Molecular phylogeny of the Neoplecostominae and Hypoptopomatinae (Siluriformes: Loricariidae) using multiple genes

Phasmids are remarkable mimics of twigs, sticks, and leaves. This extreme adaptation for crypsis can easily lead to the convergent evolution of morphology, making it difficult to establish a taxonomic system of phasmids. Accordingly, there are multiple phylogenetic hypotheses that conflict with each other. Phylogenetic arrangements suggested by molecular data disagree with the morphology-based taxonomy in some instances. We collected 13 phasmatodean species, sequenced their mitochondrial genomes, and recovered their molecular phylogeny. Our analyses did not support the monophyly of Areolatae or Anareolatae, two major infraorders of Phasmatodea. The position of Neohirasea was also quite different from the conventional taxonomic systems, thus challenging the previously assumed monophyly of the subfamily Lonchodinae. The enigmatic taxon, Timema, was shown to be distantly related to other phasmatodeans.     

Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes

The order Rodentia contains half of all extant mammal species, and from an evolutionary standpoint, there are persistent controversies surrounding the monophyly of the order, divergence dates for major lineages, and relationships among families. Exons of growth hormone receptor (GHR) and breast cancer susceptibility (BRCA1) genes were sequenced for a wide diversity of rodents and other mammals and combined with sequences of the mitochondrial 12S rRNA gene and previously published sequences of von Willebrand factor (vWF). Rodents exhibit rates of amino acid replacement twice those observed for nonrodents, and this rapid rate of evolution influences estimates of divergence dates. Based on GHR sequences, monophyly is supported, with the estimated divergence between hystricognaths and most sciurognaths dating to about 75 MYA. Most estimated dates of divergence are consistent with the fossil record, including a date of 23 MYA for Mus-Rattus divergence. These dates are considerably later than those derived from some other molecular studies. Among combined and separate analyses of the various gene sequences, moderate to strong support was found for several clades. GHR appears to have greater resolving power than do 12S or vWF. Despite its complete unresponsiveness to growth hormone, Cavia (and other hystricognaths) exhibits a conservative rate of change in the intracellular domain of GHR.     

Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes

Dipterocarpaceae is the dominant family of Southeast Asia's climax tropical rain forest region, and it contains the region's most important commercial timber species. A molecular phylogeny of the Dipterocarpaceae subfamily Dipterocapoideae was constructed using restriction fragment length polymorphisms of polymerase chain reaction-amplified specific genes in chloroplast DNA. A total of 141 site changes were detected among ten genera and 30 species in 11 different genes: rbcL, psbA, psbD, rpoB, rpoC, petB, atpH, 16S, psaA, petA and trnK. Phylogenetic trees constructed by Wanger parsimony and neighbor-joining methods, using Upuna as the outgroup, displayed five monophytelic groups that included Upuna: HopeaShorea-Parashorea-Neobalanocarpus; Dryobalanops; Dipterocarpus; Anisoptera-Vatica-Cotylelobium; and Upuna. The phylogenetic trees clearly separate species with two different base chromosome numbers: the first group is x=7, and the other is x=11. The x=7 group is thought to be in a synapomorphic character state. Parashorea lucida is a sister to most Shorea species. Neobalanocarpus heimii and Hopea from a clade of a sister to two Shorea species, and Cotylelobium and Vatica are closely related species. Our conclusions agree with a phylogeny derived from wood anatomy data analysis, and with Symington's and Ashton's taxonomic classifications.The raw data of the PCR-RFLP analysis can be obtained from the authors     

Total evidence phylogeny of Gasterosteidae: combining molecular, morphological and behavioral data

Genealogical relationships among Gasterosteidae (Teleostei: Gasterosteiformes) were tested with 84 morphological, 48 behavioral, and 2879 molecular characters. Phylogenetic analysis of the combined data set identified a single (CI = 0.735) best‐supported hypothesis (Spinachia (Apeltes ((Pungitius + Culaea)(Gasterosteus aculeatus + G. wheatlandi)))). This hypothesis is identical to previous phylogenetic propositions proposed on the basis of behavioral, and behavioral plus morphological data. Our hypothesis, however, differed from a molecular‐based phylogeny in the placement of Apeltes. This analysis highlights the importance of combining all available evidence in order to produce the best‐supported proposition of genealogical relationships.     

