A molecular phylogeny of living primates

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (~8 Mb) from 186 primates representing 61 (~90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.     

根瘤菌多样性和系统发育研究的多相分类体系及其进展

近年来对新的根瘤菌资源的不断发掘及现代分子生物学技术的发展和应用使根瘤菌分类研究有了突破性进展。多相分类通过综合获取信息,多种方法相互印证、互为补充,推进了根瘤菌的表型、遗传型和系统发育三方面的发展,从而较全面地反映根瘤菌的生物多样性特征,是根瘤菌多样性研究工作中常常采用的技术手段。文中主要阐述了根瘤菌多相分类体系中的主要方法及现代根瘤菌系统发育地位的研究和进展。     

Remarkable ancient divergences amongst neglected lorisiform primates

Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub‐Saharan Africa and South/South‐East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ～80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group. © 2015 The Linnean Society of London     

Genetic Determinism vs. Phenotypic Plasticity in Protist Morphology

Untangling the relationships between morphology and phylogeny is key to building a reliable taxonomy, but is especially challenging for protists, where the existence of cryptic or pseudocryptic species makes finding relevant discriminant traits difficult. Here we use Hyalosphenia papilio (a testate amoeba) as a model species to investigate the contribution of phylogeny and phenotypic plasticity in its morphology. We study the response of H. papilio morphology (shape and pores number) to environmental variables in (i) a manipulative experiment with controlled conditions (water level), (ii) an observational study of a within‐site natural ecological gradient (water level), and (iii) an observational study across 37 European peatlands (climate). We showed that H. papilio morphology is correlated to environmental conditions (climate and water depth) as well as geography, while no relationship between morphology and phylogeny was brought to light. The relative contribution of genetic inheritance and phenotypic plasticity in shaping morphology varies depending on the taxonomic group and the trait under consideration. Thus, our data call for a reassessment of taxonomy based on morphology alone. This clearly calls for a substantial increase in taxonomic research on these globally still under‐studied organisms leading to a reassessment of estimates of global microbial eukaryotic diversity.     

Disparate Data Sets Resolve Squirrel Monkey (Saimiri) Taxonomy: Implications for Behavioral Ecology and Biomedical Usage

Squirrel monkeys (Saimiri spp.) are the most commonly used neotropical (platyrrhine) monkeys in biomedical research; however, no consensus exists as to the phylogenetic relationships amongst geographic variants or whether these variants represent species or subspecies. Here we report a strongly supported squirrel monkey phylogeny, congruent across multiple data sets, including new field data and the first molecular (mtDNA) cladogram. These data support species-level classification for the three major groups in this study. Approximately the same amount of molecular divergence exists among Saimiri oerstedii, S. sciureus, and S. boliviensis. The S. sciureus/S. oerstedii ancestor diverged from S. boliviensis and shortly thereafter S. sciureus and S. oerstedii diverged. Until now, lack of a robust taxonomy has hindered exploitation of the massive potential of Saimiri for comparative studies. No other primate genus displays such widely divergent, genetically-based social behaviors. Our taxonomy also provides robust support for previous warnings against the widespread use of hybrid squirrel monkeys as research models.     

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004–0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04–98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.     

车轮虫分类与系统发育研究进展

车轮虫属一大类寄生性纤毛虫原生动物,可不同程度地给宿主造成危害,故对其研究既具有理论意义,又具有经济价值。文中简单回顾了车轮虫的分类研究和系统发育研究的历史。在分类学研究领域方面,全面介绍了目前车轮虫科已发现属的寄生部位和地理分布等;而系统发育研究领域方面,则介绍了车轮虫研究在萌芽期、探索期和发展期这三个时期的进展,包括形态学和分子生物学两方面的研究内容。并对该领域今后应进行的研究提出了建议。     

The Influence of Phylogeny on the Social Behaviour of Macaques (Primates: Cercopithecidae, genus Macaca)

The macaques are the most geographically widespread and behaviourally diverse primate genus. Many of the diversified features of social behaviour and organization in this genus have been attributed to socio-ecological differences. However, some core aspects of social behaviour and organization appear to be highly conservative, suggesting a high degree of phylogenetic inertia. A recently derived classification of macaque social organization, as well as a large range of social and physical traits, were analysed for 16 species to ascertain the role of phylogeny in explaining the distribution of these traits within the genus Macaca . These traits were mapped onto two alternative phylogenies. The pattern of social organization, based on the degree of asymmetry in social relations, exhibited a high and significant level of phylogenetic inertia, as did seven of the 22 individual traits compared. A profile constructed of the most likely ancestral state for this character matrix showed that it most closely resembles the pattern present in the Barbary macaque ( M. sylvanus ), which, based on both molecular and morphological data, most closely resembles the ancestral macaque.     

Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny,morphology, and distribution

Resolving the infrageneric classification of species-rich genera has been challenging in plant taxonomy. Ilex L. is a subcosmopolitan genus with over 600 species of dioecious trees and shrubs. Many classification systems based on morphological data have been proposed during the past 250 years. However, these systems (such as Loesener's and Galle's systems) may not truly reflect Ilex's evolutionary trajectories because most of those system's infrageneric hierarchies are not monophyletic. In this study, we reconstructed a phylogeny of Ilex L. comprising 15 moderately to highly supported clades using rigorously identified samples (202 species) and closely authenticated gene sequences of three nuclear genes [internal transcribed spacer (ITS), external transcribed spacer (ETS), and nepGS]. The newly generated phylogenetic tree resembles essentially that of the nuclear tree of Manen et al., but shows conspicuous topological differences with the phylogeny of Yao et al. Closely scrutinizing morphological variation and distributional patterns of 202 species, this study found that most lineages of Ilex identified herein are well defined by a particular trait or a combination of morphological and distributional traits, displaying phylogeny–morphology–distribution conformity that has seldom been uncovered in previous studies. Given the general phylogeny–morphology–distribution conformity revealed in this genus, we put forward an updated sectional classification system for Ilex that temporarily contains 14 sections. The new classification will provide a robust framework for studying the evolution and diversification of this ecologically and economically important genus.     

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.     

Phylogenetics of gall-inducing thrips on Australian Acacia

Analysis of DNA sequence data from four genes ( Elongation Factor-1 α, wingless , 16S rDNA and cytochrome oxidase I ) yielded a well-resolved, well-supported phylogeny for all 21 species of gall-inducing thrips found on Australian Acacia. This phylogeny was then used to investigate the evolution of various behavioural and life history traits, and to examine the level of agreement with the taxonomy of the group. Our results suggest that there may have been a single origin of soldier castes in gall-inducing thrips. Examination of the distribution of the three primary life history strategies employed by these thrips (pupating in the gall, pupating in soil with soldier castes and pupating in soil without soldier castes) indicates that two of the strategies may have evolved as a result of factors associated with host plant affiliations or through parasite pressure. Our phylogeny does not support the existing generic classification of the group in that the genera are not monophyletic, nor does it lend itself to a clear solution to improve the classification in accordance with the phylogeny.     

祖先性状重建法揭示铁线蕨属植物孢子表面纹饰的形态多样性及其演化

蕨类植物孢子表面的纹饰形态复杂多样, 在分类学和古生物学研究中具有重要意义, 目前探索祖先性状演化常用形态学与系统发育学结合的方法。本文选取一回羽叶铁线蕨类植物为材料, 用扫描电子显微镜观察其孢子形态, 用5个叶绿体基因序列构建系统树, 用最大似然法和最大简约法来分析孢子性状的演化。结果表明: 一回羽叶铁线蕨类的孢子纹饰有5种类型, 即光滑、粗糙、颗粒、疣状及瘤状; 这一类群的祖先孢子纹饰有很大的可能是瘤状纹饰; 疣状纹饰可能是由瘤状纹饰演化而来; 孢子纹饰由简单向复杂演化, 越进化的物种其孢子纹饰越复杂。     

Fungal evolution: diversity,taxonomy and phylogeny of the Fungi

The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a ‘Third Kingdom’, embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum‐level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.     

