Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy.

BACKGROUND AND AIMS: Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance and ecological significance, a well-resolved phylogeny for global Artemisia, a natural generic delimitation and infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling and insufficient information on DNA markers. Its morphological characters, such as capitulum, life form and leaf, show marked variations and are widely used in its infrageneric taxonomy. However, their evolution within Artemisia is poorly understood. Here, we aimed to reconstruct a well-resolved phylogeny for global Artemisia via a phylogenomic approach, to infer the evolutionary patterns of its key morphological characters and to update its circumscription and infrageneric taxonomy. METHODS: We sampled 228 species (258 samples) of Artemisia and its allies from both fresh and herbarium collections, covering all the subgenera and its main geographical areas, and conducted a phylogenomic analysis based on nuclear single nucleotide polymorphisms (SNPs) obtained from genome skimming data. Based on the phylogenetic framework, we inferred the possible evolutionary patterns of six key morphological characters widely used in its previous taxonomy. KEY RESULTS: The genus Kaschgaria was revealed to be nested in Artemisia with strong support. A well-resolved phylogeny of Artemisia consisting of eight highly supported clades was recovered, two of which were identified for the first time. Most of the previously recognized subgenera were not supported as monophyletic. Evolutionary inferences based on the six morphological characters showed that different states of these characters originated independently more than once. CONCLUSIONS: The circumscription of Artemisia is enlarged to include the genus Kaschgaria. The morphological characters traditionally used for the infrageneric taxonomy of Artemisia do not match the new phylogenetic tree. They experienced a more complex evolutionary history than previously thought. We propose a revised infrageneric taxonomy of the newly circumscribed Artemisia, with eight recognized subgenera to accommodate the new results.

The emergence of the hyperinvasive vine, Mikania micrantha (Asteraceae), via admixture and founder events inferred from population transcriptomics.

Biological invasions that involve well-documented rapid adaptations to new environments provide unequalled opportunities for testing evolutionary hypotheses. Mikania micrantha Kunth (Asteraceae), a perennial herbaceous vine native to tropical Central and South America, successfully invaded tropical Asia in the early 20th century. It is regarded as one of the most aggressive weeds in the world. To elucidate the molecular and evolutionary processes underlying this invasion, we extensively sampled this weed throughout its invaded range in South-East and South Asia and surveyed its genetic structure using variants detected from population transcriptomics. Clustering results suggest that more than one source population contributed to this invasion. Computer simulations using genomewide genetic variation support a scenario of admixture and founder events during invasion. The genes differentially expressed between native and invasive populations were found to be involved in oxidative and high light intensity stress responses, pointing to a possible ecological mechanism of adaptation. Our results provide a foundation for further detailed mechanistic and population studies of this ecologically and economically important invasion. This line of research promises to provide new mitigation strategies for invasive species as well as insights into mechanisms of adaptation.

The Use of DNA Barcoding on Recently Diverged Species in the Genus Gentiana (Gentianaceae) in China.

DNA barcoding of plants poses particular challenges, especially in differentiating, recently diverged taxa. The genus Gentiana (Gentianaceae) is a species-rich plant group which rapidly radiated in the Himalaya-Hengduan Mountains in China. In this study, we tested the core plant barcode (rbcL + matK) and three promising complementary barcodes (trnH-psbA, ITS and ITS2) in 30 Gentiana species across 6 sections using three methods (the genetic distance-based method, Best Close Match and tree-based method). rbcL had the highest PCR efficiency and sequencing success (100%), while the lowest sequence recoverability was from ITS (68.35%). The presence of indels and inversions in trnH-psbA in Gentiana led to difficulties in sequence alignment. When using a single region for analysis, ITS exhibited the highest discriminatory power (60%-74.42%). Of the combinations, matK + ITS provided the highest discrimination success (71.43%-88.24%) and is recommended as the DNA barcode for the genus Gentiana. DNA barcoding proved effective in assigning most species to sections, though it performed poorly in some closely related species in sect. Cruciata because of hybridization events. Our analysis suggests that the status of G. pseudosquarrosa needs to be studied further. The utility of DNA barcoding was also verified in authenticating 'Qin-Jiao' Gentiana medicinal plants (G. macrophylla, G. crassicaulis, G. straminea, and G. dahurica), which can help ensure safe and correct usage of these well-known Chinese traditional medicinal herbs.

Development and characterization of EST-SSR markers in the invasive weed Mikania micrantha (Asteraceae).

PREMISE OF THE STUDY: Microsatellite markers were developed for the invasive species Mikania micrantha to investigate its invasion history. Transcriptome sequencing projects offer a potential source for the development of new markers. METHODS AND RESULTS: Sixteen polymorphic simple sequence repeat (SSR) markers derived from ESTs were identified and screened in 36 samples of M. micrantha. The number of alleles per locus ranged from two to four, with an average of 2.7 alleles per locus. The expected heterozygosity and observed heterozygosity ranged from 0 to 0.7754 and 0 to 0.8333, respectively. CONCLUSIONS: These EST-SSR markers may be useful for further investigation of the population genetics of M. micrantha as additional tools to trace its invasion history.

Slatkin's Paradox: when direct observation and realized gene flow disagree. A case study in Ficus.

In flying insects, there is frequently a lack of congruence between empirical estimates of local demographic parameters and the prediction that differentiation between populations should decrease with increasing dispersal, a puzzling phenomenon known as Slatkin's Paradox. Here, we generalize Slatkin's Paradox to other taxa, drawing from available information on dispersal to predict the relative importance of pollen vs. seed migration in structuring broad-scale patterns of genetic variation in Ficus hirta, a dioecious fig whose pollen is dispersed by minute, species-specific fig wasps and whose seeds are disseminated by a variety of vagile vertebrates (especially bats and birds). Local-scale observational and genetic studies of dioecious understory figs suggest comparable rates of pollen and seed migration. In contrast, we found unusually low nuclear differentiation (F(ST) =0.037, R(ST) =0.074) and high chloroplast differentiation (G(ST) =0.729, N(ST) =0.798) among populations separated by up to 2850km, leading us to reject the hypothesis of equal pollen and seed migration rates and to obtain an equilibrium estimate of the ratio of pollen to seed migration of r=16.2-36.3. We reconcile this example of Slatkin's Paradox with previously published data for dioecious figs and relate it to the picture of exceptionally long-distance wasp-mediated pollen dispersal that is emerging for large monoecious fig trees. More generally, we argue that Slatkin's Paradox is a general phenomenon and suggest it may be common in plants and animals.