Canonical phylogenetic ordination

A phylogenetic comparative method is proposed for estimating historical effects on comparative data using the partitions that compose a cladogram, i.e., its monophyletic groups. Two basic matrices, Y and X, are defined in the context of an ordinary linear model. Y contains the comparative data measured over t taxa. X consists of an initial tree matrix that contains all the xj monophyletic groups (each coded separately as a binary indicator variable) of the phylogenetic tree available for those taxa. The method seeks to define the subset of groups, i.e., a reduced tree matrix, that best explains the patterns in Y. This definition is accomplished via regression or canonical ordination (depending on the dimensionality of Y) coupled with Monte Carlo permutations. It is argued here that unrestricted permutations (i.e., under an equiprobable model) are valid for testing this specific kind of groupwise hypothesis. Phylogeny is either partialled out or, more properly, incorporated into the analysis in the form of component variation. Direct extensions allow for testing ecomorphological data controlled by phylogeny in a variation partitioning approach. Currently available statistical techniques make this method applicable under most univariate/multivariate models and metrics; two-way phylogenetic effects can be estimated as well. The simplest case (univariate Y), tested with simulations, yielded acceptable type I error rates. Applications presented include examples from evolutionary ethology, ecology, and ecomorphology. Results showed that the new technique detected previously overlooked variation clearly associated with phylogeny and that many phylogenetic effects on comparative data may occur at particular groups rather than across the entire tree.     

Profiling phylogenetic informativeness

The resolution of four controversial topics in phylogenetic experimental design hinges upon the informativeness of characters about the historical relationships among taxa. These controversies regard the power of different classes of phylogenetic character, the relative utility of increased taxonomic versus character sampling, the differentiation between lack of phylogenetic signal and a historical rapid radiation, and the design of taxonomically broad phylogenetic studies optimized by taxonomically sparse genome-scale data. Quantification of the informativeness of characters for resolution of phylogenetic hypotheses during specified historical epochs is key to the resolution of these controversies. Here, such a measure of phylogenetic informativeness is formulated. The optimal rate of evolution of a character to resolve a dated four-taxon polytomy is derived. By scaling the asymptotic informativeness of a character evolving at a nonoptimal rate by the derived asymptotic optimum, and by normalizing so that net phylogenetic informativeness is equivalent for all rates when integrated across all of history, an informativeness profile across history is derived. Calculation of the informativeness per base pair allows estimation of the cost-effectiveness of character sampling. Calculation of the informativeness per million years allows comparison across historical radiations of the utility of a gene for the inference of rapid adaptive radiation. The theory is applied to profile the phylogenetic informativeness of the genes BRCA1, RAG1, GHR, and c-myc from a muroid rodent sequence data set. Bounded integrations of the phylogenetic profile of these genes over four epochs comprising the diversifications of the muroid rodents, the mammals, the lobe-limbed vertebrates, and the early metazoans demonstrate the differential power of these genes to resolve the branching order among ancestral lineages. This measure of phylogenetic informativeness yields a new kind of information for evaluation of phylogenetic experiments. It conveys the utility of the addition of characters a phylogenetic study and it provides a basis for deciding whether appropriate phylogenetic power has been applied to a polytomy that is proposed to be a rapid radiation. Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies.     

Refuting phylogenetic relationships

Background  

Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. Here we address this dimension in the context of concatenation approaches to phylogeny.     

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.     

The phylogenetic mixed model

The phylogenetic mixed model is an application of the quantitative-genetic mixed model to interspecific data. Although this statistical framework provides a potentially unifying approach to quantitative-genetic and phylogenetic analysis, the model has been applied infrequently because of technical difficulties with parameter estimation. We recommend a reparameterization of the model that eliminates some of these difficulties, and we develop a new estimation algorithm for both the original maximum likelihood and new restricted maximum likelihood estimators. The phylogenetic mixed model is particularly rich in terms of the evolutionary insight that might be drawn from model parameters, so we also illustrate and discuss the interpretation of the model parameters in a specific comparative analysis.     

Fast phylogenetic DNA barcoding

We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria for determining the taxonomic level at which a particular DNA sequence can be assigned.     

