Ophioglossaceae: a hypothetical archetype for the angiosperm carpel

KATO, M., 1990.Ophioglossaceae: a hypothetical archetype for the angiosperm carpel. In the light of a recently proposed phylogenetic position of Ophioglossaceae as living progymnosperms, a new archetype model for the angiosperm carpel is proposed. The three-dimensional construction of ophioglossoid fertile leaves with epiphyllous sporophores may be comparable to angiosperm carpels with adaxial ovules. The orientation of erect sporangia on young sporophores dorsiventrally facing the trophophores resembles that of anatropous ovuleS. Glossopterid fructifications may be interpreted as having the same construction as ophioglossoid leaveS. In the present hypothesis, the adaxial position of the ovules arose prior to the evolutionary process leading from gymnospermy to angiospermy. Previous hypotheses involving origins from Caytonia and Glossopteris are criticized.     

Phylogenetic signal, evolutionary process, and rate

A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species). In this study, we use individual-based numerical simulations on stochastic phylogenetic trees to clarify the relationship between phylogenetic signal, rate, and evolutionary process. Under the simplest model for quantitative trait evolution, homogeneous rate genetic drift, there is no relation between evolutionary rate and phylogenetic signal. For other circumstances, such as functional constraint, fluctuating selection, niche conservatism, and evolutionary heterogeneity, the relationship between process, rate, and phylogenetic signal is complex. For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal.     

Characterization of the ysa Pathogenicity Locus in the Chromosome of Yersinia enterocolitica and Phylogeny Analysis of Type III Secretion Systems

Several Gram negative bacteria use a complex system called "type III secretion system" (TTSS) to engage their host. The archetype of TTSS is the plasmid-encoded "Yop virulon" shared by the three species of pathogenic Yersinia (Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica). A second TTSS, called Ysa (for Yersinia secretion apparatus) was recently described in Y. enterocolitica 8081, a strain from serotype O:8. In this study, we describe the ysa locus from A127/90, another strain of serotype O:8, and we extend the sequence to several new genes encoding Ysp proteins which are the substrates of this secretion system, and a putative chaperone SycB. According to the deduced protein sequences, the ysa system from A127/90 is identical to that of 8081. It is different from the chromosome-encoded TTSS of Y. pestis but is instead closely related to the Mxi-Spa TTSS of Shigella and to the SPI-1 encoded TTSS of Salmonella enterica. We further demonstrated that the ysa locus is only present in biotype IB strains of Y. enterocolitica. Including this new Ysa system, a phylogenetic analysis of the 26 known TTSSs was carried out, based on the sequence analysis of three conserved proteins. All the TTSSs fall into five different clusters. The phylogenetic tree of these TTSSs is completely different from the evolutionary tree based on 16S RNA, indicating that TTSSs have been distributed by horizontal transfer.     

Evolutionary Models and Phylogenetic Signal Assessment via Mantel Test

Phylogenetically closely related species tend to be more similar to each other than to more distantly related ones, a pattern called phylogenetic signal. Appropriate tests to evaluate the association between phylogenetic relatedness and trait variation among species are employed in a myriad of eco-evolutionary studies. However, most tests available to date are only suitable for datasets describing continuous traits, and are most often applicable only for single trait analysis. The Mantel test is a useful method to measure phylogenetic signal for multiple (continuous, binary and/or categorical) traits. However, the classical Mantel test does not incorporate any evolutionary model (EM) in the analysis. Here, we describe a new analytical procedure, which incorporates explicitly an evolutionary model in the standard Mantel test (EM-Mantel). We run numerical simulations to evaluate its statistical properties, under different combinations of species pool size, trait type and number. Our results showed that EM-Mantel test has appropriate type I error and acceptable power, which increases with the strength of phylogenetic signal and with species pool size but depended on trait type. EM-Mantel test is a good alternative for measuring phylogenetic signal in binary and categorical traits and for datasets with multiple traits.     

