Hsi-Wen Li

Phylogenetic relationships within the ‘core’ Laureae (Litsea complex, Lauraceae) inferred from sequences of the chloroplast gene matK and nuclear ribosomal DNA ITS regions

Abstract.A phylogenetic analysis of the ‘core’ Laureae (Litsea complex) was conducted using the chloroplast gene matK and nuclear ribosomal DNA ITS sequences to investigate generic relationships and boundaries within the complex. Despite low genetic divergence for matK, rooting of the tree with Sassafras resulted in Iteadaphne as the basal member of the complex and five resolved clades: a Neolitsea clade and then Laurus, Parasassafras, Litsea and Lindera clades in a large polytomy with unresolved Lindera sections plus Umbellularia. A combined analysis of the data (identical to the ITS results) provided a more resolved phylogeny of the Laureae, with four major lineages: the Laurus, Litsea, Lindera and Actinodaphne II clades. These clades also appear to reflect the importance of inflorescence structure and ontogeny within the Laureae, as well as data from cuticular micromorphology, but there was no support for traditional generic characters such as 2- versus 4- celled anthers. As a result, genera such as Actinodaphne, Litsea, Neolitsea and Lindera were polyphyletic in all analyses. Parasassafras was related to Sinosassafras by the matK data, but distant from it in the ITS and combined analyses.

MOLECULAR PHYLOGENETIC ANALYSIS OF THE PERSEA GROUP (LAURACEAE) AND ITS BIOGEOGRAPHIC IMPLICATIONS ON THE EVOLUTION OF TROPICAL AND SUBTROPICAL AMPHI-PACIFIC DISJUNCTIONS

UNLABELLED PREMISE OF THE STUDY The Persea group (Lauraceae) has a tropical and subtropical amphi-pacific disjunct distribution with most of its members, and it includes two Macaronesian species. The relationships within the group are still controversial, and its intercontinental disjunction has not been investigated with extensive sampling and precise time dating. • METHODS ITS and LEAFY intron II sequences of 78 Persea group species and nine other Lauraceae species were analyzed with maximum parsimony and Bayesian inference. Divergence time estimation employed Bayesian Markov chain Monte Carlo method under a relaxed clock. • KEY RESULTS Several traditional genera or subgenera within the Persea group form well-supported monophyletic groups except Alseodaphne and Dehaasia. The divergence time of the Persea group is estimated as ∼55.3 (95% higher posterior densities [HPD] 41.4-69.9) million years ago (mya). Two major divergences within the Persea group are estimated as ∼51.9 (95% HPD 38.9-63.9) mya and ∼48.5 (95% HPD 35.9-59.9) mya. • CONCLUSIONS Persea can be retained as a genus by the inclusion of Apollonias barbujana and exclusion a few species that do not fit into the established subgenera. A major revision is recommended for the delimitation between Alseodaphne, Dehaasia, and Nothaphoebe. We suggest that the Persea group originated from the Perseeae-Laureae radiation in early Eocene Laurasia. Its amphi-pacific disjunction results from the disruption of boreotropical flora by climatic cooling during the mid- to late Eocene. The American-Macaronesian disjunction may be explained by the long-distance dispersal.

Phylogeny and historical biogeography of Isodon (Lamiaceae): Rapid radiation in south-west China and Miocene overland dispersal into Africa

Rapid organismal radiations occurring on the Qinghai-Tibetan Plateau (QTP) and the mechanisms underlying Asia-Africa intercontinental disjunctions have both attracted much attention from evolutionary biologists. Here we use the genus Isodon (Lamiaceae), a primarily East Asian lineage with disjunct species in central and southern Africa, as a case study to shed light upon these processes. The molecular phylogeny and biogeographic history of Isodon were reconstructed using sequences of three plastid markers, the nuclear ribosomal internal transcribed spacer (nrITS), and a low-copy nuclear gene (LEAFY intron II). The evolution of chromosome numbers in this genus was also investigated using probabilistic models. Our results support a monophyletic Isodon that includes the two disjunct African species, both of which likely formed through allopolyploidy. An overland migration from Asia to Africa through Arabia during the early Miocene is proposed as the most likely explanation for the present disjunct distribution of Isodon. The opening of the Red Sea in the middle Miocene may appear to have had a major role in disrupting floristic exchange between Asia and Africa. In addition, a rapid radiation of Isodon was suggested to occur in the late Miocene. It corresponds with one of the major uplifts of the QTP and subsequent aridification events. Our results support the hypothesis that geological and climatic events play important roles in driving biological diversification of organisms distributed in the QTP area.

