RAPD problems in phylogenetics

This paper is intended to clarify some of the questions related with the application of RAPD for phylogenetic reconstruction purposes. Using different specimens of mammals selected across various taxonomic levels, we assessed the validity of RAPD to recover a known phylogeny, using four distance coefficients (simple matching, Russell & Rao, Jaccard, and Dice). We assessed the minimum number of primers required in the computations to obtain stable results in terms of distance estimates and/or topologies of the derived trees. These results based on distance methods were compared with those obtained with parsimony analyses of RAPD markers. Both approaches have shown to be equally problematic for comparing taxa above the family level. On the basis of these comparisons among various indices and methods, we recommend the use of Jaccard or Dice coefficients, with no less than twelve primers. We also suggest validation of any phylogeny based on RAPD data with a resampling procedure (i.e. the bootstrap or the jackknife) before any sound conclusion can be drawn.     

Molecular phylogenetics of DNA 5mC-methyltransferases.

We have identified a total of 88 members of the DNA-(cytosine-5) methyltransferase (5mC MTase) family whose sequences have been deposited in the databases. The results of a comparison of these sequences is presented in the form of an alignment-based phylogenetic tree and sequence logos for 10 conserved motifs. Phylogenetic analysis showed that members of the family aggregate into subfamilies which are usually consistent with their target specificity. However, it was also shown that similar target specificity does not necessarily imply close homology of the catalytic domain of MTases, which strongly supports the hypothesis that target recognition evolved independently of catalytic properties. This analysis also indicate that the 5mC MTase was present in the cenancestor (last common ancestor) of eubacteria, archaebacteria, and eukaryotes. The phylogeny of the 5mC MTases catalytic domain provides the basis for establishing the patterns of evolutionary change that characterize this family of proteins with conserved structural core and variable and mobile modules not directly involved in formation of the active site.     

Species concepts and phylogenetics

Concepts of species proposed within the phylogenetic paradigm arecritically reviewed. Most so called phylogenetic species concepts relyheavily on factors immaterial to phylogenetic hypotheses. Thus, theyhave limited empirical content and offer weak bases on which to makedecisions about real problems related to species. Any workable notion ofspecies relies on an explicit character analysis, rather than onabstract properties of lineages, narrative predications and speculationson tokogenetic relationships. Species only exist conjecturally, as thesmallest meaningful units for phylogenetic analysis, as based oncharacter evidence. Such an idea considers species to be conjecturesbased on similarity, that are subsequently subject to testing by theresults of analysis. Species, thus, are units of phylogenetic analysisin the same way as hypotheses of homology are units of comparablesimilarities, i.e. conjectures to be tested by congruence. Althoughmonophyly need not be demonstrated for species-level taxa, hypotheses ofrelationships are the only basis to refute species limits and guidenecessary rearrangements. The factor that leads to recognition ofspecies is similarity in observed traits. The concept of life cycle isintroduced as an important element in the discussion of species, as anefficient way to convey subsidiary notions of sexual dimorphism,polymorphism, polytypy and clusters of diagnosable semaphoronts. Thenotion of exemplars is used to expand the concept ofspecies-as-individual-organisms into a more generally usable concept.Species are therefore proposed for a diagnosable sample of(observed or inferred) life cycles represented by exemplars all of whichare hypothesized to attach to the same node in a cladogram, and whichare not structured into other similarly diagnosable clusters. Thisdefinition is character-based, potentially testable by reference to abranching diagram, and dispenses with reference to ancestor-descendantrelationships or regression into population concepts. It provides aworkable basis on which to proceed with phylogenetic analysis and abasis for that analysis to refute or refine species limits. A protocolis offered for testing hypotheses of species boundaries in cladograms.     

Heterotachy and long-branch attraction in phylogenetics

Background  

Probabilistic methods have progressively supplanted the Maximum Parsimony (MP) method for inferring phylogenetic trees. One of the major reasons for this shift was that MP is much more sensitive to the Long Branch Attraction (LBA) artefact than is Maximum Likelihood (ML). However, recent work by Kolaczkowski and Thornton suggested, on the basis of simulations, that MP is less sensitive than ML to tree reconstruction artefacts generated by heterotachy, a phenomenon that corresponds to shifts in site-specific evolutionary rates over time. These results led these authors to recommend that the results of ML and MP analyses should be both reported and interpreted with the same caution. This specific conclusion revived the debate on the choice of the most accurate phylogenetic method for analysing real data in which various types of heterogeneities occur. However, variation of evolutionary rates across species was not explicitly incorporated in the original study of Kolaczkowski and Thornton, and in most of the subsequent heterotachous simulations published to date, where all terminal branch lengths were kept equal, an assumption that is biologically unrealistic.     

