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Asymmetric introgression reveals the genetic architecture of a plumage trait.

https://arctichealth.org/en/permalink/ahliterature303524
Source
Nat Commun. 2021 02 15; 12(1):1019
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
02-15-2021
Author
Georgy A Semenov
Ethan Linck
Erik D Enbody
Rebecca B Harris
David R Khaydarov
Per Alström
Leif Andersson
Scott A Taylor
Author Affiliation
Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA. georgy.semenov@colorado.edu.
Source
Nat Commun. 2021 02 15; 12(1):1019
Date
02-15-2021
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Chimera
Color
Epistasis, Genetic
Feathers - anatomy & histology - metabolism
Female
Genetic Introgression
Genome
Male
Passeriformes - anatomy & histology - classification - genetics
Pigmentation - genetics
Quantitative Trait, Heritable
Siberia
Uzbekistan
Abstract
Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of their hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. Here we show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.
PubMed ID
33589637 View in PubMed
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Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird.

https://arctichealth.org/en/permalink/ahliterature266673
Source
Mol Ecol. 2015 Jun;24(12):3009-25
Publication Type
Article
Date
Jun-2015
Author
Nicholas A Mason
Scott A Taylor
Source
Mol Ecol. 2015 Jun;24(12):3009-25
Date
Jun-2015
Language
English
Publication Type
Article
Keywords
Animals
Arctic Regions
Beak - anatomy & histology
Ecosystem
Feathers - anatomy & histology
Female
Finches - anatomy & histology - classification
Gene Flow
Genetics, Population
High-Throughput Nucleotide Sequencing
Linear Models
Male
Models, Genetic
North America
Phenotype
Phylogeny
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Transcriptome
Abstract
Understanding the patterns and processes that contribute to phenotypic diversity and speciation is a central goal of evolutionary biology. Recently, high-throughput sequencing has provided unprecedented phylogenetic resolution in many lineages that have experienced rapid diversification. The Holarctic redpoll finches (Genus: Acanthis) provide an intriguing example of a recent, phenotypically diverse lineage; traditional sequencing and genotyping methods have failed to detect any genetic differences between currently recognized species, despite marked variation in plumage and morphology within the genus. We examined variation among 20 712 anonymous single nucleotide polymorphisms (SNPs) distributed throughout the redpoll genome in combination with 215 825 SNPs within the redpoll transcriptome, gene expression data and ecological niche modelling to evaluate genetic and ecological differentiation among currently recognized species. Expanding upon previous findings, we present evidence of (i) largely undifferentiated genomes among currently recognized species; (ii) substantial niche overlap across the North American Acanthis range; and (iii) a strong relationship between polygenic patterns of gene expression and continuous phenotypic variation within a sample of redpolls from North America. The patterns we report may be caused by high levels of ongoing gene flow between polymorphic populations, incomplete lineage sorting accompanying very recent or ongoing divergence, variation in cis-regulatory elements, or phenotypic plasticity, but do not support a scenario of prolonged isolation and subsequent secondary contact. Together, these findings highlight ongoing theoretical and computational challenges presented by recent, rapid bouts of phenotypic diversification and provide new insight into the evolutionary dynamics of an intriguing, understudied non-model system.
Notes
Comment In: Mol Ecol. 2015 Jun;24(12):2901-326095582
PubMed ID
25735539 View in PubMed
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Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist.

https://arctichealth.org/en/permalink/ahliterature304721
Source
Syst Biol. 2020 Sep 17; :
Publication Type
Journal Article
Date
Sep-17-2020
Author
Erik R Funk
Garth M Spellman
Kevin Winker
Jack J Withrow
Kristen C Ruegg
Erika Zavaleta
Scott A Taylor
Author Affiliation
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder CO, USA.
Source
Syst Biol. 2020 Sep 17; :
Date
Sep-17-2020
Language
English
Publication Type
Journal Article
Abstract
Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. While different signals can be difficult to separate, the application of high throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole genome sequence data.
PubMed ID
32941630 View in PubMed
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