基于孢子形态和分子证据探讨鳞盖蕨属(碗蕨科)系统分类

孢粉学是解决植物分类中疑难类群物种微形态分化的重要方法, 随着分子系统学的发展, 结合这两门学科的优势可以更加有效地解决疑难类群的分类学问题。鳞盖蕨属(Microlepia)是一个分类困难的疑难类群, 采用孢粉学与分子系统学一一对应的方法, 以及居群取样方式, 选取280份样本, 联合4个叶绿体片段(rbcL、trnL-F、psbA-trnH和rps4), 采用最大似然法和贝叶斯法构建该属的系统发生关系, 在此基础上对凭证标本中100份材料的孢子进行观察和分析。综合分子系统学和孢粉学的研究结果, 得出结论: (1) 在形态学研究中广泛被接受的15个物种得到了单系支持, 并厘清了分类困难的复合群; (2) 发现边缘鳞盖蕨(M. marginata)可能存在隐性种; (3) 建议恢复过去归并处理为异名的瑶山鳞盖蕨(M. yaoshanica)、罗浮鳞盖蕨(M. lofoushanensis)、四川鳞盖蕨(M. szechuanica)以及滇西鳞盖蕨(M. subspeluncae); (4) 提出鳞盖蕨属可能存在杂交现象; (5) 提出鳞盖蕨属完整的属下分类建议。     

Phylogenetic relationships of glassfrogs (Centrolenidae) based on mitochondrial and nuclear genes

Glassfrogs (family Centrolenidae) represent an exceptionally diverse group among Neotropical anurans, but their evolutionary relationships never have been assessed from a molecular perspective. Mitochondrial and nuclear markers were used to develop a novel hypothesis of centrolenid phylogeny. Ingroup sampling included 100 terminals, with 78 (53%) of the named species in the family, representing most of the phenotypic diversity described for the group. Thirty-five species representing taxa traditionally associated with glassfrogs were used as outgroups. Gene sampling consisted of complete or partial sequences of three mitochondrial (12S, 16S, ND1) and three nuclear markers (c-myc exon 2, RAG1, POMC) for a total of 4362 bp. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analyses for individual genes and combined datasets. The separate analysis of mitochondrial and nuclear datasets allowed us to clarify the relationships within glassfrogs; also, we corroborate the sister-group relationship between Allophryne ruthveni and glassfrogs. The new phylogeny differs significantly from all previous morphology-based hypotheses of relationships, and shows that hypotheses based on few traits are likely to misrepresent evolutionary history. Traits previously hypothesized as unambiguous synapomorphies are shown to be homoplastic, and all genera in the current taxonomy (Centrolene, Cochranella, Hyalinobatrachium, Nymphargus) are found to be poly- or paraphyletic. The new topology implies a South American origin of glassfrogs and reveals allopatric speciation as the most important speciation mechanism. The phylogeny profoundly affects the traditional interpretations of glassfrog taxonomy, character evolution, and biogeography—topics that now require more extensive evaluation in future studies.     

The 10kTrees website: A new online resource for primate phylogeny

The comparative method plays a central role in efforts to uncover the adaptive basis for primate behaviors, morphological traits, and cognitive abilities. 1 - 4 The comparative method has been used, for example, to infer that living in a larger group selects for a larger neocortex, 5 , 6 that primate territoriality favors a longer day range relative to home range size, 7 and that sperm competition can account for the evolution of primate testes size. 8 , 9 Comparison is fundamental for reconstructing behavioral traits in the fossil record, for example, in studies of locomotion and diet. 10 - 13 Recent advances in comparative methods require phylogenetic information, 2 , 14 - 16 but our knowledge of phylogenetic information is imperfect. In the face of uncertainty about evolutionary relationships, which phylogeny should one use? Here we provide a new resource for comparative studies of primates that enables users to run comparative analyses on multiple primate phylogenies Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes, given the dataset. The trees also reflect uncertainty about branch lengths.     

The subspecies concept in primatology: The case of mountain gorillas

The criteria for the application of subspecific units in living primate populations have received little attention relative to other vertebrate taxa, even though they have important implications for conservation strategies for many nonhuman primate populations. One of the most critically endangered primates is the mountain gorilla,Gorilla gorilla beringei, of which 600 animals exist in east-central Africa. FollowingSarmiento et al. (1996), taxonomists have proposed splitting these populations into two subspecies as part of a revised taxonomy of the genusGorilla. In this paper I review the application of the subspecies concept in primatology, using the gorillas of Bwindi Impenetrable National Park and the Virungas as case studies. An examination of genetic, morphological, biogeographic, ecological, and behavioral evidence indicates that reclassifying Bwindi gorillas as taxonomically distinct from those in the Virungas is not well supported and needs further study. Because taxonomy provides the basis of conservation management policies, a cautious and conservative approach to the subspecies question is warranted in the case of endangered primate populations.     

