Asian Endemic Genus Research Articles

Comparative phylogenomic study of East Asian endemic genus, Corchoropsis Siebold & Zucc. (Malvaceae s.l.), based on complete plastome sequences

BackgroundEndemic plants are key to understanding the evolutionary history and enhancing biodiversity within their unique regions, while also offering significant economic potential. The East Asian endemic genus Corchoropsis Siebold & Zucc., classified within the subfamily Dombeyoideae of Malvaceae s.l., comprises three species.ResultsThis study characterizes the complete plastid genomes (plastomes) of C. crenata var. crenata Siebold & Zucc. and C. crenata var. hupehensis Pamp., which range from 160,093 to 160,724 bp. These genomes contain 78 plastid protein-coding genes, 30 tRNA, and four rRNA, except for one pseudogene, infA. A total of 316 molecular diagnostic characters (MDCs) specific to Corchoropsis were identified. In addition, 91 to 92 simple sequence repeats (SSRs) in C. crenata var. crenata and 75 in C. crenata var. hupehensis were found. Moreover, 49 long repeats were identified in both the Chinese C. crenata var. crenata and C. crenata var. hupehensis, while 52 were found in the South Korean C. crenata var. crenata. Our phylogenetic analyses, based on 78 plastid protein-coding genes, reveal nine subfamilies within the Malvaceae s.l. with high support values and confirm Corchoropsis as a member of Dombeyoideae. Molecular dating suggests that Corchoropsis originated in the Oligocene, and diverged during the Miocene, influenced by the climate shift at the Eocene–Oligocene boundary.ConclusionsThe research explores the evolutionary relationships between nine subfamilies within the Malvaceae s.l. family, specifically identifying the position of the Corchoropsis in the Dombeyoideae. Utilizing plastome sequences and fossil data, the study establishes that Corchoropsis first appeared during the Eocene and experienced further evolutionary divergence during the Miocene, paralleling the evolutionary patterns observed in other East Asian endemic species.

Temporal and Spatial Pattern of Holcoglossum Schltr. (Orchidaceae), an East Asian Endemic Genus, Based on Nuclear and Chloroplast Genes

East Asia is characterized by high levels of species diversity and endemism. However, the biogeographic patterns and processes of endemic epiphytic plants within East Asia are still poorly known. In this study, we used eleven plastid and one nuclear DNA sequences to infer the historical biogeography of Holcoglossum Schltr. (Orchidaceae), an eastern Asian endemic genus. Phylogenetic analyses strongly support Holcoglossum as monophyletic, and contains three major clades (TC, HC and AC). Our results suggest that the most recent common ancestor of Holcoglossum occurred in Palaeotropical region in the late Miocene (6.29 Ma). Within Asian mainland, three dispersal and one vicariant events were hypothesized to explain the expansion of Holcoglossum from Palaeotropical region to Sino-Himalayan and Sino-Japanese region. These events occurred in the latest Miocene to middle Pleistocene, which may be associated with the uplift of the southeastern Tibetan Plateau and intensification of East Asia monsoon around that period. A disjunct distribution between Asian mainland and Taiwan was inferred in the latest Pliocene-early Pleistocene, which supports the close floristic affinity between Taiwan and Asian mainland. This study contributes to our knowledge on the historical biogeography of endemic epiphytic plants in East Asia.

