DOI: 10.5061/dryad.4hg2p
title: Data from: Population genetic structure of Oryza rufipogon and O. nivara: implications for the origin of O. nivara

description: 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 unclear. Here, based on sequences of 10 nuclear and two
 chloroplast loci from 26 wild populations across the entire geographic
 ranges of the two species, we conducted comprehensive analyses using
 population genetics, phylogeography and species distribution modelling
 (SDM) approaches. In addition to supporting the two previously reported
 major subdivisions, we detected four genetically distinct groups within O.
 rufipogon and found no correlation between the genetic groups and either
 species identity or geographical regions. The SDM clearly showed
 substantial change in the distribution range of O. rufipogon in history,
 demonstrating that the repeated extinction and colonization of local
 populations due to multiple glacial–interglacial cycles during the
 Quaternary was most likely the main factor shaping the confounding
 population genetic structure of O. rufipogon. Moreover, we found
 significant differences between the two species in climate preferences,
 suggestive of an important role for climatic factors in the adaptation,
 persistence and expansion of O. nivara. Finally, based on the genetic
 pattern and dynamics of the O. nivara populations, we hypothesize that O.
 nivara might have independently originated multiple times from different
 O. rufipogon populations.
description: KS1-alignmentAligned sequences of KS1 gene fragment from 307 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.LHS1-alignmentAligned sequences of LHS1 gene fragment from 306 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.SSII1-alignmentAligned sequences of SSII1 gene fragment from 307 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.WAXY-alignmentAligned sequences of WAXY gene fragment from 307 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.HD3A-alignmentAligned sequences of HD3A gene fragment from 296 individuals of Oryza nivara and O. rufipogon and one individual of O.barthii used as outgroup.GBSS-alignmentAligned sequences of GBSS gene fragment from 294 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.NP23-alignmentAligned sequences of NP23 gene fragment from 294 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.NP39-alignmentAligned sequences of NP39 gene fragment from 293 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.NP81-alignmentAligned sequences of NP81 gene fragment from 293 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.NP122-alignmentAligned sequences of NP122 gene fragment from 293 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.NDHC_TRNV-alignmentAligned sequences of NDHC_TRNV gene fragment from 306 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.TRNP_RPL33-alignmentAligned sequences of TRNP_RPL33 gene fragment from 306 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.Structure_input_file