Growth rates and phylogeny in primates

There is sufficient evidence to indicate that man grows for a longer period of time than chimpanzee who in turn has a greater duration of growth than rhesus monkey. The problem of this paper was to determine if there was a concomitant decrease in a rate of growth. Using the relative growth rate of Fisher ('21), it appears that for most of their period of growth, the rate of change is the same. Immediately after birth, when we have no data for children, rhesus monkey grows significantly faster than chimpanzee. By a year and a half their rates are the same, and neither species shows a sex difference. From seven years (age of youngest children) until children start through puberty, there is no sex difference in Homo sapiens, and the human rate does not differ from the chimpanzee rate. Because of the resemblance between the primate curve for rate and that for dairy cattle, it is postulated that this curve is more mammalian than primate and that during phylogeny the primates have merely increased the duration of time when growth is possible. Man does show one new feature, the puberal growth spurt, which is not found in the non-human data considered. The implications of these conclusions for primate phylogeny and for growth are discussed.     

THE QUANTITATIVE ASSESSMENT OF PHYLOGENETIC CONSTRAINTS IN COMPARATIVE ANALYSES: SEXUAL DIMORPHISM IN BODY WEIGHT AMONG PRIMATES

We have presented a formal model for the quantitative analysis of phylogenetic and specific effects on the distribution of trait values among species. Total trait values are divided into phylogenetic values, inherited from an ancestral species, and specific values, the result of independent evolution. This allows a quantitative assessment of the strength of the phylogenetic inertia, or burden, displayed by a character in a lineage, so that questions concerning the relative importance of phylogenetic constraints in evolution can be answered. The separation of phylogenetic from specific effects proposed here also allows phylogenetic factors to be explicitly included in cross-species comparative analyses of adaptation. This solves a long-standing problem in evolutionary comparative studies. Only species' specific values can provide information concerning the independent evolution of characters in a set of related species. Therefore, only correlations among specific values for traits may be used as evidence for adaptation in cross-species comparative analyses. The phylogenetic autocorrelation model was applied to a comparative analysis of the determinants of sexual dimorphism in weight among 44 primate species. In addition to sexual dimorphism in weight, mating system, habitat, diet, and size (weight itself) were included in the analysis. All of the traits, except diet, were substantially influenced by phylogenetic inertia. The comparative analysis of the determinants of sexual dimorphism in weight indicates that 50% of the variation among primate species is due to phylogeny. Size, or scaling, could account for a total of 36% of the variance, making it almost as important as phylogeny in determining the level of dimorphism displayed by a species. Habitat, mating system, and diet follow, accounting for minor amounts of variation. Thus, in attempting to explain why a particular modern primate species is very dimorphic compared to other primates, we would say first because its ancestor was more dimorphic than average, second because it is a relatively large species, and third because it is terrestrial, polygynous, and folivorous.     

Within-species differences in primate social structure: evolution of plasticity and phylogenetic constraints

Primate socioecological studies have attempted to derive general frameworks using the average behavioural traits of species or genera to place them into categories. However, with the accumulation of primate studies, it is timely to place more emphasis on understanding within-species variation in social structure. In this review we have four objectives. First, we examine within-species variation in the potential determinants of social structure, including diet, demography, predation and infanticide, and document considerable variation. Second, we present case studies of within-species variation in social structure to illustrate the potential magnitude of this variation. For example, there are cases within a single interbreeding population where multi-male, uni-male, fission–fusion and monogamous groups are found. Third, by examining widespread primate lineages that occur in a variety of habitats, we note that there are differences in the magnitude of variation in social structures across different lineages and as a result we consider phylogenetic constraints on phenotypic variation in social structure. Finally, we reflect on the implications of extensive variation in social structure. We suggest that primate social structure will represent a combination of adaptation to present-day environment and phylogenetic inertia. To advance our understanding of the relative contribution of phylogeny versus ecology we propose two approaches. One approach is to compare groups in the same interbreeding population that inhabit different ecological conditions. Any differences that are found can be attributed to ecological differences, since phylogeny should not play a role within a single population. The second approach is to study distantly related species that have similar social structures to illustrate how similar ecological pressures might be operating to select for parallel social structures.