树鼩进化分类地位的分子证据

树鼩隶属攀鼩目,广泛分布于东南亚、南亚和中国南部等地区。由于其独特的特点,如体型小、脑-体重比例高、生殖周期短、寿命短和饲养成本低等,在生物医学研究中被认为是可望替代灵长类动物的新型实验动物。然而,关于树鼩与灵长类动物的亲缘关系一直存在争议。明确树鼩的分类地位是创建实验动物的重要研究基础。该文介绍了近年来关于树鼩分类地位探讨的分子证据。在现有的研究中,大部分核DNA序列研究,包括近期树鼩全基因组序列分析,都支持树鼩是灵长动物的近缘旁系群,然而绝大部分基于线粒体DNA序列的研究却显示树鼩与啮齿动物的亲缘关系更为接近。这样的分歧主要是由于线粒体序列和核基因数据的差异以及不同的算法导致。综合现有不同DNA数据的研究结果,作者认为树鼩作为灵长类的近亲这一结论应该成为共识。     

Rooting the tree of life by transition analyses

Background

Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed – the most difficult problems in phylogeny. Protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution; ribosome-related and DNA-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it within eubacteria but in contradictory places. Palaeontology shows that eubacteria are much more ancient than eukaryotes, and, together with phylogenetic evidence that archaebacteria are sisters not ancestral to eukaryotes, implies that the root is not within the neomura. Transition analysis, involving comparative/developmental and selective arguments, can polarize major transitions and thereby systematically exclude the root from major clades possessing derived characters and thus locate it; previously the 20 shared neomuran characters were thus argued to be derived, but whether the root was within eubacteria or between them and archaebacteria remained controversial.

Results

I analyze 13 major transitions within eubacteria, showing how they can all be congruently polarized. I infer the first fully resolved prokaryote tree, with a basal stem comprising the new infrakingdom Glidobacteria (Chlorobacteria, Hadobacteria, Cyanobacteria), which is entirely non-flagellate and probably ancestrally had gliding motility, and two derived branches (Gracilicutes and Unibacteria/Eurybacteria) that diverged immediately following the origin of flagella. Proteasome evolution shows that the universal root is outside a clade comprising neomura and Actinomycetales (proteates), and thus lies within other eubacteria, contrary to a widespread assumption that it is between eubacteria and neomura. Cell wall and flagellar evolution independently locate the root outside Posibacteria (Actinobacteria and Endobacteria), and thus among negibacteria with two membranes. Posibacteria are derived from Eurybacteria and ancestral to neomura. RNA polymerase and other insertions strongly favour the monophyly of Gracilicutes (Proteobacteria, Planctobacteria, Sphingobacteria, Spirochaetes). Evolution of the negibacterial outer membrane places the root within Eobacteria (Hadobacteria and Chlorobacteria, both primitively without lipopolysaccharide): as all phyla possessing the outer membrane β-barrel protein Omp85 are highly probably derived, the root lies between them and Chlorobacteria, the only negibacteria without Omp85, or possibly within Chlorobacteria.

Conclusion

Chlorobacteria are probably the oldest and Archaebacteria the youngest bacteria, with Posibacteria of intermediate age, requiring radical reassessment of dominant views of bacterial evolution. The last ancestor of all life was a eubacterium with acyl-ester membrane lipids, large genome, murein peptidoglycan walls, and fully developed eubacterial molecular biology and cell division. It was a non-flagellate negibacterium with two membranes, probably a photosynthetic green non-sulphur bacterium with relatively primitive secretory machinery, not a heterotrophic posibacterium with one membrane.

Reviewers

This article was reviewed by John Logsdon, Purificación López-García and Eric Bapteste (nominated by Simonetta Gribaldo).     

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. Availability: DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree     

Improved description of the bipolar ciliate,Euplotes petzi,and definition of its basal position in the Euplotes phylogenetic tree

Data improving the characterization of the marine Euplotes species, E. petzi Wilbert and Song, 2008, were obtained from morphological, ecological and genetic analyses of Antarctic and Arctic wild-type strains. This species is identified by a minute (mean size, 46 μm × 32 μm) and ellipsoidal cell body which is dorsally decorated with an argyrome of the double-patella type, five dorsal kineties (of which the median one contains 8–10 dikinetids), five sharp-edged longitudinal ridges, and a right anterior spur. Ventrally, it bears 10 fronto-ventral, five transverse, two caudal and two marginal cirri, 30–35 adoral membranelles, and three inconspicuous ridges. Euplotes petzi grows well at 4 °C on green algae, does not produce cysts, undergoes mating under the genetic control of a multiple mating-type system, constitutively secretes water-borne pheromones, and behaves as a psychrophilic microorganism unable to survive at >15 °C. While the α-tubulin gene sequence determination did not provide useful information on the E. petzi molecular phylogeny, the small subunit rRNA (SSU rRNA) gene sequence determination provided solid evidence that E. petzi clusters with E. sinicus Jiang et al., 2010a, into a clade which represents the deepest branch at the base of the Euplotes phylogentic tree.     

