Molecular phylogenetics of Thysanoptera

Analyses of morphological data on the higher-level phylogenetics of Thysanoptera have suggested two alternative hypotheses: (1) sister-taxon status of the monophyletic suborders Terebrantia and Tubulifera. and (2) paraphyly of Terebrantia with respect to Tubulifera. Analyses of nucleotide sequence data from the mitochondrial gene cytochrome oxidase I and the nuclear gene I8S rONA using maximum parsimony. neighbour joining. and maximum likelihood provide strong support for the hypothesis of a sister-taxon relationship between the Terebrantia and Tubulifera. These data resolve this long-standing controversy in thysanopteran phylogenetics and provide a framework for further studies of higher-level relationships in this order.     

Molecular phylogenetics of Candida albicans

We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then alpha/alpha types and was lowest for heterozygous a/alpha types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.     

Molecular phylogenetics of western North American frogs of the Rana boylii species group

Phylogenetic relationships among frogs of the genus Rana from western North America are investigated using 2013 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (O(L)) between the tRNA(Asn) and tRNA(Cys) genes. The aligned sequences contain 401 phylogenetically informative characters. A well-resolved phylogenetic hypothesis in which the Rana boylii species group (R. aurora, R. boylii, R. cascadae, R. muscosa, and R. pretiosa) is monophyletic is obtained. Molecular sequence divergence suggests that the R. boylii species group is approximately 8 million years old. The traditional hypothesis showing monophyly of the yellow-legged frogs (R. boylii and R. muscosa) is statistically rejected in favor of a hypothesis in which R. aurora, R. cascadae, and R. muscosa form a clade. Reanalyses of published nuclear ribosomal DNA restriction-site data and allozymic data support a monophyletic R. boylii group, but do not effectively resolve relationships among species within this group. Eight populations of R. muscosa form two major clades separated by a biogeographic break in the Sierra Nevada of California. This biogeographic break is broadly concordant with breaks found in four other amphibian and reptilian taxa. The two major clades within R. muscosa are estimated to have diverged approximately 2.2 million years before present. Each of these major clades contains two subgroups showing approximately 1.5 million years divergence, implicating climatic effects of Pleistocene glaciation in vicariance. The four distinct subgroups of R. muscosa separated by at least 1.4 million years of evolutionary divergence are suggested as potential units for conservation.     

分子系统学在生物保护中的意义

本文综述了近年来分子系统学的原理和方法及其在生物多样性保护中的应用和发展。分子系统学方法可以很好地确定物种保护的基本单元——进化显著性单元,并可用于推测群体的发展状态,从而为物种的保护提供了一项新的具很强操作性的科学手段。     

Molecular phylogenetics and reproductive incompatibility in a complex of cryptic species of aphid parasitoids

We infer the phylogeny of a complex of cryptic species and populations of parasitic wasps and examine how reproductive incompatibility maps onto the molecular phylogeny. We used four nuclear (28S-D2, ITS1, ITS2, ArgK) and two mitochondrial (COI, COII) gene regions to analyze relationships among populations in the Aphelinus varipes species complex (Hymenoptera: Aphelinidae) from throughout Eurasia (France, Georgia, Israel, China, Korea and Japan) and from three aphid hosts (Aphis glycines, Diuraphis noxia and Rhopalosiphum padi; Hemiptera: Aphididae). A combined analysis of 21 genotypes of Aphelinus resulted in six most-parsimonious trees, and successive approximations character-weighting selected two of these as best supported by the data. All six gene regions were necessary to fully resolve the relationships among taxa. Four clades within the A. varipes complex were distinguished: (1) Aphelinus kurdjumovi, (2) Aphelinus hordei, (3) Aphelinus atriplicis, Aphelinus varipes, and Aphelinus albipodus, and (4) Aphelinus certus (populations from China, Korea, and Japan). Based on rates of nucleotide substitutions, these clades diverged between 78 and 526 thousand years ago during a period of repeated glaciations in Eurasia. In laboratory crosses, A. kurdjumovi, A. hordei, and A. varipes were reproductively incompatible with one another and all other populations. A. atriplicis was incompatible with these three species, but not with A. certus. The populations of A. certus from China, Japan, and Korea were reproductively compatible with one another but not with the other populations. Thus, with one exception, entities that were phylogenetically distinct were also reproductively incompatible with one another. Our evidence on molecular differentiation and reproductive incompatibility supports recognition of at least five cryptic species in the A. varipes complex. We discuss likely reasons for the high rate of speciation in this complex.     