Closure operations in phylogenetics

Closure operations are a useful device in both the theory and practice of tree reconstruction in biology and other areas of classification. These operations take a collection of trees (rooted or unrooted) that classify overlapping sets of objects at their leaves, and infer further tree-like relationships. In this paper we investigate closure operations on phylogenetic trees; both rooted and unrooted; as well as on X-splits, and in a general abstract setting. We derive a number of new results, particularly concerning the completeness (and incompleteness) and complexity of various types of closure rules.     

Phenotypic diversification and island evolution of pipistrelle bats (Pipistrellus pipistrellus group) in the Mediterranean region inferred from geometric morphometrics and molecular phylogenetics

Aim The Mediterranean Basin is a centre of radiation for numerous species groups. To increase our understanding of the mechanisms underlying speciation and radiation events in this region, we assessed the phenotypic variability within the Pipistrellus pipistrellus–pygmaeus–hanaki species complex. Although bats form the second largest mammalian order, studies of insular evolution in this group are scarce. We approached this problem from a microevolutionary perspective and tested for the recurrence of the insular syndrome. Location The Mediterranean Basin, with a special focus on isolated populations from Corsica, the Maghreb, Cyprus, Cyrenaica and Crete. Methods Phenotypic variability was assessed by cranial morphometrics using the coordinates of 41 3D landmarks and associated geometric‐morphometric methods. We analysed 125 specimens representing all of the lineages in the species complex. Differences between taxa and between insular and continental populations in cranial size, shape, form and allometries were tested using analyses of variance and visualized using boxplots and canonical variate analysis. Relationships between molecular data from a previous study (cytochrome b sequences) and morphometric data were tested with co‐inertia analyses (RV test) and multivariate regressions. Results The three species were relatively well differentiated in cranial size and shape, and each species showed a significant amount of inter‐population variability. Comparisons of pairs of insular versus continental populations revealed heterogeneities in cranial patterns among island phenotypes, suggesting no recurrent insular syndrome. Molecular and phenotypic traits were correlated, except for molecular and lateral cranium shape. Main conclusions The Pipistrellus pipistrellus – pygmaeus – hanaki species complex exhibits phenotypic variability as a result of the fragmentation of its distribution (especially on islands), its phylogenetic and phylogeographic history and, most probably, other evolutionary factors that were not investigated in this study. We found no recurrent pattern of evolution on islands, indicating that site‐specific factors play a prevailing role on Mediterranean islands. The correlation between molecular and phenotypic data is incomplete, suggesting that factors other than phylogenetic relationships, potentially connected with feeding ecology, have played a role in shaping cranial morphology in this species complex.     

分子系统学在生物保护中的意义

本文综述了近年来分子系统学的原理和方法及其在生物多样性保护中的应用和发展。分子系统学方法可以很好地确定物种保护的基本单元——进化显著性单元,并可用于推测群体的发展状态,从而为物种的保护提供了一项新的具很强操作性的科学手段。     

Adaptation and functional integration in primate phylogenetics

In two areas of phylogenetics, contrary predictions have been developed and maintained for character analysis and weighting. With regard to adaptation, many have argued that adaptive characters are poorly suited to phylogenetic analysis because of a propensity for homoplasy, while others have argued that complex adaptive characters should be given high weight because homoplasy in complex characters is unlikely. Similarly, with regard to correlated sets of characters, one point of view is that such sets should be collapsed into a single character-a single piece of phylogenetic evidence. Another point of view is that a suite of correlated characters should be emphasized in phylogenetics, again because recurrence of detailed similarity in the same suite of features is unlikely. In this paper, I discuss the theoretical background of adaptation and functional integration with respect to phylogenetic systematics of primates. Several character examples are reviewed with regard to their functional morphology and phylogenetic signal: postorbital structures, tympanic morphology, fusion of the mandibular symphysis, the tooth comb, strepsirrhine talar morphology, and the prehensile tail. It is clear when considering characters such as these that some characters are synapomorphic of major clades and at the same time functionally important. This appears particularly to be the case when characters are integrated into a complex and maintained as stable configurations. Rather than being simply a problem in character analysis, processes of integration may help to explain the utility of phylogenetically informative characters. On the other hand, the character examples also highlight the difficulty in forming a priori predictions about a character's phylogenetic signal. Explanations of patterns of character evolution are often clade-specific, which does not allow for a simple framework of character selection and/or weighting.     

