Molecular Systematics of the Subfamily Caprinae (Artiodactyla, Bovidae) as Determined from Cytochrome b Sequences

We have sequenced the complete mitochondrial DNA cytochrome b gene from 18 species of the subfamily Caprinae and two outgroup taxa. Additional sequences retrieved from the literature were used to constitute a data set of 32 cytochrome b sequences comprising all genera usually included within the Caprinae. Phylogenetic relationships were assessed by PAUP using three new weighting schemes based on homoplasy analyses. Each type of substitution considered at each of the three codon positions was weighted according to its homoplasy level, as measured by the consistency index (CI), the slope of saturation (S), or their product (CIS). These differentially weighted parsimony analyses indicate that (1) the subfamily Caprinae is monophyletic, but only with the exclusion of Saiga from the group; (2) there is no support for monophyly of the four tribes currently recognized (Caprini, Rupicaprini, Ovibovini, and Saigini), suggesting relationships different from those traditionally accepted; (3) the caprine group consists of three major clades corresponding to (a) Budorcas and Ovis, (b) Capricornis, Ovibos, and Naemorhedus, and (c) Capra, Hemitragus, and Pseudois; and (4) the basal branching pattern is very weakly supported by bootstrap or branch support values except for the sister-group relationship of Pantholops with all other caprines, and the phylogenetic positions of Ammotragus, Oreamnos, and Rupicapra remain unclear.     

基于Cyt b基因探讨羚羊亚科原羚属系统发生关系

原羚属物种在羚羊亚科中的分类地位尚存在很多争议。本文测定了原羚属的黄羊和藏原羚细胞色素b基因全序列(1140bp),并与牛科其它属31个种的同源序列进行比较,对其碱基组成变异情况及核苷酸序列差异进行了分析。基于细胞色素b基因全序列,用简约法(MP)、邻接法(NJ)和似然法(ML)构建了系统进化树。结果表明：黄羊和藏原羚的序列差异为3．78％,颠换数目近乎为0,其突变远未饱和;原羚属内黄羊和藏原羚为不同种,单系发生;原羚属与赛加羚羊属、犬羚属及跳羚属等并系发生,原羚属隶属于羚羊亚科,应为独立属;羚羊亚科组成属间多为并系起源。根据序列差异值2％／百万年的细胞色素6分子钟,推测黄羊和藏原羚分歧时间大约为1～2百万年;原羚属与羚羊亚科其它属分歧时间大约在5．7～8百万年。     

Molecular phylogeny of caprines (Bovidae, Antilopinae): the question of their origin and diversification during the Miocene

Caprines include all bovids related to sheep and goat. The composition of the group is controversial and inter-generic relationships have been widely debated. Here, we analysed 2469 characters draw from three distinct molecular markers, i.e. two mitochondrial genes (cytochrome b and 12S rRNA) and one nuclear fragment (exon 4 of the κ -casein gene). The taxonomic sampling includes all genera putatively described as caprines, as well as several other bovid genera in order to elucidate the position of caprines within the family Bovidae, and to determine the exact composition of the group. Phylogenetic analyses confirm firstly that Pseudoryx and Saiga do not belong to caprines, and secondly, that all tribes classically defined in the literature are not monophyletic, supporting the inclusion of all caprine species into a unique enlarged tribe Caprini sensu lato . Our results are in contradiction with previous investigations suggesting a sister-group relationship between Ovis (sheep and mouflons) and Budorcas (takins). By using a molecular calibration point at 18.5 Mya for the first appearance of bovids, we estimated divergence times with our molecular data. We also performed biogeographic inferences to better understand the origin and diversification of caprines during the Neogene. Our analyses suggest that caprines shared a common ancestor with Alcelaphini and Hippotragini in the middle-late Miocene (13.37 ± 0.70 Mya). Our results also indicate that the extant generic diversity of caprines resulted from a rapid adaptive radiation during the late Miocene, at 10.96 ± 0.73 Mya. We propose that this adaptive radiation resulted from the acquisition of reduced metacarpals, a key innovation which occurred during the late Miocene as a consequence of insularity isolation in the mountainous mega-archipelago between Mediterranean and Paratethys Seas.     