Plastome phylogenomics of the East Asian endemic genus Dobinea

Dobinea is a dioecious genus endemic to East Asia that consists of two extant species: Dobinea delavayi and Dobinea vulgaris. Although the genus is morphologically distinct, its phylogenetic position remains controversial. In this study, we investigated the phylogenetic relationships between Dobinea and related taxa by sequencing the whole plastome DNA sequences for both extant species of Dobinea and comparing them to published plastomes within Sapindales. The complete plastomes of D. vulgaris and D. delavayi were 160,683 and 160, 154 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 26,889 and 26,759 bp) divided by the large single-copy region (LSC, 87,962 and 87,555 bp) and small single-copy region (SSC, 18,943 and 19,081 bp), and identically encoded 113 unique genes (79 protein-coding genes, 30 tRNAs, and 4 rRNA genes). Plastid phylogenomic analyses showed that Dobinea was a well-supported monophyletic unit and sister to the clade including tribes Anacardieae and Rhoideae, which suggests that Dobinea is a member of Anacardiaceae. In addition, molecular dating inferred D. delavayi and D. vulgaris diverged approximately 10.76 Ma, suggesting the divergence between these two species may have been driven by the intensification of the Asian summer monsoon and the establishment of distinct monsoon regimes in East Asia.

First fossil record of an East Asian endemic genus Sladenia (Sladeniaceae) from its modern range: Implications for floristic evolution and conservation biology

AbstractFossil records of endemic plants play an important role in recognizing the floristic history of East Asia and thereby facilitate the conservation of plant diversity in the region. However, the fossil record of many extant East Asian endemic genera remains poorly documented thus far. Here, we report an infructescence fossil of an East Asian endemic genus, Sladenia (Sladeniaceae), from the early Miocene of southeastern Yunnan, China. The fossil is characterized by: (i) dichasial cymes; and (ii) flask‐shaped ovary with dense subparallel ribs on the surface extending from the base to the distal end of the united style. It represents the first fossil record of Sladenia in Asia, showing that the genus was established in the region at least by the early Miocene. Given that a much older fossil record of Sladeniaceae has been reported from Africa and the sister group of Sladenia is distributed only in Africa, Sladenia is not likely of East Asian origin. The present endemic status of Sladenia was possibly achieved by regional extirpation in Africa and taking refuge in East Asia. This case thus supports the “Museum” rather than “Cradle” hypothesis for the genesis of high plant species in the flora of East Asia. A comparison of the present fossil with extant Sladenia infructescence shows morphological stasis from the early Miocene to present. Such evolutionary tardiness might have resulted in the reduced fitness of the genus, which further caused its current endangered situation.

Phylogeographic Analyses of the East Asian Endemic Genus Prinsepia and the Role of the East Asian Monsoon System in Shaping a North-South Divergence Pattern in China.

Prinsepia Royle (Rosaceae) is a genus native to China and the Himalayan region. In order to explain its current fragmented distribution pattern and to compare the impact of relatively recent climate changes on the genetic structure of Prinsepia species in different regions of China, a total of 66 populations and 617 individuals of four species of Prinsepia were genotyped, using three cpDNA markers. Meanwhile, phylogenetic reconstructions and divergence dating were conducted using the cpDNA haplotypes dataset and the nuclear ribosomal internal transcribed spacer (ITS) dataset, respectively. Ecological niche modeling (ENM) was performed to predict the potential distribution of each species of Prinsepia at present and during the Last Glacial Maximum. Both ITS and cpDNA gene trees support a north-south divergence of Prinsepia species in China. The divergence time of the northern and southern Clades occurred around the late Oligocene epoch. Combining the present distribution of Prinsepia species and their habitats, we inferred that the transition to a monsoon climate system in East Asia during the late Oligocene epoch, created a humid forest vegetation zone from central to East China, which potentially gave rise to the north-south divergence of Prinsepia species. Both regional climates and allopatric divergence may have played an important role in the speciation of P. sinensis and P. uniflora. P. sinensis had the lowest genetic diversity and a putative northward post-glacial colonization. The distribution range of P. uniflora was also extremely sensitive to interglacial-glacial cycles. P. utilis from southwestern China preserved more haplotypes than P. sinensis and P. uniflora due to its multiple and isolated refugia.

