COMPARATIVE GENOMIC AND POPULATION GENETIC ANALYSES INDICATE HIGHLY POROUS GENOMES AND HIGH LEVELS OF GENE FLOW BETWEEN DIVERGENT<i>HELIANTHUS</i>SPECIES

Kane, Nolan C.; King, M.; Barker, Michael S.; Raduski, Andrew R.; Karrenberg, Sophie; Yatabe, Yoko; Knapp, Steven J.; Rieseberg, Loren H.

doi:10.1111/j.1558-5646.2009.00703.x

Cited by 109 publications

(125 citation statements)

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“…Multiple postglacial migration sources are common in many plant species in Taiwan, because plant species retreated into refugia in different geographic areas (Wu et al, 2006;Kuo et al, 2010). Our population estimates of y from MIGRATE-N ranged 0.62-0.99 (Supplementary Figure 2a-c), which are comparable to those of long-lived Eucalyptus (Field et al, 2011) and annual Helianthus species (Kane et al, 2009). The long-term mutation-scaled N e ranged 1550-2475 individuals per population, suggesting large long-term effective population sizes in R. oldhamii, when a mutation rate of 10 À4 per allele per generation commonly found in plant microsatellites was used in the calculations (Marriage et al, 2009).…”

Section: Historical Connectivity and Contemporary Isolationsupporting

confidence: 64%

Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

et al. 2013

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Elucidation of the evolutionary processes that constrain or facilitate adaptive divergence is a central goal in evolutionary biology, especially in non-model organisms. We tested whether changes in dynamics of gene flow (historical vs contemporary) caused population isolation and examined local adaptation in response to environmental selective forces in fragmented Rhododendron oldhamii populations. Variation in 26 expressed sequence tag-simple sequence repeat loci from 18 populations in Taiwan was investigated by examining patterns of genetic diversity, inbreeding, geographic structure, recent bottlenecks, and historical and contemporary gene flow. Selection associated with environmental variables was also examined. Bayesian clustering analysis revealed four regional population groups of north, central, south and southeast with significant genetic differentiation. Historical bottlenecks beginning 9168-13,092 years ago and ending 1584-3504 years ago were revealed by estimates using approximate Bayesian computation for all four regional samples analyzed. Recent migration within and across geographic regions was limited. However, major dispersal sources were found within geographic regions. Altitudinal clines of allelic frequencies of environmentally associated positively selected outliers were found, indicating adaptive divergence. Our results point to a transition from historical population connectivity toward contemporary population isolation and divergence on a regional scale. Spatial and temporal dispersal differences may have resulted in regional population divergence and local adaptation associated with environmental variables, which may have played roles as selective forces at a regional scale.

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Section: Historical Connectivity and Contemporary Isolationsupporting

confidence: 64%

Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

et al. 2013

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“…Computer simulations and models of gene flow predict widespread introgression under different demographic scenarios (for example, Currat et al, 2008), but until now genome-wide studies of introgression have been limited to a handful of model organisms (for example, sunflowers; Kane et al, 2009). In this review, we promote the use of NGS technologies to design molecular markers spread throughout the genome, and encourage the use of high-throughput assays to genotype large numbers of individuals, especially in non-model organisms.…”

Section: Resultsmentioning

confidence: 99%

“…Comparative sequencing of EST libraries for multiple individuals is an effective method for reducing the complexity of the genome, and still allows the sequencing of a genome-wide sample of loci (Kane et al, 2009). The main drawback with sequencing EST collections, apart from its cost, is that RNA is required rather than DNA, and the high rate of RNA degradation makes this technique impractical for sampling a large number of wild-collected individuals for many organisms (Bräutigam and Gowik, 2010).…”

Section: How Can Ngs Technologies Help Us To Get Around These Limitatmentioning

confidence: 99%

“…These include loci with a high rate of introgression, which are under positive selection (or tightly linked to a gene undergoing positive selection, 'hitchhiking' markers), as well as loci that are likely to have a decreased frequency of introgression. These include genes involved in co-adapted gene complexes (epistatic interactions) or structurally divergent areas of the chromosome where recombination is suppressed (Rieseberg et al, 1995;Kane et al, 2009). The identification of regions that show no introgression is of particular importance, as these areas may contain genes responsible for reproductive isolation, which have a role in maintaining the distinct identities of species which co-occur in allopatry (Turner et al, 2005).…”

