Using median sets for inferring phylogenetic trees

MOTIVATION: Algorithms for phylogenetic tree reconstruction based on gene order data typically repeatedly solve instances of the reversal median problem (RMP) which is to find for three given gene orders a fourth gene order (called median) with a minimal sum of reversal distances. All existing algorithms of this type consider only one median for each RMP instance even when a large number of medians exist. A careful selection of one of the medians might lead to better phylogenetic trees. RESULTS: We propose a heuristic algorithm amGRP for solving the multiple genome rearrangement problem (MGRP) by repeatedly solving instances of the RMP taking all medians into account. Algorithm amGRP uses a branch-and-bound method that branches over medians from a selected subset of all medians for each RMP instance. Different heuristics for selecting the subsets have been investigated. To show that the medians for RMP vary strongly with respect to different properties that are likely to be relevant for phylogenetic tree reconstruction, the set of all medians has been investigated for artificial datasets and mitochondrial DNA (mtDNA) gene orders. Phylogenetic trees have been computed for a large set of randomly generated gene orders and two sets of mtDNA gene order data for different animal taxa with amGRP and with two standard approaches for solving the MGRP (GRAPPA-DCM and MGR). The results show that amGRP outperforms both other methods with respect to solution quality and computation time on the test data. AVAILABILITY: The source code of amGRP, additional results and the test instances used in this paper are freely available from the authors.     

Secator: a program for inferring protein subfamilies from phylogenetic trees

With the huge increase of protein data, an important problem is to estimate, within a large protein family, the number of sensible subsets for subsequent in-depth structural, functional, and evolutionary analyses. To tackle this problem, we developed a new program, Secator, which implements the principle of an ascending hierarchical method using a distance matrix based on a multiple alignment of protein sequences. Dissimilarity values assigned to the nodes of a deduced phylogenetic tree are partitioned by a new stopping rule introduced to automatically determine the significant dissimilarity values. The quality of the clusters obtained by Secator is verified by a separate Jackknife study. The method is demonstrated on 24 large protein families covering a wide spectrum of structural and sequence conservation and its usefulness and accuracy with real biological data is illustrated on two well-studied protein families (the Sm proteins and the nuclear receptors).     

Estimation of evolutionary distance for reconstructing molecular phylogenetic trees

The most commonly used measure of evolutionary distance in molecular phylogenetics is the number of nucleotide substitutions per site. However, this number is not necessarily most efficient for reconstructing a phylogenetic tree. In order to evaluate the accuracy of evolutionary distance, D(t), for obtaining the correct tree topology, an accuracy index, A(t), was proposed. This index is defined as D'(t)/square root of[D(t)], where D'(t) is the first derivative of D(t) with respect to evolutionary time and V[D(t)] is the sampling variance of evolutionary distance. Using A(t), namely, finding the condition under which A(t) gives the maximum value, we can obtain an evolutionary distance which is efficient for obtaining the correct topology. Under the assumption that the transversional changes do not occur as frequently as the transitional changes, we obtained the evolutionary distances which are expected to give the correct topology more often than are the other distances.      

Biochemical identification of thymosin alpha-1: its phylogenetic distribution and evolutionary implications

1. Thymosin alpha-1, like reactivity, was found in several different species (insects, crab, protozoan, fungus and bacteria) by radioimmunoassay and immune fluorescence and as an extracellular product from the bacterial genus Mycobacterium. 2. Biochemically, thymosin alpha-1 has been isolated from combined crab visceral and nervous tissue by reverse phase HPLC. 3. The identification of thymosin alpha-1 in lower life forms suggests a more generalized exocrine origin in unicellular organisms prior to the development of the immune system or exocrine differentiation.     

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.     

