Molecular systematics and historical biogeography of the Black-browed Barbet species complex (Megalaima oorti)

Although Southeast Asia is a global biodiversity hotspot, the tempo and mode of avian diversification there has not been well studied. We investigated the history of the diversification of an endemic Asian tropical bird, the Black-browed Barbet Megalaima

A reappraisal of complete mtDNA variation in East Asian families with hearing impairment

In a number of recent studies, we summarized the obvious errors and shortcomings that can be spotted in many (if not most) mitochondrial DNA (mtDNA) data sets published in medical genetics. We have reanalyzed here the complete mtDNA genome data published

CLASSIFICATION AND EVOLUTION OF ASIAN COLOBINES

In order to study the differentiation of Asian colobines, 14 variables measured on 123 skulls, including Rhinopithecus, Presbytis, Presbytiscus (Rhinopithecus avunculus), Pygathrix and Nasalis were analyzed by one-way, cluster and discriminant function analyses. Information on paleoenvironmental changes in China and southeast Asia since the late Tertiary was used to examine the influences of migratory routes and range of distribution in Asian colobines. A cladogram for 6 genera of Asian colobines was constructed from the results of various analyses. Some new points or revisions were suggested: (1) Following one of two migratory routes, ancient species of Asian colobines perhaps passed through Xizang (Tibet) along the northern bank of the Tethys sea and through the Heng Duan Shan regions of Yunnan into Vietnam. An ancient landmass linking Yunnan and Xizang was already present on the east bank of the Tethys sea. Accordingly, Asian colobines would have two centers of evolutionary origin: Sundaland and the Heng Duan Shan regions of China. (2) Pygathrix shares more cranial features with Presbytiscus than with Rhinopithecus. This differs somewhat from the conclusion reached by Groves. (3) Nasalis (karyotype: 2n = 48) may be the most primitive genus among Asian colobines. Certain features shared with Rhinopithecus, e.g. large body size, terrestrial activity and limb proportions, can be interpreted as symple-siomorphic characters. (4) Rhinopithecus, with respect to craniofacial features, is a special case among Asian colobines. It combines a high degree of evolutionary specialization with retention of some primitive features thought to have been present in the ancestral Asian colobine.

Phylogeny of east Asian bufonids inferred from mitochondrial DNA sequences (Anura : Amphibia)

We investigated the relationships of Asian bufonids using partial sequences of mitochondrial DNA genes. Twenty-six samples representing 14 species of Bufo from China and Vietnam and 2 species of Torrentophryne from China were examined. Three samples of Bufo viridis from Armenia and Georgia were also sequenced to make a comparison to its sibling tetraploid species B. danatensis. Bufo americanus, from Canada, was used as the outgroup. Sequences from the 12S ribosomal RNA, 16S ribosomal RNA, cytochrome b, and the control region were analyzed using parsimony. East Asian bufonids were grouped into two major clades. One clade included B. andrewsi, B. bankorensis, B. gargarizans, B. tibetanus, B. tuberculatus, its sister clade B. cryptotympanicus, and the 2 species of Torrentophryne. The second clade consisted of B. galeatus, B. himalayanus, B. melanostictus, and a new species from Vietnam. The placement of three taxa (B. raddei B. viridis, and its sister species, B. danatensis) was problematic. The genus Torrentophryne should be synonymized with Bufo to remove paraphyly. Because B. raddei does not belong to the clade that includes B. viridis and B. danatensis, it was removed from the viridis species group. The species status of B bankorensis from Taiwan is evaluated. (C) 2000 Academic Press.

Diatom community succession in the recent history of a eutrophic Yunnan Plateau lake, Lake Dianchi, in subtropical China

Fish introduction, eutrophication and disappearance of aquatic vegetation are important disturbances of aquatic ecosystems, especially in plateau lakes, which are generally considered to be very vulnerable. Fish were introduced to Lake Dianchi, a eutrophic plateau lake in southwest China, in the late 1950s and 1970s. After the introduction, invasive fish became the dominant species, and the total fish yield increased. Meanwhile, the trophic level of Lake Dianchi had a tendency to increase in the past decades because of the increases in human activities in the watershed area. In addition, the area of aquatic vegetation decreased from more than 90 to 1.8% of the lake area from the 1950s to 2000. This study investigated the effects of fish introduction, eutrophication and aquatic vegetation on the diatom community of Lake Dianchi by examining the changes of microfossil diatom assemblage and abundance. Results showed that the absolute abundance and diatom assemblages changed after fish were introduced. The endemic species, Cyclotella rohomboideo-elliptica, disappeared with the introduction of fish and increasing trophic levels after 1958. Fragilaria crotonensis entered into the lake with the introduction of fish and gradually thrived in the lake after 1958. Diatom species numbers also decreased gradually from 21 to 9 from the past to present. Epiphytic diatoms disappeared with the decrease of aquatic vegetation after 1985. Our study indicated that eutrophication was the most important process determining diatom abundance, and fish introduction was a secondary process determining diatom abundance, while aquatic vegetation had a more important role in structuring the diatom community in this eutrophic plateau lake.