Rooting the tree of life: the phylogenetic jury is still out

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle''s Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.     

Inferring the root of a phylogenetic tree

Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.     

Molecular phylogenetic and morphological analyses of Oidium heveae, a powdery mildew of rubber tree

Powdery mildew of rubber tree caused by Oidium heveae is an important disease of rubber plantations worldwide. Identification and classification of this fungus is still uncertain because there is no authoritative report of its morphology and no record of its teleomorphic stage. In this study, we compared five specimens of the rubber powdery mildew fungus collected in Malaysia, Thailand, and Brazil based on morphological and molecular characteristics. Morphological results showed that the fungus on rubber tree belongs to Oidium subgen. Pseudoidium. Nucleotide sequence analysis of the ribosomal DNA internal transcribed spacer (ITS) region and the large subunit rRNA gene (28S rDNA) were conducted to determine the relationships of the rubber powdery mildew fungus and to link this anamorphic fungus with its allied teleomorph. The results showed that the rDNA sequences of the two specimens from Malaysia were identical to a specimen from Thailand, whereas they differed by three bases from the two Brazilian isolates: one nucleotide position in the ITS2 and two positions in the 28S sequences. The ITS sequences of the two Brazilian isolates were identical to sequences of Erysiphe sp. on Quercus phillyraeoides collected in Japan, although the 28S sequences differed at one base from sequences of this fungus. Phylogenetic trees of both rDNA regions constructed by the distance and parsimony methods showed that the rubber powdery mildew fungus grouped with Erysiphe sp. on Q. phillyraeoides with 100% bootstrap support. Comparisons of the anamorph of two isolates of Erysiphe sp. from Q. phillyraeoides with the rubber mildew did not reveal any obvious differences between the two powdery mildew taxa, which suggests that O. heveae may be an anamorph of Erysiphe sp. on Q. phillyraeoides. Cross-inoculation tests are required to substantiate this conclusion.     

Characterization of a branch of the phylogenetic tree

We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a "tortoise and hare effect": those genera with the smallest species death rate are likely to survive much longer than genera with large species birth and death rates. A complete characterization of the behavior of a branch of the phylogenetic tree corresponding to a genus and accurate mathematical representations of the various stages are obtained. We apply our results to address certain controversial issues that have arisen in paleontology such as the importance of punctuated equilibrium and whether unique Cambrian phyla have survived to the present.     

Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

Almost a decade ago, a new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly of two major groups of protostome animals: Ecdysozoa (e.g., arthropods, nematodes, onychophorans, and tardigrades) and Lophotrochozoa (e.g., annelids, molluscs, platyhelminths, brachiopods, and rotifers). However, it received little additional support. In fact, several multigene analyses strongly argued against this new phylogeny. These latter studies were based on a large amount of sequence data and therefore showed an apparently strong statistical support. Yet, they covered only a few taxa (those for which complete genomes were available), making systematic artifacts of tree reconstruction more probable. Here we expand this sparse taxonomic sampling and analyze a large data set (146 genes, 35,371 positions) from a diverse sample of animals (35 species). Our study demonstrates that the incongruences observed between rRNA and multigene analyses were indeed due to long-branch attraction artifacts, illustrating the enormous impact of systematic biases on phylogenomic studies. A refined analysis of our data set excluding the most biased genes provides strong support in favor of the new animal phylogeny and in addition suggests that urochordates are more closely related to vertebrates than are cephalochordates. These findings have important implications for the interpretation of morphological and genomic data.     

Timing of organogenesis support basal position of turtles in the amniote tree of life

Background  

The phylogenetic position of turtles is the most disputed aspect in the reconstruction of the land vertebrate tree of life. This controversy has arisen after many different kinds and revisions of investigations of molecular and morphological data. Three main hypotheses of living sister-groups of turtles have resulted from them: all reptiles, crocodiles + birds or squamates + tuatara. Although embryology has played a major role in morphological studies of vertebrate phylogeny, data on developmental timing have never been examined to explore and test the alternative phylogenetic hypotheses. We conducted a comprehensive study of published and new embryological data comprising 15 turtle and eight tetrapod species belonging to other taxa, integrating for the first time data on the side-necked turtle clade.     

Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life

Fungi are one of the most diverse groups of Eukarya and play essential roles in terrestrial ecosystems as decomposers, pathogens and mutualists. This study unifies disparate reports of unclassified fungal sequences from soils of diverse origins and anchors many of them in a well-supported clade of the Ascomycota equivalent to a subphylum. We refer to this clade as Soil Clone Group I (SCGI). We expand the breadth of environments surveyed and develop a taxon-specific primer to amplify 2.4kbp rDNA fragments directly from soil. Our results also expand the known range of this group from North America to Europe and Australia. The ancient origin of SCGI implies that it may represent an important transitional form among the basal Ascomycota groups. SCGI is unusual because it currently represents the only major fungal lineage known only from sequence data. This is an important contribution towards building a more complete fungal phylogeny and highlights the need for further work to determine the function and biology of SCGI taxa.     

Improved prediction of critical residues for protein function based on network and phylogenetic analyses

Background  

Phylogenetic approaches are commonly used to predict which amino acid residues are critical to the function of a given protein. However, such approaches display inherent limitations, such as the requirement for identification of multiple homologues of the protein under consideration. Therefore, complementary or alternative approaches for the prediction of critical residues would be desirable. Network analyses have been used in the modelling of many complex biological systems, but only very recently have they been used to predict critical residues from a protein's three-dimensional structure. Here we compare a couple of phylogenetic approaches to several different network-based methods for the prediction of critical residues, and show that a combination of one phylogenetic method and one network-based method is superior to other methods previously employed.     

Plumage-based phylogenetic analyses of the Merops bee-eaters

I review previous systematic work on the family Meropidae and present phylogenetic hypotheses derived from my analyses of colour, pattern and shape variation in 30 plumage regions among species and subspecies in this family. Consistent patterns are seen across shallow portions of the trees. Uncertainty remains concerning the placement of several deep branches within this group's phylogeny. In particular, the phylogenetic placement of Meropogon forsteni and Merops breweri , M. ornatus , M. hirundineus and M. boehmi remains uncertain. The biogeographical patterns in the resultant trees are similar with either a Southeast Asian or African origin for the family, with most of the early diversification occurring in Africa, and with multiple independent subsequent invasions of non-African areas.     

The position of the Arthropoda in the phylogenetic system

Traditionally, Panarthropoda (Euarthropoda, Onychophora, Tardigrada) are regarded as being closely related to Annelida in a taxon Articulata, but this is not supported by molecular analyses. Comparisons of gene sequences suggest that all molting taxa (Panarthropoda, Nematoda, Nematomorpha, Priapulida, Kinorhyncha, Loricifera) are related in a monophyletic taxon Ecdysozoa. An examination of the characters supporting Articulata reveals that only segmentation with a teloblastic segment formation and the existence of segmental coelomic cavities with nephridia support the Articulata, whereas all other characters are modified or reduced in the panarthropod lineage. Another set of characters is presented that supports the monophyly of Ecdysozoa: molting under influence of ecdysteroid hormones, loss of locomotory cilia, trilayered cuticle and the formation of the epicuticle from the tips of epidermal microvilli. Comparative morphology suggests Gastrotricha as the sister group of Ecdysozoa with the synapomorphies: triradiate muscular sucking pharynx and terminal mouth opening. Thus there are morphological characters that support Articulata, but molecular as well as morphological data advocate Ecdysozoa. Comparison of both hypotheses should prompt further thorough and targeted investigations. J. Morphol. 238:263–285, 1998. © 1998 Wiley-Liss, Inc.     

