Habitat filtering influences the phylogenetic structure of avian communities across a coastal gradient in southern Brazil

The evolution of a particular trait or combination of traits within lineages may affect subsequent evolutionary outcomes, leading closely related species to exhibit higher phenotypic similarity than expected under a simple Brownian‐motion evolutionary model. Niche theory postulates that phenotypes determine species distribution across environmental gradients, leading to a phylogenetic signature in the community assembly. Thus, the incorporation of species phylogeny in the analysis of community ecology structure allows one to link broader environmental, spatial and temporal factors to local, small‐scale ecological processes, thus enabling understanding of community assembly patterns in a broader context. We used the net relatedness index to assess phylogenetic structure within avian communities across a harshness gradient in coastal habitats in southern Brazil. We also evaluated phylogenetic beta diversity, to test whether closely related species exploit habitats with similar environmental conditions. In order to do so, we scaled up phylogenetic information from the species to site level using phylogenetic fuzzy weighting. We found a pattern of phylogenetic clustering in less‐vegetated habitats, namely sandy beach and dunes, which are subject to harsher conditions because of proximity to the ocean. Basal lineages were associated with the more structurally homogeneous sandy beach, while late‐divergence clades occurred in more complex habitats, which were positively related to vegetation cover and height. The observed pattern of phylogenetic clustering suggested the importance of harsh conditions in constraining the distribution of avian lineages. Furthermore, contrasting environmental features between habitats influenced phylogenetic variation, demonstrating the prevalence of phylogenetic habitat filtering. From an applied point of view, such as planning and management of biological reserves, we showed that the full array of habitat patches embedded within coastal ecological gradients must be included in order to preserve distinct evolutionary lineages.     

Reconstructing the evolutionary history of polyploids from multilabeled trees

In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/ approximately a043878/padre.html.     

中国盐生植物系统发育多样性及省域差异性

植物系统发育多样性研究服务于区域植被历史、演化规律、生物多样性保护,盐生植物作为区域植被演化的独特类群和未来农业种质资源开发的重要物质基础,其区域系统发育多样性对于揭示区域环境变化、盐生植物种质资源保护、区域开发具有重要意义,但目前为止,这方面的研究匮乏。本文应用植物系统发育多样性理论和方法,以省级行政区为单位,系统评价中国盐生植物系统发育多样性和差异性,构建65科484种,17变种,8亚种盐生植物系统发育树;净谱系亲缘关系指数大于0的只有新疆维吾尔自治区、宁夏回族自治区、甘肃省、青海省、陕西省、内蒙古自治区和北京市;系统发育多样性与科、属、种级物种丰富度相关性依次为67.01%、91.20%和96.99%;根据盐生植物分类学组成相似性和系统发育组成相似性把中国盐生植物分为4大区域。本文结果对于省级行政区域盐生植物资源评估、盐生植物种质资源收集和中国盐生植物分区具有重要的指导意义。     

The best of both worlds: Phylogenetic eigenvector regression and mapping

Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.     

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

Ecologists are increasingly adopting an evolutionary perspective, and in recent years, the idea that closely related species are ecologically similar has become widespread. In this regard, phylogenetic signal must be distinguished from phylogenetic niche conservatism. Phylogenetic niche conservatism results when closely related species are more ecologically similar that would be expected based on their phylogenetic relationships; its occurrence suggests that some process is constraining divergence among closely related species. In contrast, phylogenetic signal refers to the situation in which ecological similarity between species is related to phylogenetic relatedness; this is the expected outcome of Brownian motion divergence and thus is necessary, but not sufficient, evidence for the existence of phylogenetic niche conservatism. Although many workers consider phylogenetic niche conservatism to be common, a review of case studies indicates that ecological and phylogenetic similarities often are not related. Consequently, ecologists should not assume that phylogenetic niche conservatism exists, but rather should empirically examine the extent to which it occurs.     

