Glacial refuge areas are expected to harbor a large fraction of the intraspecific biodiversity of the temperate biota. To test this hypothesis, we studied chloroplast DNA variation in 22 widespread European trees and shrubs sampled in the same forests. Most species had genetically divergent populations in Mediterranean regions, especially those with low seed dispersal abilities. However, the genetically most diverse populations were not located in the south but at intermediate latitudes, a likely consequence of the admixture of divergent lineages colonizing the continent from separate refugia.

Interpopulation gene flow in plants is mediated by a combination of pollen and seed dispersal. The effectiveness of pollen and seeds in bringing about gene flow depends upon the mode of inheritance of the genetic marker. For nuclear and paternally inherited markers, gene flow occurs in both pollen and seed. For maternally inherited markers, genes are only dispersed in seeds. As a result, levels of population differentiation under drift-migration equilibrium are expected to differ for markers with contrasting modes of inheritance, and the extent of such differences should be related to the relative levels of pollen and seed migration among populations. A model is developed that relates expected values of population differentiation (F,) for nuclear, paternally and maternally inherited markers, to pollen and seed migration rates. The model is used to estimate the relative rates of seed and pollen flow in six species of plants where values are available for both nuclear and maternally inherited markers. Estimates of (pollen flow/seed flow) range from four in wild barley to 200 in oaks, and this pattern of variation is consistent with the reproductive characteristics of the species concerned.

No abstract

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...

The role of seed dispersal in maintaining genetic connectivity among forest fragments has largely been ignored because gene flow by pollen is expected to predominate. By using genealogical reconstruction, we investigated gene flow after establishment of seeds in a wind-pollinated, wind-dispersed tree. Our data show that seed dispersal is the main vector of gene flow among remnants and that long-distance dispersal is common across a chronically fragmented landscape. The relative importance of seed-mediated gene flow may have been underemphasized in other fragmented systems, and diagnosing the response of forest trees to current anthropogenic disturbances requires the assessment of phenomena after establishment.

The geographical structure of mitochondrial (mt)DNA variants (mitotypes) was investigated in 38 western European populations of Scots pine Pinus sylvestris using restriction fragment length polymorphism (RFLP) analysis of total DNA and a homologous cox1 probe. Three major mitotypes (designated a, b and d) were detected. Within Spain all three major mitotypes were found, gene diversity was high, HT = 0.586, and this diversity was distributed predominantly among rather than within populations (FST(M) = 0.813 for the seven Spanish populations). Mitotype d was present only in the most southerly population from the Sierra Nevada. Elsewhere in Europe, populations showed little or no mtDNA diversity within regions, but there were marked differences between regions. Italian populations were fixed for mitotype b; populations from northern France, Germany, Poland, Russia and southern Sweden were fixed for mitotype a; while populations in northern Fennoscandia were fixed for mitotype b. The isolated Scottish populations were predominantly of mitotype a, but mitotype b was present in three of the 20 populations scored. In Scotland, UK gene diversity (HT = 0.120) and genetic differentiation among populations (FST(M) = 0.37) was much lower than in Spain. When interpreted in the light of complementary data from pollen analysis and nuclear genetic markers, the results suggest that present‐day populations of P. sylvestris in western Europe have been derived from at least three different sources after glaciation.

The rates of outcrossing in sympatric populations of Ipomoea purpurea and L hederacea were estimated (using electrophoretic markers) to be 70% and 7% respectively. The difference in outcrossing rate is not apparently due to differences in pollinator service received by the species, but is associated with differences in anther-stigma distance. In L purpurea stigmas are generally exserted and there is much genetic variation for anther-stigma distance. Variation in this character has a significant effect on the ease with which selfpollination occurs. In contrast there is no variation for the character in the L hederacea population, the anthers being invariably held at the same level as the stigma, an arrangement promoting self-pollination.

SUMMARYIn plants possessing a mixed selfing and random mating system, outcrossing rate can be estimated from progeny genotype arrays. Computer simulation studies show that if there is heterogeneity of gene frequency between subpopulations, these estimates of t are severely biased downwards, the degree of bias increasing as the true value of t increases. This effect has been demonstrated in the field using experimental populations of Ipomoea purpurea. These field studies also provide evidence for pollen "carryover" in I. purpurea.