Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome‐wide admixture

Abstract

Summary• Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification.• Flow cytometry analyses detected ploidy polymorphisms of 2· and 4· in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species ⁄ subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles.• Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection.• High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

“…gemmifera (Japan) (cf. Wang et al, 2010). Young, healthy leaves were collected and dried in silica gel.…”

“…Besides, multilocus analyses that assess the genetic divergence within and between sister species also provide genealogical information for inferring the phylogeography (Stadler et al, 2005;Wright and Gaut, 2005;Zhu et al, 2007;Zou et al, 2008;Wang et al, 2010). In addition to the bifurcate topologies that interest the evolutionists, molecular dating provides much useful information (Wikstrom et al, 2001).…”

Arabidopsis hybrid speciation processes

“…It is distributed throughout the amphiBeringian region but is also found in Japan, Korea, and Taiwan. There is also evidence of past gene flow in Europe between diploid A. lyrata and A. halleri on the basis of either nuclear genes (13) or self incompatibility alleles (14).…”

Temperate origin and diversification via southward colonization in Fatsia (Araliaceae), an insular endemic genus of the West Pacific Rim

“…In this study, genetic analyses of all markers revealed non-stop gene flow between species in this genus, a pattern contradicting with the "isolation" model. It has been known that gene flow between closely related species is not rare in plants (Wang et al 2010). Besides, STRUCTURE analyses of microsatellite loci also revealed that genetic composition of some populations was mixed with alleles from other species, although with little extent, again likely indicating non-stop interspecific introgression (Fig.…”