Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing

A new method to estimate the diversification rate of a lineage from a phylogeny of recent species is presented. This uses survival models to analyse the ages of the species as derived from the phylogeny. Survival models can analyse missing data where the exact date of death is unknown (censoring). This approach allows us to include missing data (species not included in a detailed phylogenetic study) in the analysis, provided a minimum age is known for these species. Three models are presented, with emphasis on temporal variation in diversification rates. The maximum likelihood method and Akaike information criteria are used to derive estimators and tests of hypotheses. A simulation study demonstrates that the method is able to detect a temporal variation in diversification rate only when it is present, avoiding type I and type II errors. A lineage with ten species may be sufficient to detect a temporal variation in diversification rate even with 50 per cent of missing data. An application is presented with data from a phylogeny of birds of the genus Ramphocelus.     

Topology testing of phylogenies using least squares methods

Background  

The least squares (LS) method for constructing confidence sets of trees is closely related to LS tree building methods, in which the goodness of fit of the distances measured on the tree (patristic distances) to the observed distances between taxa is the criterion used for selecting the best topology. The generalized LS (GLS) method for topology testing is often frustrated by the computational difficulties in calculating the covariance matrix and its inverse, which in practice requires approximations. The weighted LS (WLS) allows for a more efficient albeit approximate calculation of the test statistic by ignoring the covariances between the distances.     

Species-pool hypothesis: Limits to its testing

The species richness of a community depends both on the pool of available species and on biotic mechanisms that lead to the exclusion of some of the species from a community. The method suggested byPärtel et al.,Oikos 75: 111–117, 1996 to test the effect of species-pool size on the species richness of a community is discussed in this paper. This method is based on the calculation of a correlation between the actual species richness of a community and the actual species-pool size, and compares the correlation found in the data with that simulated by a null model. In the null model, the species richness has a uniform distribution between zero and the size of the species pool. A correlation significantly higher than that in the null model is interpreted as evidence of the greater role of species pool than of local interactions in formation of community species richness (Zobel,Folia Geobot. 36: 3–8, 2001). It is shown that the interpretation of discrepancies between the null model and reality is difficult or impossible, because: (1) a null model with a uniform distribution of species richness is unrealistic, (2) both models based on the random selection of species from a species pool and models that include competitive interactions in the community predict a higher positive correlation of species richness and size of the species pool than the null model, and (3) local species richness might be affected by species-pool size, but a large species-pool size can also be a result of high local species richness. Caution is urged when interpreting the analyses based on the size of the filtered species-pool size.     

Selection of evolutionary models for phylogenetic hypothesis testing using parametric methods

Recent molecular studies have incorporated the parametric bootstrap method to test a priori hypotheses when the results of molecular based phylogenies are in conflict with these hypotheses. The parametric bootstrap requires the specification of a particular substitutional model, the parameters of which will be used to generate simulated, replicate DNA sequence data sets. It has been both suggested that, (a) the method appears robust to changes in the model of evolution, and alternatively that, (b) as realistic model of DNA substitution as possible should be used to avoid false rejection of a null hypothesis. Here we empirically evaluate the effect of suboptimal substitution models when testing hypotheses of monophyly with the parametric bootstrap using data sets of mtDNA cytochrome oxidase I and II (COI and COII) sequences for Macaronesian Calathus beetles, and mitochondrial 16S rDNA and nuclear ITS2 sequences for European Timarcha beetles. Whether a particular hypothesis of monophyly is rejected or accepted appears to be highly dependent on whether the nucleotide substitution model being used is optimal. It appears that a parameter rich model is either equally or less likely to reject a hypothesis of monophyly where the optimal model is unknown. A comparison of the performance of the Kishino–Hasegawa (KH) test shows it is not as severely affected by the use of suboptimal models, and overall it appears to be a less conservative method with a higher rate of failure to reject null hypotheses.     