Molecular phylogenetics and evolution of turtles

Turtles are one of Earth's most instantly recognizable life forms, distinguished for over 200 million years in the fossil record. Even so, key nodes in the phylogeny of turtles remain uncertain. To address this issue, we sequenced >90% of the nuclear recombination activase gene 1 (RAG-1) for 24 species representing all modern turtle families. RAG-1 exhibited negligible saturation and base composition bias, and extensive base composition homogeneity. Most of the relationships suggested by prior phylogenetic analyses were also supported by RAG-1 and, for at least two critical nodes, with a much higher level of support. RAG-1 also indicates that the enigmatic Platysternidae and Chelydridae, often considered sister taxa based on morphological evidence, are not closely related, although their precise phylogenetic placement in the turtle tree is still unresolved. Although RAG-1 is phylogenetically informative, our research revealed fundamental conflicts among analytical methods for estimating phylogenetic hypotheses. Maximum parsimony analyses of RAG-1 alone and in combination with two mitochondrial genes suggest the earliest phylogenetic splits separating into three basal branches, the pig-nosed turtles (Carettochelyidae), the softshell turtles (Trionychidae), and a clade comprising all remaining extant turtles. Maximum likelihood and Bayesian analyses group Carettochelyidae and Trionychidae (=Trionychoidae) in their more traditional location as the sister taxon to all other hidden-necked turtles, collectively forming the Cryptodira. Our research highlights the utility of molecular data in identifying issues of character homology in morphological datasets, while shedding valuable light on the biodiversity of a globally imperiled taxon.     

Paramecium sexaurelia of the Paramecium aurelia species complex in Thailand

The clones originating from Thailand, Phuket Island, were identified as Paramecium sexaurelia.     

Molecular phylogenetics: principles and practice

Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken phylogenetic analysis to a new height. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use.     

Molecular phylogenetics of DNA 5mC-methyltransferases.

We have identified a total of 88 members of the DNA-(cytosine-5) methyltransferase (5mC MTase) family whose sequences have been deposited in the databases. The results of a comparison of these sequences is presented in the form of an alignment-based phylogenetic tree and sequence logos for 10 conserved motifs. Phylogenetic analysis showed that members of the family aggregate into subfamilies which are usually consistent with their target specificity. However, it was also shown that similar target specificity does not necessarily imply close homology of the catalytic domain of MTases, which strongly supports the hypothesis that target recognition evolved independently of catalytic properties. This analysis also indicate that the 5mC MTase was present in the cenancestor (last common ancestor) of eubacteria, archaebacteria, and eukaryotes. The phylogeny of the 5mC MTases catalytic domain provides the basis for establishing the patterns of evolutionary change that characterize this family of proteins with conserved structural core and variable and mobile modules not directly involved in formation of the active site.     

Molecular markers and modern phylogenetics of mammals

Application of modern molecular techniques such as molecular cloning, sequences and polymerase chain reaction of DNA resulted in the increasing of resolution of the phylogenetic analysis and enhanced the role of molecular markers in the evolutionary and taxonomic studies. However, certain properties of the molecular markers are to be taken into consideration when results of the molecular phylogenetic analyses are discussed. This survey reviews the advantages and shortages of different molecular markers (mtDNA and nDNA genes, satellite sequences, long and short retroposons) at the various taxonomic levels. The most part of new phylogenetic reconstructions are established on the results of mtDNA analysis and must be interpreted cautiously because of non-mendelian inheritance of mitochondrial genome. The extremely rapid rate of nucleotide change in mtDNA as compared with nDNA reinforces the saturation in nucleotide sequence and screens the phylogenetic signal. The analysis of nuclear genomes in constrained by that only truly orthologous genes are suitable for the phylogeny reconstruction. So there is a problem to distinguish genes from pseudogenes. Besides, there are some general problems of gene reconstruction such as nucleotide and amino acid compositional shift, long branch attraction and the choice of outgroup. Short interspersed nuclear elements (SINEs) may provide the most valuable phylogenetic information. The markers of multilocus DNA analysis (RAPD-PCR, IS-PCR, RELP, ISSR-PCR), their advantages and shortages are also discussed. A brief survey of the recent studies of molecular phylogeny of mammals for the period of about ten years is presented. The results based on the combined analysis of the mitochondrial and nuclear genes reject the reliability of some previously recognized supraordinal Eutherian taxa in favour of independent range of four main super-order clades: Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria. Within these clades, monophyly of some of traditionally recognized orders was proved by molecular data. The recent advances of molecular phylogenetics are very encouraging. However, its future developments are full off serious difficulties. The problem of accumulation of the data turns into the problem of their correct analysis that is more difficult from the methodological point of view. The careful analysis of the conformities and contradictions between different data sets and looking for congruent conclusions deduced from different characters are the most fruitful way of further phylogenetic development.     

