Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region

Abstract

Allopatric divergence is often initiated by geological uplift and restriction to sky‐islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographical structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants, we used population genomic data of the Rheum palmatum complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection, to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the R. palmatum complex originated in the central Hengduan Mts and possibly in regions further east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the R. palmatum complex cannot reject a restriction to sky‐islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographical areas.

Ring distribution patterns—diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin

“…The first three subregions showed strong isolation signals in the STRucTuRe analyses (K = 3) and DAPC (Figure 3), suggesting that the populations of the two species have been historically fragmented in these subregions for long enough to give rise to the obvious phylogeographical structure. The genetic diversification is further supported by the significant signals detected in IBE (Table 1), and also observed in some other taxa cohabiting this area (Fan et al, 2013;Feng et al, 2020;Qiao et al, 2018;Qu et al, 2011). In comparison, the populations inhabiting the fourth subregion did not show strong signals of isolation in the nuclear data (K = 4, Figure 3).…”

“…We can gain some insight into the main drivers for the allopatric divergence and admixture in the two species through the phylogeographical structures. The clustering of the two species into western and eastern groups mirrors the genetic structure displayed in other taxa inhabiting the mountains of Southwest China, such as riparian shrub (Sophora davidii) (Fan et al, 2013), Rheum palmatum complex (Feng et al, 2020) and odorous frog (Qiao et al, 2018). These divisions roughly reflect the "Tanaka-Kaiyong Line" (TKL) which is a Pleistocene-origin environmental barrier to the dispersal of plants (Fan et al, 2013;Zhu & Yan, 2002).…”

“…In comparison, the populations inhabiting the fourth subregion did not show strong signals of isolation in the nuclear data ( K = 4, Figure 3). This is probably due to the lack of high mountains (mostly mountains in this subregion are below 2500 m) that can provide enough space for upward movement in the warm‐wet climate during the interglacial periods (Feng et al, 2020; Wen et al, 2014). The populations currently inhabiting this subregion may have dispersed from microrefugia farther north (e.g., site “SNJ”) (Xu et al, 2019; Zhang et al, 2018) or farther west (e.g., site “ZaT”) (Qu et al, 2011).…”

Genome‐wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation

“…The increasing availability of whole‐genome sequencing (WGS) offers opportunities to examine this process in more detail. Genomic data in conjunction with a model testing framework have been applied to address this issue in animals (Kreiner et al ., 2019), but it has rarely been done for plants (Feng et al ., 2020), and few studies have used WGS data to examine the allopatric speciation process and its outcome, especially in plants (Chen et al ., 2019).…”

Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)

“…Beyond correlative approaches such as those described above, mechanistic approaches would enable a deeper exploration of biogeographical patterns and processes that have affected chimpanzees, especially with the recent availability of comprehensive behavioral (Kühl et al, 2019) and molecular data (Lester et al, 2021) for a large number of wild chimpanzee populations. Rapid developments in the generation and analysis of genome‐wide molecular data over the past decade have revealed detailed demographic histories, enabling the identification of diversification mechanisms due to forest refugia, which are characterized by divergence, isolation, and secondary contact as refugial habitats fragment and reconnect with each other during glacial cycles (Barratt et al, 2018; Charles et al, 2018; Feng et al, in press; Leaché et al, 2019; Portik et al, 2017). The ability to distinguish signals of forest refugia from other diversification mechanisms such as landscape barriers, ecological gradients, and anthropogenic habitat fragmentation, would represent a powerful approach for gaining a more mechanistic understanding of population diversification.…”