Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

Brelsford, Alan; Toews, David P. L.; Irwin, Darren E.

doi:10.1098/rspb.2017.1106

Cited by 57 publications

(42 citation statements)

References 69 publications

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“…These patterns suggest that the differentiation of myrtle warblers from the other forms is a result of strong selection in a small subset of the genome over a relatively short span of time, rather than accumulation of genomewide differences during a long period of pure geographic isolation. Admixture mapping in the hybrid zone has indicated that some of these differentiation peaks are strongly associated with colour differences between these two taxa; for example, the differentiation peak on chromosome 20 (Figure , on the left side of that chromosome) is associated with the presence of white eye spots and lines in myrtle warblers and their absence in Audubon's warblers (Brelsford, Toews, & Irwin, ).…”

Section: Discussionmentioning

confidence: 99%

A comparison of genomic islands of differentiation across three young avian species pairs

et al. 2018

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Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in F ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in F , suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (π ) are almost as large as levels of between-group nucleotide distance (π ) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the F peaks having low π suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This "sweep-before-differentiation" model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations.

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Section: Discussionmentioning

confidence: 99%

A comparison of genomic islands of differentiation across three young avian species pairs

et al. 2018

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“…Conversely, approaches such as GWAS focus specifically on the variants underlying phenotypes of interest, but provide no information concerning the adaptive significance of these variants. We attempted to confront and ameliorate the limitations of these two approaches by integrating them; an idea that has only recently begun to gain traction [53,[56][57][58][59]. Our approach is unique in that we leverage LD generated by natural admixture between populations to identify genotype-phenotype associations (see also Brelsford et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

“…We attempted to confront and ameliorate the limitations of these two approaches by integrating them; an idea that has only recently begun to gain traction [53,[56][57][58][59]. Our approach is unique in that we leverage LD generated by natural admixture between populations to identify genotype-phenotype associations (see also Brelsford et al, 2017). We first located potential adaptive regions of the genome using scans for selection then used GWAS to reveal genomic regions that are associated with multiple potentially adaptive phenotypes.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish

et al. 2018

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Adaptive divergence between marine and freshwater environments is important in generating phyletic diversity within fishes, but the genetic basis of adaptation to freshwater habitats remains poorly understood. Available approaches to detect adaptive loci include genome scans for selection, but these can be difficult to interpret because of incomplete knowledge of the connection between genotype and phenotype. In contrast, genome wide association studies (GWAS) are powerful tools for linking genotype to phenotype, but offer limited insight into the evolutionary forces shaping variation. Here, we combine GWAS and selection scans to identify loci important in the adaptation of complex physiological traits to freshwater environments. We focused on freshwater (FW)-native and brackish water (BW)-native populations of the Atlantic killifish (Fundulus heteroclitus) as well as a population that is a natural admixture of these two populations. We measured phenotypes for multiple physiological traits that differ between populations and that may contribute to adaptation across osmotic niches (salinity tolerance, hypoxia tolerance, metabolic rate, and body shape) and used a reduced representation approach for genome-wide genotyping. Our results show patterns of population divergence in physiological capabilities that are consistent with local adaptation. Selection scans between BWnative and FW-native populations identified genomic regions that presumably affect fitness between BW and FW environments, while GWAS revealed loci that contribute to variation for each physiological trait. There was substantial overlap in the genomic regions putatively under selection and loci associated with the measured physiological traits, suggesting that these phenotypes are important for adaptive divergence between BW and FW environments. Our analysis also implicates candidate genes likely involved in physiological capabilities, some of which validate a priori hypotheses. Together, these data provide insight into the mechanisms that enable diversification of fishes across osmotic boundaries.. CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/254854 doi: bioRxiv preprint first posted online Jan. 27, 2018; 3 Author SummaryIdentifying the genes that underlie adaptation is important for understanding the evolutionary process, but this is technically challenging. We bring multiple lines of evidence to bear for identifying genes that underlie adaptive divergence. Specifically, we integrate genotypephenotype association mapping with genome-wide scans for signatures of natural selection to reveal genes that underlie phenotypic variation and that are adaptive in populations of killifish that are diverging between marine and freshwater environments. Because adaptation is likely manifest in multiple physiological traits, we focus on hypoxia tolerance, salinity tolerance, and metabolic rate; traits that are divergent be...