Phylogenetic and evolutionary analysis of Vibrio parahaemolyticus and Vibrio alginolyticus isolates based on toxR gene sequence

The Vibrio genus contains a large number of closely related bacterial species differing, in some cases, less than 1% in 16S rRNA gene sequence. The present study evaluated the usefulness of toxR gene for phylogenetic and evolution analysis on Vibrio isolates of environmental or clinical origin belonging to the two closely related species V. parahaemolyticus and V. alginolyticus. The phylogenetic analysis based on toxR gene, contrary to 16S rRNA gene, allowed a clear differentiation of the isolates belonging to the two species and showed the presence of two separate, statistically supported clusters in V. alginolyticus (subgroup A and B). Such division, partially reflected in the biochemical features of the isolates, could not be explained by spatial and/or temporal distance in the isolation, leading to the hypothesis of two distinct, co-existing clusters in the V. alginolyticus isolates analysed. The evolutionary analysis on the toxR sequence showed that while the substitutions inferred from the alignment of V. parahaemolyticus are best explained by the negative/neutral selection model, in V. alginolyticus--and particularly in subgroup B--is acting a positive evolutionary pressure. The site detected as under diversifying selection (P164L) could be related to conformational changes of ToxR protein.     

Compositional statistics: An improvement of evolutionary parsimony and its application to deep branches in the tree of life

Summary We present compositional statistics, a new method of phylogenetic inference, which is an extension of evolutionary parsimony. Compositional statistics takes account of the base composition of the compared sequences by using nucleotide positions that evolutionary parsimony ignores. It shares with evolutionary parsimony the features of rate invariance and the fundamental distinction between transitions and transversions. Of the presently available methods of phylogenetic inference, compositional statistics is based on the fewest and mildest assumptions about the mode of DNA sequence evolution. It is therefore applicable to phylogenetic studies of the most distantly related organisms or molecules. This was illustrated by analyzing conservative positions in the DNA sequences of the large subunit of RNA polymerase from three archaebacterial groups, a eubacterium, a chloroplast, and the three eukaryotic polymerases. Internally consistent results, which are in accord with our knowledge of organelle origin and archaebacterial physiology, were achieved.     

Evolutionary and ecological causes of species richness patterns in North American angiosperm trees

Climate and evolutionary factors (e.g. diversification, time‐for‐speciation, niche conservatism) are both thought to be major drivers of species richness in regional assemblages. However, few studies have simultaneously investigated the relative effects of climate and evolutionary factors on species richness across a broad geographical extent. Here, we assess their relative effects on species richness of angiosperm trees across North America. Species richness of angiosperm trees in 1175 regional assemblages were related to climate and phylogenetic structure using a structural equation modeling (SEM) approach. Climate was quantified based on the mean temperature of the coldest month and mean annual precipitation. Evolutionary factors (time‐for‐speciation vs diversification) were inferred from phylogeny‐based measures of mean root distance, phylogenetic species variability, and net relatedness index. We found that at the continental scale, species richness is correlated with temperature and precipitation with approximately similar strength. In the SEM with net relatedness index and phylogenetic species variability and with all the 1175 quadrats, the total direct effect size of phylogenetic structure on species richness is greater than the total direct effect size of climate on species richness by a factor of 3.7. The specific patterns of phylogenetic structure (i.e. greater phylogenetic distances in more species rich regions) are consistent with the idea that time and niche conservatism drive richness patterns in North American angiosperm trees. We conclude that angiosperm tree species richness in regional assemblages in North America is more strongly related to patterns of phylogenetic relatedness than to climatic variation. The results of the present study support the idea that climatic and evolutionary explanations for richness patterns are not in conflict, and that evolutionary processes explain both the relationship between climate and richness and substantial variation in richness that is independent of climate.     

