Molecular phylogeny of wood mice (Apodemus, Muridae) in East Asia

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear IRBP (1152 bp) genes were used to assess the evolutionary history of Apodemus, using the complete set of Asian species. Our results indicate that speciation in Asia involved three radiations, which supports an earlier study. The initial radiation yielded A. argenteus (Japanese endemic), A. gurkha (Nepalese endemic), and the ancestral lineage of the remaining Asian species. This lineage subsequently diverged into four groups: agrarius-chevrieri (agrarius group), draco-latronum-semotus (draco group), A. peninsulae, and A. speciosus (Japanese endemic). The final step consisted of divergence within two species groups as a consequence of the geography of the Yunnan-Guizhou plateau and Taiwan. The ecological ability of two Apodemus-species to inhabit one locality via niche partitioning likely drove the second radiation and shaped the basic geographical pattern seen today: A. argenteus and A. speciosus in Japan, A. agrarius and A. peninsulae in northern China, and the A. agrarius and A. draco groups in southern China. The three radiations are estimated to have occurred 7.5, 6.6, and 1.8-0.8 Mya respectively, using the IRBP clock, based on rat-mouse divergence 12 Mya. (C) 2003 The Linnean Society of London.

Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences

In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of ND4 and control region fragments were sequenced to examine phylogenetic relationships among Chinese hare taxa and other leporids throughout the World using maximum parsimony, maximum likelihood, and Bayesian phylogenetic reconstruction approaches. Using reconstructed phylogenies, we observed that the Chinese hare is not a single monophyletic group as originally thought. Instead, the data infers that the genus Lepus is monophyletic with three unique species groups: North American, Eurasian, and African. Ancestral area analysis indicated that ancestral Lepus arose in North America and then dispersed into Eurasia via the Bering Land Bridge eventually extending to Africa. Brooks Parsimony analysis showed that dispersal events followed by subsequent speciation have occurred in other geographic areas as well and resulted in the rapid radiation and speciation of Lepus. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches estimated the divergence time between the three major groups within Lepus. The genus appears to have arisen approximately 10.76 MYA (+/- 0.86 MYA), with most speciation events occurring during the Pliocene epoch (5.65 +/- 1.15 MYA similar to 1.12 +/- 10.47 MYA). (c) 2005 Elsevier Inc. All rights reserved.

Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited: New Insights from Ten Additional Colobines

Pancreatic RNase genes implicated in the adaptation of the colobine monkeys to leaf eating have long intrigued evolutionary biologists since the identification of a duplicated RNASE1 gene with enhanced digestive efficiencies in Pygathrix nemaeus. The recent emergence of two contrasting hypotheses, that is, independent duplication and one-duplication event hypotheses, make it into focus again. Current understanding of Colobine RNASE1 gene evolution of colobine monkeys largely depends on the analyses of few colobine species. The present study with more intensive taxonomic and character sampling not only provides a clearer picture of Colobine RNASE1 gene evolution but also allows to have a more thorough understanding about the molecular basis underlying the adaptation of Colobinae to the unique leaf-feeding lifestyle. The present broader and detailed phylogenetic analyses yielded two important findings: 1) All trees based on the analyses of coding, noncoding, and both regions provided consistent evidence, indicating RNASE1 duplication occurred after Asian and African colobines speciation, that is, independent duplication hypothesis; 2) No obvious evidence of gene conversion in RNASE1 gene was found, favoring independent evolution of Colobine RNASE1 gene duplicates. The conclusion drawn from previous studies that gene conversion has played a significant role in the evolution of Colobine RNASE1 was not supported. Our selective constraint analyses also provided interesting insights, with significant evidence of positive selection detected on ancestor lineages leading to duplicated gene copies. The identification of a handful of new adaptive sites and amino acid changes that have not been characterized previously also provide a necessary foundation for further experimental investigations of RNASE1 functional evolution in Colobinae.

Large Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid, Acyrthosiphon pisum

Gaining insight into the mechanisms of chemoreception in aphids is of primary importance for both integrative studies on the evolution of host plant specialization and applied research in pest control management because aphids rely on their sense of smell

Phylogeny and zoogeography of the cyprinid genus Epalzeorhynchos Bleeker (Cyprinidae : Ostariophysi)

