Speciation among populations connected by gene flow is driven by adaptation to different environments, but underlying gene–environment associations remain largely unknown. Here, 162 individuals from 32 populations were sampled to obtain 191,648 independent single nucleotide polymorphisms (SNPs) across the genomes of two closely related spruce species, Picea asperata and Picea crassifolia , which occur on the Qinghai–Tibet Plat...

Extinct taxa may be detectable if they were ancestors to extant hybrid species, which retain their genetic signature. In this study, we combined phylogenomics, population genetics and fluorescence in situ hybridization (GISH and FISH) analyses to trace the origin of the alpine tetraploid Allium tetraploideum (2 n = 4 x = 32), one of the five known members in the subgenus Cyathophora . We found that A. tetraploideum was an obvi...

Having a comprehensive understanding of population structure, genetic differentiation and demographic history is important for the conservation and management of threatened species. High‐throughput sequencing (HTS) provides exciting opportunities to address a wide range of factors for conservation genetics. Here, we generated HTS data and identified 266,884 high‐quality single nucleotide polymorphisms from 82 individuals of Cu...

An increasing number of species are thought to have originated by homoploid hybrid speciation ( HHS ), but in only a handful of cases are details of the process known. A previous study indicated that Picea purpurea , a conifer in the Qinghai–Tibet Plateau ( QTP ), originated through HHS from P. likiangensis and P. wilsonii . To investigate this origin in more detail, we analysed transcriptome data for 114 individuals collected...

Hybridization and introgression are believed to play important roles in plant evolution. However, few empirical studies have been designed to clarify the ways in which these processes complicate taxonomic delimitation. Recent phylogenetic studies based on a number of different DNA fragments have indicated that Picea brachytyla in the eastern Qinghai‐Tibet Plateau is polyphyletic, a finding that contrasts with traditional taxon...