Among-site rate variation and its impact on phylogenetic analyses

Although several decades of study have revealed the ubiquity of variation of evolutionary rates among sites, reliable methods for studying rate variation were not developed until very recently. Early methods fit theoretical distributions to the numbers of changes at sites inferred by parsimony and substantially underestimate the rate variation. Recent analyses show that failure to account for rate variation can have drastic effects, leading to biased dating of speciation events, biased estimation of the transition:transversion rate ratio, and incorrect reconstruction of phylogenies.     

Overcoming problems with the use of ratios as continuous characters for phylogenetic analyses

The use of quantitative morphometric information for phylogenetic inference has been an intensely debated topic for most of the history of phylogenetic systematics. Despite several drawbacks, the most common strategy to include this sort of data into phylogenetic studies is the use of ratios, that is quotients between morphometric variables. Here, we discuss one particular problem associated with such methodology: the fact that the often arbitrary election of which variable serves as numerator and which as denominator affects the phylogenetic outcome of the analysis. We describe the cause for such an effect, and study its implications with the use of several published data matrices. Alternative coding schemes for ratio characters result in very different phylogenetic hypotheses, an effect that may even be strong enough to affect studies that combine continuous and discrete morphological information. Some of the resulting incongruence is produced by the differences in magnitude of the continuous characters involved, although different rescaling techniques are shown to decrease, but not eliminate, the confounding effect. To eliminate such problematic effect, ratios should be either log‐transformed before their use or replaced by more effective ways to capture morphometric information.     

Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus

The existence and functional importance of RNA secondary structure in the replication of positive-stranded RNA viruses is increasingly recognized. We applied several computational methods to detect RNA secondary structure in the coding region of hepatitis C virus (HCV), including thermodynamic prediction, calculation of free energy on folding, and a newly developed method to scan sequences for covariant sites and associated secondary structures using a parsimony-based algorithm. Each of the prediction methods provided evidence for complex RNA folding in the core- and NS5B-encoding regions of the genome. The positioning of covariant sites and associated predicted stem-loop structures coincided with thermodynamic predictions of RNA base pairing, and localized precisely in parts of the genome with marked suppression of variability at synonymous sites. Combined, there was evidence for a total of six evolutionarily conserved stem-loop structures in the NS5B-encoding region and two in the core gene. The virus most closely related to HCV, GB virus-B (GBV-B) also showed evidence for similar internal base pairing in its coding region, although predictions of secondary structures were limited by the absence of comparative sequence data for this virus. While the role(s) of stem-loops in the coding region of HCV and GBV-B are currently unknown, the structure predictions in this study could provide the starting point for functional investigations using recently developed self-replicating clones of HCV.     

Lack of phylogenetic signal in the variation in anuran microhabitat use in southeastern Brazil

Microhabitat use is an important component of anuran behavior in both the tadpole and the adult stages. It is potentially influenced by phylogeny and extant ecological factors acting as selective pressures, such as predation, competition, or physical habitat properties. We aimed to test whether patterns of microhabitat use vary among species, habitats and sites, and how much of this variation can be explained by phylogenetic relatedness. We collected data on microhabitat use at five different sites, where we obtained a total of 4,230 records of individual tadpoles of 34 species in 15 genera and 7 families, and a total of 1,163 records of adult individuals of 39 species in 16 genera and 8 families. Mantel tests conducted to relate species dissimilarities in microhabitat use and phylogenetic relatedness indicated a weak but significant relationship for adult anurans, and no relationship for tadpoles. Our results suggest that microhabitat use is a plastic and variable trait, overcoming phylogenetic signal in tadpoles. In adult anurans, very little of the variation in microhabitat use can be explained by phylogenetic relatedness. Microhabitat use is not a good predictor of phylogeny, but it may be a very interesting subject to study natural selection and adaptation.     

Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses.