Long-distance dispersal: a framework for hypothesis testing

Tests of hypotheses about the biogeographical consequences of long-distance dispersal have long eluded biologists, largely because of the rarity and presumed unpredictability of such events. Here, we examine data for terrestrial (including littoral) organisms in the Pacific to show that knowledge of dispersal by wind, birds and oceanic drift or rafting, coupled with information about the natural environment and biology of the organisms, can be used to generate broad biogeographic predictions. We then examine the predictions in the context of the origin, frequency of arrival and location of establishment of dispersed organisms, as well as subsequent patterns of endemism and diversification on remote islands. The predicted patterns are being increasingly supported by phylogenetic data for both terrestrial and littoral organisms.     

Telomeres and longevity: testing an evolutionary hypothesis

Identifying mechanisms that underlie variation in adult survivorship provide insight into the evolution of life history strategies and phenotypic variation in longevity. There is accumulating evidence that shortening telomeres, the protective caps at the ends of chromosomes, play an important role in individual variation in longevity. Given that telomeres generally shorten with age, it was surprising to find that in a population of a long-lived seabird, Leach's storm petrel, telomeres appear to lengthen with age. This unique finding suggested that the longest lived individuals are able to elongate telomeres, an interpretation we call the "elongation hypothesis." Alternatively, the "selection hypothesis" states that the longest lived individuals start with the longest telomeres and variation in telomere length decreases with age due to the selective disappearance of individuals with short telomeres. In the same population in which evidence supporting both hypotheses was uncovered, we tested mutually exclusive predictions from the elongation and selection hypotheses by measuring telomere length with the telomere restriction fragment assay in hatchling and old, adult storm petrels. As previously found, adult birds had longer telomeres on average compared with hatchlings. We also found that 3 hatchlings had mean telomere lengths exceeding that of the most extreme old bird, old birds on average had longer initial telomere lengths than hatchlings, and the variance in mean telomere length was significantly greater for hatchlings than for old birds, all predicted by the selection hypothesis. Perhaps more surprisingly, the oldest adults also show little or no accumulation of short telomeres over time, a pattern unknown in other species. Long telomeres are thought to provide a buffer against cellular senescence and be generally indicative of genome stability and overall cell health. In storm petrels, because the progressive accumulation of short telomeres appears negligible, variation in telomere length at birth may be linked to individual variation in longevity.     

Shortest triplet clustering: reconstructing large phylogenies using representative sets

Background  

Understanding the evolutionary relationships among species based on their genetic information is one of the primary objectives in phylogenetic analysis. Reconstructing phylogenies for large data sets is still a challenging task in Bioinformatics.     

壳斗演化的假说及分子系统学和化石证据

壳斗作为壳斗科Fagaceae的重要特征, 其起源、演化和多样性形成长期以来为系统学家们所关注, 有众多的观点和假说。本文在综合这些假说的基础上, 结合分子系统学和大化石证据, 讨论了壳斗演化的规律。研究结果支持壳斗具枝性性质, 来源于二歧聚伞花序最外侧小枝的假说。在比较3个壳斗演化模型的基础上, 根据4种分子系统关系的一致性重建了壳斗的演化历史: 壳斗是单系起源; 水青冈属的2果4裂瓣壳斗是最早分化的壳斗类型, 三棱栎型壳斗是较晚分化的类型; 并支持具有内裂瓣的金鳞果类型壳斗可能与其他横切面为圆形的壳斗有较近的共同祖先。这一结果也得到了多个大化石证据的支持。壳斗科多个分子系统关系的一致性和壳斗化石证据共同证实了壳斗演化的规律是从开裂向裂瓣融合、逐步简化、多向发展; 支持开裂壳斗、坚果三角形、较小、具棱或狭翅是祖征, 融合壳斗、坚果圆形、较大、不具棱是衍征。这些结果为进一步探索壳斗科的演化历史和系统发育提供了新的证据。     

Stable tRNA-based phylogenies using only 76 nucleotides

tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures universal phylogeny to a remarkable extent, and that the resulting tree is similar to the distribution of bootstrapped rRNA trees from the same genomes. In contrast, the trees derived from tRNAs of identical specificity or of individual isoacceptors generally produced trees of lower quality. However, some tRNA isoacceptors were very good predictors of the overall pattern of organismal evolution. These results show that UniFrac can extract meaningful biological patterns from even phylogenies with high level of statistical inaccuracy and horizontal gene transfer, and that, overall, the pattern of tRNA evolution tracks universal phylogeny and provides a background against which we can test hypotheses about the evolution of individual isoacceptors.     