Molecular phylogeny of Collembola inferred from ribosomal RNA genes

The classification of taxa within Collembola (Springtails, Hexapoda) has been controversial. In this study, we combined complete 18S rRNA gene with partial 28S rRNA gene (D7-D10) sequences to investigate the phylogeny of Collembola. About 2500 aligned sites of thirty species representing 29 genera from14 families of Collembola were analyzed, including one species of Neelipleona from which no sequence has been reported previously.The phylogenetic trees were obtained by different methods (maximum parsimony, maximum likelihood, and Bayesian analysis). Our results supported the monophyly of two of the four taxonomic groups of Collembola summarized by Deharveng [Deharveng, L., 2004. Recent advances in Collembola systematics. Pedobiologia 48, 415–433.], namely of Poduromorpha and of Symphypleona. Within Poduromorpha, Neanuridae was monophyletic with high support, but Hypogastruridae was not. Entomobryomorpha was paraphyletic, as the Tomoceroidea (Tomoceridae and Oncopoduridae) was found to be apart from the other entomobryomorphs. In the latter Isotomoidea and Entomobryoidea joined into a group with moderate support. Within Symphypleona, the phylogenetic relationship [(Sminthuridae + Bourletiellidae) + Sminthurididae] was consistent with traditional morphological studies. Neelipleona grouped with Symphypleona in all trees, with moderate support in the ML and Bayesian analyses.     

Mecoptera is paraphyletic: multiple genes and phylogeny of Mecoptera and Siphonaptera

Phylogenetic relationships among members of the Mecoptera and Siphonaptera were inferred from DNA sequence data. Four loci (18S and 28S ribosomal DNA, cytochrome oxidase II and elongation factor-1α) were sequenced for 69 taxa selected to represent major flea and mecopteran lineages. Phylogenetic analyses of these data support a paraphyletic Mecoptera with two major lineages: Nannochoristidae + (Siphonaptera + Boreidae) and Meropidae + ((Choristidae + Apteropanorpidae) (Panorpidae + (Panorpidae + Bittacidae))). The flea family Ctenophthalmidae is paraphyletic, and the Ceratophylloidea is monophyletic. Morphological evidence is discussed which is congruent with the placement of Siphonaptera as sister group to Boreidae.     

Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets

Consensus on the evolutionary relationships of humans, chimpanzees, and gorillas has not been reached, despite the existence of a number of DNA sequence data sets relating to the phylogeny, partly because not all gene trees from these data sets agree. However, given the well-known phenomenon of gene tree-species tree mismatch, agreement among gene trees is not expected. A majority of gene trees from available DNA sequence data support one hypothesis, but is this evidence sufficient for statistical confidence in the majority hypothesis? All available DNA sequence data sets showing phylogenetic resolution among the hominoids are grouped according to genetic linkage of their corresponding genes to form independent data sets. Of the 14 independent data sets defined in this way, 11 support a human- chimpanzee clade, 2 support a chimpanzee-gorilla clade, and one supports a human-gorilla clade. The hypothesis of a trichotomous speciation event leading to Homo; Pan, and Gorilla can be firmly rejected on the basis of this data set distribution. The multiple-locus test (Wu 1991), which evaluates hypotheses using gene tree-species tree mismatch probabilities in a likelihood ratio test, favors the phylogeny with a Homo-Pan clade and rejects the other alternatives with a P value of 0.002. When the probabilities are modified to reflect effective population size differences among different types of genetic loci, the observed data set distribution is even more likely under the Homo-Pan clade hypothesis. Maximum-likelihood estimates for the time between successive hominoid divergences are in the range of 300,000-2,800,000 years, based on a reasonable range of estimates for long-term hominoid effective population size and for generation time. The implication of the multiple-locus test is that existing DNA sequence data sets provide overwhelming and sufficient support for a human-chimpanzee clade: no additional DNA data sets need to be generated for the purpose of estimating hominoid phylogeny. Because DNA hybridization evidence (Caccone and Powell 1989) also supports a Homo-Pan clade, the problem of hominoid phylogeny can be confidently considered solved.      

Molecular phylogeny: reconstructing the forest

Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come. To cite this article: P. Lopez, E. Bapteste, C. R. Biologies 332 (2009).     

Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes

Background  

Phylogenetic analyses of jawed vertebrates based on mitochondrial sequences often result in confusing inferences which are obviously inconsistent with generally accepted trees. In particular, in a hypothesis by Rasmussen and Arnason based on mitochondrial trees, cartilaginous fishes have a terminal position in a paraphyletic cluster of bony fishes. No previous analysis based on nuclear DNA-coded genes could significantly reject the mitochondrial trees of jawed vertebrates.     

