2478454
Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata)
Lack of resolution in a phylogenetic tree is usually represented as a polytomy, and often adding more data (loci and taxa) resolves the species tree. These are the ‘soft’ polytomies, but in other cases additional data fail to resolve relationships; these are the ‘hard’ polytomies. This latter case is often interpreted as a simultaneous radiation of lineages in the history of a clade. Although hard polytomies are difficult to address, model-based approaches provide new tools to test these hypotheses. Here, we used a clade of 144 species of the South American lizard clade Eulaemus to estimate phylogenies using a traditional concatenated matrix and three species tree methods: *BEAST, BEST, and minimizing deep coalescences (MDC). The different species tree methods recovered largely discordant results, but all resolved the same polytomy (e.g. very short internodes amongst lineages and low nodal support in Bayesian methods). We simulated data sets under eight explicit evolutionary models (including hard polytomies), tested these against empirical data (a total of 14 loci), and found support for two polytomies as the most plausible hypothesis for diversification of this clade. We discuss the performance of these methods and their limitations under the challenging scenario of hard polytomies. © 2015 The Linnean Society of London
82449414
Estimating species trees : practical and theoretical aspects
Preface. Contributors. Chapter 1 Estimating Species Trees: An Introduction to Concepts and Models (L. Lacey Knowles and Laura S. Kubatko). 1.1 Introduction. 1.1.1 Different Tree Types and Their Relationship to Phylogeny. 1.2 The Relationship Between Gene Trees and Species Trees. 1.2.1 Evolutionary Mechanisms for Gene Tree Discord. 1.2.2 The Coalescent Process and Gene Tree Distributions. 1.2.3 Phylogenetic Extensions of the Coalescent Model. 1.3 The Relationship Between Sequence Data and Gene Trees. 1.3.1 Modeling DNA Sequence Evolution along a Gene Tree. 1.4 Statistical Inference of Species Trees. 1.4.1 ML. 1.4.2 Bayesian Analysis. 1.5 Collecting DNA Sequence Data. 1.6 Conclusions. References. Chapter 2 Bayesian Estimation of Species Trees: A Practical Guide to Optimal Sampling and Analysis (Santiago Castillo-Ramirez, Liang Liu, Dennis Pearl and Scott V. Edwards). 2.1 Introduction. 2.1.1 Empirical Examples Using BEST. 2.2 Factors Influencing Confidence in Estimated Species Trees Using BEST. 2.2.1 Simulation Protocol. 2.2.2 Results of Simulations on Number and Length of Loci. 2.2.3 Multifactorial Prediction of Confidence in Species Trees. 2.2.4 Effect of the Number of Alleles Sampled per Locus on Species Tree Estimation. 2.2.5 Effect of Recombination on Species Tree Inference. 2.3 Some Tips on Running the BEST MCMC Algorithm. 2.4 Conclusions and Challenges. Acknowledgments. References. Chapter 3 Reconstructing Concordance Trees and Testing the Coalescent Model from Genome-Wide Data Sets (Cecile Ane). 3.1 Introduction. 3.2 BCA: Background. 3.2.1 Sharing of Information across Gene Trees. 3.2.2 How to Choose the A Priori Level of Discordance alpha. 3.2.3 The Choice of an Infinite alpha in BCA. 3.2.4 A Nonparametric Prior Distribution on Gene Trees. 3.3 Genomic Support versus Statistical Support. 3.4 Comparing CFs of Contradicting Clades for Reconstructing the Dominant History. 3.5 Testing the Hypothesis That All Discordance is Due to ILS. 3.6 Species Tree Reconstruction from CFs. 3.7 The Challenge of Determining Loci on Whole-Genome Alignments. 3.7.1 The Assumption of Homogeneous, Unlinked Loci for GT/ST Reconstruction. 3.7.2 Detecting Recombination Breakpoints for GT/ST Reconstruction. 3.7.3 A Minimum Description Length (MDL) Information Criterion. 