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Biotic exchanges between Taiwan and Mainland China have shaped the biodiversity and ecosystems of both regions. Exchanges from Mainland China to Taiwan have received more attention, mainly studied in terrestrial vertebrates, while the reverse direction and invertebrates have largely been overlooked. Here, we explore the dispersal events between these two regions based on the moths of three species groups of Obeidia, including Taiwan taxa and its relatives from mainland. We conducted mixed methods and analysis, including reconstructing a phylogenetic tree, estimating associated divergence times and inferring ancestral areas and source regions, to explore the phylogeographical structure and genetic pattern of three groups based on eight genes. Our results revealed a structure of three clades and every clade included at least one Taiwanese taxa and its closest relatives of mainland of China, and also served Taiwan as an important source region of two mainland taxa. Our study revealed various origin pattern and dispersal models on the basis of three species groups of Obeidia. Bi‐directional biotic exchange via a land bridge were found: four Taiwanese taxa originated from mainland, and two of them migrated back to mainland. Both eastern Himalayas and south China are important origin areas for Taiwan biota, and the dominant source region may need multiple insect cases to confirm. Our study also provided evidences for disjunct distribution from the perspective of insecta molecular phylogeny. [ABSTRACT FROM AUTHOR]

Freshwater mussels are known to have two types of mitochondrial DNA (mtDNA) transmitted separately through oocytes and sperms, namely, maternal (F‐type) and paternal (M‐type) mtDNA. The additional suite of mitochondrial genes provides a great opportunity to resolve phylogenetically problematic relationships. East Asian freshwater mussels of the genus Cuneopsis were considered a compact group of taxa having wedge‐shaped shells. However, preliminary results from previous studies challenged the monophyly of Cuneopsis, and the exact phylogenetic relationships among Cuneopsis and its allied genera are yet to be determined with comprehensive species sampling. Here, we evaluated species boundaries in Cuneopsis based on COI barcoding and obtained 11 new F‐ and M‐type mitogenomes via genome skimming to elucidate the evolutionary history of Cuneopsis. COI barcode data supported the validity of all sampled six Cuneopsis species (missing C. kiangsiensis). Our mitochondrial phylogenomic analyses confirmed that the currently recognized genus Cuneopsis sensu lato was polyphyletic, recovering three well‐supported clades. Molecular dating analysis suggested Cuneopsis s.l. diversified at ~58.06 million years ago in the Paleogene. Hereby, we propose two new genera, that is, Arcuneopsis gen. nov. and Pseudocuneopsis gen. nov. Additionally, we report a new species, Pseudocuneopsis sichuanensis sp. nov., from Chengdu, Sichuan, China, and a newly recorded species from China, Cuneopsis demangei. [ABSTRACT FROM AUTHOR]

The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH - psbA , and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa , which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1 , matK - trnG-GCC , rpoC1 , and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely " F. omeiensis " and " F. hupehensis " in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria , as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China. [ABSTRACT FROM AUTHOR]

Aim: The Hengduan Mountains (HDM) of southwest China is a biodiversity hotspot and harbours one of the world's richest temperate floras. However, the origin and evolution of its biota remain largely unresolved. Here we explore the impact of mountain uplift on the diversification process of biodiversity in this hotspot using alpine bamboos. Location: The HDM region, southwest China. Taxon: Alpine bamboos. Methods: We used ddRAD‐seq data from the most complete sampling of alpine bamboos undertaken to date (79% of the species diversity), to investigate their evolutionary history. The ancestral area of these bamboos was reconstructed using a time‐calibrated phylogeny in BioGeoBEARS and diversification rates were inferred using BAMM analyses. In addition, the impact of mountain uplift on the divergence of alpine bamboos was evaluated using trait‐dependent models of diversification. Results: The alpine bamboos were strongly supported as monophyletic, and the relationships within them were robustly resolved. Fargesia was found to be polyphyletic and Yushania was resolved as monophyletic. Alpine bamboos originated outside the HDM region during the late Miocene, and spread to this region in the Pliocene, undergoing a significant acceleration in net diversification, which is temporally congruent with the orogeny. The speciation rate increased with altitude and a high diversification rate, estimated to be 0.75 species per million years, was detected for alpine bamboos distributed in high elevations. Main Conclusions: Our study demonstrates that heterogeneous mountain habitats and geographical isolation of alpine bamboos, which have limited dispersal ability, are important drivers for their rapid diversification. This study also highlights the power of complementary analyses in revealing the link between species diversification and past geological changes. [ABSTRACT FROM AUTHOR]

