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Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using population genetic data from chloroplast (cp), mitochondrial (mt), and nuclear (nr) genomes. These two species occur in the Central Asian Highlands and Himalayas, respectively, where they are isolated from other Asian congeneric species by the Qinghai-Tibet Plateau (QTP) or adjacent deserts. Previous studies based on both morphological and molecular evidence suggest that they have contrasting phylogenetic relationships with Picea likiangensis or Picea wilsonii which are closely related and both located in the QTP. We examined genetic variation among 16 loci of three genomes from 30 populations of these four species. At both cpDNA loci and mtDNA loci, P. schrenkiana appeared to be closely related to P. likiangensis, although statistical support for this was weak. However, phylogenetic analyses and speciation tests based on the nuclear data from 11 loci provided evidence that P. schrenkiana and P. smithiana are sister species. These two species diverged around five million years ago (Mya) while the divergence between them and the P. likiangensis- P. wilsonii clade occurred about 18.4 Mya. We also detected gene flow accompanying these speciation events. Our results highlight the complex speciation histories of these alpine conifers due to interspecific gene flow and/or incomplete lineage sorting, and the importance of the early QTP uplifts in promoting the origin of these important conifer species in the Asian highlands. [ABSTRACT FROM AUTHOR]

Species delimitation has been a major research focus in evolutionary biology. However, the genetic delimitation of recently diverged species varies depending on the markers examined. In this study, we aimed to examine genetic differentiation and delimitations between only two species of Pugionium Gaertn (Brassicaceae)- Pugionium cornutum (L.) Gaertn and Pugionium dolabratum Maxim-that occur in the desert habitats of central Asia and have parapatric distributions. We genotyped 169 individuals from 25 populations, using two chloroplast (cp) DNA fragments ( trnV- trnM and trnS- trnfM), seven simple repeated sequence (SSR) loci and the nuclear ribosomal internal transcribed spacer (ITS). Four cp haplotypes were identified, three of which commonly occur in the two species, suggesting incomplete species-specific lineage sorting. Between-species cpDNA differentiation ( F) was low, even lower than among populations of the same species. However, we found higher than average SSR F values, and both Bayesian clustering of SSR variables and maximum-likelihood genetic analyses divided all sampled individuals into two groups, agreeing well with morphological separation, although gene flow between species was obvious according to the SSR loci data. However, two types of ITS sequences were highly consistent with the morphological delimitation of the two species in all sampled individuals. These results together suggest that these two species shared numerous ancestral cpDNA polymorphisms and point to the importance of nuclear DNA (ITS or genetic accumulation at multiple loci) in delimiting recently diverged species. [ABSTRACT FROM AUTHOR]