3.7.4 Comparisons with Other Partitioning Criteria. Acknowledgments. References. Chapter 4 Probabilities of Gene Tree Topoligies with Intraspecific Sampling Given a Species Tree (James H. Degnan). 4.1 Introduction. 4.2 Background and Terminology. 4.2.1 Incomplete Lineage Sorting. 4.2.2 Notation. 4.3 Gene Tree Topology Probabilities-Theory. 4.3.1 Enumerating Coalescent Histories. 4.3.2 The Probability of a Coalescent History. 4.3.3 Probability Mass Function for Gene Tree Topologies. 4.4 Gene Tree Topology Probabilities-Examples. 4.4.1 Enumeration of Coalescent Histories. 4.4.2 Calculation of Probabilities of Coalescent Histories. 4.5 Applications. 4.5.1 Probabilities of Multilabeled Trees. 4.5.2 Probability of Monophyletic Concordance. 4.5.3 AGTs. 4.6 Conclusions. References. Appendix: Using Coal. Using the Software. Setting Up Species Tree Branch Lengths. Chapter 5 Inference of Parsimonious Species Tree from Multilocus Data by Minimizing Deep Coalescences (Cuong Than and Luay Nakhleh). 5.1 Introduction. 5.2 Trees, Clusters, and the Compatibility Graph. 5.3 Valid Coalescent Histories, Extra Lineages, and the MDC Criterion. 5.4 Exact Algorithms for the MDC Problem. 5.4.1 An ILP Algorithm. 5.4.2 A DP Algorithm. 5.5 Handling Special Cases. 5.5.1 Multiple Individuals per Species. 5.5.2 Nonbinary Trees. 5.6 Performance of MDC. 5.7 Inference from The Clusters of The Gene Trees. 5.8 Using PhyloNet. 5.8.1 Using PhyloNet to Count Valid Coalescent Histories. 5.8.2 Using PhyloNet to Infer Species Trees Under MDC. 5.9 Conclusions. Acknowledgments. References. Chapter 6 Accommodating Hybridization in a Multilocus Phylogenetic Framework (Laura S. Kubatko and Chen Meng). 6.1 Introduction. 6.2 Methods for Detecting Hybridization in The Presence of Incomplete Lineage Sorting. 6.3 A Phylogenetic Model for Hybridization in The Presence of Incomplete Lineage Sorting. 6.3.1 Estimation and Testing for the Hybridization Parameters: Gene Tree Data. 6.3.2 Estimation and Testing for the Hybridization Parameters: Sequence Data. 6.3.3 Comparison of Hybrid Species Phylogenies Using Gene Tree Data. 6.4 Application: Hybridization in the Heliconius Butterflies. 6.4.1 Estimation and Testing for the Hybridization Parameters: Application to the Estimated Gene Trees in Heliconius. 6.4.2 Estimation and Testing for the Hybridization Parameters: Application to Sequence Data in Heliconius. 6.4.3 Comparison of Hybrid Species Phylogenies for the Heliconius Gene Tree Data. 6.5 Conclusions and Future Directions. Acknowledgment. References. Chapter 7 The Influence of Hybrid Zones on Species Tree Inference in Manakins (Robb T. Brumfi eld and Matthew D. Carling). 7.1 Introduction. 7.2 The Manacus Manakins. 7.2.1 Distribution. 7.2.2 Hybrid Zone between M. vitellinus and M. candei. 7.2.3 Two Contact Zones between M. vitellinus and M. manacus. 7.2.4 Inferring a Manacus Species Tree. 7.3 Is Introgression Across the Hybrid Zones Influencing the Species Tree Inference? 7.4 Conclusions. Acknowledgments. References. Chapter 8 Summarizing Gene Tree Incongruence at Multiple Phylogenetic Depths (Karen A. Cranston). 8.1 Introduction. 8.2 Sample Data: Rice, Flies, and Yeast. 8.3 Bayesian Inference of Gene Trees. 8.4 Detecting Convergence Across Hundreds of Genes. 8.5 A Note on Combining Trees. 8.6 BCA. 8.7 gsi. 8.8 Triplet Analysis. 8.9 Missing Data. 8.10 Genomic Distribution of Gene Tree Incongruence. 8.11 Visualization of Gene Tree Incongruence. 8.12 Concluding Remarks. Acknowledgments. References. Chapter 9 Species Tree Estimation for Complex Divergence Histories: A Case Study in Neodiprion Sawflies (Catherine R. Linnen). 9.1 Introduction. 9.2 Study System: Neodiprion Sawflies. 9.3 Sampling Strategy. 9.4 Determining the Source of Mitonuclear Discordance. 9.5 Approaches for Species Tree Estimation. 9.5.1 Concatenation with Monophyly Constraints (CMC). 9.5.2 Minimize Deep Coalescences (MDC). 