Phylogenetic relationships of the phasianidae reveals possible non-pheasant taxa

The phylogenetic relationships of 21 pheasant and 6 non-pheasant species were determined using nucleotide sequences from the mitochondrial cytochrome b gene. Maximum parsimony and maximum likelihood analysis were used to try to resolve the phylogenetic relationships within Phasianidae. Both the degree of resolution and strength of support are improved over previous studies due to the testing of a number of species from multiple pheasant genera, but several major ambiguities persist. Polyplectron bicalcaratum (grey peacock pheasant) is shown not to be a pheasant. Alternatively, it appears ancestral to either the partridges or peafowl. Pucrasia macrolopha macrolopha (koklass) and Gallus gallus (red jungle fowl) both emerge as non-pheasant genera. Monophyly of the pheasant group is challenged if Pucrasia macrolopha macrolopha and Gallus gallus are considered to be pheasants. The placement of Catreus wallichii (cheer) within the pheasants also remains undetermined, as does the cause for the great sequence divergence in Chrysolophus pictus obscurus (black-throated golden). These results suggest that alterations in taxonomic classifications may be required for some pheasant species and genera.     

鸡形目鸟类系统发生研究现状

综合形态学、行为学、分子系统发生等方面研究成果,对世界鸡形目鸟类科的系统关系以及属、种间系统发生的研究进展进行了阐述,侧重介绍与我国鸡形目鸟类相关类群的系统发生研究现状。与传统的系统关系比较,新的研究结果主要有:凤冠雉科和冢雉科不再是互为姊妹群;传统分类中的雉族和鹑族被证明并非单源而是多源的;雉族的原鸡属与鹑族的竹鸡属有很近的亲缘关系;灰山鹑、火鸡和松鸡类的系统发生关系可能很近。分子进化的研究表明雉科各属的起源主要集中在上新世。     

Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

Molecular phylogeny and biogeography of caecilians from Southeast Asia (Amphibia, Gymnophiona, Ichthyophiidae), with special reference to high cryptic species diversity in Sundaland

We investigated the phylogenetic relationships and estimated the history of species diversification and character evolution in two ichthyophiid genera: Caudacaecilia and Ichthyophis. We estimated the phylogenetic relationships of 67 samples from 33 localities in Southeast Asia from 3840-bp sequences of the mitochondrial 12S rRNA, 16S rRNA, and cyt b genes using Bayesian inference, maximum likelihood, and maximum parsimony methods. The Southeast Asian samples formed a well-supported clade differentiated from a South Asian sample. The Southeast Asian clade was divided into two subclades, one containing samples from South China, Indochina, Malay Peninsula, and Java. The other consisted of samples from Borneo and the Philippines. Neither Caudacaecilia nor Ichthyophis was monophyletic, nor did samples with or without light stripes lateral to the body form clades. We found several distinct sympatric lineages and undescribed species, especially from Sundaland.     

The complete mitogenome of the snakehead Channa argus (Perciformes: Channoidei): genome characterization and phylogenetic implications

To better understand the phylogenetic status of the snakehead, Channa argus, we determined its complete mitogenome sequence using long-polymerase chain reaction and the direct sequencing method. The complete mitogenome sequence was 16,559?bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. This was the first report of the mitogenome sequence in suborder Channoidei. Phylogenetic relationships of 14 perciform suborders based on mitogenome sequences were reconstructed using Bayesian inference and maximum likelihood methods. The results strongly supported the monophyly of Perciformes and the snakehead, as a representative species of suborder Channoidei, formed the most basal branch having sister relationship with the clade containing all other analyzed perciform fishes. The further phylogenetic analyses of six channid species, based on cytochrome b gene, suggested that two channid genera constituted reciprocally monophyletic clades. In addition, the relaxed molecular clock method was used to estimate divergence dates among major suborders of Perciformes and major species in Channoidei.     

角雉属分类地位的探讨

角雉属Tragopan两性羽色不同,雄性具有艳丽的装饰性羽毛,这与一般雉族Phasianini相似;而尾较翅为短,尾羽的换羽从中央到外侧,这些特征又与鹑族Perdicini各属相同,形态特征上角雉属被划为鹑族.通过PCR扩增鸡形目Galliformes黄腹角雉Tragopan caboti等10个属19个个体的线粒体DNA细胞色素b的部分基因,获取片段长度为828bp,以及从GenBank获取22种样本的相应序列,以角叫鸭Anhima cornuta和海龟Kachuga dhongoka为外群,分别用邻接法(Neighbor-joining,NJ)和最小进化法(Minimum-evolution,ME),对鸡形目和将雉科的15个属分为5个属及雉族和鹑族构建分子系统树,NJ和ME系统树中,都是角雉与雉类相聚.角雉出现形态解剖与基因分析分类地位的不一致,说明雉和鹑可能不是单系群.同时我们认为雌雄的色泽区别比尾羽的长短和换羽方式在对雉和鹑形态特征分类时更为重要.从分子水平分析的结果都是角雉属与雉聚类.因此角雉归为雉族更合理.     