Molecular phylogenetics and historical biogeography of the west-palearctic common toads (Bufo bufo species complex)

In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the level of the Western Palearctic, our dating estimates place most of the deepest phylogenetic structure before the Pleistocene, indicating that Pleistocene glaciations did not have a major role in splitting the major lineages. At a shallow level, the glacial dynamics contributed unevenly to the genetic structuring of populations, with a strong influence in the European-Caucasian populations, and a more relaxed effect in the Iberian populations.     

Molecular phylogenetics employing modern and ancient DNA

Comparative studies of DNA in recent populations and characterisation of ancient hereditary material have contributed very interesting facts to our understanding of evolution of modern mankind. Analysis of DNA homology in related species, assessment of mutations and polymorphisms in various populations and new DNA sequence data from prehistoric finds allowed - via sophisticated DNA extraction techniques, PCR, sequencing and digitalised processing of genetic information - insights into possible roots of Homo sapiens and related species, migration patterns and ancient cultural habits, thus enrhing the palaeoanthropological discipline. However, a presentation of this development would not be complete without pointing towards the methodological limitations and manifold presentations burdened with artifacts, data misinterpretation and unjustified conclusions. Presently, this modern field of research is in its consolidation phase and new parameters for quality control and authentication are being implemented to avoid spectacular but unfounded reports. It is expected that most of the problems connected to old biomolecules may be closely related to fossilisation parameters. The future challenge will be the full understanding of the complex and multi-faceted processes underlying diagenesis, including the elucidation of nucleic acid postmortem damage".     

Electrokaryotypes of macronuclei of several Paramecium species

A comparative study of macronuclear DNA molecules from the following Paramecium species: the P. aurelia complex, P. caudatum, P. bursaria, P. putrinum and P. multimicronucleatum was performed using pulsed-field gel electrophoresis. The electrophoretic pattern was constant and unique for each species, and is referred to herein as its electrokaryotype. Large differences were observed between Paramecium species according to the range and major size of macronuclear DNA fragments, while different strains of the same species, even belonging to different syngens, were characterized by the same electrokaryotype. In this respect sibling species from the P. aurelia complex are as similar as syngens in other Paramecium species, but are unlike conventional species. The principles and value of electrokaryotype analysis for application to ciliates are discussed.     

Molecular phylogenetics of sexual and parthenogenetic Timema walking-sticks

We inferred a phylogeny for the walking-stick genus Timema (Insecta: Phasmatoptera) using mitochondrial DNA sequence, and we used the phylogeny to infer temporal patterns of speciation and the evolutionary history of parthenogenesis. Maximum parsimony, neighbour-joining and maximum-likelihood analyses of 660 base pairs (bp) of cytochrome oxidase I (COI) yielded phylogenies that were well resolved and topologically identical or very similar. Application of an insect molecular clock for COI suggests that the genus originated in southern California, northern Mexico or Arizona about 20 million years ago and underwent a burst of speciation 1.5 to 3 million years ago during the uplifts of the Sierra Nevada, Coast, and Transverse Ranges. The phylogeny indicates that the three parthenogenetic lineages of Timema have arisen independently and are each closely related to morphologically indistinguishable or similar sexual species. Each of the three lineages exhibits an allopatric or parapatric, and more northerly, distribution with regard to their closest sexual relative. COI divergence levels between each of the three parthenogens and their closest sexual relative suggest ancient origins of parthenogenesis, 1.5 to 3 million years ago, that may coincide with the extensive glaciation that formed the North American ice sheets.     