A total of 62 variable osteological and external characters was found among the five currently recognized species of Epalzeorhynchos. When the genera Crossocheilus and Paracrossocheilus are combined as the outgroup, only 30 of these characters can be polarized. This includes six autapomorphies. The remaining 24 polarized characters form a data matrix which yields a single, 26-step tree with a Consistency Index (CI) of 1 and a Retention Index (RI) of 1, The analysis was also performed on a combined dataset in which the 32 unpolarized characters (characters for which the combined outgroup was dimorphic) were added and coded as missing data (i.e., "?"), Analyzing this data matrix with all multistate characters ordered generates the same single most-parsimonious tree with a length of 63 steps, a CI of 0.98 and a RI of 0.97, When either Crossocheilus or Paracrossocheilus is used as the sole outgroup, the same single most-parsimonious tree is produced although the numbers of informative characters and some of the polarities differ. Evidence is presented to support the following hypotheses: (1) E, kalopterus + E, frenatus + E. bicolor + E. munensis form a monophyletic group; (2) E. frenatus + E, bicolor + E, munensis form a monophyletic group with E, kalopterus as its sister group; this speciation event is congruent with the predictions of vicariant speciation mode I; and (3) E. bicolor and E. munensis are sister groups, again congruent with vicariant speciation mode I, Evidence presented here also supports the zoogeographical hypothesis that the faunas of the Indochinese region and the Greater Sundas are more closely related to each other than either of them is to the lower Salween basin fauna and that the lower Mekong, Chao Phraya, and Mac Khlong basin faunas are more closely related to each other than any of them is to the Greater Sundas, In addition, the monophyly of Epalzeorhynchos is also preliminarily discussed by including either Paracrossocheilus or Crossocheilus in the ingroup. It is demonstrated that E. bicornis clusters with Paracrossocheilus when Paracrossocheilus is included in the ingroup. It seems likely that the taxonomic position of E. bicornis will be resolved as more fishes of the Crossocheilus group are included in future studies.

Taxonomic review of the genus Sinocrossocheilus Wu (Teleostei : Cyprinidae), with a description of four new species

All Sinocrossocheilus species, except S. microstomatus, are reviewed. Four new species, S. labiata, S. papillolabra, S. nigrovittata, and S. longibulla, are described. The genus Sinocrossocheilus differs from other genera of Cyprinidae by the last simple dorsal fin ray being unserrated and unossified, the last unbranched anal fin ray being unserrated and unossified, the 5-branched anal fin rays, the mouth gap being inferior, the rostral cap covering the lower jaw and connecting directly with the lower lip, a row of fleshy lobes on the lower jaw, and a cloudy black spot above the pectoral fin. Sinocrossocheilus labiata is small and has 22 predorsal scales; S. longibulla has a very large air bladder; S. papillolabra possesses a well-developed ventral fin and a wide band covered by fleshy papillae on the lower lip; and S. nigrovittata possesses black longitudinal stripes along the lateral line. Crossocheilus bamaensis and Crossocheilus liuchengensis are transferred to the genus Sinocrossocheilus. Sinocrossocheilus species are endemic to the central and eastern Yunnan-Guizhou Plateau of China, where river systems are anfractuous, including seasonal rivers, cave rivers, underground rivers, and streamlets between mountains. These separated rivers probably provide conditions for the allopatric speciation of the Sinocrossocheilus.

Phylogeny and zoogeography of the cyprinid hemicultrine group (Cyprinidae : Cultrinae)

Ying-Gui Dai and Jun-Xing Yang (2003) Phylogeny and zoogeography of the cyprinid hemicultrine group (Cyprinidae: Cultrinae). Zoological Studies 42(1): 73-92. The hemicultrine group consists of middle-sized cyprinids in Asia which taxonomically belong to the subfamily Cultrinae in the Cyprinidae (Cypriniformes), but there has been no convincing generic phylogenetic hypothesis proposal so far. On the basis of a morphological study of 65 specimens soaked in formalin and 14 skeletal specimens of 8 species in 6 genera within the hemicultrine group as an ingroup, a 70-character matrix was obtained. The generic phylogenetic relationships of the hemicultrine group are hypothesized with the matrix by the method of cladistic analysis. When the species Rasborinus lineatus or Cultrichthys erythropterus is used as the sole outgroup, the matrix gives the same single most-parsimonious tree of generic phylogenetic relationships within the hemicultrine group which shows that the hemicultrine group forms a monophyletic group. However, when Rasborinus lineatus is used as the sole outgroup and Cultrichthys erythropterus and Paralaubuca barroni are included in the ingroup, the hemicultrine group is validated to represent a paraphyletic group, and the hemicultrine group and the genus Paralaubuca form a monophyletic group. The tree of generic relationships and zoogeography of the monophyletic group comprising the hemicultrine group and the genus Paralaubuca suggest the following: (1) The monophyletic group comprises 2 smaller monophyletic groups: the genera Hemiculterella + Pseudohemiculter + Hainania and the genera Hemiculter + Paralaubuca + Pseudolaubuca + Toxabramis. (2) The sister groups of the monophyletic group show both overlapping and vicariant distribution patterns; therefore the generic distribution pattern of the monophyletic group maybe have resulted from both dispersal and vicariance events. (3) The monophyletic group probably originated on the Asian mainland from the Yangtze River to the Pearl River and on Hainan Island in China. (4) The monophyletic group probably originated after the Japanese Archipelago was separated from the Asian mainland at the beginning of the Quaternary Period in the Cenozoic but before Taiwan, Hainan Island, and Indonesia were completely isolated from the Asian mainland after the ice age in the Quaternary Period. (5) Speciation of the genus Hemiculter should have been the earliest, and those of the genera Paralaubuca, Pseudolaubuca, and Hainania ought to be the latest in the process of evolution of this monophyletic group. http://www.sinica.edu.tw/zool/zoolstud/42.1/73.pdf.

