Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori , and drift in populations of Drosophila melanogaster . The methods are implemented in a program, structure , version 2.0, which is available at http://pritch.bsd.uchicago.edu.

/pdf/inference-of-population-structure-using-multilocus-genotype-4p91nh3fvr.pdf

Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies

MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

I. the origin of species by means of natural selection

Hybridization between species is commonplace in plants, but is often seen as unnatural and unusual in animals. Here, I survey studies of natural interspecific hybridization in plants and a variety of animals. At least 25% of plant species and 10% of animal species, mostly the youngest species, are involved in hybridization and potential introgression with other species. Species in nature are often incompletely isolated for millions of years after their formation. Therefore, much evolution of eventual reproductive isolation can occur while nascent species are in gene-flow contact, in sympatry or parapatry, long after divergence begins. Although the relative importance of geographic isolation and gene flow in the origin of species is still unknown, many key processes involved in speciation, such as 'reinforcement' of post-mating isolation by the evolution of assortative mating, will have ample opportunity to occur in the presence of continuing gene flow. Today, DNA sequence data and other molecular methods are beginning to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.

https://www.ucl.ac.uk/taxome/jim/pap/mallethyb05.pdf

Hybridization as an invasion of the genome

▪ Abstract Changes in ploidy occurred early in the diversification of some animal and plant lineages and represent an ongoing phenomenon in others. While the prevalence of polyploid lineages indicates that this phenomenon is a common and successful evolutionary transition, whether polyploidization itself has a significant effect on patterns and rates of diversification remains an open question. Here we review evidence for the creative role of polyploidy in evolution. We present new estimates for the incidence of polyploidy in ferns and flowering plants based on a simple model describing transitions between odd and even base chromosome numbers. These new estimates indicate that ploidy changes may represent from 2 to 4% of speciation events in flowering plants and 7% in ferns. Speciation via polyploidy is likely to be one of the more predominant modes of sympatric speciation in plants, owing to its potentially broad-scale effects on gene regulation and developmental processes, effects that can produce immed...

/pdf/polyploid-incidence-and-evolution-18k59e8zrk.pdf

Polyploid Incidence and Evolution

Genetic analyses of reproductive barriers represent one of the few methods by which theories of speciation can be tested. However, genetic study is often restricted to model organisms that have short generation times and are easily propagated in the laboratory. Replicate hybrid zones with a diversity of recombinant genotypes of varying age offer increased resolution for genetic mapping experiments and expand the pool of organisms amenable to genetic study. Using 88 markers distributed across 17 chromosomes, we analyze the introgression of chromosomal segments of Helianthus petiolaris into H. annuus in three natural hybrid zones. Introgression was significantly reduced relative to neutral expectations for 26 chromosomal segments, suggesting that each segment contains one or more factors that contribute to isolation. Pollen sterility is significantly associated with 16 of these 26 segments, providing a straightforward explanation of why this subset of blocks is disadvantageous in hybrids. In addition, comparison of rates of introgression across colinear vs. rearranged chromosomes indicates that close to 50% of the barrier to introgression is due to chromosomal rearrangements. These results demonstrate the utility of hybrid zones for identifying factors contributing to isolation and verify the prediction of increased resolution relative to controlled crosses.

https://www.genetics.org/content/genetics/152/2/713.full.pdf

Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species

Apomixis, the asexual production of seed, is a trait estimated to occur in fewer than 1% of flowering plant species, with an uneven distribution among lineages. In the past decade, targeted research efforts have aimed at clarifying the genetic basis of apomixis, with the goal of engineering or breeding apomictic crops. Recent work suggests a simple genetic basis for apomixis, but it also indicates that natural populations of apomicts are much more complex than is often assumed. For example, in nature, nearly all apomicts that go through a megagametophyte stage (gametophytic apomicts) are polyploid, while their sexual relatives are typically diploid. Although populations have been characterized as obligately sexual or apomictic, it is increasingly clear that many plant populations exhibit some variation in reproductive mode. Many apomicts retain residual sexual function as pollen donors and thus have the potential to spread apomixis via male gametes, thereby increasing the genetic diversity observed within...

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The dynamic nature of apomixis in the angiosperms

The development of transgenic plants has heightened concern about the possible escape of genetically engineered material into the wild. Hybridization between crops and their wild relatives provides a mechanism by which this could occur. While hybridization has been documented between several crops and wild or weedy relatives, little is known about the persistence of cultivar genes in wild populations in the generations following hybridization. Wild and weedy sunflowers occur sympatrically with cultivated sunflowers throughout much of the cultivation range, and hybridization is known to occur. We surveyed two cultivar-specific RAPD markers in 2700 progeny in a naturally occurring population of wild Helianthus annuus over five generations following a single generation of hybridization with the cultivar. Moderate levels of gene flow were detected in the first generation (42% hybrids at the crop margin) and cultivar allele frequencies did not significantly decline over four subsequent generations. These results indicate that gene flow from cultivated into wild populations of sunflowers can result in the long-term establishment of cultivar alleles in wild populations. Furthermore, we conclude that neutral or favorable transgenes have the potential to escape and persist in wild sunflower populations.

The persistence of cultivar alleles in wild populations of sunflowers five generations after hybridization

One of the striking observations from the young field of molecular evolutionary biology has been the high frequency of cases where taxon-specific markers are found to differ widely in both phylogenetic and geographic distribution. This pattern has been observed most frequently when cytoplasmic markers are compared with those of nuclear origin (Rieseberg & Soltis 1991), but similar observations are often made for comparisons among markers of nuclear origin only (Rieseberg & Ellstrand 1993). These observations are important to phylogenists because they provide ‘footprints’ of past evolutionary events, information that may be critical to elucidating true organismal phylogeny. Marker incongruence also is significant to the evolutionist because it may provide insights into the differences in the evolutionary biology of organellar versus nuclear genes (as well as differences among nuclear genes), the role of selection, linkage and recombination in controlling the frequency and spatial distribution of introgressed genes, and the effects of introgression on the maintenance of species differences. In this paper, we list some of the best examples of molecular marker incongruence from both hybrid zones and phylogenetic trees in plants. General patterns emerging from this tabulation are discussed, and possible explanations are briefly summarized. In addition, recent studies of differential introgression and its mechanistic basis in wild sunflowers of the genus Helianthus are reviewed in detail. Results from these studies appear to explain patterns of marker discordance in Helianthus, and possibly many other groups of plants as well.

https://natuurtijdschriften.nl/pub/541050/ABN1996045003001.pdf

Jeannette Whitton

Papers

Polyploid Incidence and Evolution

Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species

The dynamic nature of apomixis in the angiosperms

The persistence of cultivar alleles in wild populations of sunflowers five generations after hybridization

Molecular marker incongruence in plant hybrid zones and phylogenetic trees