Three genomic libraries were constructed using a mixture of DNA from Solanum phureja Juz. & Buk., and S. chacoense Bitt. Two of the libraries were enriched for ATT and GT repeats (a 27-fold enrichment was achieved). In total, 3500 clones of the conventional library, 1,000 of the library enriched for ATT, and 12,000 of the one enriched for GT were screened with five different repeat motifs, and a total of 18 primer pairs was obtained. Another group of 12 primer pairs was obtained from the SSR-containing sequences in the public databases (18 SSR-containing sequences were utilized). From among 30 newly developed primer pairs, 12 previously published ones, and 12 pairs developed for tomato, 7 were used to identify 12 different potato cultivars and introductions, and 12 were used to study phylogenetic distance among seven wild and cultivated potato species. Two SSR markers were sufficient to discriminate the 12 cultivars. The mean number of alleles per polymorphic locus was 5 for the 12 cultivars and 4.5 for the seven species. The results obtained in this study confirm those achieved in similar studies in other plant species regarding the abundance and use of SSR markers in identifying species and cultivars.     

Gene tree parsimony vs uninode coding for phylogenetic reconstruction

have suggested that there are important weaknesses of gene tree parsimony in reconstructing phylogeny in the face of gene duplication, weaknesses that are addressed by method of uninode coding. Here, we discuss Simmons and Freudenstein's criticisms and suggest a number of reasons why gene tree parsimony is preferable to uninode coding. During this discussion we introduce a number of recent developments of gene tree parsimony methods overlooked by Simmons and Freudenstein. Finally, we present a re-analysis of data from that produces a more reasonable phylogeny than that found by Simmons and Freudenstein, suggesting that gene tree parsimony outperforms uninode coding, at least on these data.     

On the selection of phylogenetic eigenvectors for ecological analyses

Among the statistical methods available to control for phylogenetic autocorrelation in ecological data, those based on eigenfunction analysis of the phylogenetic distance matrix among the species are becoming increasingly important tools. Here, we evaluate a range of criteria to select eigenvectors extracted from a phylogenetic distance matrix (using phylogenetic eigenvector regression, PVR) that can be used to measure the level of phylogenetic signal in ecological data and to study correlated evolution. We used a principal coordinate analysis to represent the phylogenetic relationships among 209 species of Carnivora by a series of eigenvectors, which were then used to model log‐transformed body size. We first conducted a series of PVRs in which we increased the number of eigenvectors from 1 to 70, following the sequence of their associated eigenvalues. Second, we also investigated three non‐sequential approaches based on the selection of 1) eigenvectors significantly correlated with body size, 2) eigenvectors selected by a standard stepwise algorithm, and 3) the combination of eigenvectors that minimizes the residual phylogenetic autocorrelation. We mapped the mean specific component of body size to evaluate how these selection criteria affect the interpretation of non‐phylogenetic signal in Bergmann's rule. For comparison, the same patterns were analyzed using autoregressive model (ARM) and phylogenetic generalized least‐squares (PGLS). Despite the robustness of PVR to the specific approaches used to select eigenvectors, using a relatively small number of eigenvectors may be insufficient to control phylogenetic autocorrelation, leading to flawed conclusions about patterns and processes. The method that minimizes residual autocorrelation seems to be the best choice according to different criteria. Thus, our analyses show that, when the best criterion is used to control phylogenetic structure, PVR can be a valuable tool for testing hypotheses related to heritability at the species level, phylogenetic niche conservatism and correlated evolution between ecological traits.     

Topological variation in single-gene phylogenetic trees

A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies.     

iPhy: an integrated phylogenetic workbench for supermatrix analyses

Background  

The increasing availability of molecular sequence data means that the accuracy of future phylogenetic studies is likely to by limited by systematic bias and taxon choice rather than by data. In order to take advantage of increasing datasets, user-friendly tools are required to facilitate phylogenetic analyses and to reduce duplication of dataset assembly efforts. Current phylogenetic pipelines are dependency-heavy and have significant technical barriers to use.     

