Confidence intervals in molecular dating by maximum likelihood.

Molecular dating has been widely used to infer the times of past evolutionary events using molecular sequences. This paper describes three bootstrap methods to infer confidence intervals under a penalized likelihood framework. The basic idea is to use data pseudoreplicates to infer uncertainty in the branch lengths of a phylogeny reconstructed with molecular sequences. The three specific bootstrap methods are nonparametric (direct tree bootstrapping), semiparametric (rate smoothing), and parametric (Poisson simulation). Our extensive simulation study showed that the three methods perform generally well under a simple strict clock model of molecular evolution; however, the results were less positive with data simulated using an uncorrelated or a correlated relaxed clock model. Several factors impacted, possibly in interaction, the performance of the confidence intervals. Increasing the number of calibration points had a positive effect, as well as increasing the sequence length or the number of sequences although both latter effects depended on the model of evolution. A case study is presented with a molecular phylogeny of the Felidae (Mammalia: Carnivora). A comparison was made with a Bayesian analysis: the results were very close in terms of confidence intervals and there was no marked tendency for an approach to produce younger or older bounds compared to the other.

MooSciTIC: Training of trainers in West African research and higher education.

The MooSciTIC project is a capacity-building initiative targeting West African research scientists and higher education teachers. The project aimed to improve the self-reliance of researchers and upgrade research practices by providing on-site summer schools on trans-disciplinary topics such as scientific writing, communication, and integrity. Here, we explain how this program was designed and implemented and share the positive responses from our trainees, hoping to inspire similar initiatives.

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.

Summary: After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity. Availability and implementation: ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=ape. Further information may be found at http://ape-package.ird.fr/.

The distribution of branch lengths in phylogenetic trees.

A lot of effort has been devoted to analyze the distribution of branching times observed in a phylogenetic tree. On the other hand, the distribution of branch lengths has not received similar attention. In this paper, the distribution of branch lengths is studied. It is shown that different types of branches within a tree have distinct distributions. Some equations to predict these distributions are derived with respect to diversification parameters and whether the size of the tree is known or not. A simulation study validated these predictions. The inferred distributions are used to develop graphical and statistical tools to assess the goodness-of-fit of diversification models. An application is presented on a recently published dated phylogeny of Carnivora. Some future developments are discussed.

Random phylogenies and the distribution of branching times.

Phylogenetic trees reconstructed without fossils have become an important source of information to study evolutionary processes. A widely used method to describe patterns of phylogenetic diversification is known as the lineages-through-time (LTT) plot. Recently, it has been shown that it is possible to predict the distribution of the branching times of a phylogeny, thus making possible to derive a theoretical LTT curve conditioned on diversification parameters. Here, I review some aspects related to this prediction showing how to derive it for any time-dependent model of diversification, as well as calculating a prediction interval around a theoretical LTT curve. The accuracy of the prediction interval was assessed with simulations using fixed or random tree sizes under constant-rate models as well as two models of time-dependent diversification. The prediction intervals were relatively narrower and more accurate for larger trees. The features of this approach are discussed as well as its potential applications.

Timetree of Aselloidea reveals species diversification dynamics in groundwater.

A key challenge for biologists is to document and explain global patterns of diversification in a wide range of environments. Here, we explore patterns of continental-scale diversification in a groundwater species-rich clade, the superfamily Aselloidea (Pancrustacea: Isopoda). Our analyses supported a constant diversification rate during most of the course of Aselloidea evolution, until 4-15 Ma when diversification rates started to decrease. This constant accumulation of lineages challenges the view that groundwater species diversification in temperate regions might have been primarily driven by major changes in physical environment leading to the extinction of surface populations and subsequent synchronous isolation of multiple groundwater populations. Rather than acting synchronously over broad geographic regions, factors causing extinction of surface populations and subsequent reproductive isolation of groundwater populations may act in a local and asynchronous manner, thereby resulting in a constant speciation rate over time. Our phylogeny also revealed several cases of parapatric distributions among closely related surface-water and groundwater species suggesting that species diversification could also arise from a process of disruptive selection along the surface-subterranean environmental gradient. Our results call for re-evaluating the spatial scale and timing of factors causing diversification events in groundwater.

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.

UNLABELLED: Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. One way to overcome this problem is to exclude such estimates from data analysis giving rise to an incomplete distance data set (as opposed to a complete one). So far their analysis has been out of reach for ape. To remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. In addition, we have also extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions. AVAILABILITY: ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/web/packages/ape/index.html Further information may be found at http://ape.mpl.ird.fr/pegas/

Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion.

