Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot

Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
New Phytologist (Impact Factor: 7.67). 05/2013; 199(4). DOI: 10.1111/nph.12336
Source: PubMed


The interplay of orographic uplift and climatic changes in the Himalaya-Hengduan Mountains region (HHM) have had a key role in speciation and population demography. To gain further insight into these processes, we investigated their effects on Taxus wallichiana by combining molecular phylogeography and species distribution modeling. Molecular data were obtained from 43 populations of T. wallichiana. Nineteen climatic variables were analyzed alongside genetic discontinuities. Species distribution modeling was carried out to predict potential past distribution ranges. Two distinct lineages were identified, which diverged c. 4.2 (2.0-6.5) million years ago (Ma), a timescale that corresponds well with the recent uplift of the Qinghai-Tibet Plateau and subsequent climatic changes of the region. Correlations with climatic variables also suggest that ecological factors may have further reinforced the separation of the two lineages. Both lineages experienced population expansion during the last glaciation. The high genetic divergence, long-term isolation and ecological differentiation suggest a scenario of cryptic speciation in T. wallichiana associated with geological and climatic changes in the HHM. Our findings also challenge the notion of general population 'contraction' during the last glaciation in the HHM.

Download full-text


Available from: Lian-Ming Gao,
  • Source
    • "Repeated range expansion and contraction of most plants and animals may cause migration and/or extinction of populations, followed by periods of isolation , divergence and subsequent expansion (e.g. Liu et al., 2013). Our dating estimates indicate that the diversification in T. sinensis started in the early Pleistocene (1Á02–1Á74 Ma), suggesting that haplotypes differentiated before the LGM. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The phylogeography of plant species in sub-tropical China remains largely unclear. This study used Tapiscia sinensis, an endemic and endangered tree species widely but disjunctly distributed in sub-tropical China, as a model to reveal the patterns of genetic diversity and phylogeographical history of Tertiary relict plant species in this region. The implications of the results are discussed in relation to its conservation management. Samples were taken from 24 populations covering the natural geographical distribution of T. sinensis. Genetic structure was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). Phylogenetic relationships among haplotypes were constructed with maximum parsimony and haplotype network methods. Historical population expansion events were tested with pairwise mismatch distribution analysis and neutrality tests. Species potential range was deduced by ecological niche modelling (ENM). A low level of genetic diversity was detected at the population level. A high level of genetic differentiation and a significant phylogeographical structure were revealed. The mean divergence time of the haplotypes was approx. 1·33 million years ago. Recent range expansion in this species is suggested by a star-like haplotype network and by the results from the mismatch distribution analysis and neutrality tests. Climatic oscillations during the Pleistocene have had pronounced effects on the extant distribution of Tapiscia relative to the Last Glacial Maximum (LGM). Spatial patterns of molecular variation and ENM suggest that T. sinensis may have retreated in south-western and central China and colonized eastern China prior to the LGM. Multiple montane refugia for T. sinense existing during the LGM are inferred in central and western China. The populations adjacent to or within these refugia of T. sinense should be given high priority in the development of conservation policies and management strategies for this endangered species. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email:
    Annals of Botany 07/2015; 116(5). DOI:10.1093/aob/mcv112 · 3.65 Impact Factor
  • Source
    • "Due to the complicated geological history and dramatic variations in local climates and topography, the Himalaya–Hengduan Mountains possess the highest plant and animal diversity and level of endemism in China (Wu 1988; Li & Li 1993; Sun 2002). Thus, this region is recognized as an ideal natural laboratory for research of biodiversity conservation , speciation, adaptive evolution and climate change (Wang et al. 2008; Liu et al. 2013, 2014). The Himalaya–Hengduan Mountains region includes two global biodiversity hotspots: the Eastern Himalaya and the Mountains of Southwest China. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The Himalaya-Hengduan Mountains encompass two global biodiversity hotspots with high levels of biodiversity and endemism. This area is one of the diversification centres of the genus Rhododendron, which is recognized as one of the most taxonomically challenging plant taxa due to recent adaptive radiations and rampant hybridization. In this study, four DNA barcodes were evaluated on 531 samples representing 173 species of seven sections of four subgenera in Rhododendron, with a high sampling density from Himalaya-Hengduan Mountains employing three analytical methods. The varied approaches (NJ, PWG and BLAST) had different species identification powers with BLAST performing best. With the PWG analysis, the discrimination rates for single barcodes varied from 12.21% to 25.19% with ITS < rbcL < matK < psbA-trnH. Combinations of ITS + psbA-trnH + matK and the four barcodes showed the highest discrimination ability (both 41.98%) among all possible combinations. As a single barcode, psbA-trnH performed best with a relatively high performance (25.19%). Overall, the three-marker combination of ITS + psbA-trnH + matK was found to be the best DNA barcode for identifying Rhododendron species. The relatively low discriminative efficiency of DNA barcoding in this genus (~42%) may possibly be attributable to too low sequence divergences as a result of a long generation time of Rhododendron and complex speciation patterns involving recent radiations and hybridizations. Taking the morphology, distribution range and habitat of the species into account, DNA barcoding provided additional information for species identification and delivered a preliminary assessment of biodiversity for the large genus Rhododendron in the biodiversity hotspots of the Himalaya-Hengduan Mountains. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 05/2015; 15:932-944. DOI:10.1111/1755-0998.12353 · 3.71 Impact Factor
  • Source
    • "For example, population size reductions and isolation, resulting from Pleistocene climatic fluctuations, can deepen genetic divergence induced by pre-Pleistocene (e.g. geological, climatic) changes (Liu et al., 2013a; Yan et al., 2013). However, secondary admixture following historical divergence will reduce genetic differentiation , resulting in genetic variation similar to that from incomplete lineage sorting (Qu et al., 2012). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Warm-temperate evergreen (WTE) forest represents the typical vegetation type of subtropical China, but how its component species responded to past environmental change remains largely unknown. Here, we reconstruct the evolutionary history of Tetrastigma hemsleyanum, an herbaceous climber restricted to the WTE forest.Twenty populations were genotyped using chloroplast DNA sequences and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and ecological niche modeling (ENM) of the species distributions during the Last Glacial Maximum (LGM) and at present.Lineages in Southwest vs Central-South-East China diverged through climate/tectonic-induced vicariance of an ancestral southern range during the early Pliocene. Long-term stability in the Southwest contrasts with latitudinal range shifts in the Central-South-East region during the early-to-mid-Pleistocene. Genetic and ENM data strongly suggest refugial persistence in situ at the LGM.Pre-Quaternary environmental changes appear to have had a persistent influence on the population genetic structure of this subtropical WTE forest species. Our findings suggest relative demographic stability of this biome in China over the last glacial–interglacial cycle, in contrast with palaeobiome reconstructions showing that this forest biome retreated to areas of today's tropical South China during the LGM.
    New Phytologist 01/2015; 206(2). DOI:10.1111/nph.13261 · 7.67 Impact Factor
Show more