Variable phylogeographic histories of five forest birds with populations in Upper and Lower Guinea: implications for taxonomy and evolutionary conservation

This study evaluates phylogeographic structure in selected forest bird species distributed on either side of the Dahomey Gap in West Africa to extend analyses of avian diversification across the Guineo-Congolean forest. Mitochondrial DNA sequence data were collected for five species, including four with a break in distribution across the Dahomey Gap and one with a more continuous distribution. Data for the five focal species were included in a single analysis along with appropriate outgroup taxa, allowing estimates of divergence time on a common timescale. Both phylogeographic patterns and estimated divergence times were highly variable. In two cases (Green Hylia Hylia prasina and Yellow-whiskered Greenbul Eurillas latirostris), samples from east and west of the Dahomey Gap belong to divergent mitochondrial lineages, but with substantially older divergence in Eurillas (～4.1 MY). In Western Bluebill Spermophaga haematina, relatively divergent eastern and western lineages (～1.1 MY) were sampled in the same locality in eastern Ghana, suggesting east to west gene flow across the gap following earlier vicariance. In Forest Robin Stiphrornis erythrothorax, birds sampled within Ghana were from two highly divergent lineages (～1.9 MY), one of which is more closely related to birds from Cameroon and Equatorial Guinea, such that divergence across the Dahomey Gap was comparatively recent (～0.36 MY). For both Hylia and Stiphrornis, we corroborate recent studies documenting multiple divergent lineages within each genus, some of which may represent distinct species. Consistent with previous studies, our analysis shows that the Dahomey Gap can be a significant barrier to gene flow for species restricted to forest habitats. At the same time, individual species exhibit a broad range of divergence times and phylogeographic histories of variable complexity. We discuss the taxonomic implications of our results for each focal species.     

Tales of the phylogenetic woods: The evolution and significance of evolutionary trees

The styles of continuing intellectual traditions can have a major effect on the way in which scientific findings are expressed. Darwin and Huxley, for all their intellectual daring followed the skeptical tactics of the Scottish Enlightenment and avoided the construction of human phylogenetic trees, even though they were aware of the evidence on which such could have been constructed. The romantic evolutionism of Haeckel, Keith, and many subsequent writers in English produced suggested phylogenies on the basis of largely hypothetical forms including Homo “alalus,” “stupidus,” and “Eoanthropus.” The structural aspects of phylogenetic schemes that derive from the French intellectual ethos, from catastrophism to cladistics and punctuated equilibria, have stressed discrete categorical entities in the tradition of Platonic essentialism and have tended to avoid a consideration of evolutionary dynamics.     

Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks

To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.     

On the correlation between composition and site-specific evolutionary rate: implications for phylogenetic inference

Model-based phylogenetic reconstruction methods traditionally assume homogeneity of nucleotide frequencies among sequence sites and lineages. Yet, heterogeneity in base composition is a characteristic shared by most biological sequences. Compositional variation in time, reflected in the compositional biases among contemporary sequences, has already been extensively studied, and its detrimental effects on phylogenetic estimates are known. However, fewer studies have focused on the effects of spatial compositional heterogeneity within genes. We show here that different sites in an alignment do not always share a unique compositional pattern, and we provide examples where nucleotide frequency trends are correlated with the site-specific rate of evolution in RNA genes. Spatial compositional heterogeneity is shown to affect the estimation of evolutionary parameters. With standard phylogenetic methods, estimates of equilibrium frequencies are found to be biased towards the composition observed at fast-evolving sites. Conversely, the ancestral composition estimates of some time-heterogeneous but spatially homogeneous methods are found to be biased towards frequencies observed at invariant and slow-evolving sites. The latter finding challenges the result of a previous study arguing against a hyperthermophilic last universal ancestor from the low apparent G + C content of its rRNA sequences. We propose a new model to account for compositional variation across sites. A Gaussian process prior is used to allow for a smooth change in composition with evolutionary rate. The model has been implemented in the phylogenetic inference software PHASE, and Bayesian methods can be used to obtain the model parameters. The results suggest that this model can accurately capture the observed trends in present-day RNA sequences.     

Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications

Ribosomal RNAs have secondary structures that are maintained by internal Watson-Crick pairing. Through analysis of chordate, arthropod, and plant 5S ribosomal RNA sequences, we show that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure. Insect phylogenies based on nucleotide positions involved in pairing and the production of secondary structure are incongruent with those constructed on the basis of positions that are not. Furthermore, phylogeny reconstruction using these nonpairing bases is concordant with other, morphological data.      