Genetic status of selected fish taxa in relation to conservation of genetic and species diversity in the Victoria and Kyoga Lake basins

Cichlids are known for their explosive radiation especially in the African Great Lakes marked with a high level of lake endemism. These fishes have been characterized mainly along trophic and habitat differences, by variation in morphological structures such as teeth and jaws and by differences in body shape and coloration. Cichlids are important as a microcosm of macroevolution. The explosive radiation, young evolutionary scale, and the isolation of groups characterized with high levels of endemism and presence of living fossils makes the group important for evolutionary and genetic studies. Lake Victoria region cichlids which are isolated and relatively more recent in evolution were the last to be appreciated in their diversity. Recently Ole Seehausen has found scores of rock fishes in Lake Victoria which were up to then thought to be absent from the Lake and only known to occur in Lakes Malawi and Tanganyika. Greenwood put together the species groups of Lake Victoria, and later in the early 1980's revised the classification of haplochromine species to reflect the phyletic origin and interrelationship of the various groups in Lake Victoria region. Melan Stiassny has been interested in early evolution of cichlids while the likes of Paul Fuerst and Lees Kaufman and Axel Meyer have been interested and are working to explain the speciation mechanisms responsible for the explosive radiation and evolution of cichlids. Locally S.B Wandera and his student Getrude Narnulemo are spearheading the biodiversity and taxonomic studies of cichlids in Lake Victoria region

The youngest split in sympatric schizothoracine fish (Cyprinidae) is shaped by ecological adaptations in a Tibetan Plateau glacier lake

Although new empirical evidence shows that sympatric speciation has occurred in some species, there are few indisputable model organisms for this process of speciation. The two subspecies (Gymnocypris eckloni eckloni and G. e. scoliostomus) of the schizothoracine Gymnocypris fish species complex from a small glacier lake in the Tibetan Plateau, Lake Sunmcuo, fit several of the key characteristics of the sympatric speciation model. We used combined mitochondrial control region sequences and the cytochrome b gene (1894 bp) to address the phylogenetics and population genetics of 232 specimens of G. e. eckloni and G. e. scoliostomus, as well as all of its closely related sister species. We found that: (i) a total of four old lineages were uncovered in the widespread G. e. eckloni, of which only one was shown to be shared with all G. e. scoliostomus individuals and (ii) the new subspecies (G. e. scoliostomus) evolved in Lake Sunmcuo from the ancestral G. e. eckloni population within approximately 0.057 Ma. These two taxa of the species complex are morphologically distinct, and reproductive isolation is further suggested. Ecological disruptive selection based on morphological traits (e.g. mouth cleft characters) and food utilization may be a mechanism of incipient speciation of two sympatric populations within Lake Sunmcuo. This study provides the first genetic evidence for sympatric speciation in the schizothoracine fish.

Molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei : Cypriniformes)

Connective tissue growth factor (CTGF) plays an important role in regulation of cell growth, differentiation, apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study, 19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification, cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages, respectively, with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution (dN/dS) for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini, species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 by indel (insertion/deletion) was found at the 5' end of CTGF gene of Cyprinidae, and this 6 by deletion only appeared in the Leuciscini, which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein, the most variations and indels were distributed in the signal region and IGFBP region of this protein, implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity. (c) 2007 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships within the genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae) remain unresolved. Because of the use of Takifugu as model organisms, the resolution of these relationships is crucial for the interpretation of evolutionary trends in biology. Pufferfishes of this genus are comprised of a comparatively small number of species and are mainly distributed along the coastal region of the western part of the Sea of Japan and the coastline of China. Mitochondrial gene sequences were employed to test the phylogenetic hypotheses within the genus. Seventeen species of the genus were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, neighbor-joining, maximum likelihood and Bayesian methods. Our hypothesis of internal relationships within the genus differs from previous hypotheses. Our results indicate that (1) the genus Takifugu is a monophyletic assemblage; (2) the genus is divided into 6 subgroups based on the molecular data; and (3) there is low genetic diversity among the species within this genus. In addition, speciation within Takifugu appears to be driven by hybridization and isolation by distribution. Our results also suggested that the taxonomy in the genus should be clarified based on both molecular and morphological data.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Utility of ITS1-5.8S-ITS2 sequences for species discrimination and phylogenetic inference of two closely related bucephalid digeneans (Digenea : Bucephalidae): Dollfustrema vaneyi and Dollfustrema hefeiensis