9.5.3 Shallowest Divergences (SD). 9.5.4 Bayesian Estimation of Species Trees (BEST). 9.6 Comparison of Species Tree Estimates. 9.7 Comparison of Gene Trees to Species Trees. 9.8 Conclusions and Future Directions. References. Chapter 10 Sampling Strategies for Species Tree Estimation (L. Lacey Knowles). 10.1 Introduction. 10.2 Information Content in DNA Sequences for Species Tree Inference. 10.3 Why Phylogenetic History Dictates Appropriate Sampling Strategy. 10.4 Properties of the Data That Impact Sampling Decisions. 10.5 Making Informed Decisions about Sampling Strategies. 10.5.1 Where Does the Initial Species Tree Come from? 10.5.2 Is There Consistency in the Estimated Species Tree Given the Data? 10.6 Summary. Acknowledgments. References. Chapter 11 Developing Nuclear Sequences for Species Tree Estimation in Nonmodel Organisms: Insights from a Case Study of Bottae's Pocket Gopher, Thomomys Bottae (Natalia M. Belfiore). 11.1 Introduction. 11.2 Pocket Gophers. 11.3 Marker Generation Approach and Methodological Comments. 11.3.1 Library Construction. 11.3.2 Subtraction of High-Copy-Number Regions. 11.3.3 Locus Characterization by Genomic Approaches. 11.3.4 Primer Design Experiments. 11.3.5 Locus Evaluation for Inclusion in the Study. 11.3.6 Variation within the Library Construction Species. 11.3.7 Inclusion of Loci and Data Generation within the Genus. 11.4 Data Management and Analysis. 11.4.1 Handling Data and Choosing Analysis Programs. 11.4.2 Phylogenetic Analysis. 11.5 Conclusions. Acknowledgments. References. Chapter 12 Estimating Species Relationships and Taxon Distinctiveness in Sistrurus Rattlesnakes Using Multilocus Data (Laura S. Kubatko and H. Lisle Gibbs). 12.1 Introduction. 12.1.1 Sistrurus Rattlesnakes. 12.2 Analysis of Species and Subspecific Relationships. 12.2.1 Estimation of the Species Phylogeny. 12.2.2 Distinctiveness of Subspecies. 12.2.3 Phased versus Unphased Data. 12.3 Species Tree Estimation. 12.3.1 Estimation Using Gene Trees as Data. 12.3.2 Estimation Using Sequences as Data. 12.4 Distinctiveness Among Species and Subspecies. 12.4.1 Phased Data. 12.4.2 Unphased Data and the Effect of Sample Size. 12.5 Evolutionary and Conservation Implications. 12.6 Conclusions. Acknowledgments. References. Index.
19940411
Gene Trees in Species Trees
Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal transfer (including hybridization), lineage sorting, and gene duplication and ex- tinction. Lineage sorting could also be called deep coalescence, the failure of ancestral copies to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size). A similar dependence on process is found in historical biogeography and host-parasite relation- ships. Each of the processes of discord could yield a different parsimony criterion for reconstruct- ing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and/or extinction events. Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the prob- ability that a particular gene tree would occur given a species tree (with branch lengths and widths specified). In considering these issues, one is provoked to reconsider precisely what is phylogeny. Perhaps it is misleading to view some gene trees as agreeing and other gene trees as disagreeing with the species tree; rather, all of the gene trees are part of the species tree, which can be visualized like a fuzzy statistical distribution, a cloud of gene histories. Alternatively, phylogeny might be (and has been) viewed not as a history of what happened, genetically, but as a history of what could have happened, i.e., a history of changes in the probabilities of inter- breeding. (Biogeography; coalescence; coevolution; evolution; gene duplication; gene genealogy; gene trees; horizontal transfer; hybridization; lineage sorting; parsimony; phylogeny; species con- cepts; species trees; tree reconciliation.)