The immunocompetence handicap hypothesis: testing the genetic predictions

The immunocompetence handicap hypothesis suggests that the immune system competes for resources with sexually selected ornaments; variation in ornaments might reflect genetic variation for immunocompetence. We tested this genetic prediction by mating scorpionfly females to males differing in the expression of a condition-dependent ornament trait, saliva secretion, and then comparing offspring immunocompetence. We found several indications of an immunocompetence handicap in our study: females had superior immunocompetence compared with males, the different immune traits were positively correlated, and there were indications of genetic variation in immune traits. However, we found no significant difference in the immunocompetence of offspring derived from males differing in ornament expression, only a tendency for sons of ornamented males to possess slightly better immunocompetence. The estimated effect of fathers on offspring immunocompetence was rather small, but it might be a sufficient benefit of female choice, provided that the costs of choice are small. We conclude that the genetic benefit of female choice is small concerning offspring immunocompetence, but the immunocompetence handicap principle might nevertheless work in scorpionflies.     

Testing macro-evolutionary models using incomplete molecular phylogenies.

Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.     

Calculating structural complexity in phylogenies using ancestral ontologies

Complexity is an important aspect of evolutionary biology, but there are many reasonable concepts of complexity, and its objective measurement is an elusive matter. Here we develop a simple measure of complexity based on counts of elements, incorporating the hierarchical information as represented in anatomical ontologies. Neomorphic and transformational characters are used to identify novelties and individuated morphological regions, respectively. By linking the characters to terms in an anatomical ontology a node‐driven approach is implemented, where a node ontology and a complexity score are inferred from the optimization of individual characters on each ancestral or terminal node. From the atomized vector of character scorings, the anatomical ontology is used to integrate the hierarchical structure of morphology in terminals and ancestors. These node ontologies are used to calculate a measure of complexity that can be traced on phylogenetic trees and is harmonious with usual phylogenetic operations. This strategy is compared with a terminal‐driven approach, in which the complexity scores are calculated only for terminals, and optimized as a continuous character on the internal nodes. These ideas are applied to a real dataset of 166 araneomorph spider species scored for 393 characters, using Spider Ontology (SPD, https://bioportal.bioontology.org/ontologies/SPD ); complexity scores and transitions are calculated for each node and branch, respectively. This result in a distribution of transitions skewed towards simplification; the transitions in complexity have no apparent correlation with character branch lengths. The node‐driven and terminal‐driven estimations are generally correlated in the complexity scores, but have higher divergence in the transition values. The structure of the ontology is used to provide complexity scores for organ systems and body parts of the focal groups.     

Re-examining alveolate evolution using multiple protein molecular phylogenies

Alveolates are a diverse group of protists that includes three major lineages: ciliates, apicomplexa, and dinoflagellates. Among these three, it is thought that the apicomplexa and dinoflagellates are more closely related to one another than to ciliates. However, this conclusion is based almost entirely on results from ribosomal RNA phylogeny because very few morphological characters address this issue and scant molecular data are available from dinoflagellates. To better examine the relationships between the three major alveolate groups, we have sequenced six genes from the non-photosynthetic dinoflagellate, Crypthecodinium cohnii: actin, beta-tubulin, hsp70, BiP, hsp90, and mitochondrial hsp10. Beta-tubulin, hsp70, BiP, and hsp90 were found to be useful for intra-alveolate phylogeny, and trees were inferred from these genes individually and in combination. Trees inferred from individual genes generally supported the apicomplexa-dinoflagellate grouping, as did a combined analysis of all four genes. However, it was also found that the outgroup had a significant effect on the topology within alveolates when using certain methods of phylogenetic reconstruction, and an alternative topology clustering dinoflagellates and ciliates could not be rejected by the combined data. Altogether, these results support the sisterhood of apicomplexa and dinoflagellates, but point out that the relationship is not as strong as is often assumed.     

