Ting-Shuang Yi

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications.

Background The ginseng family (Araliaceae) includes a number of economically important plant species. Previously phylogenetic studies circumscribed three major clades within the core ginseng plant family, yet the internal relationships of each major group have been poorly resolved perhaps due to rapid radiation of these lineages. Recent studies have shown that phyogenomics based on chloroplast genomes provides a viable way to resolve complex relationships. Methodology/Principal Findings We report the complete nucleotide sequences of five Araliaceae chloroplast genomes using next-generation sequencing technology. The five chloroplast genomes are 156,333–156,459 bp in length including a pair of inverted repeats (25,551–26,108 bp) separated by the large single-copy (86,028–86,566 bp) and small single-copy (18,021–19,117 bp) regions. Each chloroplast genome contains the same 114 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 80 protein coding genes. Gene size, content, and order, AT content, and IR/SC boundary structure are similar among all Araliaceae chloroplast genomes. A total of 140 repeats were identified in the five chloroplast genomes with palindromic repeat as the most common type. Phylogenomic analyses using parsimony, likelihood, and Bayesian inference based on the complete chloroplast genomes strongly supported the monophyly of the Asian Palmate group and the Aralia-Panax group. Furthermore, the relationships among the sampled taxa within the Asian Palmate group were well resolved. Twenty-six DNA markers with the percentage of variable sites higher than 5% were identified, which may be useful for phylogenetic studies of Araliaceae. Conclusion The chloroplast genomes of Araliaceae are highly conserved in all aspects of genome features. The large-scale phylogenomic data based on the complete chloroplast DNA sequences is shown to be effective for the phylogenetic reconstruction of Araliaceae.

Multi-gene analysis provides a well-supported phylogeny of Rosales

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae.

Evolution of Rosaceae fruit types based on nuclear phylogeny in the context of geological times and genome duplication

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.

Phylogenetic inferences in Prunus (Rosaceae) using chloroplast ndhF and nuclear ribosomal ITS sequences

Sequences of the chloroplast ndhF gene and the nuclear ribosomal ITS regions are employed to reconstruct the phylogeny of Prunus (Rosaceae), and evaluate the classification schemes of this genus. The two data sets are congruent in that the genera Prunus s.l. and Maddenia form a monophyletic group, with Maddenia nested within Prunus. However, the ndhF data set is incongruent with the ITS data supporting two major groups within Prunus: one consisting of subgenera Laurocerasus (including Pygeum) and Padus as well as the genus Maddenia and another of subgenera Amygdalus, Cerasus, and Prunus. The ITS data, on the other hand, support a clade composed of subgenera Amygdalus and Prunus and Prunus sect. Microcerasus in addition to a paraphyletic grade of subgenera Laurocerasus and Padus (and the genus Maddenia) taxa. In general, the subgeneric classifications of Prunus s.l. are not supported. The ITS and ndhF phylogenies differ mainly in interspecific relationships and the relative position of the Padus/Laurocerasus group. Both ITS and ndhF data sets suggest that the formerly recognized genus Pygeum is polyphyletic and that the distinction of the subgenera Padus and Laurocerasus is not supported. The biogeographic interactions of the temperate and tropical members in the Padus/Laurocerasus/Maddenia alliance including Pygeum are shown to be highly dynamic and complex.

Global legume diversity assessment : concepts, key indicators, and strategies

While many plant species are considered threatened under anthropogenic pressure, it remains uncertain how rapidly we are losing plant species diversity. To fill this gap, we propose a Global Legume Diversity Assessment (GLDA) as the first step of a global plant diversity assessment. Here we describe the concept of GLDA and its feasibility by reviewing relevant approaches and data availability. We conclude that Fabaceae is a good proxy for overall angiosperm diversity in many habitats and that much relevant data for GLDA are available. As indicators of states, we propose comparison of species richness with phylogenetic and functional diversity to obtain an integrated picture of diversity. As indicators of trends, species loss rate and extinction risks should be assessed. Specimen records and plot data provide key resources for assessing legume diversity at a global scale, and distribution modeling based on these records provide key methods for assessing states and trends of legume diversity. GLDA has started in Asia, and we call for a truly global legume diversity assessment by wider geographic collabora- tions among various scientists.

