Kuo-Fang Chung

Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora

BackgroundThe picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia, a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species.ResultsExcept for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia (SVLB), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium, Leprosae, and Petermannia, are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB, coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area.ConclusionsBased on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium: B. cavaleriei, B. pulvinifera, and B. wangii; sect. Leprosae: B. cylindrica and B. leprosa; sect. Petermannia: B. sinofloribunda). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB. Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.

Molecular systematics of the trans-pacific alpine genus Oreomyrrhis (apiaceae) : Phylogenetic affinities and biogeographic implications

The alpine ecosystem is the only terrestrial biogeographic unit that is distributed globally. Studying phylogenetics of the plant species in this widespread ecosystem can provide insights into the historical biogeographic processes that have shaped the global biodiversity. The trans-Pacific disjunct alpine genus Oreomyrrhis (Apiaceae) was investigated using nrDNA ITS sequences to test the taxonomic and biogeographic hypotheses. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference revealed that species of Oreomyrrhis form a weakly supported monophyletic clade that is nested within Chaerophyllum sect. Chaerophyllum (subtribe Scandicinae, tribe Scandiceae). The optimal solutions of dispersal-vicariance analysis indicate that the ancestor of Chaerophyllum sect. Chaerophyllum (including Oreomyrrhis) was distributed in Eurasia and subsequently dispersed to North America and southern Pacific Rim. Based on dating using ITS sequence variation, these dispersal events were most likely recent, probably during late Tertiary to Quaternary. The structure of the ITS haplotype network suggests that a rapid range expansion via long-distance dispersal had been crucial in generating the trans-Pacific disjunction of Oreomyrrhis. Furthermore, evolution toward smaller mericarp size and a transition from outcrossing to selfing during Oreomyrrhiss evolution might have increased the chances for long-distance dispersal, facilitating its range expansion and occupation on alpine environments.

A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry

Significance Paper mulberry, a common East Asian tree used for paper making, is propagated across the Pacific for making barkcloth, a practical and symbolic component of Austronesian material culture. Using chloroplast DNA sequences, we demonstrate a tight genealogical link between its populations in South China and North Taiwan, and South Taiwan and Remote Oceania by way of Sulawesi and New Guinea, presenting the first study, to our knowledge, of a commensal plant species transported to Polynesia whose phylogeographic structure concurs with expectations of the “out of Taiwan” hypothesis of Austronesian expansion. As a commensal plant likely transported across the full range of Austronesian expansion from South China to East Polynesia, paper mulberry may also be the most widely transported fiber crop in human prehistory. The peopling of Remote Oceanic islands by Austronesian speakers is a fascinating and yet contentious part of human prehistory. Linguistic, archaeological, and genetic studies have shown the complex nature of the process in which different components that helped to shape Lapita culture in Near Oceania each have their own unique history. Important evidence points to Taiwan as an Austronesian ancestral homeland with a more distant origin in South China, whereas alternative models favor South China to North Vietnam or a Southeast Asian origin. We test these propositions by studying phylogeography of paper mulberry, a common East Asian tree species introduced and clonally propagated since prehistoric times across the Pacific for making barkcloth, a practical and symbolic component of Austronesian cultures. Using the hypervariable chloroplast ndhF-rpl32 sequences of 604 samples collected from East Asia, Southeast Asia, and Oceanic islands (including 19 historical herbarium specimens from Near and Remote Oceania), 48 haplotypes are detected and haplotype cp-17 is predominant in both Near and Remote Oceania. Because cp-17 has an unambiguous Taiwanese origin and cp-17–carrying Oceanic paper mulberries are clonally propagated, our data concur with expectations of Taiwan as the Austronesian homeland, providing circumstantial support for the “out of Taiwan” hypothesis. Our data also provide insights into the dispersal of paper mulberry from South China “into North Taiwan,” the “out of South China–Indochina” expansion to New Guinea, and the geographic origins of post-European introductions of paper mulberry into Oceania.

Extreme habitats that emerged in the Pleistocene triggered divergence of weedy Youngia (Asteraceae) in Taiwan.

Weeds with broad distributions and large morphological variation are challenging for systematists and evolutionarily intriguing because their intensive dispersal would likely prevent local morphological differentiation. Study on weeds will help to understand divergence in plants unlikely to be affected by geographical and ecological barriers. We studied Youngia japonica based on nrDNA and cpDNA sequences. This is a widespread native in Asia and invasive worldwide; nevertheless, three subspecies (japonica, longiflora, and formosana) and an undescribed variant occur in Taiwan. Bayesian and the most parsimonious phylogenies revealed that subspecies longiflora is a different linage and independently arrived in Taiwan during the Pleistocene via land connection to the Asian Continent. Bayesian time estimation suggested that Youngia in Taiwan diverged in the lower Pleistocene or more recently. Extreme habitats that emerged in the Pleistocene, i.e., cold mountain ranges for subspecies formosana and xeric, raised coral reefs for the undescribed Youngia variant probably had triggered the divergence. Components of Youngia in Taiwan are not monophyletic; a coalescent-based test suggested incomplete lineage sorting. Nevertheless, the samples within each taxon share unique morphological features suggesting a common gene pool and each taxon has different dominant ITS and/or cpDNA types; these conditions suggest ongoing process toward monophyly via coalescent processes and support the delimitation of intraspecific taxa.