Molecular phylogeny of the family Tephritidae (Insecta: Diptera): New insight from combined analysis of the mitochondrial 12S, 16S,and COII genes

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.     

Boselaphines (Artiodactyla, Ruminantia, Bovidae) from the Middle Siwaliks of Hasnot, Pakistan

In this paper, boselaphine material from several localities in the area of the Hasnot Pakistan, is described, identified, and discussed. Four species that belong to three different genera of the tribe Boselaphini have been found: Selenoportax vexillarius, S. lydekkeri, Pachyportax latidens and Eotragus sp. Eotragus sp. is reported for the first time from the Hasnot and consequently from other Upper Middle Siwalik sediments of Pakistan and equivalent strata of the world, extending the range of the genus from the Lower to the Middle Siwaliks. Reviewing the Siwaliks’ Selenoportax species, S. dhokpathanensis Akhtar and S. tatrotensis Akhtar are synonymized with S. lydekkeri and S. vexillarius, respectively.     

DNA Sequence Evidence for Placement of the Ground Cuscus, Phalanger gymnotis, in the Tribe Phalangerini (Marsupialia: Phalangeridae)

A region of mitochondrial DNA, including the 3 end of tRNA phenylalanine, the complete 12S rRNA and tRNA valine genes, and the 5 end of 16S rRNA, was sequenced for four phalangerids and one burramyid; additional marsupial sequences were extracted from GenBank. Parsimony, minimum evolution, and maximum likelihood analyses show that the ground cuscus, Phalanger gymnotis, groups with the tribe Phalangerini, not with the tribe Trichosurini as had been suggested on the basis of certain morphological characters. This result is in agreement with an earlier study using DNA hybridization and is supported by some morphological evidence as well. We conclude that the character states that link the ground cuscus with the Trichosurini are the result of convergence, and therefore the placement of several other species in the trichosurin genus Strigocuscus based on the same characters should be reconsidered. The hypothesized close relationship of two fossil taxa, Strigocuscus reidi and S. notialis, to Phalanger gymnotis is also questionable because the fossils do not share morphological synapomorphies that link the ground cuscus to the Phalangerini.     

Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA) sequences were analysed within Tarentola mauritanica and other selected species of Tarentola. Several highly genetically distinct lineages occur in North Africa, revealing phylogroups in southern and central Morocco, northern Morocco, Algeria, Tunisia, and Libya. A single haplotype characterizes populations across Spain, Portugal, Italy, Menorca, Crete, and Tunisia raising the possibility of an anthropogenic introduction followed by rapid population expansion throughout southern Europe. T. mauritanica is paraphyletic with respect to T. angustimentalis, a Canary islands endemic. The high genetic diversity observed across North Africa suggests T. mauritanica may represent a species complex.     

Molecular phylogeny of the crab genus Brachynotus (Brachyura: Varunidae) based on the 16S rRNA gene

The crab genus Brachynotus de Haan, 1833 is restricted to the intertidal and shallow subtidal of the Mediterranean and northeastern Atlantic. It is presently recognized to consist of four species, of which three (B. foresti, B. gemmellari and B. sexdentatus) are endemic to the Mediterranean. The fourth species, B. atlanticus, is found along the Atlantic coasts of northern Africa and southern Europe, but also extends into the western Mediterranean. This high level of endemism suggests that speciation within Brachynotus is strongly correlated with the geography and geology of the Mediterranean Sea. A molecular phylogeny based on the mitochondrial large subunit (16S) rRNA gene indicates that the four species of Brachynotus form a monophyletic group within Atlantic Varunidae. The DNA sequence data also show that the genus Brachynotus can be subdivided into two species groups, one comprising B. atlanticus and B. foresti, and the other one B. gemmellari and B. sexdentatus. While B. atlanticus and B. foresti are clearly genetically distinct, B. gemmellari and B. sexdentatus are identical in the studied region of the 16S rRNA gene, suggesting a recent separation or continuing gene flow.     

