Abstract Background Relict species are important for enhancing the understanding of modern biogeographic distribution patterns. Although both geological and climatic changes since the Cenozoic have affected the relict flora in East Asia, the contributions of geographical processes remain unclear. In this study, we employed restriction-site associated DNA sequencing (RAD-seq) and shallow genome sequencing data, in conjunction with ecological niche modeling (ENM), to investigate the spatial genetic patterns and population differentiation history of the relict species Rehderodendron kwangtungense Chun. Results A total of 138 individuals from 16 populations were collected, largely covering the natural distribution of R. kwangtungense . The genetic diversity within the R. kwangtungense populations was extremely low ( H O = 0.048 ± 0.019; H E = 0.033 ± 0.011). Mantel tests revealed isolation-by-distance pattern (R 2 = 0.38, P &lt; 0.001), and AMOVA analysis showed that the genetic variation of R. kwangtungense occurs mainly between populations (86.88%, K = 7). Between 23 and 21 Ma, R. kwangtungense underwent a period of rapid differentiation that coincided with the rise of the Himalayas and the establishment of the East Asian monsoon. According to ENM and population demographic history, the suitable area and effective population size of R. kwangtungense decreased sharply during the glacial period and expanded after the last glacial maximum (LGM). Conclusion Our study shows that the distribution pattern of southern China mountain relict flora may have developed during the panplain stage between the middle Oligocene and the early Miocene. Then, the flora later fragmented under the force of orogenesis, including intermittent uplift during the Cenozoic Himalayan orogeny and the formation of abundant rainfall associated with the East Asian monsoon. The findings emphasized the predominant role of geographical processes in shaping relict plant distribution patterns. 

Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense.

Additional file 4 of Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

Abstract Background Relict species are important for enhancing the understanding of modern biogeographic distribution patterns. Although both geological and climatic changes since the Cenozoic have affected the relict flora in East Asia, the contributions of geographical processes remain unclear. Here, we studied the population differentiation history of the relict species Rehderodendron kwangtungense Hu during the Cenozoic. In this study, 138 individuals from 16 populations of R. kwangtungense were subjected to double digest restriction-site associated DNA sequencing (ddRAD-seq) and shallow genome sequencing. Results We studied the population structure and historical biogeography of the relict species R. kwangtungense . The genetic diversity within the R. kwangtungense populations was extremely low. Mantel tests revealed an isolation-by-distance pattern, and the evidence of pollen and fruit morphology suggested that the distribution pattern of R. kwangtungense formed prior to the Miocene. Between 23 and 21 Ma, R. kwangtungense underwent a period of rapid differentiation that coincided with the rise of the Himalayas and the establishment of the East Asian monsoon. According to ecological niche modelling (ENM) and population demographic history, the suitable area and effective population size of R. kwangtungense decreased sharply during the glacial period and expanded after the last glacial maximum (LGM). Conclusion Our study shows that the distribution pattern of southern China mountain relict flora may have developed during the panplain stage between the middle Oligocene and the early Miocene. Then, the flora later fragmented under the force of orogenesis, including intermittent uplift during the Cenozoic Himalayan orogeny and the formation of abundant rainfall associated with the East Asian monsoon. 

Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

Additional file 5 of Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

Additional file 2 of Which contributes more to the relict flora distribution pattern in East Asia, geographical processes or climate change? New evidence from the phylogeography of Rehderodendron kwangtungense

The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

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Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax