Neogene and Quaternary climate changes shaped the lineage differentiation and demographic history of Fokienia hodginsii (Cupressaceae s.l.), a Tertiary relict in East Asia

Abstract

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.

First Fossil Fokienia (Cupressaceae) in South China and Its Palaeogeographic and Palaeoecological Implications

“…In addition, combined with the obvious phylogeographic structure and ENM results, it seems the F. hodginsii survived in four refuges during the last glacial episodes, which is consistent with the multiple refugia patterns of relict species in subtropical China (Yin et al, 2020). The F. hodginsii population has a relatively high genetic diversity, which may be related to its long history in a variety of geographical habitats (Yin et al, 2018, Yin et al, 2020. However, the fossils (F. shengxianensis He, Sun & Liu, F. catenulata (Bell) R.W.…”

“…Available palaeobotanical evidence indicates that the oldest known fossil record of Fokienia is from the Oligocene of Longjing, Jilin, China (Figure 1; Guo and Zhang, 2002). Combined with the previous phylogenetic study of Cupressaceae (Mao et al, 2012;Qu et al, 2017) and fossil records, Yin et al (2020) studied the phylogeography of F. hodginsii based on the molecular markers of chloroplast and single-copy nuclear genes. This analysis revealed that F. hodginsii comprised two major phylogeographic lineages located on either side of the Tanaka-Kaiyong Line, which is considered to be a major phytogeographic boundary in southwest China, separating Sino-Japanese and Sino-Himalayan floristic subkingdoms of East Asia (Li and Li, 1997;Yin et al, 2020).…”

“…This analysis revealed that F. hodginsii comprised two major phylogeographic lineages located on either side of the Tanaka-Kaiyong Line, which is considered to be a major phytogeographic boundary in southwest China, separating Sino-Japanese and Sino-Himalayan floristic subkingdoms of East Asia (Li and Li, 1997;Yin et al, 2020). The divergence time of these two major lineages was dated to the early Ma) (Yin et al, 2020). Yin et al (2020) speculated the ancestors of Fokienia migrated from the middle latitudes of the Northern Hemisphere to the subtropical regions after the formation of the East Asian monsoon.…”

“…The divergence time of these two major lineages was dated to the early Ma) (Yin et al, 2020). Yin et al (2020) speculated the ancestors of Fokienia migrated from the middle latitudes of the Northern Hemisphere to the subtropical regions after the formation of the East Asian monsoon. In addition, combined with the obvious phylogeographic structure and ENM results, it seems the F. hodginsii survived in four refuges during the last glacial episodes, which is consistent with the multiple refugia patterns of relict species in subtropical China (Yin et al, 2020).…”

“…Yin et al (2020) speculated the ancestors of Fokienia migrated from the middle latitudes of the Northern Hemisphere to the subtropical regions after the formation of the East Asian monsoon. In addition, combined with the obvious phylogeographic structure and ENM results, it seems the F. hodginsii survived in four refuges during the last glacial episodes, which is consistent with the multiple refugia patterns of relict species in subtropical China (Yin et al, 2020). The F. hodginsii population has a relatively high genetic diversity, which may be related to its long history in a variety of geographical habitats (Yin et al, 2018, Yin et al, 2020.…”