GENIE: estimating demographic history from molecular phylogenies

GENIE implements a statistical framework for inferring the demographic history of a population from phylogenies that have been reconstructed from sampled DNA sequences. The methods are based on population genetic models known collectively as coalescent theory. AVAILABILITY: GENIE is available from http://evolve.zoo.ox.ac.uk. All popular operating systems are supported.     

PATH: a task for the inference of phylogenies

Phylogenetic Analysis Task in Husar (PATH) is a task for the inference of phylogenies. It executes three phylogenetic methods and automatically chooses the evolutionary model for each set of data. The output of the tasks shows the consensus trees together with full results obtained from all executed methods. AVAILABILITY: PATH is available at the German EMBnet node after registration via www at http://genome.dkfz-heidelberg.de     

Detection of punctuated equilibrium from molecular phylogenies

Abstract The theory of ‘punctuated equilibrium’ hypothesises that most morphological change in species takes place in rapid bursts triggered by speciation. Eldregde and Gould postulated the theory in 1972, as an alternative to the idea that morphological change slowly accumulates in the course of time, a then common belief they dubbed ‘phyletic gradualism’. Ever since its introduction the theory of punctuated equilibrium has been the subject of speculation rather than empirical validation. Here I present a method to detect punctuated evolution without reference to fossil data, based on the phenotypes of extant species and on their relatedness as revealed by molecular phylogeny. The method involves a general mathematical model describing morphological differentiation of two species over time. The two parameters in the model, the rates of punctual (cladogenetic) and gradual (anagenetic) change, are estimated from plots of morphological diversification against time since divergence of extant species.     

Trees of trees: an approach to comparing multiple alternative phylogenies

Phylogenetic analysis very commonly produces several alternative trees for a given fixed set of taxa. For example, different sets of orthologous genes may be analyzed, or the analysis may sample from a distribution of probable trees. This article describes an approach to comparing and visualizing multiple alternative phylogenies via the idea of a "tree of trees" or "meta-tree." A meta-tree clusters phylogenies with similar topologies together in the same way that a phylogeny clusters species with similar DNA sequences. Leaf nodes on a meta-tree correspond to the original set of phylogenies given by some analysis, whereas interior nodes correspond to certain consensus topologies. The construction of meta-trees is motivated by analogy with construction of a most parsimonious tree for DNA data, but instead of using DNA letters, in a meta-tree the characters are partitions or splits of the set of taxa. An efficient algorithm for meta-tree construction is described that makes use of a known relationship between the majority consensus and parsimony in terms of gain and loss of splits. To illustrate these ideas meta-trees are constructed for two datasets: a set of gene trees for species of yeast and trees from a bootstrap analysis of a set of gene trees in ray-finned fish. A software tool for constructing meta-trees and comparing alternative phylogenies is available online, and the source code can be obtained from the author.     

Dating nodes on molecular phylogenies: a critique of molecular biogeography

Taxa have been dated using three methods: equating their age with the age of the oldest known fossil, with the age of strata the taxa are endemic to, and with the age of paleogeographic events. All three methods have been adopted as methods of dating nodes in molecular phylogenies. The first method has been the most popular, but both this and the second method involve serious difficulties. Studies often, correctly, introduce oldest known fossils as providing minimum ages for divergences. However, in the actual analyses these ages, and ages derived from them, are often treated as absolute ages and earlier geological events are deemed irrelevant to the phylogeny. In fact, only younger geological events can be irrelevant. Studies correlating the age of nodes with age of volcanic islands often overlook the fact that these islands have been produced at subduction zones or hot spots where small, individually ephemeral islands are constantly being produced and disappearing, and a metapopulation can survive indefinitely. Correlating the age of taxa with that of associated paleogeographic events is probably the most promising method but has often been used in a simplistic way, for example in assuming that all divergence across the Isthmus of Panama dates to its final rise. Most workers now agree that a global molecular clock does not exist, and that rates can change between lineages and within a lineage over time. New methods of estimating branch lengths do not assume a strict clock, but the number of models for molecular evolution is then effectively infinite. Problems with calibrating the nodes, as well as with substitution models, mean that phylogeography's claim to be able to test between vicariance and dispersal is not justified. © The Willi Hennig Society 2005.     

pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies

SUMMARY: IQPNNI is a program to infer maximum-likelihood phylogenetic trees from DNA or protein data with a large number of sequences. We present an improved and MPI-parallel implementation showing very good scaling and speed-up behavior.     