Molecular Relationships of New Guinean Three-Striped Dasyures, (Myoictis, Marsupialia: Dasyuridae)

Complete nucleotide sequences of the cytochrome b and 12S rRNA genes and partial sequences of the mitochondrial 16S rRNA gene and the nuclear ɛ-globin gene were obtained from multiple exemplars of the New Guinean dasyurid, Myoictis. Allozyme data were also obtained from most of the same animals. The molecular data show that the genus comprises a number of genetically distinct lineages which correspond with groups proposed by Woolley (2005) on the basis of a number of morphological traits, including the form of the tail i.e. Myoictis leucura (sp. nov.), M. melas, M. wallacei and M. wavicus (new status). Divergence dates estimated from the weighted-average distances for the combined cytochrome b and 12S rRNA data, calibrated with a dasyurid-thylacine divergence 25 million years ago, suggest that the early cladogenic events separating Myoictis took place in the late Miocene. Subsequent separation of M. wavicus and M. leucura from a common ancestor as well as some genetic differentiation within M. melas, took place in the medial Pliocene.     

基于12S,16S和28S rRNA基因序列的中国小毛瓢虫属系统发育分析

【目的】小毛瓢虫属Scymnus Kugelann昆虫主要捕食蚜虫、蚧虫等害虫,是一类经济上重要的天敌昆虫。目前针对小毛瓢虫属的系统发育研究尚属空白,亚属之间的系统演化关系尚不明确,为了建立合理的分类系统,亟需对小毛瓢虫属的亲缘关系进行研究和探讨。【方法】以华南农业大学馆藏的小毛瓢虫属5亚属共44种为研究对象,采用PCR技术对12S, 16S和28S rRNA基因的部分序列进行扩增;运用MEGA 7.0分析了小毛瓢虫属内12S, 16S和28S rRNA基因的碱基组成,基于K2P模型计算了小毛瓢虫属44种的种间遗传距离;采用最大似然法(maximum-likelihood, ML)和贝叶斯推断法(Bayesian-inference, BI)构建该属的系统发育树。【结果】扩增获得小毛瓢虫属44种的12S rRNA基因序列平均长度为356 bp, 16S rRNA基因序列平均长度为351 bp, 28S rRNA基因序列平均长度为315 bp;序列分析表明,12S rRNA基因的A, T, G和C平均含量分别为38.8%, 43.5%, 11.9%和5.8%, 16S rRNA基因的A, T, G和C平均含量分别为37.6%, 40.3%, 14.4%和7.7%, 28S rRNA基因的A, T, G和C平均含量分别为26.7%, 18.3%, 31.4%和23.5%;基于联合序列分析的种间遗传距离为0.004～0.276,平均遗传距离为0.115。系统发育分析结果表明,小毛瓢虫属为单系起源,而小毛瓢虫亚属Scymnus(Scymnus) Kugelann、毛瓢虫亚属Scymnus(Neopullus) Sasaji、小瓢虫亚属Scymnus(Pullus) Mulsant和拟小瓢虫亚属Scymnus(Parapullus) Yang均为并系起源。【结论】基于12S, 16S和28S rRNA基因序列的小毛瓢虫属系统发育分析显示传统的形态学分类体系与基于分子数据分析的结果部分不一致,这表明应该对该属内各亚属的鉴别特征进行全面检视,筛选并确立各亚属的形态指标,同时也表明该属内的亚属分类单元需重新厘定。     

Speciation of two sympatric coastal fish species, Girella punctata and Girella leonina (Perciformes, Kyphosidae)

