Cryptic Species Diversification of the Pedicularis siphonantha Complex (Orobanchaceae) in the Mountains of Southwest China Since the Pliocene

Plant species diversification in the Himalaya-Hengduan Mountains region: an example from an endemic lineage of Pedicularis (Orobanchaceae) in the role of floral specializations and rapid range expansions

The c. 270 endemic species of Pedicularis in the Himalaya-Hengduan Mountains (HHM) region exhibit high diversity in geographic distribution, elevational range and floral morphology. Many of these, including the species with the longest corolla tubes and beaked galeas, are monophyletic and represent a putative in situ radiation. In this study, we focus on the representative Clade 3 within the HHM region. We integrate the plastid phylogeny of this clade with environmental data and species distributions to infer environmental correlates of species diversity. We estimate macroevolutionary rates and reconstructed ancestral states for geographic ranges and corolla traits, and analyse patterns of range overlap and niche evolution to assess drivers of diversification in the HHM region. Our results show that the region from northwest Yunnan to southwest Sichuan is the centre of diversity for this clade of Pedicularis. Rates of diversification are associated with precipitation and multiple environmental factors. Multiple range expansions from the Sanjiang (Three Parallel Rivers) region, followed by allopatric speciation across the HHM region, contributed to early rapid diversification. Corolla traits are not significantly associated with species diversification. This study highlights the importance of integrated evidence for understanding species diversification dynamics and contributes to our understanding of the origins of the remarkable richness of plant species in the HHM region.

Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)

BACKGROUND

Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.

RESULTS

Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.

CONCLUSIONS

The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.

Pleistocene glaciation advances the cryptic speciation of Stellera chamaejasme L. in a major biodiversity hotspot

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer-scale population-level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco-morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67-0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming-cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts.

Responses of Three Pedicularis Species to Geological and Climatic Changes in the Qinling Mountains and Adjacent Areas in East Asia

The Qinling Mountains in East Asia serve as the geographical boundary between the north and south of China and are also indicative of climatic differences, resulting in rich ecological and species diversity. However, few studies have focused on the responses of plants to geological and climatic changes in the Qinling Mountains and adjacent regions. Therefore, we investigated the evolutionary origins and phylogenetic relationships of three Pedicularis species in there to provide molecular evidence for the origin and evolution of plant species. Ecological niche modeling was used to predict the geographic distributions of three Pedicularis species during the last interglacial period, the last glacial maximum period, and current and future periods, respectively. Furthermore, the distribution patterns of climate fluctuations and the niche dynamics framework were used to assess the equivalence or difference of niches among three Pedicularis species. The results revealed that the divergence of three Pedicularis species took place in the Miocene and Holocene periods, which was significantly associated with the large-scale uplifts of the Qinling Mountains and adjacent regions. In addition, the geographic distributions of three Pedicularis species have undergone a northward migration from the past to the future. The most important environmental variables affecting the geographic distributions of species were the mean diurnal range and annual mean temperature range. The niche divergence analysis suggested that the three Pedicularis species have similar ecological niches. Among them, P. giraldiana showed the highest niche breadth, covering nearly all of the climatic niche spaces of P. dissecta and P. bicolor. In summary, this study provides novel insights into the divergence and origins of three Pedicularis species and their responses to climate and geological changes in the Qinling Mountains and adjacent regions. The findings have also provided new perspectives for the conservation and management of Pedicularis species.

Plastome phylogenomics and morphological traits analyses provide new insights into the phylogenetic position, species delimitation and speciation of Triplostegia (Caprifoliaceae)

BACKGROUND

The genus Triplostegia contains two recognized species, T. glandulifera and T. grandiflora, but its phylogenetic position and species delimitation remain controversial. In this study, we assembled plastid genomes and nuclear ribosomal DNA (nrDNA) cistrons sampled from 22 wild Triplostegia individuals, each from a separate population, and examined these with 11 recently published Triplostegia plastomes. Morphological traits were measured from herbarium specimens and wild material, and ecological niche models were constructed.

RESULTS

Triplostegia is a monophyletic genus within the subfamily Dipsacoideae comprising three monophyletic species, T. glandulifera, T. grandiflora, and an unrecognized species Triplostegia sp. A, which occupies much higher altitude than the other two. The new species had previously been misidentified as T. glandulifera, but differs in taproot, leaf, and other characters. Triplotegia is an old genus, with stem age 39.96 Ma, and within it T. glandulifera diverged 7.94 Ma. Triplostegia grandiflora and sp. A diverged 1.05 Ma, perhaps in response to Quaternary climate fluctuations. Niche overlap between Triplostegia species was positively correlated with their phylogenetic relatedness.

CONCLUSIONS

Our results provide new insights into the species delimitation of Triplostegia, and indicate that a taxonomic revision of Triplostegia is needed. We also identified that either rpoB-trnC or ycf1 could serve as a DNA barcode for Triplostegia.

Chromosome-scale assembly and analysis of Melilotus officinalis genome for SSR development and nodulation genes analysis

Melilotus officinalis is an important legume crop with forage and Chinese medicinal value. The unknown genome of M. officinalis restricted the domestication and utilization of the species and its germplasm resource diversity. A chromosome-scale assembly of the M. officinalis genome was assembled and analysed. The 976.27 Mb of genome was divided into eight chromosomes covering 99.16% of the whole genome. A total of 50022 genes were predicted in the genome. M. officinalis and Melilotus albus shared a common ancestor 0.5-5.65 million years ago (MYA). A genome-wide doubling event occurred 68.93 MYA according to the synonymous nucleotide-substitution values. A total of 552102 tandem repeats were predicted, and 46004 SSR primers of TRs with 10 or more base pairs were developed and designed. The elucidation of the M. officinalis genome provides a compelling model system for studying the genetic, evolutionary and biosynthesis of this legume.