Inclusion of the South Pacific Alpine Genus Oreomyrrhis (Apiaceae) in Chaerophyllum Based on Nuclear and Chloroplast DNA Sequences

Abstract To test the hypotheses that Oreomyrrhis species form the sister clade of North American Chaerophyllum and thus render the mainly Eurasian Chaerophyllum paraphyletic, two chloroplast intergenic spacers (atpB-rbcL and trnS-trnG) were analyzed. Phylogenetic estimates using maximum parsimony, maximum likelihood, and Bayesian inference of separate and combined matrices strongly support the monophyly of Oreomyrrhis and its sister-group relationship with North American Chaerophyllum. Chaerophyllum temulum, the type species of Chaerophyllum, is the sister taxon to the clade composed of Oreomyrrhis and North American Chaerophyllum. Relationships among other major clades of Chaerophyllum are congruent with previous studies. Based on these phylogenetic estimates, all currently recognized taxa of Oreomyrrhis are synonymised with Chaerophyllum. The unranked names, North American clade and Oreomyrrhis clade, are advocated to designate the two well-supported clades within Chaerophyllum sect. Chaerophyllum. The proposed nomenclatural changes include three new names, Chaerophyllum australianum, Chaerophyllum guatemalense, and Chaerophyllum novae-zelandiae, and 26 new combinations, Chaerophyllum andicola, Chaerophyllum argentum, Chaerophyllum azorellaceum, Chaerophyllum basicola, Chaerophyllum borneense, Chaerophyllum brevipes, Chaerophyllum buwaldianum, Chaerophyllum colensoi, Chaerophyllum colensoi var. delicatulum, Chaerophyllum colensoi var. hispidum, Chaerophyllum colensoi var. multifidum, Chaerophyllum daucoides, Chaerophyllum eriopodum, Chaerophyllum gunnii, Chaerophyllum involucratum, Chaerophyllum lineare, Chaerophyllum nanhuense, Chaerophyllum orizabae, Chaerophyllum papuanum, Chaerophyllum plicatum, Chaerophyllum pulvinificum, Chaerophyllum pumilum, Chaerophyllum ramosum, Chaerophyllum sessiliflorum, Chaerophyllum taiwanianum, and Chaerophyllum tolucanum.

Novelties in Begonia sect. Coelocentrum : B. longgangensis and B. ferox from limestone areas in Guangxi, China

BackgroundThe spectacular karst limestone landscape in Guangxi harbors high-level diversity and endemism of Begonia species, especially those of sect. Coelocentrum. In continuation of our studies in this area, we report the discovery of two attractive new species from southwestern Guangxi: Begonia longgangensis and B. ferox.ResultsBegonia longgangensis resembles B. liuyanii, also from Longgang Nature Reserve, in the broadly ovate to suborbicular leaf blade, differing by the much smaller leaves, subglabrous leaf surface, pink flowers, dichasial cymes and the remarkably long stolons sent out from rhizomes. Unexpectedly, both diploid (2n = 30) and triploid counts (2n = 45) were observed in plants collected from the type locality. Begonia ferox probably has the most prominent bullate leaves for the genus. In this aspect, it is similar to B. nahangensis reported from northern Vietnam recently, but is readily distinguishable by the ovate, chartaceous leaves with an acuminate apex; tomentose peduncle not exceeding petioles; and the much larger stature in vegetative parts. A diploid count of 2n = 30 was determined for this unique new species.ConclusionsAll available data support the recognition of the two new species. Begonia longgangensis has remarkably long stolons and B. ferox is characterized by the prominent bullate leaves. Line drawings, color plates and comparisons are provided to aid in identification of the novelties.

Intraspecific karyotypic polymorphism is highly concordant with allozyme variation in Lysimachia mauritiana (Primulaceae: Myrsinoideae) in Taiwan: implications for the colonization history and dispersal patterns of coastal plants.