Girella punctata and Girella leonina are sympatric sister species showing extensive distributional overlap in shallow rocky reefs in the Pacific Ocean south of the Japanese Islands. Differences between the two species in external morphological characters, such as number of pored lateral line scales, colour of opercular flap and shape of caudal fin, are congruent with genetic divergence. Nucleotide identity between the two species in the 3.3 kbp region of partial mitochondrial DNA containing the D-loop region, in 12S and 16S ribosomal RNA (rRNA) and transfer RNA genes is 95%. To estimate divergence time, Bayesian analysis was conducted using a dataset comprising concatenated nucleotide sequences from the two rRNA genes of three girellid and nine other fish species. Using the Elopomorpha – Clupeocephala split (265 million years ago (mya)) as a calibration point, divergence between G. punctata and G. leonina is estimated as having occurred 6.0±1.4 mya. Speciation is suggested to have been caused by geographical isolation associated with formation of the Japanese Islands, which resulted in disjunction of Girella habitat.     

Molecular Relationships of the Extinct Pig-Footed Bandicoot Chaeropus ecaudatus (Marsupialia: Perameloidea) Using 12S rRNA Sequences

The pig-footed bandicoot, Chaeropus ecaudatus, is presumed to be extinct as no specimens have been collected or seen since early this century. Usually classified as a specialized member of the family Peramelidae, there is nevertheless still some doubt as to its taxonomic affinities, because this animal is highly specialized and shows several uniquely derived characters. We report here the first attempt to determine the molecular relationships of this animal using mitochondrial 12S rRNA sequences derived from spirit-preserved museum specimens. Phylogenetic analysis shows that the sequence derived from the Chaeropus sample is clearly that of a bandicoot. Within the bandicoot clade, the pig-footed bandicoot is quite distinct from all other taxa. Divergence-time estimates from the 12S rRNA sequences suggest that Chaeropus diverged from the other bandicoot genera in the late Oligocene or early Miocene and that bandicoots diverged from other Australian families in the late Paleocene–early Eocene.     

甘肃临夏盆地首次发现乌米兽(牛科,偶蹄类)头骨化石（英文）

报道并描述了一件来自甘肃临夏盆地的中间乌米兽(Urmiatherium intermedium)头骨化石新材料,该材料产自柳树组上部,属于晚中新世晚期杨家山动物群。中间乌米兽是一种大型的晚中新世牛科动物,角心特化,短且呈薄板状,并且在基部相互靠近。在角心前后方的额骨和顶骨上,发育大片赘生骨疣,这些骨疣与角心一起,合称角器。20世纪初,步林报道了中国北方晚中新世地层中的大量中间乌米兽化石,包括产自山西保德和甘肃庆阳的20多件头骨以及很多破碎的齿列和骨骼。本文报道的乌米兽头骨化石是乌米兽在甘肃临夏盆地的首次发现,将其在中国北方的分布向西扩展到了青藏高原东北缘地带。乌米兽被普遍认为与近旋角羊(Plesiaddax)、和政羊(Hezhengia)和柴达木兽(Tsaidamotherium)等晚中新世"麝牛类"牛科动物具有较近的亲缘关系,但其系统发育地位仍存有争议。相比其他晚中新世"麝牛类"牛科动物,乌米兽的分布较广,从伊朗至中国北方都有分布,但它鲜与其他晚中新世"麝牛类"牛科动物伴生。在临夏盆地,与其伴生的牛科动物目前仅发现中华羚(Sinotragus)一种。     

Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources

During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed > 4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN243(T)).     

牛科(哺乳纲:偶蹄目)动物与食物有关的适应形态模式

利用逐步分辨分析方法（Stepwise discriminant analysis,SCDA）检测了广义牛科动物的颅齿部结构,这些结构特征可以作为采食行为生态适应特征。在本研究中,测量了72种广义牛科动物的28个颅齿部结构。逐步分辨分析方法得出了6种采食方式适应类型：一般粗食者、新鲜禾草粗食者、开阔生境混合型采食者、精食者、郁闭生境混合型采食者、食果者。用103个标本检测了分辨指标的预测能力,所用标本为缺损标本,大多数缺少一项或多项结构。从这些标本获得的分辨函数的平均预测能力为94％,比用72种广义牛科动物标本建立的分辨函数的平均预测能力（98％）低一些。从一个颅齿部结构小样本建立的分辨函数可以用于考古发掘物中不完整标本的研究。这些指标与用颅下结构测量建立的运动能力和生境选择的指标相结合,可以推断古牛科动物的个体生态学以及古环境重建。     

