Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity
Historical climate oscillations and tectonic events have influenced the speciation and evolutionary history of many organisms. In this study, we chose Fokienia hodginsii (Dunn) A. Henry & H. H. Thomas (Cupressaceae s.l.), a Tertiary relict conifer, for the inference of the demographic history since the Neogene. Five chloroplast regions and two single‐copy nuclear genes were amplified and sequenced in 497 individuals from 28 populations. The chloroplast data showed that F. hodginsii presented a high level of genetic diversity (H
T
= 0.860 ± 0.0279) and significant phylogeographic structure (N
ST
> G
ST
, P < 0.05). According tobeast analysis, the divergence time of the two major lineages indicated by the phylogenetic construction produced from chloroplast and nuclear data could be dated to the early Miocene (ca. 19.34–19.95 Ma), which coincided with the onset and intensification of the Asian monsoon. During this time, environmental adaption under the different climatic conditions on either side of the Tanaka Line could have played important roles in maintaining and/or reinforcing the divergence of the two major lineages. The ecological niche modeling results showed that F. hodginsii experienced habitat fragmentation and strengthening of genetic barriers during the Last Glacial Maximum, followed by local expansion during postglacial periods. Our findings show that paleoclimate changes since the Neogene might have triggered the extinction of all but one Fokienia species and its intraspecific lineage differentiation. This study also suggests that Tertiary relicts in subtropical and tropical areas might have had a complex evolutionary history and their intraspecific differentiation time might have been earlier than expected.
Fokienia hodginsii is a Tertiary relict conifer of the monotypic genus Fokienia (Cupressaceae s.l.). Currently, the species is distributed in southern China, northern Vietnam, and northern Laos and listed as a “near threatened” species by the IUCN. In this study, a total of 427 individuals of F. hodginsii were sampled from China and Vietnam to characterize its genetic diversity and population differentiation. Based on the profiles of 12 simple sequence repeat (SSR) markers, we observed a high level of genetic diversity in F. hodginsii at the species level (H
e =0.635), albeit slightly lower than that of its sister species Chamaecyparis obtusa. Signals of bottleneck events were detected in the populations GXDMS, GXHJ, V‐PXB, and V‐HB, probably due to Pleistocene glaciations or overexploitation in recent years. Pronounced genetic differentiation (F
st
= 0.157) was found in this species. The inbreeding index (F
is
= 0.176 ± 0.024) indicated that F. hodginsii has a mixed mating system. Significant correlation was found between the pairwise genetic differentiation and geographic distance (r = 0.882, p = 0.01), suggesting that genetic differentiation among the populations follows the model of isolation by distance (IBD). STRUCTURE analysis and principal coordinate analysis revealed that these populations were divided into four groups: the western China group located mainly in the Yunnan–Guizhou Plateau, the central China group located mostly in the Luoxiao Mountains and Nanling Mountains, the eastern China group located in the Wuyi Mountains and the Vietnam group containing two populations in Vietnam. The different terrains and elevations of populations may be the most likely factors leading to the differentiation between the western China group and the central China group, while the geographic isolation caused by the lack of appropriate habitats may greatly contribute to the differentiation between the central China group and the eastern China group. Based on the results, some conservation suggestions for this species are provided, such as establishing seed orchards and multiple nature reserves.
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