Concordance analysis in mitogenomic phylogenetics

Here I advocate the utility of Bayesian concordance analysis as a mechanism for exploring the magnitude and source of phylogenetic signal in concatenated mitogenomic phylogenetic studies. While typically applied to the study of independently evolving gene trees, Bayesian concordance analysis can also be applied to linked, but individually analyzed, gene regions using a prior probability that reflects the expectation of similar phylogenetic reconstructions. For true branches in the mitogenomic tree, concordance factors should represent the number of gene regions that contain phylogenetic signal for a particular clade. As a demonstration of the application of Bayesian concordance analysis to empirical data, I analyzed two different salamander (Hynobiidae and Plethodontidae) mitogenomic data sets using a gene-based partitioning strategy. The results revealed many strongly supported clades in the concatenated trees that have high concordance factors, permitting the inference that these are robustly resolved through phylogenetic signal distributed across the mitogenome. In contrast, a number of strongly supported clades in the concatenated tree received low concordance factors, indicating that their reconstruction is either driven primarily by phylogenetic signal in a small number of gene regions, or that they are inconsistent reconstructions influenced by properties of the data that can produce inaccurate trees (e.g., compositional bias, selection, etc.). Exploration of the Bayesian joint posterior distribution of trees highlighted partitions that contribute phylogenetic information to similar clade reconstructions. This approach was particularly insightful in the hynobiid data, where different combinations of genes were identified that support alternative tree reconstructions. Concatenated analysis of these different subsets of genes highlighted through Bayesian concordance analysis produced strongly supported and contrasting trees, demonstrating the potential for inconsistency in concatenated mitogenomic phylogenetics. The overall results presented here suggest that Bayesian concordance analysis can serve as an effective exploration of the influence of different gene regions in mitogenomic (and other organellar genomic) phylogenetic studies.     

Nuclear DNA and salmonid phylogenetics

There are many unresolved problems in salmonid systematics, both at the interspecific and sub-specific levels. Some of the major systematic problems in the subfamily Salmoninae are briefly reviewed along with the available molecular methods for their analysis. Nuclear DNA markers available for use in molecular systematics include localized and dispersed highly repetitive DNA sequences, moderately repetitive sequences such as the ribosomal RNA genes (rDNA), and single copy DNA sequences. Both coding and non-coding sequences can be examined in the rDNA and single copy DNA. The rDNA is especially suitable for use in phylogenetic analysis, since different regions evolve at different rates and can be used for comparisons at different taxonomic levels. Comparison of restriction maps of the entire rDNA repeating unit in 17 salmonid species from Hucho. Sahelinus, Salmo and Oncorhynchus has shown that the transcribed spacer regions are the most informative for interspecific comparisons and that the intergenic spacer has potential for use in intraspecific comparisons. Our current approach is to amplify selected regions from each of these spacers for analysis by DNA sequencing. DNA sequence analysis of the internal transcribed spacers should be very informative in elucidating interspecific relationships in Salvelinus and Oncorhynchus . Analysis of a hypervariable region in the intergenic spacer has potential for identification of geographically separated stocks. The relative utility of different types of nuclear DNA sequences for identification of stocks and subspecies is examined.     

Bayesian model adequacy and choice in phylogenetics

Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.     

What's old and new in molecular phylogenetics

While it is fairly easy to devise a phylogenetic tree based on molecular data, it has proven difficult to tell how reliable any such tree is. Thus while the genetic inference that humans, chimpanzees, and gorillas cluster together is widely accepted, the genetic inference that the primary division among Old World human populations is between Asia and EurAfrica is not. A molecular phylogenetic inference linking humans and chimpanzees was proposed in the 1980s based on the technique of DNA hybridization. Despite several recent publications in primary and secondary source material, much confusion still exists surrounding the work. This paper tries to clarify issues that may still be confusing to physical anthropologists, and proposes criteria upon which to judge the robusticity of a phylogenetic inference based on DNA hybridization, in light of a recent published claim of replication. The claim of replication is considered critically. Interestingly, the original DNA hybridization data may actually show a chimp-gorilla link, in harmony with other phylogenetic results.     

Horizontal gene transfer and phylogenetics

The initial analysis of complete genomes has suggested that horizontal gene transfer events are very frequent between microorganisms. This could potentially render the inference, and even the concept itself, of the organismal phylogeny impossible. However, a coherent phylogenetic pattern has recently emerged from an analysis of about a hundred genes, the so-called 'core', strongly suggesting that it is possible to infer the phylogeny of prokaryotes. Also, estimation of the frequency of horizontal gene transfers at the genome level in a phylogenetic context seems to indicate that it is rather low, although of significant biological impact. Nevertheless, it should be emphasized that the history of microorganisms cannot be properly represented by the phylogeny of the core, which represents only a tiny fraction of the genome. This history, even if horizontal gene transfers are rare, should be represented by a network surrounding the core phylogeny.     