Phylogeny of Isodon (Schrad. ex Benth.) Spach (Lamiaceae) and Related Genera Inferred from Nuclear Ribosomal ITS, trnL-trnF Region, and rps16 Intron Sequences and Morphology

Abstract Phylogenetic analyses of Isodon and related genera using the nuclear ribosomal internal transcribed spacer (nrITS), cpDNA regions (trnL—trnF region and rps16 intron), and morphological data are presented. The results clarify the relationships among Isodon and its putative related genera and the question of the monophyly of Isodon and its relationship with Siphocranion. Siphocranion is a monophyletic genus and the sister clade to the remaining species; the new subtribe Siphocranioninae of tribe Ocimeae is described to accommodate it. Isodon, as currently circumscribed, is only monophyletic if Skapanthus oreophilus is included in it. Isodon forms a distinct subtribe Isodoninae within tribe Ocimeae and three strongly supported subclades are identified within the genus. In addition, a close relationship between Hanceola and Hyptis is indicated in the combined nrITS + cpDNA data set with Bayesian inference and this is also supported in morphological analyses, but more studies are needed to confirm this relationship. It is evident that subtribe Hanceolinae is polyphyletic as currently defined, so subtribe Hanceolinae is restricted to accommodate Hanceola alone. The relationships between Isodon and other genera within tribe Ocimeae are still unresolved; the newly erected subtribe Isodoninae is a monophyletic group representing a distinct lineage in subtribe Ociminae. The relationships among the species of the largest subclade C of Isodon are still poorly known. Additional studies of this group with additional data and more intensive taxon sampling might help to resolve these issues.

Origins and evolution of cinnamon and camphor: a phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae)

Tropical and subtropical amphi-Pacific disjunction is among the most fascinating distribution patterns, but received little attention. Here we use the fossil-rich Cinnamomum group, a primarily tropical and subtropical Asian lineage with some species distributed in Neotropics, Australasia and Africa to shed light upon this disjunction pattern. Phylogenetic and biogeographic analyses were carried out using sequences of three nuclear loci from 94 Cinnamomum group and 13 outgroup samples. Results show that although there are three clades within a monophyletic Cinnamomum group, Cinnamomum and previously recognized subdivisions within this genus were all rejected as natural groups. The Cinnamomum group appears to have originated in the widespread boreotropical paleoflora of Laurasia during the early Eocene (ca. 55Ma). The formation and breakup of the boreotropics seems to have then played a key role in the formation of intercontinental disjunctions within the Cinnamomum group. The first cooling interval (50-48Ma) in the late early Eocene resulted in a floristic discontinuity between Eurasia and North America causing the tropical and subtropical amphi-Pacific disjunction. The second cooling interval in the mid-Eocene (42-38Ma) resulted in the fragmentation of the boreotropics within Eurasia, leading to an African-Asian disjunction. Multiple dispersal events from North into South America occurred from the early Eocene to late Miocene and a single migration event from Asia into Australia appears to have occurred in the early Miocene.

Phylogeny of the Southeast Asian endemic genus Neocinnamomum H. Liu (Lauraceae)

A phylogenetic analysis of Neocinnamomum H. Liu and related genera was conducted using psbA–trnH, trnK cpDNA regions, and the ITS nrDNA segment. Neocinnamomum was confirmed to be monophyletic, and an evolutionary series of inflorescence development within the genus was recognized. The compound thyrse seen in N. caudatum is reduced to the few- to many-flowered condensed inflorescences with a poorly defined branching system seen in most species and ultimately to the 1-flowered inflorescence seen in N. atjehense. Consensus network analysis (CNA) suggested that long-branch attraction is responsible for the observed close relationship between Neocinnamomum and Cassytha L. in a combined analysis of the complete data. In contrast, the sister relationship of Neocinnamomum and Caryodaphnopsis seen in the Bayesian analyses of the partial combined matrix was supported by CNA and is also supported by morphology and wood and bark anatomy. The close similarity of the compound thyrse of less derived Neocinnamomum species to the thyrsoid inflorescences of some Caryodaphnopsis species is also seen as strong support for their affinity.