Phylogenetic position of the East Asian endemic genus Hattoria (Anastrophyllaceae) based on chloroplast DNA sequences

Phylogenetic position of the East Asian endemic genus Hattoria (Anastrophyllaceae) based on chloroplast DNA sequences

Revision of the Central Asian Scorpion Genus Anomalobuthus Kraepelin, 1900, with Descriptions of Three New Species and a Generic Synonymy (Scorpiones: Buthidae)

We revise the Central Asian endemic genus Anomalobuthus Kraepelin, 1900, which was considered monotypic for more than 100 years until the recent addition of a second species from Iran (Teruel et al., 2014). We redefine the generic diagnosis of Anomalobuthus and reveal that it is composed of no less than six species, three of which are described as new: A. krivochatskyi, sp. n. (central Uzbekistan and extreme southern Kazakhstan), A. lowei, sp. n. (southeastern Kazakhstan), and A. pavlovskyi, sp. n. (south-central Kazakhstan and extreme northern Turkmenistan). The monotypic genus Psammobuthus Birula, 1911 (described from the Ferghana Valley at the border of Uzbekistan and Tajikistan) is synonymized under Anomalobuthus; its single species is transferred as Anomalobuthus zarudnyi (Birula, 1911), comb. n. We also clarify the type locality of the type species A. rickmersi Kraepelin, 1900, from accurate data published by its collector Rickmer Rickmers (1913) but overlooked since its very original description: it is Baljuvon in Tajikistan. Occurrence of A. rickmersi in southern and southeastern Turkmenistan is confirmed. All available species are fully illustrated with color photos of habitus and morphologically diagnostic characters, and a key covering all six recognized species of Anomalobuthus is included.

Unravelling the phylogeny of the root‐hemiparasitic genus Odontites (tribe Rhinantheae, Orobanchaceae): Evidence for five main lineages

AbstractDespite the recent publication of several phylogenies focused on Rhinantheae, which has been expanded to include three Asian endemic genera, few studies so far have dealt with particular genera within the tribe. Here, we focus on Odontites and related genera because of the high morphological variability of the group and its unclear generic boundaries. Phylogenetic analyses were performed for nrDNA (ITS) and cpDNA (trnK region and rps16 intron) datasets, using Bayesian and Parsimony analyses. Our results cast doubt on the inclusion of Pterygiella and related genera within the Rhinantheae and support the para‐ phyly of Phtheirospermum, making it necessary to propose three new combinations to avoid it. Odontites is recircumscribed to include Bartsiella, Bornmuellerantha, and Macrosyringion, but not Odontitella. Within Odontites, five distinct lineages are identified. These are distinguishable either by morphological synapomorphies or by a combination of several character states. Most of the Odontites species are regarded as monophyletic. In the O. vernus and O. luteus complexes, some taxonomic changes are made to avoid paraphyly, which results in three new combinations.

Resolving the phylogenetic relationships and evolutionary history of the East Asian endemic genus Rodgersia (Saxifragaceae) using multilocus data

The East Asian endemic genus Rodgersia comprises five species and several variants. These species exhibit variation in ploidy level and a fragmented distribution across the whole of East Asia. In order to explain their present distribution pattern under a robust phylogeny, we employed multiple copy nuclear genes (ITS and ETS), cpDNA (rpl32-trnL, trnV-ndhC, ndhF-rpl32) and a low copy nuclear gene (GBSSI) to reconstruct the species’ relationships within Rodgersia. Identification of ploidy levels was also carried out for most of samples. The early-diverging positions of R. nepalensis and R. podophylla were confirmed in different gene trees. Much topological incongruence among gene trees was found in the shallower branches, which comprised the species of central-southwest China. Both incomplete lineage sorting and ancient introgression may be responsible for the incongruent pattern observed. Ancient introgressions may have occurred between diploid species and the diploid progenitors of tetraploid species in different areas of southwest China. Rodgersia probably originated in Northeast Asia during the Pliocene. This genus is a rare example in which two early-diverging species occur at opposite ends of the distribution area, likely resulting from successive vicariance events. Unlike many vicariance events shaped simply by forest fragmentation during the Pleistocene, the contemporary biogeographic pattern of Rodgersia is more the result of rapid sympatric evolution (reticulate events and polyploidization) of the taxa in the central area.