Phylogenies and traits provide distinct insights about the historical and contemporary assembly of aquatic insect communities

The assumption that traits and phylogenies can be used as proxies of species niche has faced criticisms. Evidence suggested that phylogenic relatedness is a weak proxy of trait similarity. Moreover, different processes can select different traits, giving opposing signals in null model analyses. To circumvent these criticisms, we separated traits of stream insects based on the concept of α and β niches, which should give clues about assembling pressures expected to act independently of each other. We investigated the congruence between the phylogenetic structure and trait structure of communities using all available traits and all possible combinations of traits (4095 combinations). To account for hierarchical assembling processes, we analyzed patterns on two spatial scales with three pools of genera. Beta niche traits selected a priori – i.e., traits related to environmental variation (e.g., respiration type) – were consistently clustered on the smaller scale, suggesting environmental filtering, while α niche traits – i.e., traits related to resource use (e.g., trophic position) – did not display the expected overdispersion, suggesting a weak role of competition. Using all traits together provided random patterns and the analysis of all possible combinations of traits provided scenarios ranging from strong clustering to overdispersion. Communities were phylogenetically overdispersed, a pattern previously interpreted as phylogenetic limiting similarity. However, our results likely reflect the co‐occurrence of ancient clades due to the stability of stream habitats along the evolutionary scale. We advise ecologists to avoid using combinations of all available traits but rather carefully traits based on the objective under consideration. Both trait and phylogenetic approaches should be kept in the ecologist toolbox, but phylogenetic distances should not be used as proxies of traits differences. Although the phylogenetic structure revealed processes operating at the evolutionary scale, only specific traits explained local processes operating in our communities.     

The Effect of Recombination on the Accuracy of Phylogeny Estimation

Phylogenetic studies based on DNA sequences typically ignore the potential occurrence of recombination, which may produce different alignment regions with different evolutionary histories. Traditional phylogenetic methods assume that a single history underlies the data. If recombination is present, can we expect the inferred phylogeny to represent any of the underlying evolutionary histories? We examined this question by applying traditional phylogenetic reconstruction methods to simulated recombinant sequence alignments. The effect of recombination on phylogeny estimation depended on the relatedness of the sequences involved in the recombinational event and on the extent of the different regions with different phylogenetic histories. Given the topologies examined here, when the recombinational event was ancient, or when recombination occurred between closely related taxa, one of the two phylogenies underlying the data was generally inferred. In this scenario, the evolutionary history corresponding to the majority of the positions in the alignment was generally recovered. Very different results were obtained when recombination occurred recently among divergent taxa. In this case, when the recombinational breakpoint divided the alignment in two regions of similar length, a phylogeny that was different from any of the true phylogenies underlying the data was inferred.     

SPIn: model selection for phylogenetic mixtures via linear invariants

In phylogenetic inference, an evolutionary model describes the substitution processes along each edge of a phylogenetic tree. Misspecification of the model has important implications for the analysis of phylogenetic data. Conventionally, however, the selection of a suitable evolutionary model is based on heuristics or relies on the choice of an approximate input tree. We introduce a method for model Selection in Phylogenetics based on linear INvariants (SPIn), which uses recent insights on linear invariants to characterize a model of nucleotide evolution for phylogenetic mixtures on any number of components. Linear invariants are constraints among the joint probabilities of the bases in the operational taxonomic units that hold irrespective of the tree topologies appearing in the mixtures. SPIn therefore requires no input tree and is designed to deal with nonhomogeneous phylogenetic data consisting of multiple sequence alignments showing different patterns of evolution, for example, concatenated genes, exons, and/or introns. Here, we report on the results of the proposed method evaluated on multiple sequence alignments simulated under a variety of single-tree and mixture settings for both continuous- and discrete-time models. In the simulations, SPIn successfully recovers the underlying evolutionary model and is shown to perform better than existing approaches.     

Chromosomal evolution in the lizard genus Varanus (reptilia).

The karyotypes have been determined of 16 of the 32 species of the genus Varanus, including animals from Africa, Israel, Malaya and Australia. A constant chromosome number of 2n = 40 was observed. The karyotype is divided into eight pairs of large chromosomes and 12 paris of microchromosomes. A series of chromosomal rearrangements have become established in both size groups of the karyotype and are restricted to centromers shifts, probably caused by pericentric inversion. Species could be placed in one of six distinct karyotype groups which are differentiated by these rearrangements and whose grouping does not always correspond with the current taxonomy. An unusual sex chromosome system of the ZZ/ZW type was present in a number of the species examined. The evolutionary significance of these chromosomal rearrangements, their origin and their mode of establishment are discussed and related to the current taxonomic groupings. The most likely phylogenetic model based on chromosome morphology, fossil evidence and the current distribution of the genus Varanus is presented.     