Molecular phylogeny of the nettle family (Urticaceae) inferred from multiple loci of three genomes and extensive generic sampling

Urticaceae is one of the larger Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae, using maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) to analyze the DNA sequence data from two nuclear (ITS and 18S), four chloroplast (matK, rbcL, rpll4-rps8-infA-rpl36, trnL-trnF) and one mitochondrial (matR) loci. We sampled 169 accessions representing 122 species, representing 47 of the 54 recognized genera within Urticaceae, including four of the six sometimes separated as Cecropiaceae. Major results included: (1) Urticaceae including Cecropiaceae was monophyletic; (2) Cecropiaceae was biphyletic, with both lineages nested within Urticaceae; (3) Urticaceae can be divided into four well-supported clades; (4) previously erected tribes or subfamilies were broadly supported, with some additions and alterations; (5) the monophyly of many genera was supported, whereas Boehmeria, Pellionia, Pouzolzia and Urera were clearly polyphyletic, while Urtica and Pilea each had a small genus nested within them; (6) relationships between genera were clarified, mostly with substantial support. These results clarify that some morphological characters have been overstated and others understated in previous classifications of the family, and provide a strong foundation for future studies on biogeography, character evolution, and circumscription of difficult genera.

Genetic Diversity and Population Structure: Implications for Conservation of Wild Soybean (Glycine soja Sieb. et Zucc) Based on Nuclear and Chloroplast Microsatellite Variation

Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from 43 locations sampled across its range in China, Japan and Korea were analyzed using 20 nuclear (nSSRs) and five chloroplast microsatellite markers (cpSSRs) to reveal its genetic diversity and population structure. Relatively high nSSR diversity was found in wild soybean compared with other self-pollinated species, and the region of middle and lower reaches of Yangtze River (MDRY) was revealed to have the highest genetic diversity. However, cpSSRs suggested that Korea is a center of diversity. High genetic differentiation and low gene flow among populations were detected, which is consistent with the predominant self-pollination of wild soybean. Two main clusters were revealed by MCMC structure reconstruction and phylogenetic dendrogram, one formed by a group of populations from northwestern China (NWC) and north China (NC), and the other including northeastern China (NEC), Japan, Korea, MDRY, south China (SC) and southwestern China (SWC). Contrib analyses showed that southwestern China makes the greatest contribution to the total diversity and allelic richness, and is worthy of being given conservation priority.

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.

Biogeographic disjunction between eastern Asia and North America in the Adiantum pedatum complex (Pteridaceae)

PREMISE OF THE STUDY Biogeographic analyses of ferns with an eastern Asian-North American disjunction are few. The Adiantum pedatum complex has such a disjunct distribution. The monophyly of the complex needs to be tested and diversification history of the four species needs to be reconstructed. METHODS Plastid (atpA, atpB, rbcL, trnL-F, and rps4-trnS) sequences of 100 accessions representing the biogeographic diversity of Adiantum were analyzed with parsimony and Bayesian inference. Biogeography of the Adiantum pedatum complex was inferred using programs DIVA and LAGRANGE. Divergence times of clades were estimated with the program BEAST. KEY RESULTS The A. pedatum complex is monophyletic and sister to the eastern Asian A. edentulum. Accessions of A. pedatum do not form a clade; instead three subgroups are recognizable. The clade of A. aleuticum and A. viridimontanum is nested within A. pedatum. The Asian A. myriosorum is sister to the A. pedatum-A. aleuticum clade. Both DIVA and LAGRANGE analyses suggest an eastern Asian origin of the A. pedatum complex. The age of the crown A. pedatum complex is dated to be at 4.27 (2.24-6.57) million years ago. CONCLUSIONS The currently recognized eastern Asian-North American disjunct species A. pedatum needs to be segregated into three species, corresponding to populations in eastern North America, China, and Japan. The eastern Asian-North American disjunction in the complex is inferred to be the result of two intercontinental migrations, one from eastern Asia into North America in the late Tertiary and the other from North America back to eastern Asia in the Pleistocene.