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“…The use of both metrics simultaneously ensured that the relationships observed are method agnostic. This multi-metric approach, including a combination of association and F ST outliers, has been utilized repeatedly to identify genomic regions associated with domestication in both dogs and cats (Axelsson et al 2013; Montague et al 2014), variation in feather coloration in warblers (Brelsford et al 2017), and the architecture and modularity of wing pattern variation in Heliconius butterflies (Nadeau et al 2014; Van Belleghem et al 2017). The relationship between the two metrics was explored by plotting both a correlation and a quantile-quantile plot (Q-Q plot) of the F ST and association for all variants (Fig.…”

Section: Methodsmentioning

confidence: 99%

Multiple loci control eyespot number variation on the hindwings ofBicyclus anynanabutterflies

Rivera‐Colón

Westerman

Belleghem

et al. 2019

Preprint

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27The underlying genetic changes that regulate the appearance and disappearance of 28 repeated traits, or serial homologs, remain poorly understood. One hypothesis is 29 that variation in genomic regions flanking master regulatory genes, also known as 30 input-output genes, controls variation in trait number, making the locus of 31 evolution almost predictable. Other hypotheses implicate genetic variation in up-32 stream or downstream loci of master control genes. Here, we use the butterfly 33Bicyclus anynana, a species which exhibits natural variation in eyespot number 34 on the dorsal hindwing, to test these two hypotheses. We first estimated the 35 heritability of dorsal hindwing eyespot number by breeding multiple butterfly 36 families differing in eyespot number, and regressing eyespot number of offspring 37 on mid-parent values. We then estimated the number and identity of independent 38 genetic loci contributing to eyespot number variation by performing a genome-39 wide association study with restriction site-associated DNA Sequencing (RAD-seq) 40 from multiple individuals varying in number of eyespots sampled across a freely 41 breeding lab population. We found that dorsal hindwing eyespot number has a 42 moderately high heritability of approximately 0.50. In addition, multiple loci near 43 previously identified genes involved in eyespot development display high 44 association with dorsal hindwing eyespot number, suggesting that homolog 45 number variation is likely determined by regulatory changes at multiple loci that 46 build the trait and not by variation at single master regulators or input-output 47 49 Body plans often evolve through changes in the number of repeated parts or serial 50 homologs by either addition or subtraction. For instance, the pelvic fins of 51 vertebrates are inferred to have originated by addition to a body plan displaying 52 only pectoral fins, perhaps via co-option of the pectoral or caudal fin 53 developmental programs to a novel location in the body (Ruvinsky and Gibson-54 Brown 2000; Larouche et al. 2017). In insects, the absence of limbs and wings in 55 the abdomen is inferred to be due to a process of subtraction, i.e. via the repression 56 or modification of limbs and wings in these segments by hox genes (Galant and 57 Carroll 2002; Ronshaugen et al. 2002; Tomoyasu et al. 2005; Ohde et al. 2013). 58 Regulatory targets of abdominal hox genes are likely to underlie loss of limb/wing 59 number in these body segments (Tomoyasu et al. 2005; Ohde et al. 2013), 60 although these mutations have not yet been identified. Thus, while serial homolog 61 number variation is a common feature in the evolution of organisms' body plans, 62 the underlying genetic changes that regulate the appearance and disappearance of 63 these repeated traits remain poorly understood. 64 65 Studies in Drosophila have contributed most to the identification of the genetic 66 basis underlying the evolution of serial homolog number. Larvae of different 67 species have different numbers of small hairs, or tr...

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Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

Cited by 57 publications

References 69 publications

A comparison of genomic islands of differentiation across three young avian species pairs

A comparison of genomic islands of differentiation across three young avian species pairs

Genome-wide selection scans integrated with association mapping reveal mechanisms of physiological adaptation across a salinity gradient in killifish

Multiple loci control eyespot number variation on the hindwings ofBicyclus anynanabutterflies

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