◽

Innovative Techniques ◽

Current Behaviour

Darwin's finches are a classic example of adaptive radiation. The ecological diversity of the Galápagos in part explains that radiation, but the fact that other founder species did not radiate suggests that other factors are also important. One hypothesis attempting to identify the extra factor is the flexible stem hypothesis, connecting individual adaptability to species richness. According to this hypothesis, the ancestral finches were flexible and therefore able to adapt to the new and harsh environment they encountered by exploiting new food types and developing new foraging techniques. Phenotypic variation was initially mediated by learning, but genetic accommodation entrenched differences and supplemented them with morphological adaptations. This process subsequently led to diversification and speciation of the Darwin's finches. Their current behaviour is consistent with this hypothesis as these birds use unusual resources by extraordinary means. In this paper, we identify cognitive capacities on which flexibility and innovation depend. The flexible stem hypothesis predicts that we will find high levels of these capacities in all species of Darwin's finches (not just those using innovative techniques). Here, we test that prediction, and find that while most of our data are in line with the flexible stem hypothesis, some are in tension with it.

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Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Genome Research ◽

10.1101/gr.212522.116 ◽

2017 ◽

Vol 27 (6) ◽

pp. 1004-1015 ◽

Cited By ~ 57

Author(s):

Fan Han ◽

Sangeet Lamichhaney ◽

B. Rosemary Grant ◽

Peter R. Grant ◽

Leif Andersson ◽

...

Keyword(s):

Gene Flow ◽

Ecological Adaptation ◽

Darwin's Finches ◽

Darwin’S Finches ◽

Genomic Landscape

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Cranial shape evolution in adaptive radiations of birds: comparative morphometrics of Darwin's finches and Hawaiian honeycreepers

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0481 ◽

2017 ◽

Vol 372 (1713) ◽

pp. 20150481 ◽

Cited By ~ 31

Author(s):

Masayoshi Tokita ◽

Wataru Yano ◽

Helen F. James ◽

Arhat Abzhanov

Keyword(s):

Adaptive Radiation ◽

Molecular Mechanisms ◽

Rapid Evolution ◽

Oceanic Islands ◽

Shape Variation ◽

Skull Morphology ◽

Darwin's Finches ◽

Hawaiian Honeycreepers ◽

Darwin’S Finches ◽

Adaptive Radiations

Adaptive radiation is the rapid evolution of morphologically and ecologically diverse species from a single ancestor. The two classic examples of adaptive radiation are Darwin's finches and the Hawaiian honeycreepers, which evolved remarkable levels of adaptive cranial morphological variation. To gain new insights into the nature of their diversification, we performed comparative three-dimensional geometric morphometric analyses based on X-ray microcomputed tomography (µCT) scanning of dried cranial skeletons. We show that cranial shapes in both Hawaiian honeycreepers and Coerebinae (Darwin's finches and their close relatives) are much more diverse than in their respective outgroups, but Hawaiian honeycreepers as a group display the highest diversity and disparity of all other bird groups studied. We also report a significant contribution of allometry to skull shape variation, and distinct patterns of evolutionary change in skull morphology in the two lineages of songbirds that underwent adaptive radiation on oceanic islands. These findings help to better understand the nature of adaptive radiations in general and provide a foundation for future investigations on the developmental and molecular mechanisms underlying diversification of these morphologically distinguished groups of birds. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

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The genomic impact of European colonization of the Americas

10.1101/676437 ◽

2019 ◽

Cited By ~ 1

Author(s):

Linda Ongaro ◽

Marilia O. Scliar ◽

Rodrigo Flores ◽

Alessandro Raveane ◽

Davide Marnetto ◽

...

Keyword(s):

Gene Flow ◽

Demographic History ◽

Colonial Era ◽

Genome Wide ◽

A Genome ◽

European Colonization ◽

High Degree ◽

The Impact ◽

North And South America ◽

North And South

AbstractThe human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas.We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

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THE EVOLUTIONARY HISTORY OF DARWIN'S FINCHES: SPECIATION, GENE FLOW, AND INTROGRESSION IN A FRAGMENTED LANDSCAPE

Evolution ◽

10.1111/evo.12484 ◽

2014 ◽

Vol 68 (10) ◽

pp. 2932-2944 ◽

Cited By ~ 43

Author(s):

Heather L. Farrington ◽

Lucinda P. Lawson ◽

Courtney M. Clark ◽

Kenneth Petren

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Fragmented Landscape ◽

Darwin's Finches ◽

Darwin’S Finches ◽

History Of

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Population-genomic inference of the strength and timing of selection against gene flow

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1616755114 ◽

2017 ◽

Vol 114 (27) ◽

pp. 7061-7066 ◽

Cited By ~ 56

Author(s):

Simon Aeschbacher ◽

Jessica P. Selby ◽

John H. Willis ◽

Graham Coop

Keyword(s):

Gene Flow ◽

Recombination Rate ◽

Divergent Selection ◽

Adaptive Divergence ◽

Serpentine Soils ◽

Evolutionary Mechanisms ◽

Local Conditions ◽

Local Environments ◽

Genome Wide ◽

A Genome

The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus, we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genome-wide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation.

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