Speciation and Phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: Analysis of the Cytochrome b Gene of mtDNA from Diverse Populations

Gao-Yan Li, Xu-Zhen Wang, Ya-Hui Zhao, Jie Zhang, Chun-Guang Zhang, and Shun-Ping He (2009) Speciation and phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: analysis of the cytochrome b gene of mtDNA from diverse populations. Zoological Studies 48(4): 569-583. The cyprinid fish Opsariichthys bidens Gunther is distributed in all major river systems of continental East Asia, and represents an attractive model for phylogeographic studies among cyprinid species or within a given species. In this study, we investigated the phylogeographic and demographic history of this species, using partial sequences of the cytochrome (cyt) b gene in mitochondrial (mt)DNA. Fish samples were collected from almost all major river systems where O. bidens is distributed in China. Sequence analysis showed remarkably high polymorphism, with 125 haplotypes in the 234 specimens examined, and with 89.8% of haplotypes occurring in only 1 specimen. A neutrality test indicated that some groups were not at mutation-drift equilibrium, suggesting a past population expansion. These results were supported by a mismatch distribution analysis. Based on our analysis, O. bidens consists of 4 groups belonging to 2 clades. The divergence time of the 2 clades was estimated to be 11.06-8.04 my. This value corresponds to the time of the 2nd uplift of the Qinghai-Tibet Plateau, the emergence of the East Asian monsoon, and the Epoch-6 Event. A two species scheme is proposed. http://zoolstud.sinica.edu.tw/Journals/48.4/569.pdf

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Molecular evidence for diphyly of the Asian catfish family Amblycipitidae (Teleostei: Siluriformes) and exclusion of the South American Aspredinidae from Sisoroidea

Amblycipitidae Day, 1873 is an Asian family of catfishes (Siluriformes) usually considered to contain 28 species placed in three genera: Amblyceps (14 spp.), Liobagrus (12 spp.) and Xiurenbagrus (2 spp.). Morphology-based systematics has supported the monophyly of this family, with some authors placing Amblycipitidae within a larger group including Akysidae, Sisoridae and Aspredinidae, termed the Sisoroidea. Here we investigate the phylogenetic relationships among four species of Amblyceps, six species of Liobagrus and the two species of Xiurenbagrus with respect to other sisoroid taxa as well as other catfish groups using 6100 aligned base pairs of DNA sequence data from the rag1 and rag2 genes of the nuclear genome and from three regions (cyt b, COL ND4 plus tRNA-His and tRNA-Ser) of the mitochondrial genome. Parsimony and Bayesian analyses of the data indicate strong support for a diphyletic Amblycipitidae in which the genus Amblyceps is the sister group to the Sisoridae and a clade formed by genera Liobagrus and Xiurenbagrus is the sister group to Akysidae. These taxa together form a well supported monophyletic group that assembles all Asian sisoroid taxa, but excludes the South American Aspredinidae. Results for aspredinids are consistent with previous molecular studies that indicate these catfishes are not sisoroids, but the sister group to the South American doradoid catfishes (Auchenipteridae + Doradidae). The redefined sisoroid clade plus Bagridae, Horabagridae and (Ailia + Laides) make up a larger monophyletic group informally termed "Big Asia." Likelihood-based SH tests and Bayes Factor comparisons of the rag and the mitochondrial data partitions considered separately and combined reject both the hypothesis of amblycipitid monophyly and the hypothesis of aspredinid inclusion within Sisoroidea. This result for amblycipitids conflicts with a number of well documented morphological synapomorphies that we briefly review. Possible nomenclatural changes for amblycipitid taxa are noted.

Multiple invasions of europe by east asian cobitid loaches (Teleostei : Cobitidae)