Section: How Can Ngs Best Be Used To Study Hybridization and Introgrementioning

confidence: 99%

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Next-generation hybridization and introgression

2011

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Hybridization has a major role in evolution-from the introgression of important phenotypic traits between species, to the creation of new species through hybrid speciation. Molecular studies of hybridization aim to understand the class of hybrids and the frequency of introgression, detect the signature of ancient hybridization, and understand the behaviour of introgressed loci in their new genomic background. This often involves a large investment in the design and application of molecular markers, leading to a compromise between the depth and breadth of genomic data. New techniques designed to assay a large sub-section of the genome, in association with next-generation sequencing (NGS) technologies, will allow genome-wide hybridization and introgression studies in organisms with no prior sequence data. These detailed genotypic data will unite the breadth of sampling of loci characteristic of population genetics with the depth of sequence information associated with molecular phylogenetics. In this review, we assess the theoretical and methodological constraints that limit our understanding of natural hybridization, and promote the use of NGS for detecting hybridization and introgression between non-model organisms. We also make recommendations for the ways in which emerging techniques, such as pooled barcoded amplicon sequencing and restriction site-associated DNA tags, should be used to overcome current limitations, and enhance our understanding of this evolutionary significant process. Heredity (2012) 108, 179-189; doi:10.1038/hdy.2011.68; published online 7 September 2011Keywords: next-generation sequencing; hybridization; introgression; reticulate evolution; single-nucleotide polymorphisms (SNPs); restriction site-associated DNA (RAD) tags INTRODUCTION Hybridization, the crossbreeding between individuals of different species, and introgression, the transfer of genes between species mediated primarily by backcrossing, have been the focus of evolutionary studies over many decades (see Anderson, 1949;Arnold, 1992;Rieseberg and Carney, 1998). Hybridization is potentially a creative evolutionary process, allowing genetic novelties to accumulate faster than through mutation alone (Anderson and Hubricht, 1938;Martinsen et al., 2001). This may increase allelic variation at selectively neutral loci, and transfer adaptively important genetic variation, which may increase the fitness of the introgressed lineage (Choler et al., 2004;Martin et al., 2006;Castric et al., 2008;Kim et al., 2008). Moreover, hybridization can have a role in speciation. Hybridization in association with whole-genome duplication (polyploidy) is considered a likely route to speciation, particularly in plants ( Hegarty and Hiscock, 2008). The difference in ploidy levels between the polyploid hybrid and diploid progenitors acts as a strong reproductive barrier (Soltis et al., 2004), although there are examples of introgression across ploidy levels (for example, Senecio; Chapman and Abbott, 2010). Hybrid speciation can also occur without a change i...

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“…Remarkable progress has been accomplished in an increasing number of organisms, both in plants (e.g. Schemske & Bierzychudek 2007;Kane et al 2009) and animals (e.g. Hoekstra et al 2006;Joron et al 2006;Storz et al 2007;Barrett et al 2008; other papers in this issue).…”

Section: Introductionmentioning

confidence: 99%

On the origin of species: insights from the ecological genomics of lake whitefish

Bernatchez

Renaut

Whiteley

et al. 2010

Phil. Trans. R. Soc. B

228

317

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In contrast to the large amount of ecological information supporting the role of natural selection as a main cause of population divergence and speciation, an understanding of the genomic basis underlying those processes is in its infancy. In this paper, we review the main findings of a long-term research programme that we have been conducting on the ecological genomics of sympatric forms of whitefish (Coregonus spp.) engaged in the process of speciation. We present this system as an example of how applying a combination of approaches under the conceptual framework of the theory of adaptive radiation has yielded substantial insight into evolutionary processes in a non-model species. We also discuss how the joint use of recent biotechnological developments will provide a powerful means to address issues raised by observations made to date. Namely, we present data illustrating the potential offered by combining next generation sequencing technologies with other genomic approaches to reveal the genomic bases of adaptive divergence and reproductive isolation. Given increasing access to these new genomic tools, we argue that non-model species studied in their ecological context such as whitefish will play an increasingly important role in generalizing knowledge of speciation.

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COMPARATIVE GENOMIC AND POPULATION GENETIC ANALYSES INDICATE HIGHLY POROUS GENOMES AND HIGH LEVELS OF GENE FLOW BETWEEN DIVERGENTHELIANTHUSSPECIES

Cited by 109 publications

References 105 publications

Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

Next-generation hybridization and introgression

On the origin of species: insights from the ecological genomics of lake whitefish

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