BibSonomy publications for /tag/for:compevolFri Apr 15 03:22:04 CEST 2011Systematic Biology3307-321New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.592010PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.Tue Feb 01 23:03:06 CET 2011Proceedings of the National Academy of Sciences4920646The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography1062009moa myown Tue Feb 01 22:30:47 CET 2011The Journal of Physical Chemistry A12733--12740Extinction Times in Autocatalytic Systems2010autocatalytic myown Tue Feb 01 22:29:46 CET 2011BMC biology1114Bayesian random local clocks, or one rate to rule them all82010bayesian myown Tue Feb 01 22:28:08 CET 2011Molecular biology and evolution4811Epidemic dynamics revealed in dengue evolution272010myown phylodynamics Tue Feb 01 22:22:56 CET 2011Molecular Biology and Evolution2879--887A Bayesian phylogenetic method to estimate unknown sequence ages282011imported myown Tue Sep 28 00:32:56 CEST 2010Mol Biol Evolfeb2245-248Accommodating the effect of ancient DNA damage on inferences of demographic histories262009bayesian coalescent myown DNA sequences extracted from ancient remains are increasingly used to generate large population data sets, often spanning tens of thousands of years of population history. Bayesian coalescent methods such as those implemented in the software package BEAST can be used to estimate the demographic history of these populations, sometimes resulting in complex scenarios of fluctuations in population size, which can be correlated with the timing of environmental events, such as glaciations. Recently, however, Axelsson et al. (Axelsson E, Willerslev E, Gilbert MTP, Nielsen R. 2008. The effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol 25:2181-2187.) claimed that many of these complex demographic trends are likely to be the result of postmortem DNA damage, a problem that they investigate by removing all sites involving transitions from ancient sequences prior to analysis. When this solution is applied to a previously published data set of Pleistocene bison, they show that the demographic signal of population expansion and decline disappears. Although some apparently segregating mutations in ancient sequences may be due to postmortem damage, we argue that discarding the data will result in loss of power to detect patterns of population change. Instead, to accommodate this problem, we implement a model in which sequences are the result of a joint process of molecular evolution and postmortem DNA damage within a probabilistic inference framework. Through simulation, we demonstrate the ability of this model to accurately recover evolutionary parameters, demographic history, and DNA damage rates. When this model is applied to the bison data set, we find that the rate of DNA damage is significant but low and that the reconstruction of population size history is nearly identical to previously published estimates.Tue Sep 28 00:30:22 CEST 2010Mol Biol Evolmar3570-580Bayesian inference of species trees from multilocus data272010bayesian coalescent multispecies-coalescent myown phylogenetics Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With technological advances, it is now becoming more common to collect data sets containing multiple gene loci and multiple individuals per species. These data sets often reveal the need to directly model intraspecies polymorphism and incomplete lineage sorting in phylogenetic estimation procedures. For a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. Here, we present a Bayesian Markov chain Monte Carlo method for the multispecies coalescent. Our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. The inference is made possible by multilocus data from multiple individuals per species. Using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. These simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. Finally, we compare our new method to both an existing method (BEST 2.2) with similar goals and the supermatrix (concatenation) method. We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation.Tue Sep 28 00:23:10 CEST 2010PLoS Comput Biolsep9Bayesian phylogeography finds its roots52009Bayesian myown phylogeography As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. In addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. To visualize the spatial and temporal information, we summarize inferences using virtual globe software. We describe how Bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza A H5N1 origin and H5N1 epidemiological linkage among sampling localities. Analysis of rabies in West African dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms.Sun Oct 18 05:01:59 CEST 2009Los Alamitos, CA, USAIEEE/ACM Transactions on Computational Biology and Bioinformatics3420-426Computing the Distribution of a Tree Metric62009Sun Oct 18 05:00:02 CEST 2009BMC Evolutionary Biology111Species delimitation and phylogeny of a New Zealand plant species radiation92009Background Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the use of genome-wide molecular markers, such as amplified fragment length polymorphisms (AFLPs) and single nucleotide polymorphisms (SNPs), to identify distinct metapopulation lineages as taxonomic species. Here we investigate the properties of AFLP data, and the usefulness of tree-based and non-tree-based clustering