While it has been widely suggested that freshwater fishes from East Asia invaded the western Palaearctic, details about this process are largely unknown. Here, using the cytochrome b gene, we evaluated the phylogenetic relationships of a small group of Eurasian primary freshwater fishes (Cobitidae), which are widely distributed and species rich in East Asia and Europe, with the purpose of inferring their invasion process of Europe from East Asia. Though phylogenetic relationships of cobitids were not well resolved, our analysis could identify three sister groups formed by the European and East Asian cobitids, which brought new insights into the biogeography of the genera Cobitis, Misgurnus, and Sabanejewia. The present results support the view that Asian cobitid fishes may have invaded Europe at least five times independently, and once reverse colonization of European cobitids to East Asia could also be found. Ancestral Sabanejewia might have been the first cobitids to cross Siberia and invade the EMZS (Euro-Mediterranean zoogeographic subregion) about 33.54 million years ago (MYA). One lineage of Cobitis and the ancestor of Misgurnus fossilis (Linnaeus) almost in the same time invaded the Europe, responding to 16.71 MYA and 16.59 MYA, respectively. Three different lineages of Cobitis were found to have invaded the EMZS from East Asia, and once reverse invasion to East Asia occurred to one subclade of European Cobitis. And our data also suggest that the diversity of East Asian cobitid fishes, especially of the genus Cobitis, is greatly underestimated.

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub-species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree-building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub-species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8.89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4.78 mya from the Chinese group. The northern-southern clades of S. nigripinnis began to diverge c. 2.12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0.34 mya. (C) 2008 The Authors Journal compilation (C) 2008 The Fisheries Society of the British Isles.

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei : Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence (1140bp). Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G. eckloni of the Yellow River specific haplotype A1 was a founder and it radiated all haplotypes of G. przewalskii which suggested G. przewalskii might only originate from one of two maternals of G. eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades A1 and A21 with the most recent common ancestor (TMRCA) about 0.2308 +/- 0.01 Ma and 0.1319 +/- 0.015 Ma, respectively, which were within the geological age range of "Gonghe Movement" event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qinghai-Tibetan Plateau in the Late Pleistocene.

Changes in the life history of Abbottina fivularis in Lake Fuxian

After invading Lake Fuxian, China, Abbottina rivularis showed marked changes in its life history traits, including alterations in annuli formation, extension to the length of the breeding season, and an increase in fecundity and growth rate. The results are explained in the context of the enemy release hypothesis. (c) 2007 The Authors. Journal compilation (c) 2007 The Fisheries Society of the British Isles.

MtDNA phylogeny provides evidence of generic polyphyleticism for East Asian bagrid catfishes

We explore the intrafamilial relationships of East Asian bagrid catfishes (Hemibagrus, Pseudobagrus, Pelteobagrus, and Leiocassis) based on 245 sequences of 1092 bp mitochondrial cytochrome b fragments. Four haplotypes were found to be shared by Pseudobagrus ussuriensis, Pelteobagrus vachelli and Pelteobagrus nitidus. Phylogenetic trees were performed using the neighbor joining, maximum parsimony, maximum likelihood, and Bayesian likelihood methods. The phylogenetic trees based on NJ, MP, ML and BL inferences strongly support polyphyleticism for the currently recognized genera Pseudobagrus, Pelteobagrus and Leiocassis. However, the species currently assigned to these three genera form a robustly monophyletic group with relatively low genetic divergence. The structure of maxillary barbels and serrations on the anterior edge of the pectoral spines seem to be indicatory of appropriate phylogenetic traits. We propose that only Hemibagrus and Pseudobagrus are the only valid genera of East Asian bagrids.

Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei : Cypriniformes) derived from the nuclear recombination activating gene 2 sequences

The family Cyprinidae is one of the largest families of fishes in the world and a well-known component of the East Asian freshwater fish fauna. However, the phylogenetic relationships among cyprinids are still poorly understood despite much effort paid on the cyprinid molecular phylogenetics. Original nucleotide sequence data of the nuclear recombination activating gene 2 were collected from 109 cyprinid species and four non-cyprinid cypriniform outgroup taxa and used to infer the cyprinid phylogenetic relationships and to estimate node divergence times. Phylogenetic reconstructions using maximum parsimony, maximum likelihood, and Bayesian analysis retrieved the same clades, only branching order within these clades varied slightly between trees. Although the morphological diversity is remarkable, the endemic cyprinid taxa in East Asia emerged as a monophyletic clade referred to as Xenocypridini. The monophyly for the subfamilies including Cyprininae and Leuciscinae, as well as the tribes including Labeonini, Gobionini, Acheilognathini, and Leuciscini, was also well resolved with high nodal support. Analysis of the RAG2 gene supported the following cyprinid molecular phylogeny: the Danioninae is the most basal subfamily within the family Cyprinidae and the Cyprininae is the sister group of the Leuciscinae. The divergence times were estimated for the nodes corresponding to the principal clades within the Cyprinidae. The family Cyprinidae appears to have originated in the mid-Eocene in Asia, with the cladogenic event of the key basal group Danioninae occurring in the early Oligocene (about 31-30 MYA), and the origins of the two subfamilies, Cyprininae and Leuciscinae, occurring in the mid-Oligocene (around 26 MYA). (c) 2006 Elsevier Inc. All rights reserved.