Lack of premating isolation at the base of a phylogenetic tree

Darwin's finches in the Galápagos archipelago are an unusual example of adaptive radiation in that the basal split separates two lineages of warbler finches (Certhidea olivacea and Certhidea fusca) believed until recently to be only one species. The large genetic difference between them contrasts with their similarity in plumage, size, shape, and courtship behavior. They differ in song, which is a key factor in premating isolation of other sympatric Darwin's finches. We conducted playback experiments to see whether members of the population of C. olivacea on Santa Cruz Island would respond to songs of C. fusca from two islands, Genovesa and Pinta, and songs of C. olivacea from another island (Isabela). Another set of experiments was performed, using the same playback tapes, with C. fusca on Genovesa. Some members of both populations responded to all playbacks; therefore, the hypothesis of complete premating isolation on the basis of song is rejected. Discrimination between songs of the two lineages was inconsistent. We conclude that premating barriers to interbreeding among the tested populations have not arisen in the 1.5-2.0 m.yr. of their geographical isolation on different islands. This contrasts with strong premating barriers between more recently derived sympatric species. Early learning of song associated with morphology is later used in mate recognition. This explains why sympatric species that are vocally and morphologically distinct yet genetically less differentiated than Certhidea do not interbreed, whereas the Certhidea lineages that are genetically well differentiated but vocally and morphologically similar have no apparent premating barrier. We discuss this unusual situation in terms of the forces that have produced similarities and differences in song, morphology, and ecology and their relevance to phylogenetic and biological species concepts. Neither principles nor details are unique to Darwin's finches, and we conclude by pointing out strong parallels with some continental birds.     

Phylogenetic analyses of mtDNA sequences corroborate taxonomic designations based on cuticular hydrocarbons in subterranean termites

Cuticular hydrocarbons (CHCs) are valuable characters for the analysis of cryptic insect species with few discernible morphological characters. Yet, their use in insect systematics, specifically in subterranean termites in the genus Reticulitermes (Isoptera: Rhinotermitidae), remains controversial. In this paper, we show that taxonomic designations in Reticulitermes from California (USA) suggested in light of differences among CHC phenotypes are corroborated by phylogenetic analyses using mtDNA sequences. Analyses based on CHC phenotypes and supported, in part, by behavioral and ecological differences have suggested the presence of more species than the two currently recognized: R. hesperus Banks and R. tibialis Banks. We analyze a 680 base pair fragment of the mitochondrial DNA cytochrome oxidase (COII) gene from 45 new (21 collection localities) and two previously recorded samples of Reticulitermes from California using parsimony and maximum likelihood methods. Both methods result in trees with highly similar topologies. Bootstrapping indicates support for six clades of Reticulitermes, and corroborates groupings based on cuticular hydrocarbons. One of the clades, R. hesperus, is already recognized in California, while four clades appear to be previously undescribed taxa. Although identification of the final clade is inconclusive, it includes a sample putatively identified as R. tibialis. Therefore, using phylogenetic analyses we corroborate chemical characters used to identify taxa, associate a chemical phenotype with a previously described species, and provide additional support for undescribed taxa of Reticulitermes.     

Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century

Phylogenies, or evolutionary trees, are fundamental to biology. Systematists have laboured since the time of Darwin to discover the tree of life. Recent developments in systematics, such as cladistics and molecular sequencing, have led practitioners to believe that their phylogenies are more testable now than equivalent efforts from the 1960s or earlier. Whole trees, and nodes within trees, may be assessed for their robustness. However, these quantitative approaches cannot be used to demonstrate that one tree is more likely to be correct than another. Congruence assessments may help. Comparison of a sample of 1000 published trees with an essentially independent standard (dates of origin of groups in geological time) shows that the order of branching has improved slightly, but the disparity between estimated times of origination from phylogeny and stratigraphy has, if anything, become worse. Controlled comparisons of phylogenies of four major groups (Agnatha, Sarcopterygii, Sauria and Mammalia) do not show uniform improvement, or decline, of fit to stratigraphy through the twentieth century. Nor do morphological or molecular trees differ uniformly in their performance.     

The assembly of tropical tree communities – the advances and shortcomings of phylogenetic and functional trait analyses

Tropical tree communities present one of the most challenging systems for studying the processes underlying community assembly. Most community assembly hypotheses consider the relative importance of the ecological similarity of co‐occurring species. Quantifying this similarity is a daunting and potentially impossible task in species‐rich assemblages. During the past decade tropical tree ecologists have increasingly utilized phylogenetic trees and functional traits to estimate the ecological similarity of species in order to test mechanistic community assembly hypotheses. A large amount of work has resulted with many important advances having been made along the way. That said, there are still many outstanding challenges facing those utilizing phylogenetic and functional trait approaches to study community assembly. Here I review the conceptual background, major advances and major remaining challenges in phylogenetic‐ and trait‐based approaches to community ecology with a specific focus on tropical trees. I argue that both approaches tremendously improve our understanding of tropical tree community ecology, but neither approach has fully reached its potential thus far.