Spirometra erinaceieuropaei is an important diphyllobothriid cestode whose larval plerocercoid (sparganum) can parasitise humans, causing sparganosis. In China, sparganosis is an important foodborne parasitic zoonosis and poses a serious threat to human health. However, our knowledge of the taxonomic classification of S. erinaceieuropaei and its relationship with other diphyllobothriid cestodes, such as Diphyllobothrium , remains fragmentary. In this study, we determined the complete sequences of cytochrome b ( cytb ) and cytochrome c oxidase subunit I ( cox1 ) genes from 61 isolates of S. erinaceieuropaei collected from 11 geographical locations in eastern China and compared them to the sequences of Diphyllobothrium species from the GenBank database. Then, we evaluated the genetic variation of S. erinaceieuropaei and the phylogenetic relationship between S. erinaceieuropaei and Diphyllobothrium . Both negative Tajima’s D and Fu’s F S values of neutrality tests and unimodal curve of mismatch distribution analyses supported demographic population expansion. Bayesian skyline plot (BSP) analyses indicated that a population expansion occurred in the Pleistocene. Phylogenetic analysis based on cytb , cox1 , and cytb + cox1 under all three methods tested (neighbour-joining, maximum parsimony, and maximum likelihood) suggested that the S. erinaceieuropaei isolates from eastern China and the genus Diphyllobothrium are separate monophyletic groups. Furthermore, the uncorrelated log-normal relaxed molecular-clock model suggested that divergence between Spirometra and Diphyllobothrium began in the late Miocene. [ABSTRACT FROM AUTHOR]

Based on three chloroplast markers ( psbA- trnH, trnL- trnF, and trnT- trnL), we identified eight haplotypes in 23 samples of Litsea coreana collected from seven provinces across southern and southwestern China. The Hap6 was the most widely distributed haplotype. The genetic diversity was highest in Sichuan Province and its adjacent regions. Therefore, these regions should be areas of priority for conservation of L. coreana in the future. In addition, our molecular dating analyses indicated that the uplift of the Tibetan Plateau and past climate changes accounted for the diversification of L. coreana in China. Finally, we found that the chemical components of L. coreana were significantly affected by both collection time and postharvest handling methods. [ABSTRACT FROM AUTHOR]

[Display omitted] • Six Phrynarachne species are delimited using multiple species delimitation methods. • Multigene phylogenetic analyses support the monophyly of the genus Phrynarachne. • Relationships within Phrynarachne are consistent. • The ancestor of Phrynarachne in China originated in the middle Miocene. Evolutionary biologists have long been fascinated by the striking resemblance to bird droppings of the sit-and-wait crab spiders of the genus Phrynarachne. In doing so, species of Phrynarachne have evolved not to avoid detection, but rather, to cause predators to misidentify them as inedible and/or inanimate bird droppings. However, the lack of a phylogeny for Phrynarachne impedes our understanding of the evolution of this trait in the genus. Here we explore species boundaries in species of Phrynarachne from China using single- and multi-locus species delimitation approaches based on 30 Phrynarachne samples. All species delimitation approaches supported six species of Phrynarachne in China. We further present the first phylogenetic analysis of the genus Phrynarachne and estimate divergence times using two mitochondrial and three nuclear genes. All of our phylogenetic analyses supported the monophyly of Phrynarachne in China, with the genus still included within the higher ' Thomisus group' based on our results. Our dating analyses place the crown age of Phrynarachne in China to the middle Miocene. Taken together, our study provides a time-calibrated phylogeny of the genus Phrynarachn e in China for testing hypotheses regarding the evolution of the lineage and bird dropping masquerade. [ABSTRACT FROM AUTHOR]

Abstract: Mahonia bealei (Berberidaceae) is a frequently-used traditional Chinese medicinal plant with efficient anti-inflammatory ability. This plant is one of the sources of berberine, a new cholesterol-lowering drug with anti-diabetic activity. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of M. bealei. The complete cp genome of M. bealei is 164,792bp in length, and has a typical structure with large (LSC 73,052bp) and small (SSC 18,591bp) single-copy regions separated by a pair of inverted repeats (IRs 36,501bp) of large size. The Mahonia cp genome contains 111 unique genes and 39 genes are duplicated in the IR regions. The gene order and content of M. bealei are almost unarranged which is consistent with the hypothesis that large IRs stabilize cp genome and reduce gene loss-and-gain probabilities during evolutionary process. A large IR expansion of over 12kb has occurred in M. bealei, 15 genes (rps19, rpl22, rps3, rpl16, rpl14, rps8, infA, rpl36, rps11, petD, petB, psbH, psbN, psbT and psbB) have expanded to have an additional copy in the IRs. The IR expansion rearrangement occurred via a double-strand DNA break and subsequence repair, which is different from the ordinary gene conversion mechanism. Repeat analysis identified 39 direct/inverted repeats 30bp or longer with a sequence identity ≥90%. Analysis also revealed 75 simple sequence repeat (SSR) loci and almost all are composed of A or T, contributing to a distinct bias in base composition. Comparison of protein-coding sequences with ESTs reveals 9 putative RNA edits and 5 of them resulted in non-synonymous modifications in rpoC1, rps2, rps19 and ycf1. Phylogenetic analysis using maximum parsimony (MP) and maximum likelihood (ML) was performed on a dataset composed of 65 protein-coding genes from 25 taxa, which yields an identical tree topology as previous plastid-based trees, and provides strong support for the sister relationship between Ranunculaceae and Berberidaceae. Molecular dating analyses suggest that Ranunculaceae and Berberidaceae diverged between 90 and 84mya, which is congruent with the fossil records and with recent estimates of the divergence time of these two taxa. [Copyright &y& Elsevier]

