Today East Asia harbors many “relict” plant species whose ranges were much larger during the Paleogene-Neogene and earlier. The ecological and climatic conditions suitable for these relict species have not been identified. Here, we map the abundance and distribution patterns of relict species, showing high abundance in the humid subtropical/warm-temperate forest regions. We further use Ecological Niche Modeling to show that these patterns align with maps of climate refugia, and we predict species’ chances of persistence given the future climatic changes expected for East Asia. By 2070, potentially suitable areas with high richness of relict species will decrease, although the areas as a whole will probably expand. We identify areas in southwestern China and northern Vietnam as long-term climatically stable refugia likely to preserve ancient lineages, highlighting areas that could be prioritized for conservation of such species.

Classification of the tribe Cardueae in natural subtribes has always been a challenge due to the lack of support of some critical branches in previous phylogenies based on traditional Sanger markers. With the aim to propose a new subtribal delimitation, we applied a Hyb-Seq approach to a set of 76 Cardueae species representing all the subtribes and informal groups defined in the tribe, targeting 1061 nuclear conserved orthology loci (COS) designed for Compositae and obtaining chloroplast coding regions as byproduct of off-target reads. For the extraction of target nuclear data, we used two strategies, PHYLUCE and HybPiper, and 776 and 1055 COS loci were recovered with each of them, respectively. Additionally, 87 chloroplast genes were assembled and annotated. With the three datasets, phylogenetic relationships within the tribe were reconstructed under approaches of concatenation (using supermatrices as input for maximum likelihood analysis with RAxML) and coalescence (species tree estimated with ASTRAL based on the individual gene trees of each COS locus). The phylogenetic analyses of the nuclear datasets fully resolved virtually all nodes with very high support. Although nuclear and plastid tree topologies are highly congruent, they still present some incongruences, which are shortly discussed. On the basis of the phylogenies obtained, we propose a new taxonomic scheme of 12 monophyletic and morphologically consistent subtribes: Carlininae, Cardopatiinae, Echinopsinae, Dipterocominae (new), Xerantheminae (new), Berardiinae (new), Staehelininae (new), Onopordinae (new), Carduinae (redelimited), Arctiinae (new), Saussureinae (new), and Centaureinae. Another main key result of the study was the high resolution recovered at the backbone of the Cardueae tree, which led to obtain better inter-subtribal relationships. Using as tree base the nuclear HybPiper phylogeny, we updated the temporal framework for the origin and diversification of the tribe and subtribes. Overall, the power of Hyb-Seq is demonstrated to solve relationships traditionally suggested by morphology but never recovered with support using Sanger sequencing of a few DNA markers.

This study, using species distribution modeling (involving a new approach that allows for uncertainty), predicts the distribution of climatically suitable areas prevailing during the mid-Holocene, the Last Glacial Maximum (LGM), and at present, and estimates the potential formation of new habitats in 2070 of the endangered and rare Tertiary relict tree Davidia involucrata Baill. The results regarding the mid-Holocene and the LGM demonstrate that south-central and southwestern China have been long-term stable refugia, and that the current distribution is limited to the prehistoric refugia. Given future distribution under six possible climate scenarios, only some parts of the current range of D. involucrata in the mid-high mountains of south-central and southwestern China would be maintained, while some shift west into higher mountains would occur. Our results show that the predicted suitable area offering high probability (0.5‒1) accounts for an average of only 29.2% among the models predicted for the future (2070), making D. involucrata highly vulnerable. We assess and propose priority protected areas in light of climate change. The information provided will also be relevant in planning conservation of other paleoendemic species having ecological traits and distribution ranges comparable to those of D. involucrata.

2019. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. Applications in Plant Sciences 7(10): e11295. PREMISE:Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS:Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS:Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION:The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.

Saussurea is one of the largest genera of Asteraceae tribe Cardueae, comprising about 460 species from the Northern Hemisphere with most species distributed on the Qinghai-Tibetan Plateau (QTP) and adjacent areas. A well-supported phylogenetic framework was established based on whole chloroplast genomes of 126 taxa of Saussurea and 14 additional Cardueae taxa analyzed with Bayesian inference and Maximum Likelihood. Our results, however, are inconsistent with previous subgeneric classification of Saussurea on the whole. Some groups shown certain relationships: subgenus Eriocoryne was almost completely delimited, and subgenus Theodorea, subgenus Saussurea section Laguranthera and section Rosulascentes appear closely related. Molecular dating and biogeographic analysis suggest that Saussurea originated in Hengduan Mountains about 18.54 Mya and rapid diversification in this area and a dispersal northwards took place since then in several migration patterns. The barrier effect of QTP might the main reason for the origin especially for the diversification of Saussurea. Both continuous uplift of the QTP and global cooling since mid-Miocene played important roles in the geographic expansion and diffusion; the later, especially, accelerated northward dispersal.