Genomic islands of divergence are not affected by geography of speciation in sunflowers

Renaut, Sébastien; Grassa, Christopher J.; Yeaman, Sam; Moyers, Brook T.; Lai, Zhao; Kane, Nolan C.; Bowers, John E.; Burke, John M.; Rieseberg, Loren H.

doi:10.1038/ncomms2833

Cited by 271 publications

(364 citation statements)

References 50 publications

(52 reference statements)

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“…Therefore, the cluster definitions need to take into account the different scales of genome coverage if comparisons between both types of studies are to be made. Data from Renaut et al (2013) clearly illustrate this issue, as the 0.3-0.6 cM outlier clusters from their study must be different to the 20 cM clusters used to define DH (Via and West, 2008;Via, 2009) and the 10 cM clusters found in this study. One concern regarding outlier clusters is co-variation among linked loci (Nosil and Feder, 2012;Faria et al, 2013).…”

Section: Confounding Effects On Neutrality Testingmentioning

confidence: 61%

“…Clustering of F ST outlier loci around QTLs that are involved in ecologically based reproductive isolation was first quantified by Via and West (2008), who estimated that DH regions could reach 20 cM within the genome of the pea aphid Acyrthosiphon pisum. Later studies involving other species pairs, together with next-generation sequencing markers, apparently failed to find the outlier clusters (for example, in threespine sticklebacks by Hohenlohe et al, 2010; in manakins by Parchman et al, 2013); or their patterns were interpreted as opposed to DH expectations (for example, in sunflowers by Renaut et al, 2013). However, the threespine stickleback data were reinterpreted by Via (2012) to support the existence of DH regions in such species, and a similar reinterpretation could be likely made for the other studies.…”

Section: Confounding Effects On Neutrality Testingmentioning

confidence: 99%

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A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

et al. 2014

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We analyzed the genetic mosaic of speciation in two hybridizing Mediterranean white oaks from the Iberian Peninsula (Quercus faginea Lamb. and Quercus pyrenaica Willd.). The two species show ecological divergence in flowering phenology, leaf morphology and composition, and in their basic or acidic soil preferences. Ninety expressed sequence tag-simple sequence repeats (EST-SSRs) and eight nuclear SSRs were genotyped in 96 trees from each species. Genotyping was designed in two steps. First, we used 69 markers evenly distributed over the 12 linkage groups (LGs) of the oak linkage map to confirm the species genetic identity of the sampled genotypes, and searched for differentiation outliers. Then, we genotyped 29 additional markers from the chromosome bins containing the outliers and repeated the multilocus scans. We found one or two additional outliers within four saturated bins, thus confirming that outliers are organized into clusters. Linkage disequilibrium (LD) was extensive; even for loosely linked and for independent markers. Consequently, score tests for association between two-marker haplotypes and the 'species trait' showed a broad genomic divergence, although substantial variation across the genome and within LGs was also observed. We discuss the influence of several confounding effects on neutrality tests and review the evolutionary processes leading to extensive LD. Finally, we examine how LD analyses within regions that contain outlier clusters and quantitative trait loci can help to identify regions of divergence and/or genomic hitchhiking in the light of predictions from ecological speciation theory.

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Section: Confounding Effects On Neutrality Testingmentioning

confidence: 61%

Section: Confounding Effects On Neutrality Testingmentioning

confidence: 99%

A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

et al. 2014

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“…For example, a recent study of sunflowers showed that regions of greater differentiation were strongly associated with reduced recombination (Renaut et al 2013). We used the revised genetic map to estimate the recombination rate for 5-Mb intervals of the mouse genome (Shifman et al 2006;Cox et al 2009).…”

Section: Recombination and Inversionsmentioning

confidence: 99%

“…The idea that the genomes of closely related species are mosaics of differentiated and less differentiated regions is not new and first emerged in the literature on hybrid zones (e.g., Key 1968;Harrison 1986;Tucker et al 1992;Rieseberg et al 1999;reviewed in Harrison 2012). The advent of genomic methods has fueled a renewed interest in studying patterns of differentiation between closely related species, including work on mosquitoes (Turner et al 2005;Lawniczak et al 2010;Neafsey et al 2010), mice (Harr 2006), Drosophila (Kulathinal et al 2009), Heliconius butterflies (Nadeau et al 2012), flycatchers (Ellegren et al 2012), crickets (Andrés et al 2013), sunflowers (Renaut et al 2013), and others.…”

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confidence: 99%

Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

2014

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One approach to understanding the genetic basis of speciation is to scan the genomes of recently diverged taxa to identify highly differentiated regions. The house mouse, Mus musculus, provides a useful system for the study of speciation. Three subspecies (M. m. castaneus, M. m. domesticus, and M. m. musculus) diverged 350 KYA, are distributed parapatrically, show varying degrees of reproductive isolation in laboratory crosses, and hybridize in nature. We sequenced the testes transcriptomes of multiple wild-derived inbred lines from each subspecies to identify highly differentiated regions of the genome, to identify genes showing high expression divergence, and to compare patterns of differentiation among subspecies that have different demographic histories and exhibit different levels of reproductive isolation. Using a sliding-window approach, we found many genomic regions with high levels of sequence differentiation in each of the pairwise comparisons among subspecies. In all comparisons, the X chromosome was more highly differentiated than the autosomes. Sequence differentiation and expression divergence were greater in the M. m. domesticus-M. m. musculus comparison than in either pairwise comparison with M. m. castaneus, which is consistent with laboratory crosses that show the greatest reproductive isolation between M. m. domesticus and M. m. musculus. Coalescent simulations suggest that differences in estimates of effective population size can account for many of the observed patterns. However, there was an excess of highly differentiated regions relative to simulated distributions under a wide range of demographic scenarios. Overlap of some highly differentiated regions with previous results from QTL mapping and hybrid zone studies points to promising candidate regions for reproductive isolation. U NDERSTANDING the genetic basis of speciation is a fundamental goal of evolutionary biology. This problem has primarily been approached in two ways: through laboratory studies using crosses and through studies of genetic variation in natural populations. Laboratory studies control for genetic background and environment, and they make it possible to connect genotype and phenotype. These types of studies have produced some spectacular successes including the identification of individual genes underlying postzygotic isolation in Drosophila (e.g., Ting et al. 1998;Presgraves et al. 2003;Brideau et al. 2006;Masly et al. 2006), Arabidopsis (Bomblies et al. 2007;Bikard et al. 2009), Mus (Mihola et al. 2009), and others (reviewed in Presgraves 2010 and Nosil and Schluter 2011).Studies of natural populations rely on the idea that regions of the genome that are important in reproductive isolation may be more differentiated than other regions of the genome. Therefore, by studying patterns of differentiation, one may gain insight into the genomic regions that underlie isolation. The idea that the genomes of closely related species are mosaics of differentiated and less differentiated regions is not new and first e...

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“…A recently much cited scenario for speciation without strong geographical isolation, derived 188 from earlier models 65,66 , ) on sex chromosomes [98][99][100] . Heterogeneity in genomic divergence seen in allopatry might 240 also result from gene-flow-selection balance that has occurred in the past 47,76 . Regardless of whether identified DMI alleles are the first step in the origin of reproductive isolation, a 278 striking pattern to emerge from recent work is that they have evolved under strong positive selection 279 rather than genetic drift and that genomic conflict is often implicated as the source of this selection.…”

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confidence: 99%