Coalescent histories for discordant gene trees and species trees

Given a gene tree and a species tree, a coalescent history is a list of the branches of the species tree on which coalescences in the gene tree take place. Each pair consisting of a gene tree topology and a species tree topology has some number of possible coalescent histories. Here we show that, for each n≥7, there exist a species tree topology S and a gene tree topology G≠S, both with n leaves, for which the number of coalescent histories exceeds the corresponding number of coalescent histories when the species tree topology is S and the gene tree topology is also S. This result has the interpretation that the gene tree topology G discordant with the species tree topology S can be produced by the evolutionary process in more ways than can the gene tree topology that matches the species tree topology, providing further insight into the surprising combinatorial properties of gene trees that arise from their joint consideration with species trees.     

Morphology of locomotor appendages in Arachnida: evolutionary trends and phylogenetic implications

The morphological diversity of locomotor appendages in Arachnida is surveyed lo reconstruct phylogenetic relationships and discover evolutionary trends in form and function. The appendicular skeleton and musculature of representatives from the ten living arachnid orders ate described, and a system of homology is proposed. Character polarities are established through comparison with an outgroup. Limulus polyphemus Xiphosura). Cladistic analysis suggests that Arachnida is monophyletic and that absence of extensor muscles is a primitive condition. Extensors are primitively absent in Araneae. Amblypygi, Uropygi, Palpigradi, Ricinulei and Acari. Most similarities in the appendages of these orders are symplesiomorphic so that phylogenetic relationships among the 'extensorless' groups cannot be resolved solely on the basis of appendicular characters. Extensor muscles appear to have evolved once, and their presence is considered a synapomorphic feature of Opiliones, Scorpiones, Pseudoscorpiones and Solifugae. Solifugae lack extensors, but a parsimonious interpretation of other characters indicates that this is a secondary, derived condition. The phylogenetic relationships among these four orders are clarified by modifications of the patellotibial joint. Cladistic analysis indicates that Opiliones may be the sister group of the other three orders and that Scorpiones is the sister group of Pseudoscorpiones and Solifugae. Conclusions concerning phylogenetic relationships and evolutionary morphology presented here differ substantially from those of earlier studies on the locomotor appendages of Arachnida.     

Aflatoxigenicity in Aspergillus: molecular genetics, phylogenetic relationships and evolutionary implications

Aflatoxins (AFs) are toxic and carcinogenic secondary metabolites produced by isolates of Aspergillus section Flavi as well as a number of Aspergillus isolates that are classified outside of section Flavi. Characterization of the AF and sterigmatocystin (ST) gene clusters and analysis of factors governing regulation of their biosynthesis has resulted in these two mycotoxins being the most extensively studied of fungal secondary metabolites. This wealth of information has allowed the determination of the molecular basis for non-production of AF in natural isolates of A. flavus and domesticated strains of A. oryzae. This review provides an overview of the molecular analysis of the AF and ST gene clusters as well as new information on an AF gene cluster identified in the non-section Flavi isolate, Aspergillus ochraceoroseus. Additionally, molecular phylogenetic analysis using AF biosynthetic gene sequences as well as ribosomal DNA internal transcribed spacer (ITS) sequences between various section Flavi and non-section Flavi species has enabled determination of the probable evolutionary history of the AF and ST gene clusters. A model for the evolution of the AF and ST gene clusters as well as possible biological roles for AF are discussed.     