牛科动物HSL基因序列分析及其分子进化研究

在对牛科中4种动物即牦牛、瘤牛、普通牛和水牛HSL基因外显子Ⅰ部分核苷酸序列进行测定的基础上,与Gen-Bank中其他物种相应基因核苷酸序列、氨基酸序列进行了比对分析,并构建了牦牛与其他物种间分子系统进化树。结果表明:牦牛与普通牛、瘤牛、水牛、猪、人、小鼠、大鼠7个物种HSL基因外显子Ⅰ部分核苷酸序列间保守性较高,同源性大小依次为99.8%、99.6%、97.4%、90.6%、88.4%、83.5%、82.3%。相应氨基酸序列间保守性更高,同源性分别为100%、100%、98.2%、94.0%、92.2%、89.8%、89.8%。牦牛与各物种该基因部分核苷酸序列间碱基变异类型主要表现为碱基转换和颠换,无碱基插入和缺失发生,碱基转换的频率高于颠换的频率;在核苷酸水平上的多数碱基替换都是同义替换;序列间单碱基变异位点大多出现在同一位点,多发生在密码子第3位,其次是第1位,最少发生在第2位,符合分子进化的中性学说。HSL基因外显子Ⅰ部分核苷酸序列进行多序列对位排列构建的各物种间分子系统进化树结果表明,普通牛和瘤牛首先聚为一类,再分别与牦牛、水牛、猪、人聚类,最后与大鼠、小鼠聚为一类。该聚类结果与动物学上的分类结果一致,表明HSL基因外显子Ⅰ部分核苷酸序列适合于构建物种间分子系统进化树。研究表明,牦牛、普通牛和瘤牛3个物种间的遗传距离大小相近,牦牛和水牛间的遗传距离与普通牛、瘤牛和水牛间的遗传距离大小相当。牦牛、普通牛和瘤牛3个物种间的遗传距离远小于它们各自与水牛这一物种的遗传距离,它们三者之间的亲缘关系也相对于它们各自与水牛间的亲缘关系都较近,故将牦牛、普通牛和瘤牛划分在同一个属——牛属(Bos)更为合理。     

Molecular Phylogeny and Species Identification of Pufferfish of the Genus Takifugu (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships and species identification of pufferfishes of the genus Takifugu were examined by use of randomly amplified polymorphic DNA (RAPD) and sequencing of the amplified partial mitochondrial 16S ribosomal RNA genes. Amplifications with 200 ten-base primers under predetermined optimal reaction conditions yielded 1962 reproducible amplified fragments ranging from 200 to 3000 bp. Genetic distances between 5 species of Takifugu and Lagocephalus spadiceus as the outgroup were calculated from the presence or absence of the amplified fragments. Approximately 572 bp of the 16S ribosomal RNA gene was amplified, using universal primers, and used to determine the genetic distance values. Topological phylogenic trees for the 5 species of Takifugu and outgroup were generated from neighbor-joining analysis based on the data set of RAPD analysis and sequences of mitochondrial 16S rDNA. The genetic distance between Takifugu rubripes and Takifugu pseudommus was almost the same as that between individuals within each species, but much smaller than that between T. rubripes, T. pseudommus, and the other species. The molecular data gathered from both analysis of mitochondria and nuclear DNA strongly indicated that T. rubripes and T. pseudommus should be regarded as the same species. A fragment of approximately 900 bp was amplified from the genome of all 26 T. pseudommus individuals examined and 4 individuals of intermediate varieties between T. rubripes and T. pseudommus. Of the 32 T. rubripes individuals, only 3 had the amplified fragment. These results suggest that this fragment may be useful in distinguishing between T. rubripes and T. pseudommus. Received September 29, 2000; accepted February 26, 2001.     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.