A DNA barcode library for woody plants in tropical and subtropical China.

The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.

Adaptive genetic diversity of dominant species contributes to species co-existence and community assembly.

The synthesis of evolutionary biology and community ecology aims to understand how genetic variation within one species can shape community properties and how the ecological properties of a community can drive the evolution of a species. A rarely explored aspect is whether the interaction of genetic variation and community properties depends on the species' ecological role. Here we investigated the interactions among environmental factors, species diversity, and the within-species genetic diversity of species with different ecological roles. Using high-throughput DNA sequencing, we genotyped a canopy-dominant tree species, Parashorea chinensis, and an understory-abundant species, Pittosporopsis kerrii, from fifteen plots in Xishuangbanna tropical seasonal rainforest and estimated their adaptive, neutral and total genetic diversity; we also surveyed species diversity and assayed key soil nutrients. Structural equation modelling revealed that soil nitrogen availability created an opposing effect in species diversity and adaptive genetic diversity of the canopy-dominant Pa. chinensis. The increased adaptive genetic diversity of Pa. chinensis led to greater species diversity by promoting co-existence. Increased species diversity reduced the adaptive genetic diversity of the dominant understory species, Pi. kerrii, which was promoted by the adaptive genetic diversity of the canopy-dominant Pa. chinensis. However, such relationships were absent when neutral genetic diversity or total genetic diversity were used in the model. Our results demonstrated the important ecological interaction between adaptive genetic diversity and species diversity, but the pattern of the interaction depends on the identity of the species. Our results highlight the significant ecological role of dominant species in competitive interactions and regulation of community structure.

Plastome-based phylogeny improves community phylogenetics of subtropical forests in China.

Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

Founder effects, post-introduction evolution and phenotypic plasticity contribute to invasion success of a genetically impoverished invader.

Multiple mechanisms may act synergistically to promote success of invasive plants. Here, we tested the roles of three non-mutually exclusive mechanisms-founder effects, post-introduction evolution and phenotypic plasticity-in promoting invasion of Chromolaena odorata. We performed a common garden experiment to investigate phenotypic diversification and phenotypic plasticity of the genetically impoverished invader in response to two rainfall treatments (ambient and 50% rainfall). We used ancestor-descendant comparisons to determine post-introduction evolution and the QST-FST approach to estimate past selection on phenotypic traits. We found that eight traits differed significantly between plants from the invasive versus native ranges, for two of which founder effects can be inferred and for six of which post-introduction evolution can be inferred. The invader experienced strong diversifying selection in the invasive range and showed clinal variations in six traits along water and/or temperature gradients. These clinal variations are likely attributed to post-introduction evolution rather than multiple introductions of pre-adapted genotypes, as most of the clinal variations were absent or in opposite directions from those for native populations. Compared with populations, rainfall treatments explained only small proportions of total variations in all studied traits for plants from both ranges, highlighting the importance of heritable phenotypic differentiation. In addition, phenotypic plasticity was similar for plants from both ranges although neutral genetic diversity was much lower for plants from the invasive range. Our results showed that founder effects, post-introduction evolution and phenotypic plasticity may function synergistically in promoting invasion success of C. odorata.

Tertiary origin and pleistocene diversification of dragon blood tree (Dracaena cambodiana-Asparagaceae) populations in the Asian tropical forests.

BACKGROUND: The origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests. METHODS: WE ANALYZED NUCLEOTIDE SEQUENCE DATA OF TWO CHLOROPLAST DNA (CPDNA: atpB-rbcL and trnD-trnT) regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively) distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa) and BEAST software programs. RESULTS: A significant phylogeographic structure (N ST = 0.876, G ST = 0.796, F ST-SSR = 0.329, R ST = 0.449; N ST>G ST, R ST>F ST-SSR, P<0.05) and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period. CONCLUSIONS: The results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction-recolonization during the Pleistocene may have contributed to the fast diversification in D. cambodiana.