Challenges of phylogenetic analyses of aDNA sequences

One of the crucial steps of authentication of aDNA sequences is phylogenetic consistency. Amplified sequences should fit into the phylogenetic framework of their supposed origin. An inherent property of aDNA sequences however, is their short sequence length. Additionally, genes for aDNA studies are often chosen by their preservation potential rather than by phylogenetically informative content. This poses potential challenges regarding their analyses, and might result in an inaccurate reflection of the supposed phylogenetic history of the sequence or organism under study. In this paper some fundamental problems of phylogenetic analysis and interpretation of aDNA datasets are discussed. Suggestions for character sampling and treatment of missing data are made. The publication is the result of a talk from the 1st PAMINSA Meeting in Rio de Janeiro, July 2005.     

Character transformation and relationships in Corallorhiza (Orchidaceae: Epidendroideae). II. Morphological variation and phylogenetic analysis

Morphological and anatomical study of Corallorhiza, a genus of primarily New World leafless mycoparasitic orchids, was undertaken in order to produce a hypothesis of relationships among the species and to gain some understanding of character transformations. Cladistic analysis of the resulting data set gave two most parsimonious trees. Analysis of combined plastid DNA and morphological data yielded a single topology, identical to one of the two from the analysis of morphological data alone. Molecular data do not conflict with the morphological data set, and provide more resolution within the C. maculata complex. The combined data indicate that C. striata is the sister group to the remainder of the genus; the circumboreal C. trifida also occupies a basal position. Corallorhiza wisteriana and C. odontorhiza comprise the sister group to the C. maculata + C. mertensiana + C. bulbosa clade. Only two synapomorphies, presence of the coralloid rhizome and loss of leaves, unite the species of Corallorhiza. The coralloid rhizome appears to be a paedomorphic development, due to its similarity to a protocorm; if so, it too is a loss character and may be considered only weak support for monophyly of the genus. Predominant autogamy, seen in C. trifida and cleistogamous C. odontorhiza, has probably arisen independently in these taxa.     

Representing supraspecific taxa in higher-level phylogenetic analyses: guidelines for palaeontologists

Abstract:  As phylogenetic analyses become larger, one of the greatest methodological difficulties is representing speciose supraspecific clades in higher-level analyses (e.g. trilobites within studies of arthropod phylogeny). Several strategies have been proposed, including using representative single composite terminals or species-level exemplars, and various methods are currently used in the palaeontological literature. However, this is problematic, as simulation studies and empirical arguments in the systematics literature have clearly identified multiple exemplars as the optimal method. The continuing usage of suboptimal strategies in palaeontology may lessen the accuracy of phylogenies and hampers comparison between alternative studies. Here, I outline problems with suboptimal strategies, review arguments in support of multiple exemplars and provide guidelines for palaeontologists undertaking higher-level phylogenetic analyses.     

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.     

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16.     

The performance of morphological characters in broad-scale phylogenetic analyses

In view of their propositional content (i.e. they can be right or wrong), character statements (i.e. statements that predicate characters of organisms) are treated as low-level hypotheses. The thesis of the present study is that such character statements, as do more complex scientific theories, come with variable scope. The scope of a hypothesis, or theory, is the domain of discourse over which the hypothesis, or theory, ranges. A character statement is initially introduced within the context of a certain domain of discourse that is defined by the scale of the initial phylogenetic analysis. The doctrine of 'total evidence' requires the inclusion of previously introduced characters in subsequent studies. As a consequence, the initial scope of character statements is widened to the extent that the scale of subsequent analyses is broadened. Scope expansion for character statements may result in incomplete characters, in the subdivision of characters, or in ambiguity of reference (indeterminacy of the extension of anatomical terms). Character statements with a wide scope are desirable because they refer to characters with the potential to resolve deep nodes in phylogenetic analyses. Care must be taken to preserve referential unambiguity of anatomical terms if the originally restricted scope of a character statement is expanded to match a broad-scale phylogenetic analysis.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 297–308.     