Clade composition of a plant community indicates its phylogenetic diversity

Phylogenetic diversity quantification is based on indices computed from phylogenetic distances among species, which are derived from phylogenetic trees. This approach requires phylogenetic expertise and available molecular data, or a fully sampled synthesis‐based phylogeny. Here, we propose and evaluate a simpler alternative approach based on taxonomic coding. We developed metrics, the clade indices, based on information about clade proportions in communities and species richness of a community or a clade, which do not require phylogenies. Using vegetation records from herbaceous plots from Central Europe and simulated vegetation plots based on a megaphylogeny of vascular plants, we examined fit accuracy of our proposed indices for all dimensions of phylogenetic diversity (richness, divergence, and regularity). For real vegetation data, the clade indices fitted phylogeny‐based metrics very accurately (explanatory power was usually higher than 80% for phylogenetic richness, almost always higher than 90% for phylogenetic divergence, and often higher than 70% for phylogenetic regularity). For phylogenetic regularity, fit accuracy was habitat and species richness dependent. For phylogenetic richness and divergence, the clade indices performed consistently. In simulated datasets, fit accuracy of all clade indices increased with increasing species richness, suggesting better precision in species‐rich habitats and at larger spatial scales. Fit accuracy for phylogenetic divergence and regularity was unreliable at large phylogenetic scales, suggesting inadvisability of our method in habitats including many distantly related lineages. The clade indices are promising alternative measures for all projects with a phylogenetic framework, which can trade‐off a little precision for a significant speed‐up and simplification, such as macroecological analyses or where phylogenetic data is incomplete.     

Altitudinal biodiversity patterns of seed plants along Gongga Mountain in the southeastern Qinghai–Tibetan Plateau

The mechanisms underlying elevation patterns in species and phylogenetic diversity remain a central issue in ecology and are vital for effective biodiversity conservation in the mountains. Gongga Mountain, located in the southeastern Qinghai–Tibetan Plateau, represents one of the longest elevational gradients (ca. 6,500 m, from ca. 1,000 to 7,556 m) in the world for studying species diversity patterns. However, the elevational gradient and conservation of plant species diversity and phylogenetic diversity in this mountain remain poorly studied. Here, we compiled the elevational distributions of 2,667 native seed plant species occurring in Gongga Mountain, and estimated the species diversity, phylogenetic diversity, species density, and phylogenetic relatedness across ten elevation belts and five vegetation zones. The results indicated that species diversity and phylogenetic diversity of all seed plants showed a hump‐shaped pattern, peaking at 1,800–2,200 m. Species diversity was significantly correlated with phylogenetic diversity and species density. The floras in temperate coniferous broad‐leaved mixed forests, subalpine coniferous forests, and alpine shrublands and meadows were significantly phylogenetically clustered, whereas the floras in evergreen broad‐leaved forests had phylogenetically random structure. Both climate and human pressure had strong correlation with species diversity, phylogenetic diversity, and phylogenetic structure of seed plants. Our results suggest that the evergreen broad‐leaved forests and coniferous broad‐leaved mixed forests at low to mid elevations deserve more conservation efforts. This study improves our understanding on the elevational gradients of species and phylogenetic diversity and their determinants and provides support for improvement of seed plant conservation in Gongga Mountain.     

The complete chloroplast genome sequence of the endangered species Syringa pinnatifolia (Oleaceae)

Syringa pinnatifolia is an endangered endemic species in China with important ornamental and medicinal value, and it needs urgent protection. Here, we report the complete chloroplast (cp) genome structure of S. pinnatifolia and its evolution is inferred through comparative studies with related species. The S. pinnatifolia cp genome was 155 326 bp and contained a large single copy region (LSC) of 86 167 bp and a small single copy region (SSC) of 17 775 bp, as well as a pair of inverted repeat regions (IRs) of 25 692 bp. A total of 113 unique genes were annotated, including 79 protein‐coding genes, 30 tRNA genes and four rRNA genes. The GC content of the S. pinnatifolia cp genome was 37.9%, and the corresponding values in the LSC, SSC and IR regions were 36.0, 32.1, 43.2% respectively. Repetitive sequences analysis revealed that the S. pinnatifolia cp genome contained 38 repeats. Microsatellite marker detection analysis identified 253 simple sequence repeats (SSRs), which provides opportunities for future studies of the population genetics and phylogenetic relationships of Syringa. Phylogenetic analysis of 29 selected cp genomes revealed that S. pinnatifolia is closely related to Syringa vulgaris and all 27 Lamiales species formed a clade separate from the two outgroup species. This newly characterized S. pinnatifolia chloroplast genome will provide a useful genomic resource of phylogenetic inference and the development of more genetic markers for species discrimination and population studies in the genus Syringa.     