Molecular phylogenetics, vocalizations, and species limits in Celeus woodpeckers (Aves: Picidae)

Species limits and the evolutionary mechanisms that have shaped diversification of woodpeckers and allies (Picidae) remain obscure, as inter and intraspecific phylogenetic relationships have yet to be comprehensively resolved for most genera. Herein, we analyzed 5020 base pairs of nucleotide sequence data from the mitochondrial and nuclear genomes to reconstruct the evolutionary history of Celeus woodpeckers. Broad geographic sampling was employed to assess species limits in phenotypically variable lineages and provide a first look at the evolution of song and plumage traits in this poorly known Neotropical genus. Our results strongly support the monophyly of Celeus and reveal several novel relationships across a shallow phylogenetic topology. We confirm the close sister relationship between Celeus spectabilis and the enigmatic Celeus obrieni, both of which form a clade with Celeus flavus. The Mesoamerican Celeus castaneus was placed as sister to a Celeus undatus-grammicus lineage, with the species status of the latter drawn into question given the lack of substantial genetic, morphological, and vocal variation in these taxa. We recovered paraphyly in Celeus elegans; however, this result appears to be the consequence of mitochondrial introgression from Celeus lugubris considering the monophyly of elegans at the ?-FIBI7 locus. A second instance of paraphyly was observed in Celeus flavescens with deep genetic splits and substantial phenotypic variation indicating the presence of two distinct species in this broadly distributed lineage. As such, we advocate elevation of Celeus flavescens ochraceus to species status. Our analysis of Celeus vocalizations and plumage characters demonstrates a pattern of lability consistent with a relatively recent origin of the genus and potentially rapid speciation history.     

Molecular phylogenetics and historical biogeography of Rhinolophus bats

The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated that the two rhinolophid clades diverged approximately 35 million years ago and results from Dispersal Vicariance (DIVA) analysis suggest that the horseshoe bats arose in Asia and subsequently dispersed into Europe and Africa.     

Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe

Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.     

Modelling habitat distributions for multiple species using phylogenetics

In this paper, we describe an empirical approach to model community structure using phylogenetic signals. That approach combines information about the species (i.e. traits and phylogeny) with information about the habitat (i.e. environmental conditions and spatial distribution of sampling sites) and their interactions to predict the species responses (e.g. the local densities). As an application, we use the approach to model fish densities in rivers. In the model, the different species and size classes were described using a functional trait, body length, and phylogenetic eigenvectors maps whereas the sites were described using water velocity, depth, substrate composition, macrophyte cover, degree‐days, total phosphorus, and spatial eigenvector maps. The model (estimated using a regularised Poisson‐family generalised linear modelling approach) fitted the data well (likelihood‐based R²_adj = 0.512) and showed fair predictive power (likelihood‐based cross‐validation R² = 0.283) to predict the density of fish pertaining to 48 species totalling 143 combinations of species and size classes in 15 unregulated Canadian rivers. Using the model as a baseline to estimate the effect of flow regulation on community composition, we found that, with few exceptions, the densities of most fish species were lower in regulated than in unregulated rivers. Phylogenetics have been proposed to study community structure, but this is, to our knowledge, the first time phylogenetic information is used explicitly for numerical habitat modelling. We expect that models of that type will be in increasing demand now that development projects are routinely assessed through impact studies.     

Molecular phylogenetics of Uvaria (Annonaceae): relationships with Balonga,Dasoclema and Australian species of Melodorum

An extended molecular phylogenetic analysis of Uvaria (Annonaceae) is presented, using maximum parsimony, maximum likelihood and Bayesian methods, based on sequences of four plastid DNA regions (matK, psbA‐trnH spacer, rbcL and trnL‐F). The additional taxa include the monotypic West African genus Balonga, the monotypic South‐East Asian genus Dasoclema and seven Australian representatives of the genus Melodorum. The results indicate that all of these taxa are nested within a well‐supported clade otherwise consisting of Uvaria species, indicating that their taxonomic treatment needs to be reassessed. The distinguishing morphological characteristics of the taxa are re‐evaluated and interpreted as specialized adaptations of the basic Uvaria structure. The genus Uvaria is accordingly extended following the transfer of these species, necessitating six new nomenclatural combinations and two replacement names. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 33–43.