介形纲丽足目和速足目及相关类群18S rDNA分子系统发育的研究

文中分析现生介形类 (Ostracoda) 4目 2 1科 2 9属的 18SrDNA部分序列 ,采用最大似然法 (ML)、邻接法 (NJ)和最大简约法 (MP) ,尝试构建介形类的分子系统树 ;结合介形类的形态特征和化石记录 ,主要对速足目(Podocopida)、丽足目 (Myodocopida)及其超科级分类阶元的系统发生关系进行探讨。 3种分析方法均支持形态学上Podocopida ,Myodocopida和海萤超科 (Cypridinacea)的界定 ;但对Podocopida目土菱介超科 (Bairdiacea)的系统地位提出质疑 ,该类群可能不是单系发生的自然类群。上述分析显示 ,Podocopida,Myodocopida,Platycopida和Halo cypridina组成一个单系群 ;介形类在目、超科、科和属的水平上可能发生过多次辐射分化     

两种锦鸡和环颈雉线粒体DNA(mtDNA)的比较研究

本文以10种限制性内切酶分析雉科中环颈雉,红腹锦鸡和白腹锦鸡线粒体DNA（mtDNA）。雉属与锦鸡属之间的遗传距离P为0.076（0.067-0.085）,红腹锦鸡与白腹锦鸡的P为0.012。推算雉属和锦鸡属的分化大约发生在3.8×10[6]年以前,红腹锦鸡与白腹锦鸡的分化大约在6×10[5]年以前。这些结果表明：1.在雉科系统发生中,雉属与锦鸡属是近缘的属;2.红腹锦鸡和白腹锦鸡的分化较晚,关系密切,可能只是两个亚种。     

Resolution of the phylogenetic position of the Congo peafowl,Afropavo congensis: a biogeographic and evolutionary enigma.

Afropavo congensis, the Congo peafowl, has long fascinated ornithologists because of its uncertain phylogenetic position and unusual geographic distribution. While some researchers have placed Afropavo as a sister taxon to the true peafowl, Pavo species, others have suggested relationships with the guineafowl or an Old World partridge, Francolinus. These divergent opinions are due, at least in part, to (i) the unique morphological characteristics, lack of elaborate ornamentation, and monogamous mating system in Afropavo which differentiates it from Pavo; and (ii) the restricted distribution of Afropavo in Zaire, which is far removed from the Asian distribution of all other pheasant species. We obtained complete cytochrome b and partial D-loop sequences of Afropavo and compared them to Pavo, guineafowl, Francolinus and other galliform taxa. Our results strongly support a close relationship between Afropavo and Pavo, and we were able to reject alternative phylogenetic hypotheses. Molecular clock estimates of the divergence time place the separation of Afropavo and Pavo in the late Miocene. We also discuss other relatives of Afropavo and Pavo and use this information to propose hypotheses regarding the evolution of ornamentation and sexual dimorphism within this group of pheasants.     

Parasite-mediated competition between pheasant and grey partridge: a preliminary investigation

Pheasants (Phasianus colchicus) and grey partridges (Perdix perdix) were maintained together on land known to be contaminated with eggs of the caecal nematode Heterakis gallinarum to examine the hypothesis that this shared parasite has a greater impact on grey partridges than on pheasants. Since an inverse relationship between worm intensity and partridge body condition was detected, while no such relationship with pheasant body condition was observed, we were unable to refute this hypothesis. Furthermore, that there was no relationship between worm intensity after the exposure period and partridge body mass prior to the infection trial implies that infection caused the decrease in partridge body condition, and not vice versa. Data consistent with previous observations that H. gallinarum fecundity and survival is greater in pheasants than in partridges suggest that the bulk source of nematode infection to wild grey partridges is reared pheasants, and not the partridges themselves. This, and the differential impact on host body condition, supports the hypothesis that the spread of parasites from increasing numbers of released pheasants has contributed to the decline in wild grey partridge populations in the UK within the past 50 years. Received: 11 September 1998 / Accepted: 13 February 1999     

Phylogenetic relationships of mullets (Mugilidae) in China Seas based on partial sequences of two mitochondrial genes

Phylogenetic analyses of Mugilidae species from the China coast were carried out based on 16S and 12S rRNA mitochondrial gene sequences by maximum parsimony, maximum likelihood, Bayesian inference and neighbor joining analysis in the present study. The results suggested that Mugil cephalus is the most genetically divergent species among the Mugilidae. The four Liza species clustered together and formed a monophyletic group. The genera Osteomugil showed closer affiliation with Valamugil than with Ellochelon; these three genera then grouped together to form a monophyletic clade presenting as the sister group to Liza. Analyses of phylogenetic and genetic distance indicated that Southern and Northern lineages of Liza haematocheila may be two different species; likewise, strong genetic divergence existed between Southern and Northern M. cephalus lineages. In addition, our results supported the Southern origin of Chinese Mugilids, which is contrary to the hypothesis based on morphological characters.     

Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights

Comprehensive taxonomic sampling can vastly improve the accuracy of phylogenetic reconstruction. Here, we present the most inclusive phylogenetic analysis of Arvicolinae (Mammalia, Rodentia) to date, combining all published cytochrome  b gene sequences of greater than 1097 bp and new sequences from two monotypic genera. Overall, the phylogenetic relationships between 69 species of voles and lemmings, representing 18 genera and 10 tribes, were studied. By applying powerful modern approaches to phylogenetic reconstruction, such as maximum likelihood and Bayesian analysis, we provide new information on the early pulse of evolution within the Arvicolinae. While the position of two highly divergent lineages, Phenacomys and Ondatra , could not be resolved, the tribe Lemmini, appeared as the most basal group of voles. The collared lemmings (Dicrostonychini) grouped together with all of the remaining tribes. The two previously unstudied monotypic genera Dinaromys and Prometheomys form a moderately well-supported monophyletic clade, possibly a sister group to Ellobius (Ellobiusini). Furthermore, with one exception, all tribes ( sensu Musser & Carleton, 2005) proved to be monophyletic and can thus be regarded as meaningful evolutionary entities. Only the tribe Arvicolini emerged as paraphyletic in both analyses because of the unresolved phylogenetic position of Arvicola terrestris . Steppe voles of the genus Lagurus were solidly supported as a sister group to the Microtus and allies clade.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 825–835.     

Genetic divergence and phylogenetic independence of Far Eastern species in subfamily Leuciscinae (Pisces: Cyprinidae) inferred from mitochondrial DNA analyses

Classification of freshwater fish in the subfamily Leuciscinae, Cyprinidae is hampered by complexity or lack of morphological diversity. In this study, analyses based on mtDNA sequences were undertaken to clarify phylogenetic relationships among Far Eastern, North American and European species in the Leuciscinae. Evolutionary rate in cytochrome b gene (Cyt-b) and D-loop sequences appear to be almost constant in Leuciscinae. The topology of phylogenetic trees generated by neighbor-joining (NJ) and maximum likelihood (ML) methods based on Cyt-b gene and D-loop sequences was similar. Five major clades, designated clades 1-5, and a minor clade were discriminated. Most of the Far Eastern, North American and European species were included in the major clades. Clade 1, comprised almost entirely of Far Eastern phoxinins, is monophyletic and greatly diverged from the other species of Leuciscinae. From the present phylogenetic relationships and the previous studies, we present the following hypotheses with respect to the evolutionary history of the Far Eastern phoxinins. The Far Eastern species should be classified into Far Eastern-specific genera, although ichthyologists have still insisted that the species should be included in the European genera. The Far Eastern clade 1 consists of two subclades, including genera Pseudaspius-Tribolodon and Far Eastern Phoxinus species. According to our phylogenetic analyses, Pseudaspius leptocephalus and Tribolodon species should be reclassified into the same genus. On the basis of evolutionary rate in Cyt-b gene in Cyprinidae, it is estimated that the Far Eastern lineage diverged approximately 10-14 million years ago (mya) from the common ancestor of Leuciscinae. It is deduced that speciation of the Far Eastern species occurred until approximately 4 mya, in relation to the formation of the Sea of Japan and the Japanese Islands.     

Phylogenetic position of the genus Tetraophasis (Aves, Galliformes, Phasianidae) as inferred from mitochondrial and nuclear sequences

The genus Tetraophasis is endemic to China and the systematic relationships of the genus in Phasianidae based solely on their morphology are not clear. The phylogenetic position of this genus and other genera in Phasianidae was investigated in this study using the mitochondrial genes cytochrome b (CYT B), NADH dehydrogenase subunit 2 (ND2) and nuclear ovomucoid intron G (OVO-G). Maximum parsimony, Bayesian and maximum likelihood analyses were employed. Comparison between the mitochondrial and nuclear findings suggested that our final combined data had higher resolving power than the separate data. Both separate data and combined data yielded a sister relationship between Tetraophasis and Lophophorus with strong support, which provided new evidence that pheasants and partridges were not monophyletic. In addition, our results indicated a basal position of Ithaginis, but the position of Perdix and Pucrasia were still unresolved. The result of this study provided a phylogenetic background for a revised classification of Galliformes.     

