Climatic niche divergence explains angiosperm diversification across clades in China

Diversification rates are critically important for understanding patterns of species richness among clades. However, the effects of climatic niche width on plant diversification rates remain to be elucidated. Based on the phylogenetic, climatic, and distributional information of angiosperms in China, a total of 26 906 species from 182 families were included in this study. We aimed to test relationships between diversification rate and climatic niche width and climatic niche width related variables (including climatic niche divergence, climatic niche position, geographic extent, and climatic niche evolutionary rate) using phylogenetic methods. We found that climatic niche divergence had the largest unique contribution to the diversification rate, while the unique effects of climatic niche width, climatic niche position, geographic extent, and climatic niche evolutionary rate on the diversification rate were negligible. We also observed that the relationship between diversification rate and climatic niche divergence was significantly stronger than the null assumption (artefactual relationship between diversification and clade-level climatic niche width by sampling more species). Our study supports the hypothesis that wider family climatic niche widths explain faster diversification rates through a higher climatic niche divergence rather than through higher geographic extent, higher climatic niche evolutionary rate, or separated climatic niche position. Hence, the results provide a potential explanation for large-scale diversity patterns within families of plants.     

Genomic analyses reveal natural selection on reproduction related genes between two closely related Populus (Salicaceae) species

Identifying the factors that cause reproductive isolation and their relative importance in species divergence is crucial to our understanding of speciation processes. In most species, natural selection is commonly considered to play a large role in driving speciation. Based on whole genome re-sequencing data from 27 Populus alba and 28 Populus adenopoda individuals, we explored the factors related to reproductive isolation of these two closely related species. The results showed that the two species diverged ~5–10 million years ago (Ma), when the Qinghai–Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid. In highly differentiated genomic regions, the relative divergence (F_ST) and absolute divergence (d_xy) were significantly higher than the genomic background, θπ and shared polymorphisms decreased whereas fixed differences increased, which indicated that natural selection played a key role in the reproductive isolation of the two species. In addition, we found several genes that were related to reproduction that may be involved in explaining the reproductive isolation. Using phylogenetic trees resolved from haplotype data of Populus tomentosa and P. adenopoda, the maternal origin of P. tomentosa from P. adenopoda was likely to be located in Hubei and Chongqing Provinces.     

Mutational meltdown or controlled chain reaction: The dynamics of rapid plastome evolution in the hyperdiversity of Poaceae

The study of genomic structural evolution associated with accelerated evolutionary rates that result in avoidance of meltdown and increase biodiversity is becoming ever more possible as the number of available plastomes increases. To more comprehensively analyze rate heterogeneity among monocots and within Poaceae, we sequenced plastomes from four Poaceae species, combined them with publicly available data from ~200 plastomes, and conducted comparative analyses to quantify the pattern of rate heterogeneity between different lineages, functional groups, and periods of evolutionary time. We compared structural differences across the Poaceae to quantify how changes in plastome size correspond to different genomic subunits and the evolution of IR–SC junction boundaries. The substitution rates among ancestral Poaceae were inferred to be exceptionally rapid compared to other monocots but slowed after divergence into extant lineages, which could not be sufficiently explained by positive selection. As such, rapid rates in the ancestral lineage leading to Poaceae might be more closely linked to large-scale structural changes like the loss of ycf1 and ycf2. The total increase in plastome size across Poaceae was positively correlated with the total length of intergenic spacers, tandem repeats, and dispersed repeats as well as large single copy, and inverted repeats (IRs). The continuous evolution of IR–SC junction boundaries was asynchronous with sizes of total genome and subunits across Poaceae. Future work is needed to better understand what factors in ancestral Poaceae evolved to harness such rapid rates of plastome evolution, avoid a mutational meltdown, and escape the stagnation of strong purifying selection as well as if these factors could be utilized to synthetically control rates.     

Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana

Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global F_ST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.     

Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data

Oresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. The taxonomy of Mukdenia, especially of M. acanthifolia, has been controversial. To address this, we produced plastid and mitochondrial data using genome skimming for Mukdenia acanthifolia and Mukdenia rossii, including three individuals of each species. We assembled complete plastomes, mitochondrial CDS and nuclear ribosomal ETS/ITS sequences using these data. Comparative analysis shows that the plastomes of Mukdenia and Oresitrophe are relatively conservative in terms of genome size, structure, gene content, RNA editing sites and codon usage. Five plastid regions that represent hotspots of change (trnH-psbA, psbC-trnS, trnM-atpE, petA-psbJ and ccsA-ndhD) are identified within Mukdenia, and six regions (trnH-psbA, petN-psbM, trnM-atpE, rps16-trnQ, ycf1 and ndhF) contain a higher number of species-specific parsimony-informative sites that may serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between Mukdenia and Oresitrophe, we combined our data with published data based on three different datasets. The monophyly of each species (Oresitrophe rupifraga, M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M. acanthifolia), O. rupifraga) are well supported in trees reconstructed using the complete plastome sequences, but M. acanthifolia and M. rossii did not form a separate clade in the trees based on ETS + ITS data, while the mitochondrial CDS trees are not well-resolved. We found low recovery of genes in the Angiosperms353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordance between trees reconstructed from organellar and nuclear data. Considering its morphological distinctiveness and our molecular phylogenetic results, we strongly recommend that M. acanthifolia be treated as a distinct species.