Reconstructing Indian-Australian phylogenetic link

Background  

An early dispersal of biologically and behaviorally modern humans from their African origins to Australia, by at least 45 thousand years via southern Asia has been suggested by studies based on morphology, archaeology and genetics. However, mtDNA lineages sampled so far from south Asia, eastern Asia and Australasia show non-overlapping distributions of haplogroups within pan Eurasian M and N macrohaplogroups. Likewise, support from the archaeology is still ambiguous.     

Flavonoids and phylogenetic reconstruction

Flavonoids have been used successfully for interpreting evolutionary relationships in many groups of angiosperms. These interpretations often have been presented in narrative fashion without specific indications of the kinds of relationships expressed. In this paper a method of phylogeny reconstruction with flavonoid data showing cladistic, patristic, and phenetic relationships is presented. Such a phylogram contains maximal information about flavonoid evolution. As an example, relationships in the North American species ofCoreopsis (Compositae), containing 46 species in 11 sections, are analyzed by this approach. A phylogeny of sections of the genus from previous morphological, chromosomal and hybridization data is compared with that from data on anthochlors (chalcones and aurones). Strong correspondence of these evolutionary interpretations gives support to the hypothesized evolutionary trends within the group.     

Statistics for phylogenetic trees

This paper poses the problem of estimating and validating phylogenetic trees in statistical terms. The problem is hard enough to warrant several tacks: we reason by analogy to rounding real numbers, and dealing with ranking data. These are both cases where, as in phylogeny the parameters of interest are not real numbers. Then we pose the problem in geometrical terms, using distances and measures on a natural space of trees. We do not solve the problems of inference on tree space, but suggest some coherent ways of tackling them.     

Reconstruction of phylogenetic relationships

In this paper, we provide an introductory overview to the field of phylogenetic analysis, which has wide applications in modern biology.     

BIMLR: A method for constructing rooted phylogenetic networks from rooted phylogenetic trees

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The C_ASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved C_ASS algorithm, BIMLR. We show that BIMLR is faster than C_ASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/.     

Testing for phylogenetic signal in phenotypic traits: new matrices of phylogenetic proximities

Abouheif adapted a test for serial independence to detect a phylogenetic signal in phenotypic traits. We provide the exact analytic value of this test, revealing that it uses Moran's I statistic with a new matrix of phylogenetic proximities. We introduce then two new matrices of phylogenetic proximities highlighting their mathematical properties: matrix A which is used in Abouheif test and matrix M which is related to A and biodiversity studies. Matrix A unifies the tests developed by Abouheif, Moran and Geary. We discuss the advantages of matrices A and M over three widely used phylogenetic proximity matrices through simulations evaluating power and type-I error of tests for phylogenetic autocorrelation. We conclude that A enhances the power of Moran's test and is useful for unresolved trees. Data sets and routines are freely available in an online package and explained in an online supplementary file.     

物种谱系不确定性对群落谱系格局指标的影响

物种谱系关系常被用于衡量群落谱系格局及推断格局背后的生态过程,但多数研究往往忽视谱系关系的不确定性及其可能对群落谱系格局造成的影响.为此,本文以浙江天童20 hm^2样地内150个树种为研究对象,采用这些物种叶绿体DNA的rbcL和matK碱基序列构建1棵一致系统发育树和反映谱系不确定性的999棵系统发育树,然后结合样地物种分布数据计算标准化净亲缘指数(NRI)和最近亲缘指数(NTI),最后运用独立置换零模型衡量样地群落谱系格局.结果表明:物种系统发育树在拓扑结构和物种谱系分支节点年龄上均存在较大的不确定性,谱系不确定性随着谱系分支节点年龄的减小而增大,也随物种间平均谱系距离的增加而增加;在样方尺度上,物种谱系的不确定性增加了标准化NRI和NTI指数的变异,但对两个指数的影响几乎独立;其对两指数的空间分布影响不同,且程度不一,其中标准化NRI受到的影响相对更大;在群落尺度上,物种谱系的不确定性增加了标准化NRI和NTI的变异,平均变异系数分别为0.37和0.077,表明群落水平的标准化NRI更易受到谱系不确定性的影响.这说明物种谱系不确定性会传递到常用的群落谱系格局指标中,且不同指标受影响的程度不同,进而影响对群落谱系格局的衡量及相关生态过程的推断.该结论也暗示以往不考虑谱系不确定性的研究中,非随机的群落谱系格局比例可能被高估.