A molecular phylogeny of Dichocarpum (Ranunculaceae): Implications for eastern Asian biogeography

East Asia is characterized by high levels of species diversity and endemism. However, the biogeographical patterns and processes underlying the distribution of biodiversity within the area are still poorly known. In this study, we used plastid (matK, trnL-F, and trnH-psbA) and nuclear (ITS) DNA sequences to investigate the historical biogeography of Dichocarpum (Ranunculaceae), an eastern Asian endemic genus throughout warm-temperate and subtropical forests of the area. Phylogenetic analyses strongly support Dichocarpum as monophyletic, which contains two major clades. Clade I corresponds to section Hutchinsonia, and clade II includes sections Dichocarpum and Fargesia. Section Dichocarpum and its subsections Dalzielia and Dichocarpum are not recognized as monophyletic. Our results suggest that the most recent common ancestor of Dichocarpum occurred in central China and Japan in the earliest Early Miocene, and thus support an ancient vicariance event between Japan and China. Within mainland China, three migrations at the species level were hypothesized to explain the expansion of Dichocarpum from central China to southeastern Yunnan, Hengduan mountains, and eastern Himalaya. These migration events occurred in the Late Miocene to Early Pliocene, which may be associated with the uplift of the southeastern Qinghai-Tibetan Plateau and accordingly the expansion of subtropical forests in China around that period. A migration or dispersal from central China to Taiwan was inferred in the Early Pleistocene, which supports the close floristic affinity between Taiwan and mainland China. This study contributes to our knowledge on the historical biogeography of plants in eastern Asia.

Floral organogenesis in Urophysa rockii, a rediscovered endangered and rare species of Ranunculaceae

Urophysa is an Asian endemic genus in the Ranunculaceae, but data on floral organogenesis, which would be a useful complement to molecular data in clarifying the relationship with closely related taxa (Aquilegia and Semiaquilegia) in Ranunculaceae, are completely lacking. We used scanning electron microscopy and light microscopy to study the floral development of Urophysa rockii Ulbrich, a recently rediscovered species in this genus. The sepals are initiated spirally, whereas other organs are nonsimultaneously whorled; the floral phyllotaxis is whorled. Primordia of the sepals are lunular and truncate, but those of the petals and stamens are hemispherical and rounded. After sepal initiation, there is a delay in development, but the initiation of petals and stamens is continuous. The developmental sequence of the microspores in the stamens is centrifugal, although the stamens are initiated centripetally. The early developmental stages of the staminodes are similar to those of the stamens, although much smaller, so they may be phylogenetically homologous organs. The carpel primordia are lunular in shape and plicate. The mature ovule is anatropous and bitegmic. Urophysa shows similar floral development features as Aquilegia and Semiaquilegia, although with some differences, which supports the relationship inferred by DNA sequence data.

Two species of the Asian endemic genus Keteleeria form ectomycorrhizas with diverse fungal symbionts in southwestern China

The ectomycorrhizal status of Keteleeria species is reported for the first time based on morphological and molecular analyses of root tips from southwestern China. Based on internal transcribed spacer rDNA sequences, we detected 26 ectomycorrhizal (ECM) fungal species on roots of Keteleeria evelyniana and Keteleeria davidiana collected from natural sites and a botanical garden in Kunming, China. These ECM symbionts represent six fungal lineages, including /russula-lactarius, /inocybe, /sebacina, /tomentella-thelephora, /wilcoxina, and /cenococcum. Our results provide the first evidence of ECM formation by Keteleeria and also supply ecologically important information for conservation and restoration efforts to recover populations of Keteleeria.

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.