Molecular phylogeny of the hexagrammid fishes using a multi-locus approach

Ideally, organisms are grouped into monophyletic assemblages reflecting their evolutionary histories. Single (molecular) markers can reflect the evolutionary history of the marker, rather than the species in question, therefore, phylogenetic relationships should be inferred from adequate sampling of characters. Because the use of multiple loci greatly improves the resolving power of the molecular assay, we constructed a molecular phylogeny of the family Hexagrammidae based on six loci, including two mitochondrial and four nuclear loci. The resulting molecular phylogeny, from the combined data, was significantly different from the morphological topology suggested by Shinohara [Memoirs of the Faculty of Fisheries, Hokkaido University 41 (1994) 1]. Our data support a monophyletic assemblage for the genera Hexagrammos and Pleurogrammus. However, other taxa traditionally included in the family Hexagrammidae did not form a monophyletic assemblage. The monotypic genus Ophiodon was more closely associated with cottids than with other hexagrammids. Our data concur with the morphological topology in that the genera Zaniolepis and Oxylebius formed a monophyletic clade, which was distinct and basal to the remaining hexagrammids, seven cottids and one agonid.     

Horned lizard (Phrynosoma) phylogeny inferred from mitochondrial genes and morphological characters: understanding conflicts using multiple approaches

The genus Phrynosoma includes 13 species of North American lizards characterized by unique and highly derived morphologies and ecologies. Understanding interspecific relationships within this genus is essential for testing hypotheses about character evolution in this group. We analyzed mitochondrial ND4 and cytochrome b gene sequence data from all species of Phrynosoma in conjunction with a previously published dataset including 12S and 16S rRNA gene sequences and morphological characters. We used multiple phylogenetic methods and diagnostic tests for data combinability and taxonomic congruence to investigate the data in separate and combined analyses. Separate data partitions resulted in several well-supported lineages, but taxonomic congruence was lacking between topologies from separate and combined analyses. Partitioned Bremer support analyses also reveals conflict between data partitions in certain tree regions. When taxa associated with well-supported clades were removed from analyses, phylogenetic signal was lost. Combined, our results initially suggest conflict between data partitions, but further tests show the data are only appropriate for phylogenetic reconstruction of those parts of the topology that were well resolved. Nonetheless, our data analyses reveal five well-supported clades: (1) Phrynosoma ditmarsi and Phrynosoma hernandesi, (2) P. ditmarsi, P. hernandesi, and Phrynosoma douglasii, (3) P. ditmarsi, P. hernandesi, P. douglasii, and Phrynosoma orbiculare, (4) Phrynosoma mcallii and Phrynosoma platyrhinos, and (5) Phrynosoma braconnieri and Phrynosoma taurus.     

Molecular phylogeny and rearrangement of rRNA genes in Rickettsia species.

It has previously been observed that Rickettsia prowazekii has an unusual arrangement of the rRNA genes. In this species, the three rRNA genes, 16S (rrs), 23S (rrl), and 5S (rrf), are not linked in the typical arrangements for bacteria. Rather, the 16S rRNA gene has been separated from the 23S and 5S rRNA gene cluster, and the 23S rRNA gene is preceded by a gene which codes for methionyl-tRNAf(Met) formyltransferase (fmt). In this study, we screened the genus Rickettsia for the fmt-rrl motif in order to examine the phylogenetic depth of this unusual rRNA gene organization. A rearranged operon structure was observed in Rickettsia conorii, Rickettsia parkeri, Rickettsia sibirica, Rickettsia rickettsii, Rickettsia amblyomii, Rickettsia montana, Rickettsia rhipicephali, Rickettsia australis, Rickettsia akari, Rickettsia felis, Rickettsia canada, and Rickettsia typhi. There is also evidence for a divided operon in Rickettsia belli, but in this species, the fmt gene could not be identified upstream of the 23S rRNA gene. In order to place the rearrangement event in the evolutionary history of the Rickettsia, phylogenetic analyses were performed based on the fmt-rrl spacer regions and the 23S rRNA genes. Based on these phylogenies, we suggest that the genomic rearrangement of the rRNA genes preceded the divergence of the typhus group and the spotted fever group Rickettsia. The unique organization of the 23S rRNA genes provides a simple diagnostic tool for identification of Rickettsia species.     

Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes

Extant vertebrates are divided into three major groups: hagfishes (Hyperotreti, myxinoids), lampreys (Hyperoartia, petromyzontids), and jawed vertebrates (Gnathostomata). The phylogenetic relationships among the groups and within the jawed vertebrates are controversial, for both morphological and molecular studies have rendered themselves to conflicting interpretations. Here, we use the sequences of 35 nuclear protein-encoding genes to provide definitive evidence for the monophyly of the Agnatha (jawless vertebrates, a group encompassing the hagfishes and lampreys). Our analyses also give a strong support for the separation of Chondrichthyes (cartilaginous fishes) before the divergence of Osteichthyes (bony fishes) from the other gnathostomes.     

Molecular phylogeny of the Entomophthoromycota

The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.     