Perils of paralogy: using HSP70 genes for inferring organismal phylogenies

Conserved genes have found their way into the mainstream of molecular systematics. Many of these genes are members of multigene families. A difficulty with using single genes of multigene families for phylogenetic inference is that genes from one species may be paralogous to those from another taxon. We focus attention on this problem using heat shock 70 (HSP70) genes. Using polymerase chain reaction techniques with genomic DNA, we isolated and sequenced 123 distinct sequences from 12 species of sharks. Phylogenetic analysis indicated that the sequences cluster with constituitively expressed cytoplasmic heat shock-like genes. Three highly divergent gene clades were sampled. A number of similar sequences were sampled from each species within each distinct gene clade. Comparison of published species trees with an HSP70 gene tree inferred using Bayesian phylogenetic analysis revealed several cases of gene duplication and differential sorting of gene lineages within this group of sharks. Gene tree parsimony based on the objective criteria of duplication and losses showed that previously published hypotheses of species relationships and two novel hypothesis based on Bayesian phylogenetics were concordant with the history of HSP70 gene duplication and loss. By contrast, two published hypotheses based on morphological data were not significantly different from the null hypothesis of a random association between species relatedness and the HSP70 gene tree. These results suggest that gene tree parsimony using data from multigene families can be used for inferring species relationships or testing published alternative hypotheses. More importantly, the results suggest that systematic studies relying on phylogenetic inferences from HSP70 genes may by plagued by unrecognized paralogy of sampled genes. Our results underscore the distinction between gene and species trees and highlight an underappreciated source of discordance between gene trees and organismal phylogeny, i.e., unrecognized paralogy of sampled genes.     

Warriors and peacekeepers: testing a biosocial implicit leadership hypothesis of intergroup relations using masculine and feminine faces

This paper examines the impact of facial cues on leadership emergence. Using evolutionary social psychology, we expand upon implicit and contingent theories of leadership and propose that different types of intergroup relations elicit different implicit cognitive leadership prototypes. It is argued that a biologically based hormonal connection between behavior and corresponding facial characteristics interacts with evolutionarily consistent social dynamics to influence leadership emergence. We predict that masculine-looking leaders are selected during intergroup conflict (war) and feminine-looking leaders during intergroup cooperation (peace). Across two experiments we show that a general categorization of leader versus nonleader is an initial implicit requirement for emergence, and at a context-specific level facial cues of masculinity and femininity contingently affect war versus peace leadership emergence in the predicted direction. In addition, we replicate our findings in Experiment 1 across culture using Western and East Asian samples. In Experiment 2, we also show that masculine-feminine facial cues are better predictors of leadership than male-female cues. Collectively, our results indicate a multi-level classification of context-specific leadership based on visual cues imbedded in the human face and challenge traditional distinctions of male and female leadership.     

Deactivation of Src family kinases: hypothesis testing using a Monte Carlo sensitivity analysis of systems-level properties.

Src family tyrosine kinases play a key role in many cellular signalling networks, but due to the high complexity of these networks their precise function remains elusive. Many factors involved in Src regulation, such as specific kinases and phosphatases, are still unknown. Mathematical models have been constructed to improve the understanding of the system and its dynamic behavior. Using a computational random parameter search, we characterized and compared the dynamics of three alternative models in order to assess their likelihoods. For this, we investigated how systems-level properties such as bistability and excitable behavior relate to kinetic and physiological parameters and how robust these properties were. Our results suggest the existence of a putative negative feedback loop in the Src system. A previously suggested role for PTPalpha in the deactivation of Src was not supported by the model.