Molecular phylogeny of the endemic fern genera Cyrtomidictyum and Cyrtogonellum (Dryopteridaceae) from East Asia

Cyrtomidictyum Ching and Cyrtogonellum Ching are two eastern Asian endemic genera whose taxonomic affinities and phylogenetic relationships have long been controversial. The main uncertainty surrounds the separation of the two genera from the species-rich genus Polystichum. Here we present a phylogenetic study focusing on the phylogenetic relationships of these polystichoid ferns. We reconstructed the relationships based on DNA sequence variation in four chloroplast genome regions, rbcL, atpB, and the intergenic spacers (IGS) rps4-trnS and trnL-trnF. Maximum likelihood and Bayesian inference analyses confirm earlier results that were based on less comprehensive taxon sampling and either only a single gene (rbcL) or two IGS (rps4-trnS and trnL-trnF). Cyrtomidictyum is the sister of the clade of polystichoid ferns that includes Cyrtogonellum, Cyrtomium subser. Balansana and three sections of Polystichum. Cyrtogonellum groups with several species of Polystichum, and constitutes the sister taxon to Polystichum sect. Sphaenopolystichum. We support the recognition of Cyrtomidictyum as circumscribed initially, rather than expansion of the genus to include either several Polystichum species or Cyrtogonellum, some Polystichum and Cyrtomium species. The monophyly of Cyrtomidictyum is supported by morphological characters such as once-pinnate leaves, free venation, prolongated leaf apices, and exindusiate sori. Two synapomorphic indels in the chloroplast genome, one 15-bp deletion in rps4-trnS, and one 3-bp insertion in trnL-trnF further differentiate Cyrtomidictyum from other polystichoid ferns. The close affinity of Cyrtogonellum to section Sphaenopolystichum of Polystichum s.s. is highly supported by molecular data. However, no shared morphological characters or molecular indels have been detected, although the distinctness of Cyrtogonellum is shown by a 13-bp insertion in the rps4-trnS alignment.

Hamawilsonia boglei gen. et sp. nov. (Hamamelidaceae) from the Late Paleocene Almont Flora of Central North Dakota

Hamawilsonia boglei Benedict, Pigg & DeVore gen. et sp. nov. (Hamamelidaceae) is described from the Late Paleocene Almont flora of central North Dakota. The infructescence is an anatomically preserved spike with up to 20 sessile, robust, cuboidal to ovoid capsules borne on an elongate, thick axis up to $$9.2\,\mathrm{cm}\,\,\mathrm{long}\,\times 0.5\,\mathrm{cm}\,\,\mathrm{wide}\,$$ . Individual fruits are 10–12 mm across and bilocular, with paired persistent, recurved styles borne on the distal carpel face. One locule is often larger than the other. Anatomically, the fruit wall is composed of a sclerified endocarp and a poorly preserved exocarp. Seeds are elliptical to slightly obovate with a sclerotic seed coat. Hamawilsonia is an extinct Late Paleocene genus with a combination of characters not seen in any extant hamamelid genus. Hamawilsonia is similar to the Asian endemic genus Sinowilsonia in its elongate spikelike infructescence, resembles the witch hazel Hamamelis in fruit and seed morphology, and has seed anatomy that combines features found in several extant genera. Affinities with Sinowilsonia are further supported by the co‐occurrence of associated pollen catkins and in situ tricolpate pollen with a distinctive reticulate sculpturing. Like several other Almont taxa (Amersinia, Beringiaphyllum, Davidia, and Palaeocarpinus), Hamawilsonia is a genus with strong North American–Asian affinities.

A Taxonomic Reassessment of Microdendron Inferred from Molecular and Morphological Evidence

Abstract Microdendron Broth., an eastern Asian endemic genus, was initially described based mainly on the tree-like gametophytes, but there have been several conflicting taxonomic treatments. In this study, we sequenced three DNA regions of Microdendron: the nuclear 18S, and chloroplast rbcL and trnL-F. Phylogenetic analyses indicate that Microdendron is nested within Pogonatum, suggesting that the genus should not be recognized. Additionally we found an indel in the trnL intron region shared by the two genera, which also indicates the close relationship between them. Moreover, the probable allies of Microdendron sinense Broth. within Pogonatum are suggested based on detailed investigation under the scanning electron microscope.