Dating the divergence in a phylogenetic tree is a fundamental step in evolutionary analysis. Some extensions and improvements of the penalised likelihood method originally presented by Sanderson are introduced. The improvements are the introduction of alternative models, including one with non-correlated rates of molecular substitution ("relaxed" model), a completely reworked fitting algorithm that considers the high-dimensionality of the optimisation problem, and the development of a new information criterion for model selection in the presence of a penalised term. It is also shown that the strict clock model is a special case of the present approach. An extensive simulation study was conducted to assess the statistical performance of these improvements. Overall, the different estimators studied here appeared as unbiased though their variance varied depending on the fitted and the simulated models and on the number of calibration points. The strict clock model gave good estimates of branch lengths even in the presence of heterogeneous substitution rates. The correlated model gave the best estimates of substitution rates whatever the model used to simulate the data. These results, which are certainly the first from an extensive simulation study of a molecular dating method, call for more comparison with alternative methods, as well as further work on the developments introduced here.

Information-energy equivalence and the emergence of self-replicating biological systems.

Biological processes are characterized by a decrease in entropy in apparent violation of the second law of thermodynamics. Information stored in genomes help to solve this paradox when interpreted under the relationship between information and energy stated by Brillouin in the 1950's. However, the origins of living forms from inanimate matter which have no information storage device remains an open question. In this paper, a theoretical approach is developed on this issue. The replication of a simple entity with a binary genome is assumed to require an information-equivalent energy in addition to the standard activation energy. It is found that, in some conditions, a decrease in entropy can be accomplished together with a decrease in Gibbs free energy. An equation of the total energy for the replication of this entity is derived. Three factors are predicted to lower this energy: a small number of states of the coding sequence, a lower temperature, and a high ratio of the reaction on diffusion coefficients. These factors may have favoured the emergence of evolutionary demons-information storage devices that are able to decrease entropy. It is evaluated that some short, single-stranded RNA sequences made only of G and of C may conform to this model. The consequences of this model and its predictions on the origins of life on Earth and on other planets are discussed.

Seed Size Variation of Trees and Lianas in a Tropical Forest of Southeast Asia: Allometry, Phylogeny, and Seed Trait - Plant Functional Trait Relationships.

Seed size is a key trait for understanding and predicting ecological processes in a plant community. In a tropical forest, trees and lianas are major components driving ecosystem function and biogeochemical processes. However, seed ecological research on both components remains limited, particularly phylogenetic patterns and relationships with other traits. Here, we compiled a unique dataset of seed size (seed mass and geometrical size metrics) based on collections of more than 5,200 seeds of 196 woody plant species, covering >98 and 70% of tree and liana stems, respectively, located on a 30-ha plot in a tropical evergreen forest in central Thailand. We aimed to (1) develop allometric equations among seed size metrics to predict seed mass; (2) examine phylogenetic influence on seed size variation; and (3) examine relationships among seed traits and several other functional plant traits. Our allometric equations relating seed mass, seed volume, and width were well-fitted with data (R 2 = 0.94, 0.87 respectively). A phylogenetic signal test found that seed size was randomly distributed across the phylogeny. To study the functional trait relationships, we separately tested seed size data of the tree and liana communities (146 and 50 species, respectively), against mean body size of frugivores, successional niches, leaf, and structural traits. For the tree community, seed size was significantly related to mean body size of frugivores, which we believe is a basic driver of seed size because it is related to the gape width affecting dispersal effectiveness. Nearly all leaf traits were significantly positively correlated with seed size (p < 0.03). The significant positive correlation of leaf area and greenness suggested the high-energy demand of large-seeded species. We found a strong positive correlation between seed size and leaf toughness, suggesting a coordination between seed size and leaf defense. However, all these patterns disappeared in the same analysis applied to the liana community. Liana seed size variation was lower than that of trees, perhaps because lianas grow in relatively more uniform conditions in the forest canopy. Frugivore size was the strongest driver of seed size variation. Our study shows a surprising contrast between trees and lianas that is worth further investigation.

pegas: an R package for population genetics with an integrated-modular approach.

SUMMARY: pegas (Population and Evolutionary Genetics Analysis System) is a new package for the analysis of population genetic data. It is written in R and is integrated with two other existing R packages (ape and adegenet). pegas provides functions for standard population genetic methods, as well as low-level functions for developing new methods. The flexible and efficient graphical capabilities of R are used for plotting haplotype networks as well as for other functionalities. pegas emphasizes the need to further develop an integrated-modular approach for software dedicated to the analysis of population genetic data. AVAILABILITY: pegas is distributed through the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/pegas/index.html. Further information may be found at: http://ape.mpl.ird.fr/pegas/.

Parallel life history evolution in mouthbrooding cichlids from the African Great Lakes.

The existence of ancient deep-water lakes provides an opportunity to study the independent adaptation of aquatic organisms to pelagic, benthic, and rocky shore habitats. With improving resolution of their phylogenetic relationships, the many cichlid fish species endemic to the African Great Lakes Malawi, Tanganyika, and Victoria provide a significant resource for the comparative study of such evolutionary processes. Here, we show that cichlid lineages colonizing rocky shores and pelagic habitats in the different lakes have independently evolved larger eggs and lower fecundities than benthic lineages, suggesting parallel adaptive life-history evolution. By contrast, other pelagic teleost fishes in both marine and freshwater habitats, including African lakes, typically produce large numbers of very small eggs. Our results also suggest that decreased fecundity and increased egg size not only occurred independently in each lake but occurred independently in the colonization of rocky and pelagic habitats.