Identifiability and inference of non-parametric rates-across-sites models on large-scale phylogenies

Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general rates-across-sites models. Our results imply, in particular, that large phylogenies are typically identifiable under rate variation. We also derive sequence-length requirements for high-probability reconstruction. Our main contribution is a novel algorithm that clusters sites according to their mutation rate. Following this site clustering step, standard reconstruction techniques can be used to recover the phylogeny. Our results rely on a basic insight: that, for large trees, certain site statistics experience concentration-of-measure phenomena.     

The biased reptation model of DNA gel electrophoresis: mobility vs molecular size and gel concentration

The biased reptation model provides a good framework for interpreting the results of continuous field DNA electrophoresis experiments performed in agarose gels. Here we discuss the main features of the mobility-molecular size and mobility-gel concentration diagrams as obtained from new extensive computer simulations of the model. Our aim is to suggest a global and coherent picture of this widely used yet poorly understood experimental technique, and to point out the areas where a systematic experimental study is still needed.     

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.     

Reproductive mode evolution in nematodes: insights from molecular phylogenies and recently discovered species

The Phylum Nematoda has long been known to contain a great diversity of species that vary in reproductive mode, though our understanding of the evolutionary origins, causes and consequences of nematode reproductive mode change have only recently started to mature. Here we bring together and analyze recent progress on reproductive mode evolution throughout the phylum, resulting from the application of molecular phylogenetic approaches and newly discovered nematode species. Reproductive mode variation is reviewed in multiple free-living, animal-parasitic and plant-parasitic nematode groups. Discussion ranges from the model nematode Caenorhabditis elegans and its close relatives, to the plant-parasitic nematodes of the Meloidogyne genus where there is extreme variation in reproductive mode between and even within species, to the vertebrate-parasitic genus Strongyloides and related genera where reproductive mode varies across generations (heterogony). Multiple evolutionary transitions from dioecous (obligately outcrossing) to hermaphroditism and parthenogenesis in the phylum are discussed, along with one case of an evolutionary transition from hermaphroditism to doioecy in the Oscheius genus. We consider the roles of underlying genetic mechanisms in promoting reproductive plasticity in this phylum, as well as the potential evolutionary forces promoting transitions in reproductive mode.     

Dinoflagellate phylogeny revisited: reconciling morphological and molecular based phylogenies

Ultrastructural and molecular phylogenetic data suggest that dinoflagellates diverged as a lineage possibly as early as the Precambrian. However, the fossil record is problematic before the Mesozoic. From the mid Triassic, though, the fossil record of dinoflagellates is a rich source of information on Mesozoic-Cenozoic dinoflagellates, especially the gonyaulacoids and peridinioids. From the sequence of appearance of species and tabulation types and the impression of early morphological experimentation and later stabilization, the early Mesozoic radiation of dinoflagellates appears to be a real evolutionary event: indeed, dinoflagellate morphology as we know it today may originate in that event. This would explain why it is so difficult to interpret earlier fossils as dinoflagellates. However, that the dinoflagellate lineage existed in some form in the pre-Mesozoic is supported by biogeochemical data, early results of which indicate that certain early Paleozoic acanthomorph acritarchs may belong to the lineage.

A surprising degree of consistency is observed between ultrastructural (including tabulational), coarse biochemical and molecular sequence data. For example, sequence data provided by small subunit (SSU) rRNA support the hypothesis of progressive loss of histones within the dinoflagellates. Gymnodinioids have long been considered to be polyphyletic but are thought of generally as forerunners to the strongly thecate groups such as gonyaulacoids and peridinioids. In molecular trees they appear in both early-derived and late-derived positions, but mostly the latter. SSU data clearly support the gonyaulacoid/peridinioid ordinal separation, as does the fossil record. Prorocentroids are now thought to be the among the most derived dinoflagellates (and presumably the morphologically similar dinophysoids), but SSU sequences have so far failed to resolve the relationships of most gymnodinioids, peridinioids and prorocentroids (the so-called GPP complex) to one another. However, they do suggest the origin of prorocentroids from peridinioids rather than gonyaulacoids and that gymnodinioids probably had several origins.     