2236567
How should species phylogenies be inferred from sequence data?
levels as follows: (1) Separate gene trees are inferred from each linkage partition, and (2) the species phylogeny is then inferred from the set of gene trees. A method (Maddison, 1997; Page and Charleston, 1997a, 1997b; Slowinski et al., 1997) termed gene tree parsimony by Slowinski et al. (1997) is the appropriate method for implementing the second step. Gene tree parsimony operates by finding the species tree or trees that minimizes the number of hypothesized gene tree/ species tree conflict-producing events required to fit each gene tree to the species tree(s). Central to gene tree parsimony is the concept of fitting trees to other trees (Page, 1994a). Gene tree parsimony implements Doyle’s (1992) insightful concept that nucleotides are characters of gene trees, whereas gene trees are characters of species trees. An important caveat relates to the serious question raised by Maddison (1997) of just what a species phylogeny is meant to represent. The search for a species phylogeny assumes that such a diagram has some meaning. This is a difficult issue that we leave to other workers. Below, we briefly discuss the sources of conflict between gene and species trees, identify problems with previous methods for inferring species trees from molecular sequence data, define gene tree parsimony, and then illustrate the application of gene tree parsimony by using the computer program GeneTree (Page, 1998), which is free and available at http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html; it requires Mac OS 7.5 or later running on a PowerMac, or an Intel-based PC running Windows 95/NT 4.0 or later. The issues explored in this article bear directly on the controversial question of whether or not There are two levels of potential error in the inference of species phylogenies from molecular sequence data: (1) A gene tree (herein, we use the term gene for any contiguous block of nucleotides, regardless of whether it codes for a protein or not) for a set of molecular sequences will be incorrectly inferred if there is sufficient random or systematic error (Swofford et al., 1996), and (2) even if a gene tree is correctly inferred, the phenomena of deep coalescence, gene duplication, and horizontal gene transfer can produce a gene tree different from the true species tree (Goodman et al., 1979; Avise et al., 1983; Pamilo and Nei, 1988; Doyle, 1992; Maddison, 1996, 1997). The second level of error would be quite worrisome if all nucleotides of genomes were historically linked (as is generally true with organellar genomes). In this situation, there would only be one gene tree, which might not be the same as the true species tree. But happily, because of intraand interchromosomal recombination, the nuclear genome is composed of many historically linked sets of nucleotides with different histories. We call these linkage partitions (the cgenes of Doyle, 1992, 1997). Sequences sampled from several species and forming a single linkage partition are related by a unique, binary gene tree. Contrary to claims that natural data partitions do not exist (e.g., Kluge and Wolf, 1993; Siddall, 1997), linkage partitions are natural partitions of molecular sequence data and can be considered as independent estimators of the overlying species phylogeny. This strongly suggests that the molecular phylogenetic analysis of species by using 814 SYSTEMATIC BIOLOGY VOL. 48
1599605
BEAST: Bayesian evolutionary analysis by sampling trees
BackgroundThe evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented.ResultsBEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license.ConclusionBEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.
3087479
Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions.
The desire to infer the evolutionary history of a group of species should be more viable now that a considerable amount of multilocus molecular data is available. However, the current molecular phylogenetic paradigm still reconstructs gene trees to represent the species tree. Further, commonly used methods of combining data, such as the concatenation method, are known to be inconsistent in some circumstances. In this paper, we propose a Bayesian hierarchical model to estimate the phylogeny of a group of species using multiple estimated gene tree distributions, such as those that arise in a Bayesian analysis of DNA sequence data. Our model employs substitution models used in traditional phylogenetics but also uses coalescent theory to explain genealogical signals from species trees to gene trees and from gene trees to sequence data, thereby forming a complete stochastic model to estimate gene trees, species trees, ancestral population sizes, and species divergence times simultaneously. Our model is founded on the assumption that gene trees, even of unlinked loci, are correlated due to being derived from a single species tree and therefore should be estimated jointly. We apply the method to two multilocus data sets of DNA sequences. The estimates of the species tree topology and divergence times appear to be robust to the prior of the population size, whereas the estimates of effective population sizes are sensitive to the prior used in the analysis. These analyses also suggest that the model is superior to the concatenation method in fitting these data sets and thus provides a more realistic assessment of the variability in the distribution of the species tree that may have produced the molecular information at hand. Future improvements of our model and algorithm should include consideration of other factors that can cause discordance of gene trees and species trees, such as horizontal transfer or gene duplication.