The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from 60 specimens belonging to two closely related bucephalid digeneans (Dollfustrema vaneyi and Dollfustrema hefeiensis) from different localities, hosts, and microhabitat sites were cloned to examine the level of sequence variation and the taxonomic levels to show utility in species identification and phylogeny estimation. Our data show that these molecular markers can help to discriminate the two species, which are morphologically very close and difficult to separate by classical methods. We found 21 haplotypes defined by 44 polymorphic positions in 38 individuals of D. vaneyi, and 16 haplotypes defined by 43 polymorphic positions in 22 individuals of D. hefeiensis. There is no shared haplotypes between the two species. Haplotype rather than nucleotide diversity is similar between the two species. Phylogenetic analyses reveal two robustly supported clades, one corresponding to D. vaneyi and the other corresponding to D. hefeiensis. However, the population structures between the two species seem to be incongruent and show no geographic and host-specific structure among them, further indicating that the two species may have had a more complex evolutionary history than expected.

The c-myc coding DNA sequences of cyprinids (Teleostei : Cypriniformes): Implications for phylogeny

The family Cyprinidae is one of the largest fish families in the world, which is widely distributed in East Asian, with obvious difference in characteristic size among species. The phylogenetic analysis of cyprinid taxa based on the functionally important genes can help to understand the speciation and functional divergench of the Cyprinidae. The c-myc gene is an important gene regulating individual growth. In the present study, the sequence variations of the cyprinid c-myc gene and their phylogenetic significance were analyzed. The 41 complete sequences of the c-myc gene were obtained from cyprinids and outgroups through PCR amplification and clone. The coding DNA sequences of the c-myc gene were used to infer molecular phylogenetic relationships within the Cyprinidae. Myxocyprinus asiaticus (Catostomidae), Misgurnus anguillicaudatus (Cobitidae) and Hemimyzon sinensis (Homalopteridae) were assigned to the outgroup taxa. Phylogenetic analyses using maximum parsimony (MP), maximum likelihood (ML), and Bayesian retrieved similar topology. Within the Cyprinidae, Leuciscini and Barbini formed the monophyletic lineage respectively with high nodal supports. Leuciscini comprises Xeno-cyprinae, Cultrinae, East Asian species of Leuciscinae and Danioninae, Gobioninae and Acheilognathinae, and Barbini contains Schizothoracinae, Barbinae, Cyprininae and Labeoninae. Danio rerio, D. myersi and Rasbora trilineata were supposed to separate from Leuciscinae and Barbini and to form another lineage, The positions of some Danioninae species were still unresolved. Analyses of both amino acid variation with parsimony information and two high variation regions indicated that there is no correlation between variations of single amino acid or high variation regions and characteristic size of cyprinids. In,addition, the species with smaller size were usually found to be basal within clades in the tree, which might be the results of the adaptation to the primitive ecology and survival pressure.

Simultaneous determination of chromium(VI) and chromium(III) of bioavailable fraction in bottom mud by flow injection-atomic absorption spectroscopy

A rapid and sensitive method for separation and determination of Cr(VI) and Cr(III) in bottom mud of lake by flow injection on-line preconcentrtion system and GFAAS was developed. The available Cr(VI) and Cr(III) were extracted by HOAc or EDTA + NH4 NO3 and adsorbed simultaneously by an anion and a cation resin microclummn and then eluted simultaneously by 2 mol/L NH4 NO3 + 0.05 mol/L ascorbate and 2 mol/L H2SO4, respectively. The elution was performed for 50 s after adsorption for 2 min, and the efficiencies of elution were 85.4% - 94.8% and 96.7% - 106% for Cr(VI) and Cr(M) respectively. The detection limits of the method were 0.9 mu g/L and 2.7 mu g/L with relative standard deviations of 3.5% and 6.4% for the determination of Cr(VI) and Cr(III) in sample, respectively.