BACKGROUND AND AIMS Investigating intraspecific karyotypic and genetic variations jointly can provide unique insights into how historical, ecological and cytogenetic factors influence microevolution. A coastal herb, Lysimachia mauritiana, exhibits extensive karyotypic polymorphism and displays a complex cytogeographic pattern across the Ryukyus. To explore whether a similar degree of chromosomal variation exists south of the Ryukyus, and in an attempt to ascertain the mechanisms that may have generated the patterns, comprehensive sampling was conducted in Taiwan. METHODS Karyotypes were analysed at mitotic metaphase for 550 individuals from 42 populations throughout Taiwan Proper and its adjacent islands. In addition, genetic variation was estimated using 12 allozymes (21 loci) of 314 individuals sampled from 12 localities. KEY RESULTS Four chromosome numbers and eight cytotypes, including four endemic cytotypes, were detected. Cytotype distributions were highly structured geographically, with single cytotypes present in most populations and four major cytotypes dominating the north, east and south of Taiwan and the Penghu Archipelago. Allozyme variation was very low and F-statistics indicated an extremely high level of population differentiation, implying limited gene flow among populations. Cluster analysis of allozyme variation uncovered four geographic groups, each corresponding perfectly to the four dominant cytotypes. The geographic structure of cytotype distribution and allozyme variation probably resulted from severe genetic drift triggered by genetic bottlenecks, suggesting that Taiwanese populations were likely to be derived from four independent founder events. In the few localities with multiple cytotypes, cytogeographic patterns and inferences of chromosomal evolution revealed a trend of northward dispersal, consistent with the course of the Kuroshio Current that has been influential in shaping the coastal biota of the region. CONCLUSIONS The data elucidate the patterns of colonization and the effects of the Kuroshio Current on the distribution of L. mauritiana in Taiwan. These inferences are highly relevant to other coastal plant species in the region and will stimulate further studies.

Petrocodon (Gesneriaceae) in the Limestone Karsts of Guangxi, China: Three New Species and a New Combination Based on Morphological and Molecular Evidence

Abstract Based on morphological and molecular data, three new species of the Old World Didymocarpoid Gesneriaceae, Petrocodon laxicymosus, P. longgangensis, and P. pseudocoriaceifolius, are described and illustrated from Guangxi, China. The three new species are most similar to P. coriaceifolius, differing by their texture, size, and shape of leaves, size and pubescence of inflorescence and corolla, anther shape, and pistil length. Additionally, Primulina guangxiensis, one of two species included in Primulina before its recent recircumscription, was unexpectedly found to be nested within Petrocodon in our ongoing phylogenetic analyses, prompting us to make the new combination Petrocodon guangxiensis. The four species of Petrocodon treated here are all rare, known only from a single or a few localities of limestone karsts in Guangxi.

Primulina cardaminifolia (Gesneriaceae), a rare new species from limestone areas in Guangxi, China

BackgroundPrimulina cardaminifolia Yan Liu & W.B. Xu (Gesneriaceae), a distinct new species with imparipinnate leaves, is described and illustrated from a limestone valley in Guangxi Zhuangzu Autonomous Region, China. To assure its generic placement and phylogenetic affinity, phylogenetic analyses were performed using DNA sequences of nuclear ITS and chloroplast trnL-F intron spacer region. Additionally, somatic chromosome number was counted and pollen stainability was tested.ResultsPhylogenetic analyses support its placement in Primulina; however, two phylogenetically distinct ITS sequence types were detected, suggesting a probable hybrid origin. Its pollen stainability is 100% and its chromosome number, 2n = 36, is congruent with all known counts of diploid species of the genus.ConclusionAll available data support the recognition of the new species Primulina cardaminifolia and suggest that it could have derived from homoploid hybrid speciation. Color plates, line drawings and a distribution map are provided to aid in identification.

The Miocene to Pleistocene colonization of the Philippine archipelago by Begonia sect. Baryandra (Begoniaceae)

PREMISE OF THE STUDY One third of the species-rich Philippine flora is endemic, and most of the islands in the archipelago have never been connected to a continental region. We currently lack any well-sampled angiosperm phylogenies that span the archipelago, prohibiting the formation of informed hypotheses as to the evolution of this rich and highly endemic flora. METHODS We produced time-calibrated phylogenetic trees from both nuclear (ITS) and chloroplast (ndhA intron, ndhF-rpl32 spacer, rpl32-trnL spacer, trnC-trnD spacer) regions of 41 species of Begonia sect. Baryandra, all except one endemic to the Philippines. Historical biogeography was reconstructed across the chloroplast phylogeny using a Bayesian binary method of character optimization. Comparison of phylogenies from the two genomes permitted insight into the prevalence of hybridization in the group. KEY RESULTS The Philippine archipelago was colonized by Begonia sect. Baryandra in the late Miocene, via long-distance dispersal from western Malesia and a point of entry likely to be in the northwestern region of the archipelago. Palawan, Luzon, and Panay all bear early-branching lineages from this initial colonization. There have been Plio-Pleistocene dispersals from these islands into Borneo and Mindanao. Hybridization was common between species as evidenced by haplotype sharing and phylogenetic incongruence. CONCLUSIONS The phylogenies show a high degree of geographic structure, which millions of years of exposure to typhoons have not blurred, showing long-term species and population stability. The recent dispersals to Mindanao are congruent with the geologically recent arrival of the island at its current latitude in the southern Philippines.