Morphology and phylogenetics of Stomatisora,including Stomatisora psychotriicola sp. nov.

The morphology of the type specimen of Stomatisora geophilicola, the only species of the genus Stomatisora (Pucciniales) recognised till now, was restudied. Thin-walled probasidia (teliospores) develop exclusively in substomatal chambers, and mature metabasidia emerge through the stomata and develop suprastomatally. Uredinia are erumpent through the upper epidermis. A new species, S. psychotriicola, parasitizing Psychotria capensis (Rubiaceae) from South Africa, is described and illustrated. Only telia have been found which also develop in stomatal cavities, and, as in the type species, have partly repetitive probasidia and suprastomatal metabasidia that easily detach from fragile stalks. The similarities of telial morphology, as well as the same host family, indicate a close relationship and a generic separation from other rust genera. Molecular data support this interpretation and a possible relationship within a phakopsoroid clade.     

Genomic biodiversity, phylogenetics and coevolution in proteins

Comprehensive sampling of genomic biodiversity is fast becoming a reality for some genomic regions and complete organelle genomes. Genomic biodiversity is defined as large genomic sequences from many species, and here some recent work is reviewed that demonstrates the potential benefits of genomic biodiversity for molecular evolutionary analysis and phylogenetic reconstruction. This work shows that using likelihood-based approaches, taxon addition can dramatically improve phylogenetic reconstruction. Features or dynamics of the evolutionary process are much more easily inferred with large numbers of taxa, and large numbers are essential for discriminating differences in evolutionary patterns between sites. Accurate prediction of site-specific patterns can improve phylogenetic reconstruction by an amount equivalent to quadrupling sequence length. Genomic biodiversity is particularly central to research relating patterns of evolution, adaptation and coevolution to structural and functional features of proteins. Research on detecting coevolution between amino acid residues in proteins demonstrates a clear need for much greater numbers of closely related taxa to better discriminate site-specific patterns of interaction, and to allow more detailed analysis of coevolutionary interactions between subunits in protein complexes. It is argued that parsing out coevolutionary and other context-dependent substitution probabilities is essential for discriminating between coevolution and adaptation, and for more realistically modelling the evolution of proteins. Also reviewed is research that argues for increasing the efficiency of acquiring genomic biodiversity, and suggests that this might be done by simultaneously shotgun cloning and sequencing genomic mixtures from many species. Increased efficiency is a prerequisite if genomic biodiversity levels are to rapidly increase by orders of magnitude, and thus lead to dramatically improved understanding of interactions between protein structure, function and sequence evolution.     

Zinc proteomes, phylogenetics and evolution

Evolution has not been studied in detail with reference to the changing environment. This requires a study of the inorganic chemistry of organisms, especially metalloproteins. The evolution of organisms has been analysed many times previously using comparative studies, fossils, and molecular sequences of proteins, DNA and 16s rRNA (Zhang and Gladyshev, Chem. Rev., 2009, 109, 4828). These methods have led to the confirmation of Darwin's original proposal that evolution followed from natural selection in a changing environment often pictured as a tree. In all cases, the main tree in its upper later reaches has been well studied but its lower earlier parts are not so well defined. To approach this topic we have treated evolution as due to the intimate combination of the effect of chemical changes in the environment and in the organisms (Williams and da Silva, The Chemistry of Evolution, 2006, Elsevier). The best chemicals to examine are inorganic ions as they are common to both. As a more detailed example of the chemical study of organisms we report in this paper a bioinformatic approach to the characterization of the zinc proteomes. We deduce them from the 821 totally sequenced DNA of organisms available on NCBI, exploiting a published method developed by one of us (Andreini, Bertini and Rosato, Acc. Chem. Res., 2009, 42, 1471). Comparing the derived zinc-finger-containing proteins and zinc hydrolytic enzymes in organisms of different complexity there is a correlation in their changes during evolution related to environmental change.     

Likelihood-based tests of topologies in phylogenetics

Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is the Kishino-Hasegawa test. However, the assumptions that have to be made to ensure the validity of the Kishino-Hasegawa test place important restrictions on its applicability. In particular, it is only valid when the topologies being compared are specified a priori. Unfortunately, this means that the Kishino-Hasegawa test may be severely biased in many cases in which it is now commonly used: for example, in any case in which one of the competing topologies has been selected for testing because it is the maximum likelihood topology for the data set at hand. We review the theory of the Kishino-Hasegawa test and contend that for the majority of popular applications this test should not be used. Previously published results from invalid applications of the Kishino-Hasegawa test should be treated extremely cautiously, and future applications should use appropriate alternative tests instead. We review such alternative tests, both nonparametric and parametric, and give two examples which illustrate the importance of our contentions.