Phylogenetic relationships of the Litsea complex and core laureae (Lauraceae) using ITS and ETS sequences and morphology

Abstract Nuclear DNA ITS and ETS sequences of 71 representatives from nine genera and 11 sections of the core Laureae were combined with a matrix of morphological characters, analyzed using maximum parsimony with both equally and successively weighted characters, and analyzed for Bayesian inference, minimum evolution by neighbor joining, and maximum likelihood inference for molecular data alone. The large genera Actinodaphne Nees, Lindera Thunb., and Litsea Lam. were polyphyletic, as were Lindera sect. Aperula (Blume) Benth. and Litsea sections Conodaphne (Blume) Benth. & Hook. f., Cylicodaphne (Nees) Hook. f., and Tomingodaphne (Blume) Hook. f. In contrast, Neolitsea (Benth.) Merr. was monophyletic and terminal in a larger monophyletic lineage above an Actinodaphne grade. A major disparity exists between these molecular results and traditional morphology-based classifications within Lauraceae. These results suggest that the use of two- versus four-celled anthers for Laureae generic delimitation has resulted in polyphyletic or paraphyletic genera, and the character of dimerous versus trimerous flowers is of only limited phylogenetic value. Several of the major lineages in Laureae are supported by inflorescence morphology and ontogeny, with Laureae defined by short shoots with a vegetative terminal bud, splitting into thyrsoid (Actinodaphne and Neolitsea) versus racemose (Laurus, Litsea s. str., and Lindera s. str. and Lindera sect. Aperula), although there appear to be at least two different pathways to form the Laureae pseudo-umbel. Similarly, imbricate, early deciduous inflorescence basal involucral bracts defined an Actinodaphne–Neolitsea–Parasassafras–Sinosassafras clade, although within it, Neolitsea was defined in part by decussate, persistent bracts. Accordingly, our study indicates the need for caution in the use of morphology for assessing affinity in Laureae, as virtually all traditional morphological characteristics show high levels of homoplasy and/or reversal, but future research may help to resolve whether this indicates problems of homology or ontogenetic convergence.

DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China

Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH–psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China. We tested the ability of DNA barcoding to distinguish species and as an alternative tool for correcting species misidentification. We also used the rbcL+matK+trnH–psbA+ITS loci to investigate the phylogenetic relationships of the species examined. Among the gene regions and their combinations, ITS was the most efficient for identifying species (57.5%) and genera (70%). DNA barcoding also had a positive role for correcting species misidentification (10.8%). Furthermore, based on the results of the phylogenetic analyses, Chinese Lauraceae species formed three supported monophyletic clades, with the Cryptocarya group strongly supported (PP = 1.00, BS = 100%) and the clade including the Persea group, Laureae and Cinnamomum also receiving strong support (PP = 1.00, BS = 98%), whereas the Caryodaphnopsis–Neocinnamomum received only moderate support (PP = 1.00 and BS = 85%). This study indicates that molecular barcoding can assist in screening difficult to identify families like Lauraceae, detecting errors of species identification, as well as helping to reconstruct phylogenetic relationships. DNA barcoding can thus help with large-scale biodiversity inventories and rare species conservation by improving accuracy, as well as reducing time and costs associated with species identification.

Alseodaphnopsis: A new genus of Lauraceae based on molecular and morphological evidence

An investigation of a questionable species of the genus Alseodaphne led to the discovery of a new genus Alseodaphnopsis H. W. Li & J. Li, gen. nov., separated from Alseodaphne Nees, and a new species Alseodaphnopsis ximengensis H. W. Li & J. Li, sp. nov., endemic to Yunnan province, China. This new species is characterized by having big, axillary, paniculate inflorescences, as well as large, subglobose fruits. Based on DNA sequence data from two gene regions (nuclear ribosomal ITS and LEAFY intron II), we investigate its phylogenetic position within the Persea group. Phylogenies using maximum parsimony (MP) and Bayesian inference (BI) support the recognition of Alseodaphnopsis as a distinct genus but do not resolve well its relationship within the Persea group. The new genus is circumscribed, eight new combinations for its species are made, and a description and illustration of the new species are provided.