10543839
Bayesian estimation of concordance among gene trees.
Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species.
13453831
Inferring phylogeny despite incomplete lineage sorting.
It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to phylogenetic inference designed to consider retention and sorting of ancestral polymorphism. We examine how the reconstructability of a species (or population) phylogeny is affected by (a) the number of loci used to estimate the phylogeny and (b) the number of individuals sampled per species. Even in difficult cases with considerable incomplete lineage sorting (times between divergences less than 1 N(e) generations), we found the reconstructed species trees matched the "true" species trees in at least three out of five partitions, as long as a reasonable number of individuals per species were sampled. We also studied the tradeoff between sampling more loci versus more individuals. Although increasing the number of loci gives more accurate trees for a given sampling effort with deeper species trees (e.g., total depth of 10 N(e) generations), sampling more individuals often gives better results than sampling more loci with shallower species trees (e.g., depth = 1 N(e)). Taken together, these results demonstrate that gene sequences retain enough signal to achieve an accurate estimate of phylogeny despite widespread incomplete lineage sorting. Continued improvement in our methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. [Coalescence; divergence; population; speciation.].
607101
Species Tree Inference by Minimizing Deep Coalescences
In a 1997 seminal paper, W. Maddison proposed minimizing deep coalescences, or MDC, as an optimization criterion for inferring the species tree from a set of incongruent gene trees, assuming the incongruence is exclusively due to lineage sorting. In a subsequent paper, Maddison and Knowles provided and implemented a search heuristic for optimizing the MDC criterion, given a set of gene trees. However, the heuristic is not guaranteed to compute optimal solutions, and its hill-climbing search makes it slow in practice. In this paper, we provide two exact solutions to the problem of inferring the species tree from a set of gene trees under the MDC criterion. In other words, our solutions are guaranteed to find the tree that minimizes the total number of deep coalescences from a set of gene trees. One solution is based on a novel integer linear programming (ILP) formulation, and another is based on a simple dynamic programming (DP) approach. Powerful ILP solvers, such as CPLEX, make the first solution appealing, particularly for very large-scale instances of the problem, whereas the DP-based solution eliminates dependence on proprietary tools, and its simplicity makes it easy to integrate with other genomic events that may cause gene tree incongruence. Using the exact solutions, we analyze a data set of 106 loci from eight yeast species, a data set of 268 loci from eight Apicomplexan species, and several simulated data sets. We show that the MDC criterion provides very accurate estimates of the species tree topologies, and that our solutions are very fast, thus allowing for the accurate analysis of genome-scale data sets. Further, the efficiency of the solutions allow for quick exploration of sub-optimal solutions, which is important for a parsimony-based criterion such as MDC, as we show. We show that searching for the species tree in the compatibility graph of the clusters induced by the gene trees may be sufficient in practice, a finding that helps ameliorate the computational requirements of optimization solutions. Further, we study the statistical consistency and convergence rate of the MDC criterion, as well as its optimality in inferring the species tree. Finally, we show how our solutions can be used to identify potential horizontal gene transfer events that may have caused some of the incongruence in the data, thus augmenting Maddison's original framework. We have implemented our solutions in the PhyloNet software package, which is freely available at: http://bioinfo.cs.rice.edu/phylonet.
269331
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
UNLABELLED
STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree.


AVAILABILITY
The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/.


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
18951975
The accuracy of species tree estimation under simulation: a comparison of methods.