饶氏藻系统位置的研究

用18S rDNA基因序列分析饶氏藻属(Jaoa)与相关藻类的亲缘关系。结果表明:饶氏藻18S rDNA的长度为1632 bp,GC%为50.6%,泡状饶氏藻18S rDNA的长度为1639 bp,GC%为50.3%。用最大简约法与饶氏藻上一级分类单元(目)构建的系统树表明有4个大的分支。两种饶氏藻与石莼目的 Ulva curvata、U.rigida、Enteromorpha intestinalis和Monostroma grevillei构成很强的支持分支(分支B),它们之间的核苷酸趋异性最低仅0.041,而与胶毛藻目的 Chaetophora incrassata的趋异性则很显著,达0.112,因此,饶氏藻应属于石莼目的一个类群,且饶氏藻和泡状饶氏藻构成一单系起源的分支,这两个物种的趋异性仅0.002,显示出它们具有非常紧密的亲缘关系,很可能是1种1变种而不是2种。     

Are phylogenies derived from family‐level supertrees robust for studies on macroecological patterns along environmental gradients?

Ecologists frequently use a supertree method to generate phylogenies in ecological studies. However, the robustness of research results based on phylogenies generated with a supertree method has not been well evaluated. Here, we use the angiosperm tree flora of North America as a model system to test the robustness of phylogenies generated with a supertree method for studies on the relationship between phylogenetic properties and environment, by comparing the relationship between phylogenetic metrics and environmental variables derived from a phylogeny reconstructed with a supertree method to that derived from a phylogeny resolved at species level. North America was divided into equal area quadrats of 12 100 km². Nine indices of phylogenetic structure were calculated for angiosperm tree assemblages in each quadrat using two phylogenies resolved at different levels (one resolved at the family level and the other resolved at the species level). Scores of phylogenetic indices were related to two major climatic variables (temperature and precipitation) using correlation and regression analyses. Scores of phylogenetic indices resulting from the two phylogenies are perfectly or nearly perfectly correlated. On average, there is no difference in the variation explained by the two climatic variables between scores of phylogenetic indices derived from the two phylogenies. Our study suggests that a phylogeny derived from a well resolved family-level supertree as backbone with genera and species attached to the backbone as polytomies is robust for studies investigating the relationship between phylogenetic structure and environment in biological assemblages at a broad spatial scale.     

Museums and cradles of diversity are geographically coincident for narrowly distributed Neotropical snakes

Factors driving the spatial configuration of centres of endemism have long been a topic of broad interest and debate. Due to different eco-evolutionary processes, these highly biodiverse areas may harbour different amounts of ancient and recently diverged organisms (paleo- and neo-endemism, respectively). Patterns of endemism still need to be measured at distinct phylogenetic levels for most clades and, consequently, little is known about the distribution, the age and the causes of such patterns. Here we tested for the presence of centres with high phylogenetic endemism (PE) in the highly diverse Neotropical snakes, testing the age of these patterns (paleo- or neo-endemism), and the presence of PE centres with distinct phylogenetic composition. We then tested whether PE is predicted by topography, by climate (seasonality, stability, buffering and relictualness), or biome size. We found that most areas of high PE for Neotropical snakes present a combination of both ancient and recently diverged diversity, which is distributed mostly in the Caribbean region, Central America, the Andes, the Atlantic Forest and on scattered highlands in central Brazil. Turnover of lineages is higher across Central America, resulting in more phylogenetically distinct PE centres compared to South America, which presents a more phylogenetically uniform snake fauna. Finally, we found that elevational range (topographic roughness) is the main predictor of PE, especially for paleo-endemism, whereas low paleo-endemism levels coincide with areas of high climatic seasonality. Our study highlights the importance of mountain systems to both ancient and recent narrowly distributed diversity. Mountains are both museums and cradles of snake diversity in the Neotropics, which has important implications for conservation in this region.     