A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping

Traditional phylogenetic analysis is based on multiple sequence alignment. With the development of worldwide genome sequencing project, more and more completely sequenced genomes become available. However, traditional sequence alignment tools are impossible to deal with large-scale genome sequence. So, the development of new algorithms to infer phylogenetic relationship without alignment from whole genome information represents a new direction of phylogenetic study in the post-genome era. In the present study, a novel algorithm based on BBC (base-base correlation) is proposed to analyze the phylogenetic relationships of HEV (Hepatitis E virus). When 48 HEV genome sequences are analyzed, the phylogenetic tree that is constructed based on BBC algorithm is well consistent with that of previous study. When compared with methods of sequence alignment, the merit of BBC algorithm appears to be more rapid in calculating evolutionary distances of whole genome sequence and not requires any human intervention, such as gene identification, parameter selection. BBC algorithm can serve as an alternative to rapidly construct phylogenetic trees and infer evolutionary relationships.     

The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process

Determining the influence of horizontal gene transfer (HGT) on phylogenomic analyses and the retrieval of a tree of life is relevant for our understanding of microbial genome evolution. It is particularly difficult to differentiate between phylogenetic incongruence due to noise and that resulting from HGT. We have performed a large-scale, detailed evolutionary analysis of the different phylogenetic signals present in the genomes of Xanthomonadales, a group of Proteobacteria. We show that the presence of phylogenetic noise is not an obstacle to infer past and present HGTs during their evolution. The scenario derived from this analysis and other recently published reports reflect the confounding effects on bacterial phylogenomics of past and present HGT. Although transfers between closely related species are difficult to detect in genome-scale phylogenetic analyses, past transfers to the ancestor of extant groups appear as conflicting signals that occasionally might make impossible to determine the evolutionary origin of the whole genome.     

Community Structure of Skipper Butterflies (Lepidoptera,Hesperiidae) along Elevational Gradients in Brazilian Atlantic Forest Reflects Vegetation Type Rather than Altitude

Species turnover across elevational gradients has matured into an important paradigm of community ecology. Here, we tested whether ecological and phylogenetic structure of skipper butterfly assemblages is more strongly structured according to altitude or vegetation type along three elevation gradients of moderate extent in Serra do Mar, Southern Brazil. Skippers were surveyed along three different mountain transects, and data on altitude and vegetation type of every collection site were recorded. NMDS ordination plots were used to assess community turnover and the influence of phylogenetic distance between species on apparent community patterns. Ordinations based on ecological similarity (Bray-Curtis index) were compared to those based on phylogenetic distance measures (MPD and MNTD) derived from a supertree. In the absence of a well-resolved phylogeny, various branch length transformation methods were applied together with four different null models, aiming to assess if results were confounded by low-resolution trees. Species composition as well as phylogenetic community structure of skipper butterflies were more prominently related to vegetation type instead of altitude per se. Phylogenetic distances reflected spatial community patterns less clearly than species composition, but revealed a more distinct fauna of monocot feeders associated with grassland habitats, implying that historical factors have played a fundamental role in shaping species composition across elevation gradients. Phylogenetic structure of community turned out to be a relevant additional tool which was even superior to identify faunal contrasts between forest and grassland habitats related to deep evolutionary splits. Since endemic skippers tend to occur in grassland habitats in the Serra do Mar, inclusion of phylogenetic diversity may also be important for conservation decisions.     

Evolutionary model of protein secondary structure capable of revealing new biological relationships

Ancestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylogenetic analyses of remote homologues must handle extreme amino acid sequence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesized in their immediate ancestors. We implemented maximum likelihood-based phylogenetic inference to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of comparative modeling and sequence-based prediction; the reconstruction extracts information not available from modern structures or the ancestral sequences alone. Based on a phylogenetic analysis of a sequence-diverse protein family, we showed that the model can highlight relationships that are evolutionarily rooted in structure and not evident in amino acid-based analysis.     