The inference of evolutionary trees from molecular data.

1. Procedures for multiple alignment of sequence data, subsequent phylogenetic inference, and testing of the trees derived are presented. 2. The assumptions underlying different approaches and the extent to which they are valid are discussed.     

Probabilistic inference of molecular networks from noisy data sources

Information on molecular networks, such as networks of interacting proteins, comes from diverse sources that contain remarkable differences in distribution and quantity of errors. Here, we introduce a probabilistic model useful for predicting protein interactions from heterogeneous data sources. The model describes stochastic generation of protein-protein interaction networks with real-world properties, as well as generation of two heterogeneous sources of protein-interaction information: research results automatically extracted from the literature and yeast two-hybrid experiments. Based on the domain composition of proteins, we use the model to predict protein interactions for pairs of proteins for which no experimental data are available. We further explore the prediction limits, given experimental data that cover only part of the underlying protein networks. This approach can be extended naturally to include other types of biological data sources.     

Artificial neural networks can learn to estimate extinction rates from molecular phylogenies

Molecular phylogenies typically consist of only extant species, yet they allow inference of past rates of extinction, because recently originated species are less likely to be extinct than ancient species. Despite the simple structure of the assumed underlying speciation-extinction process, parametric functions to estimate extinction rates from phylogenies turned out to be complex and often difficult to derive. Moreover, these parametric functions are specific to a particular process (e.g. complete species level phylogeny with constant birth and death rates) and a particular type of data (e.g. times between bifurcations). Here, it is shown that artificial neural networks can substitute for parametric estimation functions once they have been sufficiently trained on simulated data. This technique can in principle be used for different processes and data types, and because it circumvents the time-consuming and difficult task of deriving parametric estimation functions, it may greatly extend the possibilities to make macro-evolutionary inferences from molecular phylogenies. This novel approach is explained, applied to estimate speciation and extinction rates from a molecular phylogeny of the reef fish genus Naso (Acanturidae), and its performance is compared to that of maximum likelihood estimation.     

Changing the landscape: a new strategy for estimating large phylogenies

In this paper we describe a new heuristic strategy designed to find optimal (parsimonious) trees for data sets with large numbers of taxa and characters. This new strategy uses an iterative searching process of branch swapping with equally weighted characters, followed by swapping with reweighted characters. This process increases the efficiency of the search because, after each round of swapping with reweighted characters, the subsequent swapping with equal weights will start from a different group (island) of trees that are only slightly, if at all, less optimal. In contrast, conventional heuristic searching with constant equal weighting can become trapped on islands of suboptimal trees. We test the new strategy against a conventional strategy and a modified conventional strategy and show that, within a given time, the new strategy finds trees that are markedly more parsimonious. We also compare our new strategy with a recent, independently developed strategy known as the Parsimony Ratchet.     

Bayesian coalescent inference of past population dynamics from molecular sequences

We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.     

Efficient inference of haplotypes from genotypes on a large animal pedigree

We present a simple algorithm for reconstruction of haplotypes from a sample of multilocus genotypes. The algorithm is aimed specifically for analysis of very large pedigrees for small chromosomal segments, where recombination frequency within the chromosomal segment can be assumed to be zero. The algorithm was tested both on simulated pedigrees of 155 individuals in a family structure of three generations and on real data of 1149 animals from the Israeli Holstein dairy cattle population, including 406 bulls with genotypes, but no females with genotypes. The rate of haplotype resolution for the simulated data was >91% with a standard deviation of 2%. With 20% missing data, the rate of haplotype resolution was 67.5% with a standard deviation of 1.3%. In both cases all recovered haplotypes were correct. In the real data, allele origin was resolved for 22% of the heterozygous genotypes, even though 70% of the genotypes were missing. Haplotypes were resolved for 36% of the males. Computing time was insignificant for both data sets. Despite the intricacy of large-scale real pedigree genotypes, the proposed algorithm provides a practical rule-based solution for resolving haplotypes for small chromosomal segments in commercial animal populations.