methods to delimit species and reconstruct evolutionary relationships among high-elevation Ourisia species (Plantaginaceae) in the New Zealand archipelago. Results New Zealand Ourisia are shown to comprise a geologically recent species radiation based on molecular dating analyses of ITS sequences (0.4–1.3 MY). Supernetwork analyses indicate that separate tree-based clustering analyses of four independent AFLP primer combinations and 193 individuals of Ourisia produced similar trees. When combined and analysed using tree building methods, 15 distinct metapopulations could be identified. These clusters corresponded very closely to species and subspecies identified on the basis of diagnostic morphological characters. In contrast, Structure and PCO-MC analyses of the same data identified a maximum of 12 and 8 metapopulations, respectively. All approaches resolved a large-leaved group and a small-leaved group, as well as a lineage of three alpine species within the small-leaved group. We were unable to further resolve relationships within these groups as corrected and uncorrected distances derived from AFLP profiles had limited tree-like properties. Conclusion Ourisia radiated into a range of alpine and subalpine habitats in New Zealand during the Pleistocene, resulting in 13 morphologically and ecologically distinct species, including one reinstated from subspecies rank. Analyses of AFLP identified distinct metapopulations consistent with morphological characters allowing species boundaries to be delimited in Ourisia. Importantly, Structure analyses suggest some degree of admixture with most species, which may also explain why the AFLP data do not exhibit sufficient tree-like properties necessary for reconstructing some species relationships. We discuss this feature and highlight the importance of improving models for phylogenetic analyses of species radiations using AFLP and SNP data. Wed Mar 18 23:15:46 CET 2009Proceedings of the Royal Society B: Biological Sciences-Matrilocal residence is ancestral in Austronesian societies2009imported The nature of social life in human prehistory is elusive, yet knowing how kinship systems evolve is critical for understanding population history and cultural diversity. Post-marital residence rules specify sex-specific dispersal and kin association, influencing the pattern of genetic markers across populations. Cultural phylogenetics allows us to practise ‘virtual archaeology’ on these aspects of social life that leave no trace in the archaeological record. Here we show that early Austronesian societies practised matrilocal post-marital residence. Using a Markov-chain Monte Carlo comparative method implemented in a Bayesian phylogenetic framework, we estimated the type of residence at each ancestral node in a sample of Austronesian language trees spanning 135 Pacific societies. Matrilocal residence has been hypothesized for proto-Oceanic society ( 3500 BP), but we find strong evidence that matrilocality was predominant in earlier Austronesian societies 5000–4500 BP, at the root of the language family and its early branches. Our results illuminate the divergent patterns of mtDNA and Y-chromosome markers seen in the Pacific. The analysis of present-day cross-cultural data in this way allows us to directly address cultural evolutionary and life-history processes in prehistory. Wed Mar 18 23:14:24 CET 2009Proceedings of the Royal Society B: Biological Sciences-Does horizontal transmission invalidate cultural phylogenies?2009Phylogenetic methods have recently been applied to studies of cultural evolution. However, it has been claimed that the large amount of horizontal transmission that sometimes occurs between cultural groups invalidates the use of these methods. Here, we use a natural model of linguistic evolution to simulate borrowing between languages. The results show that tree topologies constructed with Bayesian phylogenetic methods are robust to realistic levels of borrowing. Inferences about divergence dates are slightly less robust and show a tendency to underestimate dates. Our results demonstrate that realistic levels of reticulation between cultures do not invalidate a phylogenetic approach to cultural and linguistic evolution. Mon Feb 02 00:53:35 CET 2009The Evolution of Cultural Diversity: Phylogenetic Approaches31-52Testing population dispersal hypotheses: Pacific settlement, phylogenetic trees and Austronesian languages2005me Mon Feb 02 00:53:35 CET 2009Evolutionary Bioinformatics271-283The Austronesian Basic Vocabulary Database: from bioinformatics to lexomics42008abvd, me Mon Feb 02 00:53:35 CET 2009Biological Theory360-375The Pleasures and Perils of Darwinizing Culture (with phylogenies)22007me rob russell Mon Feb 02 00:53:35 CET 2009Science588Languages evolve in punctuational bursts3192008evolution language mark me phylogenetics quentin Mon Feb 02 00:53:35 CET 2009Science446Parsing the Evolution of Language (Letter)3202008me Mon Feb 02 00:53:35 CET 2009Science5913479-483{Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement}3232009me Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory. Thu Jan 22 23:35:24 CET 2009Science5913479-483{Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement}3232009imported myown Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory. for:compevolCommunity for tag(s) for:compevol