Abstract:Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains… Show more
“…1). This is consistent with the results of Liu et al (2015), who found no correlation between genetic groups and geographic regions in wild rice, and ascribed the absence of a phylogeographic pattern to repeated extinctions and re-colonizations of wild populations during Quaternary glacial-interglacial cycles. If this explanation is correct, it may imply that both mutations emerged prior to the last glaciation.Fig.…”
A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the “domestication alleles” of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.Electronic supplementary materialThe online version of this article (doi:10.1007/s10722-017-0518-0) contains supplementary material, which is available to authorized users.
“…1). This is consistent with the results of Liu et al (2015), who found no correlation between genetic groups and geographic regions in wild rice, and ascribed the absence of a phylogeographic pattern to repeated extinctions and re-colonizations of wild populations during Quaternary glacial-interglacial cycles. If this explanation is correct, it may imply that both mutations emerged prior to the last glaciation.Fig.…”
A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the “domestication alleles” of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.Electronic supplementary materialThe online version of this article (doi:10.1007/s10722-017-0518-0) contains supplementary material, which is available to authorized users.
“…Previous studies of genome-wide polymorphism have clustered aus and indica together (Garris et al 2005; McNally et al 2009; Xu et al 2011), however, none have specifically tested whether aus and indica have a single or separate origins. Our results suggest that japonica , indica , and aus have their origins in distinct ancestral populations, consistent with phylogeographic studies that show population structuring and geographic subdivision within O. rufipogon , with O. nivara as a separate group (Sun et al 2002; Huang et al 2012a; Huang et al 2012b; Liu et al 2015). …”
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1–24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.
“…Aquilegia species are mainly outcrossed by different pollinators and the genetic diversity data from this study, together with other research, provide a good example for investigating how different mating systems and pollinators influence the nucleotide polymorphism between species. We also found that the genetic diversity at the species level was significantly higher than at the population level; this pattern has been reported in other research, such as A. thaliana , Oryza rufipogon Griff., O. nivara S. D. Sharma & Shastry, and Zea mays L. (Moeller & Tiffin, ; Nordborg et al, ; Liu et al, ). We suspected that the population structure might be responsible for this because segregating sites emerged when highly structured populations were put together.…”
The genus Aquilegia is emerging as the new model system for plant development, ecology, and evolution studies. Previous research showed that pollinator shift might drive the diversification of North American Aquilegia species, and natural selection on the length of petal nectar spur might play a crucial role. In this genus, A. ecalcarata Maxim. is the only taxon that has lost nectar spurs. Previous phylogenetic results indicated that A. ecalcarata, A. yabeana Kitag., A. oxysepala var. kansuensis Bruhl., and A. rockii Munz comprised a monophyletic group. However, their pattern of genetic diversity remains unknown. In addition, little is known about the evolutionary relationship among the four species on the population level. We carried out a population genetics study with 21 representative populations based on 10 single‐copy nuclear gene fragments and found that: (i) A. yabeana conserved the highest genetic diversity (both πsil and θsil) and A. oxysepala var. kansuensis had the lowest level; (ii) A. ecalcarata split into two groups, with one population clustered with A. rockii and the other five populations clustered with A. oxysepala var. kansuensis; and (iii) the allele frequency spectrum showed an excess of low frequency alleles in all four species, implying that they may undergo the mutation‐drift equilibrium. Our findings provide the first investigation of genetic diversity and evolutionary relationships in A. yabeana, A. oxysepala var. kansuensis, A. rockii, and A. ecalcarata. They lay the foundation for future evolutionary studies, such as speciation mediated by pollinators.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