Molecular phylogeny of the Rhinotermitidae

Summary. Relationships among genera in the termite family Rhinotermitidae and their relationship to the families Termitidae and Serritermitidae were investigated based on analysis of three mitochondrial genes: COI, COII and 16S rDNA. Maximum Parsimony (MP) bootstrap analysis of each of these genes indicated a low level of phylogenetic incongruence between them, and thus they were combined and analysed by MP and Bayesian analysis. Six main lineages were clearly identified, however relationships among these were not well defined. Tentative support was found for the Rhinotermitid genera Coptotermes, Heterotermes and Reticulitermes being the sister group to the Termitidae, rendering the Rhinotermitidae paraphyletic. The species Serritermes serrifer and Glossotermes oculatus were found to group with strong support, in agreement with the recent transfer of the latter species to the family Serritermitidae based on morphological characteristics. No support was found for the Rhinotermitidae being paraphyletic with respect to the Serritermitidae. A number of disagreements were found between the molecular tree and traditional classifications of genera within subfamilies.Received 20 February 2004; revised 2 April 2004; accepted 19 April 2004.     

Molecular phylogeny of Salmo of the western Balkans,based upon multiple nuclear loci

Background

Classification of species within the genus Salmo is still a matter of discussion due to their high level of diversity and to the low power of resolution of mitochondrial (mt)DNA-based phylogeny analyses that have been traditionally used in evolutionary studies of the genus. We apply a new marker system based on nuclear (n)DNA loci to present a novel view of the phylogeny of Salmo representatives and we compare it with the mtDNA-based phylogeny.

Methods

Twenty-two nDNA loci were sequenced for 76 individuals of the brown trout complex: Salmo trutta (Danubian, Atlantic, Adriatic, Mediterranean and Duero mtDNA lineages), Salmo marmoratus (marble trout), Salmo obtusirostris (softmouth trout), and Salmo ohridanus (Ohrid belvica or belushka). Sequences were phylogenetically analyzed using maximum-likelihood and Bayesian Inference methods. The divergence time of the major clades was estimated using the program BEAST.

Results

The existence of five genetic units i.e. S. salar, S. ohridanus, S. obtusirostris, S. marmoratus and the S. trutta complex, including its major phylogenetic lineages was confirmed. Contrary to previous observations, S. obtusirostris was found to be sister to the S. trutta complex and the S. marmoratus clade rather than to the S. ohridanus clade. Reticulate evolution of S. obtusirostris was confirmed and a time for its pre-glacial origin suggested. S. marmoratus was found to be a separate species as S. trutta and S. obtusirostris. Relationships among lineages within the S. trutta complex were weakly supported and remain largely unresolved.

Conclusions

Nuclear DNA-based results showed a fairly good match with the phylogeny of Salmo inferred from mtDNA analyses. The comparison of nDNA and mtDNA data revealed at least four cases of mitochondrial–nuclear DNA discordance observed that were all confined to the Adriatic basin of the Western Balkans. Together with the well-known extensive morphological and genetic variability of Balkan trouts, this observation highlights an interesting and variegated evolutionary history of Salmo in this area.     

幽门螺杆菌vacA和cagA基因全长分子系统发育分析

文章从GenBank中下载所有含有vacA和cagA基因的H.pylori菌株的VacA和CagA全长氨基酸序列,利用ClastalX 2.0和MEGA 5.05软件构建VacA和CagA分子系统发育树,探讨两基因之间的分子系统发育关系和不同聚类群的临床感染结果与基因型特征。结果显示,VacA和CagA具有高度相似的分子系统发育树,并且所有H.pylori菌株在系统发育树中具有相同的分布特点,分别聚类为东亚株群1、2和西方株群3个聚类群。其中东亚株群1患萎缩性胃炎比例较高,vacA基因型以s1c/m1b和s1a/m1b为主,cagA基因型以EPIYA-ABD为主;东亚株群2患十二指肠溃疡的比例较高,vacA基因型以s1c/m2和s1a/m2为主,cagA基因型以EPIYA-AB’C为主;西方株群患十二指肠溃疡和胃炎的比例相当,萎缩性胃炎比例较低,vacA基因型以s1a/m1a和s1b/m1a为主,cagA基因型以EPIYA-AB/B’CC为主。这些结果说明,vacA和cagA基因可能具有共进化的遗传关系;东亚株群1、2和西方株群分别具有不同的vacA和cagA基因亚型,这可能与其临床感染结果密切相关,因此,在进行H.pylori相关性疾病分析时,有必要结合vacA和cagA基因型的亚型做深入分析。     

Mammalian phylogeny: genes and supertrees

A massive effort to sample mammals for genes has yielded new proposals for the branching architecture of the great radiation of placental mammals. Some of these are notably discrepant with morphologically based analyses, but they suggest new research that should address several major outstanding issues.