Phylogeny and biogeography in the evolution of migration: shorebirds of the Charadrius complex

Aim We explore whether molecular phylogeny and biogeography can complement evolutionary ecology in developing a method to address a long-standing issue in the evolution of migration: have migrations between breeding and non-breeding grounds, which may be on different continents, evolved through origins in the breeding grounds with successive shifts of the non-breeding distribution or vice versa? Methods To accommodate the biology of migration, we treated breeding and non-breeding distributions as characters to be mapped onto a phylogeny derived from mitochondrial DNA sequence data and so examined the ancestral home issue as a study in the direction of character evolution. Results Our main findings from applying this approach to a subset of the Charadrius complex of shorebirds (Aves: Charadriinae) are that a case can be made for shifts of breeding distributions having occurred in the ancestries of C. alexandrinus and C. veredus as those species evolved their present migration patterns. Our results also argue for a southern hemisphere origin (specifically South America) for the Charadrius complex as a whole. A South American origin implies other shifts in breeding distributions having occurred in the evolution of the species C. semipalmatus and C. vociferus. On applying the methods we developed for dealing with phylogenetic uncertainty, these results are reinforced and the merit of testing them further is suggested. Conclusions By way of a new approach to the evolution of migration, our study adds to a consensus emerging from the evolutionary ecology of migrant birds, arguing that shifts of breeding distributions are commonly, though not necessarily exclusively, involved in the evolution of migration.     

Permutation tests for phylogenetic comparative analyses of high‐dimensional shape data: What you shuffle matters

Evaluating statistical trends in high‐dimensional phenotypes poses challenges for comparative biologists, because the high‐dimensionality of the trait data relative to the number of species can prohibit parametric tests from being computed. Recently, two comparative methods were proposed to circumvent this difficulty. One obtains phylogenetic independent contrasts for all variables, and statistically evaluates the linear model by permuting the phylogenetically independent contrasts (PICs) of the response data. The other uses a distance‐based approach to obtain coefficients for generalized least squares models (D‐PGLS), and subsequently permutes the original data to evaluate the model effects. Here, we show that permuting PICs is not equivalent to permuting the data prior to the analyses as in D‐PGLS. We further explain why PICs are not the correct exchangeable units under the null hypothesis, and demonstrate that this misspecification of permutable units leads to inflated type I error rates of statistical tests. We then show that simply shuffling the original data and recalculating the independent contrasts with each iteration yields significance levels that correspond to those found using D‐PGLS. Thus, while summary statistics from methods based on PICs and PGLS are the same, permuting PICs can lead to strikingly different inferential outcomes with respect to statistical and biological inferences.     

Parallel evolution of larval morphology and habitat in the snail-killing fly genus Tetanocera

In this study, we sequenced one nuclear and three mitochondrial DNA loci to construct a robust estimate of phylogeny for all available species of Tetanocera. Character optimizations suggested that aquatic habitat was the ancestral condition for Tetanocera larvae, and that there were at least three parallel transitions to terrestrial habitat, with one reversal. Maximum likelihood analyses of character state transformations showed significant correlations between habitat transitions and changes in four larval morphological characteristics (cuticular pigmentation and three characters associated with the posterior spiracular disc). We provide evidence that phylogenetic niche conservatism has been responsible for the maintenance of aquatic-associated larval morphological character states, and that concerted convergence and/or gene linkage was responsible for parallel morphological changes that were derived in conjunction with habitat transitions. These habitat-morphology associations were consistent with the action of natural selection in facilitating the morphological changes that occurred during parallel aquatic to terrestrial habitat transitions in Tetanocera.     

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.     

QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets

We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which is subsequently represented by a planar split network. To illustrate the applicability of QNet, we apply it to a previously published Salmonella data set. We conclude that QNet can provide a useful alternative to NNet if distance data are not available or a character-based approach is preferred. Moreover, it can be used as an aid for determining when a quartet-based tree-building method may or may not be appropriate for a given data set. QNet is freely available for download.