Molecular Phylogeny and Evolution of the Neurotrophins from Monotremes and Marsupials

We have investigated the phylogenetic relationships of monotremes and marsupials using nucleotide sequence data from the neurotrophins; nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3). The study included species representing monotremes, Australasian marsupials and placentals, as well as species representing birds, reptiles, and fish. PCR was used to amplify fragments encoding parts of the neurotrophin genes from echidna, platypus, and eight marsupials from four different orders. Phylogenetic trees were generated using parsimony analysis, and support for the different tree structures was evaluated by bootstrapping. The analysis was performed with NGF, BDNF, or NT-3 sequence data used individually as well as with the three neurotrophins in a combined matrix, thereby simultaneously considering phylogenetic information from three separate genes. The results showed that the monotreme neurotrophin sequences associate to either therian or bird neurotrophin sequences and suggests that the monotremes are not necessarily related closer to therians than to birds. Furthermore, the results confirmed the present classification of four Australasian marsupial orders based on morphological characters, and suggested a phylogenetic relationship where Dasyuromorphia is related closest to Peramelemorphia followed by Notoryctemorphia and Diprotodontia. These studies show that sequence data from neurotrophins are well suited for phylogenetic analysis of mammals and that neurotrophins can resolve basal relationships in the evolutionary tree. Received: 27 January 1997 / Accepted: 20 March 1997     

Phylogeny, host-parasite relationship and zoogeography

Phylogeny is the evolutionary history of a group or the lineage of organisms and is reconstructed based on morphological, molecular and other characteristics. The genealogical relationship of a group of taxa is often expressed as a phylogenetic tree. The difficulty in categorizing the phylogeny is mainly due to the existence of frequent homoplasies that deceive observers. At the present time, cladistic analysis is believed to be one of the most effective methods of reconstructing a phylogenetic tree. Excellent computer program software for phylogenetic analysis is available. As an example, cladistic analysis was applied for nematode genera of the family Acuariidae, and the phylogenetic tree formed was compared with the system used currently. Nematodes in the genera Nippostrongylus and Heligmonoides were also analyzed, and the validity of the reconstructed phylogenetic trees was observed from a zoogeographical point of view. Some of the theories of parasite evolution were briefly reviewed as well. Coevolution of parasites and humans was discussed with special reference to the evolutionary relationship between Enterobius and primates.     

phylosignal: an R package to measure,test, and explore the phylogenetic signal

Phylogenetic signal is the tendency for closely related species to display similar trait values as a consequence of their phylogenetic proximity. Ecologists and evolutionary biologists are becoming increasingly interested in studying the phylogenetic signal and the processes which drive patterns of trait values in the phylogeny. Here, we present a new R package, phylosignal which provides a collection of tools to explore the phylogenetic signal for continuous biological traits. These tools are mainly based on the concept of autocorrelation and have been first developed in the field of spatial statistics. To illustrate the use of the package, we analyze the phylogenetic signal in pollution sensitivity for 17 species of diatoms.     

Reconstructing the Clavariaceae using nuclear large subunit rDNA sequences and a new genus segregated from Clavaria

Fungi that produce clavarioid fruit bodies have evolved independently many times in the Basidiomycota. The evolutionary significance of this morphology is difficult to interpret because the phylogenetic positions of many clavarioid fungi are still unknown. In this study we examined the phylogenetic diversity of the Clavariaceae sensu lato among Homobasidiomycetidae by adding partial nuclear large subunit ribosomal DNA sequences from clavarioid and corticioid fungi to a large euagaric dataset and analyzing them both together and separately. Our results indicate that the clavarioid morphology has evolved at least five times in the euagarics while the inclusion of type species enabled us to evaluate the taxonomic consequences of this polyphyletic distribution. Although the sampling available at present is incomplete, a qualitative assessment of our phylogenetic hypotheses indicates that the clavarioid habit might not be as evolutionary labile as previously reported. We propose the new genus Alloclavaria to accommodate Clavaria purpurea, which is not related to Clavaria but is derived within the hymenochaetoid clade. The Physalacriaceae and Clavariaceae are redefined to reflect monophyletic groups, and the limits of Clavaria, Clavulinopsis and Ramariopsis should be reconsidered when additional data are available.