A phylogeny of the fish family Sparidae (porgies) inferred from mitochondrial sequence data

The porgies (Sparidae) comprise a diverse group of neritic fishes with a broad geographic distribution. We used mitochondrial DNA sequences from partial 16S ribosomal RNA and cytochrome b genes to reconstruct the phylogenetic history of these fishes. Sequences from 38 sparid species, 10 species in outgroups closely related to sparids, seven basal percoid species, and a non-perciform outgroup species were analyzed with parsimony and maximum likelihood. The Sparidae were monophyletic with the inclusion of Spicara, which is currently placed in the Centracanthidae. The genera Spicara, Pagrus, and Pagellus, were not monophyletic indicating a need for revision. Two main sparid lineages were recovered in all analyses, but the previously proposed six sparid subfamilies (Boopsinae, Denticinae, Diplodinae, Pagellinae, Pagrinae, and Sparinae) were not monophyletic. This suggests that dentition and feeding modes, upon which these subfamilies are based, were independently derived multiple times within sparid fishes. There was no evidence from the 16S or combined analyses for a monophyletic Sparoidea.     

Molecular evolution of pteridophytes and their relationship to seed plants: Evidence from complete 18S rRNA gene sequences

Complete 18S ribosomal RNA sequence data from representatives of all extant pteridophyte lineages together with RNA sequences from different seed plants were used to infer a molecular phylogeny of vascular plants that included all major land plant lineages. The molecular data indicate that lycopsids are monophyletic and are the earliest diverging group within the vascular land plants, whereasPsilotum nudum is more closely related to the seed plants than to other pteridophyte lineages. The phylogenetic trees based on maximum likelihood, parsimony and distance analyses show substantial agreement with the evolutionary relationships of land plants as interpreted from the fossil record.     

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.     

Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits

To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup consisted of 59 individuals representing six families, 12 genera, and 54 species potentially part of the Peltigerineae/Peltigerales. Our study revealed that all six families together formed a strongly supported monophyletic group within the Lecanoromycetidae. We propose here a new classification for these lichens consisting of the order Peltigerales and two suborders-Collematineae subordo nov. (Collemataceae, Placynthiaceae, and Pannariaceae) and Peltigerineae (Lobariaceae, Nephromataceae, and Peltigeraceae). To accommodate these new monophyletic groups, we redefined the Lecanorineae, Pertusariales, and Lecanorales sensu Eriksson et al. (Outline of Ascomycota-2003, Myconet 9: 1-103, 2003). Our study confirms the monophyly of the Collemataceae, Lobariaceae, Nephromataceae, and Peltigeraceae, and the genera Nephroma, Sticta, and Peltigera. However, Leptogium, Lobaria, Pseudocyphellaria, and Solorina were found to be nonmonophyletic genera. Reconstruction of ancestral symbiotic states within the Peltigerales, using maximum likelihood (ML) and a Bayesian approach to account for phylogenetic uncertainty, revealed an evolutionary scenario in which bimembered associations with cyanobacteria were ancestral, followed by multiple independent acquisitions of green algae to form tripartite symbioses and rare subsequent losses of the cyanobiont to form bimembered symbioses with green algae.     

Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes

Systematics of the red algal order Corallinales has a long and convoluted history. In the present study, molecular approaches were used to assess the phylogenetic relationships based on the analyses of two datasets: a large dataset of SSU sequences including mainly sequences from GenBank; and a combined dataset including four molecular markers (two nuclear: SSU, LSU; one plastidial: psbA; and one mitochondrial: COI). Phylogenetic analyses of both datasets re-affirmed the monophyly of the Corallinales as well as the two families (Corallinaceae and Hapalidiaceae) currently recognized within the order. Three of the four subfamilies of the Corallinaceae (Corallinoideae, Lithophylloideae, Metagoniolithoideae) were also resolved as a monophyletic lineage whereas members of the Mastophoroideae were resolved as four distinct lineages. We therefore propose to restrict the Mastophoroideae to the genera Mastophora, Metamastophora, and possibly Lithoporella in the aim of rendering this subfamily monophyletic. In addition, our phylogenies resolved the genus Hydrolithon in two unrelated lineages, one containing the generitype Hydrolithon reinboldii and the second containing Hydrolithon onkodes, which used to be the generitype of the now defunct genus Porolithon. We therefore propose to resurrect the genus Porolithon for the second lineage encompassing those species with primarily monomerous thalli, and trichocyte arrangements in large pustulate horizontal rows. Moreover, our phylogenetic analyses revealed the presence of cryptic diversity in several taxa, shedding light on the need for further studies to better circumscribe species frontiers within the diverse order Corallinales, especially in the genera Mesophyllum and Neogoniolithon.