Isolation and characterization of microsatellite markers in Beilschmiedia roxburghiana (Lauraceae).

PREMISE OF THE STUDY: Although there are as many as 250 species in the genus Beilschmiedia, their genetic diversity has been poorly investigated. Our objective was to develop microsatellite markers for B. roxburghiana to study its genetic diversity for the sustainable management of this species. • METHODS AND RESULTS: Using the microsatellite-enriched library and PCR-based screening method, 22 microsatellite markers were developed and 10 showed high polymorphism in a population. The number of alleles per locus for these 10 microsatellites ranged from five to 19. The observed and expected heterozygosities ranged from 0.298 to 1.000 and from 0.314 to 0.878, respectively. • CONCLUSIONS: Our results from the 10 highly polymorphic microsatellites indicate that the principal reproductive mode of B. roxburghiana is clonal in the studied population. These microsatellites will facilitate further studies on genetic diversity and structure in B. roxburghiana.

Isolation and characterization of microsatellite markers for a worldwide invasive weed, Chromolaena odorata (Asteraceae).

PREMISE OF THE STUDY: Microsatellite loci were isolated and characterized for a worldwide invasive weed Chromolaena odorata (Asteraceae) to elucidate the population genetic structure and invasive history. • METHODS AND RESULTS: A total of 14 microsatellite primer pairs were developed using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol, and their polymorphism was assessed in two natural populations of C. odorata from Mexico and Trinidad and Tobago. Eleven loci showed polymorphism and eight of these loci were successfully amplified in Ageratina adenophora, another invasive weed related to C. odorata. • CONCLUSIONS: These microsatellite markers are useful for investigating the population genetic structure and the history of range expansion of these invasive species.

Contrasting coarse and fine scale genetic structure among isolated relic populations of Kmeria septentrionalis.

Trees of the Magnoliaceae family are of scientific, cultural and socio-economic importance. Kmeria septentrionalis Dandy (Magnoliaceae) is a dioecious tree, found in small, isolated, relic populations in Southern China, and is subject to extensive protection due to its rarity and high economic values. To improve conservation outcomes and in particular, germplasm collection guidelines, information on spatial genetic structure of the species is required. In this study, we investigated the spatial genetic structure and genetic diversity of 161 individuals of K. septentrionalis collected from five natural populations using AFLP molecular markers. Within-population genetic variation was measured, with percentage of polymorphic bands (PPB) ranged from 63% to 87%, while H (S) (genetic diversity within population) varied from 0.185 to 0.244 with a mean of 0.215 ± 0.025. Significant genetic differentiations were revealed between pairwise populations, indicating each population existing as an independent evolutionarily significant unit. Mantel test results showed no pattern of isolation-by-distance among populations separated by large distance. Fine scale spatial patterns of genetic variation suggested significant effects of isolation-by-distance within population at distances of 22 m. The results of contrasting genetic structure at coarse and fine scale in K. septentrionalis may indicate restricted pollen flow and seed dispersal at fine scales, and separated evolution in isolated populations over long period of time at coarser scales. Finally, we make several suggestions for improved management practices that may assist in the conservation of this species.

Isolation and characterization of microsatellite markers in an endangered species Dracaena cambodiana (Liliaceae).

UNLABELLED: • PREMISE OF THE STUDY: The development of microsatellite primers in the endangered species Dracaena cambodiana will be the foundation for genetic and conservation studies of D. cambodiana and several Dracaena species. • METHODS AND RESULTS: A total of 26 microsatellite markers were developed in Chinese populations of D. cambodiana, using the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) protocol. Among them, sixteen primer pairs generated polymorphic loci (fourteen of them successfully amplified in other four Dracaena species) and ten primer pairs produced monomorphic loci. • CONCLUSIONS: These microsatellite markers could be used in the further investigation of population genetics of D. cambodiana and other Dracaena species.