Seeing the forest for the trees: partitioning ecological and phylogenetic components of Bergmann's rule in European Carnivora

Comparative methods have commonly been applied in macroecological research. However, few methods exist to map and analyze phylogenetic variation in geographical space. Here we develop a general analytical framework to partition the phylogenetic and ecological structures of macroecological patterns in geographic space. As an example, we apply the framework to evaluate interspecific patterns of body size geographic variation (Bergmann's rule) in European Carnivora. We model the components of variance attributable to ecological and phylogenetic effects, and to the shared influence of both factors. Spatial patterns in the ecological component are stronger than those in the original body size data. More importantly, the magnitude of intraspecific body size patterns (as measured by the correlation coefficient between body size and latitude) is significantly correlated with the ecological component across species, providing a unified interpretation for Bergmann's rule at multiple levels of biological hierarchy. This approach provides a better understanding of patterns in macroecological traits and allows improved understanding of their underlying ecological and evolutionary mechanisms.     

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

Background  

To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted.     

Ecological and evolutionary responses in complex communities: implications for invasions and eco‐evolutionary feedbacks

It is easier to predict the ecological and evolutionary outcomes of interactions in less diverse communities. As species are added to communities, their direct and indirect interactions multiply, their niches may shift, and there may be increased ecological redundancy. Accompanying this complexity in ecological interactions, is also complexity in selection and subsequent evolution, which may feed back to affect the ecology of the system, as species with different traits may play different ecological roles. Drawing from my own work and that of many others, I first discuss what we currently understand about ecology and evolution in light of simple and diverse communities, and suggest the importance of escape from community complexity per se in the success of invaders. Then, I examine how community complexity may influence the nature and magnitude of eco‐evolutionary feedbacks, classifying eco‐evolutionary dynamics into three general types: those generating alternative stable states, cyclic dynamics, and those maintaining ecological stasis and stability. The latter may be important and yet very hard to detect. I suggest future directions, as well as discuss methodological approaches and their potential pitfalls, in assessing the importance and longevity of eco‐evolutionary feedbacks in complex communities. Synthesis The ecology, evolution and eco‐evolutionary dynamics of simple and diverse communities are reviewed. In more diverse communities, direct and indirect interactions multiply, species’ niches often shift, ecological redundancy can increase, and selection may be less directional. Community complexity may influence the magnitude and nature of eco‐evolutionary dynamics, which are classified into three types: those generating alternative stable states, cyclic dynamics, and those maintaining ecological stasis and stability. Strengths and pitfalls of approaches to investigating eco‐evolutionary feedbacks in complex field communities are discussed.     

Foraging ecology of the mountain monkey (Cercopithecus l'hoesti): implications for its evolutionary history and use of disturbed forest

We present the first systematic field study on the feeding ecology of the mountain monkey (Circopithecus l'hoesti), a semi-terrestrial guenon. We compare our results with findings from a concurrent study of blue monkeys (C. mitis doggetti, which have an overlapping home range) conducted over ten months in the Nyungwe Forest Reserve, Rwanda. The mountain monkeys spent 35% of observation time feeding on terrestrial herbaceous vegetation. Thirty-five fruit and seed species comprised 42% of their diet, and invertebrates composed 9%. They spent 38% of observation time on the ground and 27% of observation time in canopy trees. Individuals were observed for equivalent proportions of time foraging on the ground for herbs and in canopy trees for fruits. Although mountain monkeys primarily foraged in undisturbed open areas, they also used disturbed open habitats for this purpose. Synthesizing our results with Pleistocene forest history and C. l'hoesti evolutionary history, we suggest that, although these monkeys readily use disturbed forest for herb foraging, they are a forest-adapted species which has adopted a terrestrial lifestyle to exploit the abundant herb layer common to montane forests.     

Visualizations for taxonomic and phylogenetic trees

MOTIVATION: Despite substantial efforts to develop and populate the back-ends of biological databases, front-ends to these systems often rely on taxonomic expertise. This research applies techniques from human-computer interaction research to the biodiversity domain. RESULTS: We developed an interactive node-link tool, TaxonTree, illustrating the value of a carefully designed interaction model, animation, and integrated searching and browsing towards retrieval of biological names and other information. Users tested the tool using a new, large integrated dataset of animal names with phylogenetic-based and classification-based tree structures. These techniques also translated well for a tool, DoubleTree, to allow comparison of trees using coupled interaction. Our approaches will be useful not only for biological data but as general portal interfaces.