The use of chemical analyses of umbilical cord blood for the computation of instantaneous fetal growth

From the umbilical veno-arterial differences in the concentrations of carbohydrates, lipids and amino acids, and of oxygen, carbon dioxide and urea, one can calculate what fractions of the three fuels are burned and what fractions are deposited and constitute growth of the fetus. If umbilical blood flow is also measured, it is possible to calculate the instantaneous rate of fetal growth. Blood can be sampled from the umbilical artery and vein by means of indwelling catheters in unanesthetized sheep. Measurements of umbilical blood flow in unanesthetized sheep are available also. Application of the proposed analysis to published cord blood values for the fetal lamb lead to a predicted rate of growth that was in good agreement with the observed rate of growth. It also showed that a small uptake of a lipid like fuel is still being overlooked. It is concluded that analysis of a set of cord blood samples makes possible a calculation of the fraction of fuel uptake of the fetus that is being used for growth, at the time the samples were taken.     

Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea

Microbial communities inhabiting deep-sea cold seep sediments at the northeastern Japan Sea were characterized by molecular phylogenetic and chemical analyses. White patchy microbial mats were observed along the fault offshore the Hokkaido Island and sediment samples were collected from two stations at the southern foot of the Shiribeshi seamount (M1 site at a depth of 2,961 m on the active fault) and off the Motta Cape site (M2 site at a depth of 3,064 m off the active fault). The phylogenetic and terminal-restriction fragment polymorphism analyses of PCR-amplified 16S rRNA genes revealed that microbial community structures were different between two sampling stations. The members of ANME-2 archaea and diverse bacterial components including sulfate reducers within Deltaproteobacteria were detected from M1 site, indicating the occurrence of biologically mediated anaerobic oxidation of methane, while microbial community at M2 site was predominantly composed of members of Marine Crenarchaeota group I, sulfate reducers of Deltaproteobacteria, and sulfur oxidizers of Epsilonproteobacteria. Chemical analyses of seawater above microbial mats suggested that concentrations of sulfate and methane at M1 site were largely decreased relative to those at M2 site and carbon isotopic composition of methane at M1 site shifted heavier (¹³C-enriched), the results of which are consistent with molecular analyses. These results suggest that the mat microbial communities in deep-sea cold seep sediments at the northeastern Japan Sea are significantly responsible for sulfur and carbon circulations and the geological activity associated with plate movements serves unique microbial habitats in deep-sea environments.     

The philosophical basis of character coding for the inference of phylogenetic hypotheses

The coding of observations of organisms into a data matrix for the inference of phylogenetic hypotheses has suffered from a variety of problems that have precluded development of a uniform approach to the issue. Probably the most notable consequence is that the philosophical basis for coding has been prominently ignored in lieu of emphasis placed on specific coding strategies. From an epistemic standpoint, part of the problem lies with the distinction of ‘characters’ and ‘character states’, which does not accurately convey perceptual beliefs or observation statements. The ability to perceive objects is by the nature of the properties of those objects. One's sense perceptions are of characters, not states; or more appropriately, one observes objects by way of the properties perceived of those objects. The proper distinction is therefore not one of character/state, but one of object/character, as communicated by subject–predicate relations. With observation statements referring to shared similarities among organisms distributed among two or more species, and phylogenetic hypotheses in the form of cladograms serving as at least tentative explanations for those effects, then what dictates the coding of observations is not adherence to a particular coding strategy, but the need to accurately convey the causal questions that address those observations. A phylogenetic data matrix is therefore not composed of columns as ‘characters’ and cells as ‘states’. Rather, column headings indicate the observed subjects that instantiate various characters; columns represent specifiable causal questions based on observations, and cells present the subject–predicate relations of observation statements. Since data matrices must represent one's causal questions, the inclusion of outgroup taxa is justified as components of those questions. With these criteria, the coding strategies summarized by Pleijel (1995) are critiqued. It is shown that advocacy of any one of those approaches is not possible, and that strategies that incorrectly apply the notion of ‘absence’ are especially prone to misrepresent observations.