• Comprehensive phylogenetic analyses of the Chinese Amolops frogs were performed. • Two major clades representing eastern and western Chinese torrent frogs were revealed. • Some species groups were not monophyletic, suggesting a need for revision. • The ancestor of the Chinese Amolops has appeared in the late Eocene or early Oligocene. • The dispersal routes of the Amolops frogs into China from the Indochinese Peninsula were revealed. The torrent frog genus Amolops contains nearly sixty species distributed in swift mountain streams throughout southeast Asia. The taxonomy of this genus has proven complicated due to unstable morphological diagnostic characters. The relationships of Amolops species and species groups were not readily resolved with a small number of molecular markers. Here, we applied the novel AFLP-Capture approach and acquired two large datasets (242 anonymous nuclear sequences and the mitochondrial genome) from 70 Chinese Amolops samples to study their relationships. The phylogenies inferred from the nuclear data and the mitochondrial data were both robust and revealed a primary phylogenetic split between eastern and western Chinese Amolops species. The relationships of the six species groups were clarified. While the three species groups in east China (the A. ricketti , A. daiyunensis and A. hainanensis groups) were monophyletic, the three species groups in the west (the A. mantzorum , A. monticola and A. marmoratus groups) were not monophyletic, suggesting a need for further investigation and revision. The robust phylogenies also provided new insights into species relationships, especially for the A. mantzorum group, which has been difficult to resolve due to multiple speciation events occurring approximately 7–8 million years ago. The divergence times estimated with the nuclear data indicated that the ancestor of the Chinese Amolops appeared in the late Eocene or early Oligocene, and that speciation events in the Chinese Amolops were often related to geological events (e.g. the uprising of mountains and the formation of islands). By including the mitochondrial sequences from GenBank, a more comprehensive Amolops phylogeny was constructed that reflected the origin of the Chinese Amolops. Based on all these results, a dispersal scenario of the torrent frogs was hypothesized. Our research serves as the first example of using AFLP-Capture to obtain a large amount of data for shallow-scale phylogenetic and taxonomic studies, which should be useful for other nonmodel organism groups. [ABSTRACT FROM AUTHOR]

The Oriental greenfinch, Chloris sinica , is a small seed-eating finch that breeds in the eastern Palearctic region, an area that spans from Russia in the east to China, Korea, and Japan in the south and southwest. Several subspecies have been described based on subtle morphological characteristics, although the taxonomy varies among different authors. Although many ecological studies have been performed, there has been no phylogenetic study that encompasses the species' entire geographical range. We used four regions of mitochondrial DNA to analyze the intraspecies genetic phylogeny and diversity of the Oriental greenfinch. In addition, we performed morphometric analyses using museum specimens. Genetic analysis identified two clades that diverged approximately 1.06 million years ago. These were a population from the Ogasawara Islands, Japan (subspecies kittlitzi , Clade B), and the other populations (Clade A, which could not be subdivided according to geographic context). Morphometric analyses showed that the population on the Kuril Islands (subspecies kawarahiba ) had the longest mean wing length, whereas C. s. kittlitzi had the shortest wings. Chloris s. kittlitzi also had the longest mean bill length, probably because it has adapted to feeding on the Ogasawara Islands. Based on molecular phylogeny and morphology analyses, we recommend that C. s. kittlitzi should be treated as a completely distinct species, called the Ogasawara greenfinch, Chloris kittlitzi . It is critically endangered and needs to be specially protected.

Thlaspi arvense is a well-known annual farmland weed with worldwide distribution, which can be found from sea level to above 4000 m high on the Qinghai-Tibetan Plateau (QTP). In this paper, a phylogeographic history of T. arvense including 19 populations from China was inferred by using three chloroplast (cp) DNA segments (trnL-trnF, rpl32-trnL and rps16) and one nuclear (n) DNA segment (Fe-regulated transporter-like protein, ZIP). A total of 11 chloroplast haplotypes and six nuclear alleles were identified, and haplotypes unique to the QTP were recognized (C4, C5, C7 and N4). On the basis of molecular dating, haplotypes C4, C5 and C7 have separated from others around 1.58 Ma for cpDNA, which corresponds to the QTP uplift. In addition, this article suggests that the T. arvense populations in China are a mixture of diverged subpopulations as inferred by hT/vT test (hT ≤ vT, cpDNA) and positive Tajima's D values (1.87, 0.05 < p < 0.10 for cpDNA and 3.37, p < 0.01 for nDNA). Multimodality mismatch distribution curves and a relatively large shared area of suitable environmental conditions between the Last Glacial Maximum (LGM) as well as the present time recognized by MaxEnt software reject the sudden expansion population model.