Large-scale reptile extinctions following European colonization of the Guadeloupe Islands.

Large-scale extinction is one of the defining challenges of our time, as human processes fundamentally and irreversibly reshape global ecosystems. While the extinction of large animals with popular appeal garners widespread public and research interest, the importance of smaller, less "charismatic" species to ecosystem health is increasingly recognized. Benefitting from systematically collected fossil and archaeological archives, we examined snake and lizard extinctions in the Guadeloupe Islands of the Caribbean. Study of 43,000 bone remains across six islands revealed a massive extinction of 50 to 70% of Guadeloupe's snakes and lizards following European colonization. In contrast, earlier Indigenous populations coexisted with snakes and lizards for thousands of years without affecting their diversity. Study of archaeological remains provides insights into the causes of snake and lizard extinctions and shows that failure to consider fossil-derived data probably contributes to substantial underestimation of human impacts to global biodiversity.

Publisher Correction: A thirteen-million-year divergence between two lineages of Indonesian coelacanths.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A thirteen-million-year divergence between two lineages of Indonesian coelacanths.

Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these 'living fossils' using new molecular data, including the possibility of 'cryptic' species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.

Asymmetries in phylogenetic diversification and character change can be untangled.

The analysis of diversification and character evolution using phylogenetic data attracts increasing interest from biologists. Recent statistical developments have resulted in a variety of tools for the inference of macroevolutionary processes in a phylogenetic context. In a recent paper Maddison (2006 Evolution, 60: 1743-1746) pointed out that uncareful use of some of these tools could lead to misleading conclusions on diversification or character evolution, and thus to difficulties in distinguishing both phenomena. I here present guidelines for the analyses of macroevolutionary data that may help to avoid these problems. The proper use of recently developed statistical methods may help to untangle diversification and character change, and so will allow us to address important evolutionary questions.

Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages.

Studies in insular environments have often documented a positive association of extinction risk and evolutionary uniqueness (i.e., how distant a species is from its closest living relative). However, the cause of this association is unclear. One explanation is that species threatened with extinction are evolutionarily unique because they are old, implying that extinction risk increases with time since speciation (age-dependent extinction). An alternative explanation is that such threatened species are last survivors of clades that have undergone an elevated extinction rate, and that their uniqueness results from the extinction of their close relatives. Distinguishing between these explanations is difficult but important, since they imply different biological processes determining extinction patterns. Here, we designed a simulation approach to distinguish between these alternatives using living species, and applied it to 12 insular radiations that show a positive association between extinction risk and evolutionary uniqueness. We also tested the sensitivity of results to underlying assumptions and variable extinction rates. Despite differences among the radiations considered, age-dependent extinction was supported as best explaining the majority of the empirical cases. Biological processes driving characteristic changes in abundance with species duration (age-dependency) may merit further investigation.

Linking genomics and population genetics with R.

Population genetics and genomics have developed and been treated as independent fields of study despite having common roots. The continuous progress of sequencing technologies is contributing to (re-)connect these two disciplines. We review the challenges faced by data analysts and software developers when handling very big genetic data sets collected on many individuals. We then expose how r, as a computing language and development environment, proposes some solutions to meet these challenges. We focus on some specific issues that are often encountered in practice: handling and analysing single-nucleotide polymorphism data, handling and reading variant call format files, analysing haplotypes and linkage disequilibrium and performing multivariate analyses. We illustrate these implementations with some analyses of three recently published data sets that contain between 60 000 and 1 000 000 loci. We conclude with some perspectives on future developments of r software for population genomics.

Phylogeography of Toxoplasma gondii points to a South American origin.

Toxoplasma gondii, a protozoan found ubiquitously in mammals and birds, is the etiologic agent of toxoplasmosis, a disease causing substantial public health burden worldwide, including about 200,000 new cases of congenital toxoplasmosis each year. Clinical severity has been shown to vary across geographical regions, with South America exhibiting the highest burden. Unfortunately, the drivers of these heterogeneities are still poorly understood, and the geographical origin and historical spread of the pathogen worldwide are currently uncertain. A worldwide sample of 168 T. gondii isolates gathered in 13 populations was sequenced for five fragments of genes (140 single nucleotide polymorphisms from 3153bp per isolate). Phylogeny based on Maximum likelihood methods with estimation of the time to the most recent common ancestor (TMRCA) and geostatistical analyses were performed for inferring the putative origin of T. gondii. We show that extant strains of the pathogen likely evolved from a South American ancestor, around 1.5 million years ago, and reconstruct the subsequent spread of the pathogen worldwide. This emergence is much more recent than the appearance of ancestral T. gondii, believed to have taken place about 11 My ago, and follows the arrival of felids in this part of the world. We posit that an ancestral lineage of T. gondii likely arrived in South America with felids and that the evolution of oral infectivity through carnivorism and the radiation of felids in this region enabled a new strain to outcompete the ancestral lineage and undergo a pandemic radiation.

apex: phylogenetics with multiple genes.

Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The r software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new r package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set.