Admixture as the basis for genetic mapping

Buerkle, C. Alex; Lexer, Christian

doi:10.1016/j.tree.2008.07.008

Cited by 155 publications

(210 citation statements)

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“…Natural selection can cause the fixation of advantageous alleles (or chromosomal segments) in ecologically diverged hybrids (Beaumont and Balding 2004;Buerkle and Lexer 2008;Lexer et al 2003). Introgressed alleles may often have a positive fitness effect in their new genetic background and traits responsible for adaptation can be transferred between species (Martin et al 2006).…”

Section: Discussionmentioning

confidence: 99%

Hybridization in contact zone between temperate European pine species

Wachowiak

Żukowska

Wójkiewicz

et al. 2016

Tree Genetics & Genomes

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Hybridization studies are important to advance our understanding of the interspecific gene flow and its evolutionary consequences in closely related species. Hybridization and admixture patterns were assessed in a contact zone and reference populations of European pine species using sequence data from 26 nuclear genes and a species-diagnostic cpDNA marker. Reference populations formed three distinct genetic clusters comprising Pinus sylvestris, Pinus mugo/Pinus uliginosa, and Pinus uncinata. Evidence of population structure was found only in P. uliginosa. Based on phenotypic characteristics and molecular data, we identified five groups of individuals in the contact zone in Poland, comprising forms of the parental species and intermediates that were most probably the result of interspecific crosses. A combination of nuclear gene sequence data and a diagnostic organelle marker were used to show that hybridization is frequent in the contact zone and results in hybrid trees with distinct phenotypic identity. The influence of selection in maintaining hybrid phenotypes in environments unsuited to parental species was inferred from nucleotide polymorphism data. A lack of admixture in reference populations suggests that hybridization has not occurred during post-glacial migration and so the contact zone represents a distinct, active example of ongoing evolution. Pine populations in this zone will be a valuable system for studying the genetic basis of hybrid advantage in environmental conditions untypical of pure parental species.

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Section: Discussionmentioning

confidence: 99%

Hybridization in contact zone between temperate European pine species

Wachowiak

Żukowska

Wójkiewicz

et al. 2016

Tree Genetics & Genomes

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“…(2) Linkage mapping normally uses F2 hybrids to test for statistical associations between alleles at marker loci and trait values for phenotypes (Lynch and Walsh, 1998;Rogers et al, 2012). (3) Association mapping is similar to linkage mapping but uses natural variation within or among populations (Buerkle and Lexer, 2008;Kruglyak, 2008;Flint and Mackay, 2009). (4) Genome scans use population samples to measure genetic differentiation at many loci, often with the goal of detecting loci under divergent selection, which are assumed to be high-differentiation outliers (Stinchcombe and Hoekstra, 2008;Nosil et al, 2009).…”

Section: Methods For Analysismentioning

confidence: 99%

“…(6) Candidate gene studies determine the extent to which genes of known effect contribute to phenotypic variation within or between populations (Stinchcombe and Hoekstra, 2008). These different methods have different utilities, strengths and weakness, that have been discussed extensively (Lynch and Walsh, 1998;Buerkle and Lexer, 2008;Stinchcombe and Hoekstra, 2008;Mackay et al, 2009;Stapley et al, 2010;Rockman, 2012).…”

Section: Methods For Analysismentioning

confidence: 99%

Key questions in the genetics and genomics of eco-evolutionary dynamics

Hendry

2013

Heredity

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Increasing acceptance that evolution can be 'rapid' (or 'contemporary') has generated growing interest in the consequences for ecology. The genetics and genomics of these 'eco-evolutionary dynamics' will be-to a large extent-the genetics and genomics of organismal phenotypes. In the hope of stimulating research in this area, I review empirical data from natural populations and draw the following conclusions. (1) Considerable additive genetic variance is present for most traits in most populations. (2) Trait correlations do not consistently oppose selection. (3) Adaptive differences between populations often involve dominance and epistasis. (4) Most adaptation is the result of genes of small-to-modest effect, although (5) some genes certainly have larger effects than the others. (6) Adaptation by independent lineages to similar environments is mostly driven by different alleles/genes. (7) Adaptation to new environments is mostly driven by standing genetic variation, although new mutations can be important in some instances. (8) Adaptation is driven by both structural and regulatory genetic variation, with recent studies emphasizing the latter. (9) The ecological effects of organisms, considered as extended phenotypes, are often heritable. Overall, the study of eco-evolutionary dynamics will benefit from perspectives and approaches that emphasize standing genetic variation in many genes of small-to-modest effect acting across multiple traits and that analyze overall adaptation or 'fitness'. In addition, increasing attention should be paid to dominance, epistasis and regulatory variation.

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“…Fitness changes associated with introgressed genes can be assessed using reciprocal transplant or common garden experiments (Arnold, 1992;Rieseberg et al, 2003;Martin et al, 2006). Alternatively, admixture mapping in natural populations containing a mixture of early and later generation recombinant individuals can be used to understand the genetic architecture of introgressed candidate traits (reviewed by Buerkle and Lexer, 2008).…”

Section: Population Genetic Approachmentioning

confidence: 99%

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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Admixture as the basis for genetic mapping

Cited by 155 publications

References 84 publications

Hybridization in contact zone between temperate European pine species

Hybridization in contact zone between temperate European pine species

Key questions in the genetics and genomics of eco-evolutionary dynamics

Next-generation hybridization and introgression

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