Numerous simulation studies have investigated the accuracy of phylogenetic inference of gene trees under maximum parsimony, maximum likelihood, and Bayesian techniques. The relative accuracy of species tree inference methods under simulation has received less study. The number of analytical techniques available for inferring species trees is increasing rapidly, and in this paper, we compare the performance of several species tree inference techniques at estimating recent species divergences using computer simulation. Simulating gene trees within species trees of different shapes and with varying tree lengths (T) and population sizes (), and evolving sequences on those gene trees, allows us to determine how phylogenetic accuracy changes in relation to different levels of deep coalescence and phylogenetic signal. When the probability of discordance between the gene trees and the species tree is high (i.e., T is small and/or is large), Bayesian species tree inference using the multispecies coalescent (BEST) outperforms other methods. The performance of all methods improves as the total length of the species tree is increased, which reflects the combined benefits of decreasing the probability of discordance between species trees and gene trees and gaining more accurate estimates for gene trees. Decreasing the probability of deep coalescences by reducing also leads to accuracy gains for most methods. Increasing the number of loci from 10 to 100 improves accuracy under difficult demographic scenarios (i.e., coalescent units ≤ 4N(e)), but 10 loci are adequate for estimating the correct species tree in cases where deep coalescence is limited or absent. In general, the correlation between the phylogenetic accuracy and the posterior probability values obtained from BEST is high, although posterior probabilities are overestimated when the prior distribution for is misspecified.
3028790
Deciphering ancient rapid radiations.
A deeper phylogenetic understanding of ancient patterns of diversification would contribute to solving many problems in evolutionary biology, yet many of these phylogenies remain poorly resolved. Ancient rapid radiations pose a major challenge for phylogenetic analysis for two main reasons. First, the pattern to be deciphered, the order of divergence among lineages, tends to be supported by small amounts of data. Second, the time since divergence is large and, thus, the potential for misinterpreting phylogenetic information is great. Here, we review the underlying causes of difficulty in determining the branching patterns of diversification in ancient rapid radiations, and review novel data exploration tools that can facilitate understanding of these radiations.
10670233
Coalescent‐based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)
Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species’ phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath‐Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20 000 years ago), mid‐Pleistocene (800 000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath‐Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid‐Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid‐Pleistocene. Tests for expanding populations using mismatch distributions and ‘g’ distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.
13891478
Coupling Genetic and Ecological-Niche Models to Examine How Past Population Distributions Contribute to Divergence
Understanding the impact of climate-induced distributional shifts on species divergence, like those accompanying the Pleistocene glacial cycles [1, 2], requires tools that explicitly incorporate the geographic configuration of past distributions into analyses of genetic differentiation. Depending on the historical distribution of species, genetic differences may accumulate among ancestral source populations, but there is long-standing debate whether displacements into glacial refugia promoted divergence. Here we integrate coalescent-based genetic models [3, 4] with ecological-niche modeling [5, 6] to generate expectations for patterns of genetic variation based on an inferred past distribution of a species. Reconstruction of the distribution of a montane grasshopper species during the last glacial maximum suggests that Melanoplus marshalli populations from the sky islands of Colorado and Utah were likely colonized from multiple ancestral source populations. The genetic analyses provide compelling evidence that the historical distribution of M. marshalli-namely, spatial separation of multiple refugia-was conducive to genetic differentiation. The coupling of genetic and ecological-niche modeling provides a new and flexible tool for integrating paleoenvironmental details into species-specific predictions of population structure that can increase our understanding of why the glacial cycles promoted speciation in some taxa and yet inhibited diversification in others [7, 8].
16800986
Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses
Statistical phylogeographic studies contribute to our understanding of the factors that influence population divergence and speciation, and that ultimately generate biogeographical patterns. The use of coalescent modelling for analyses of genetic data provides a framework for statistically testing alternative hypotheses about the timing and pattern of divergence. However, the extent to which such approaches contribute to our understanding of biogeography depends on how well the alternative hypotheses chosen capture relevant aspects of species histories. New modelling techniques, which explicitly incorporate spatio-geographic data external to the gene trees themselves, provide a means for generating realistic phylogeographic hypotheses, even for taxa without a detailed fossil record. Here we illustrate how two such techniques – species distribution modelling and its historical extension, palaeodistribution modelling – in conjunction with coalescent simulations can be used to generate and test alternative hypotheses. In doing so, we highlight a few key studies that have creatively integrated both historical geographic and genetic data and argue for the wider incorporation of such explicit integrations in biogeographical studies.
24155758
WHEN GAPS REALLY ARE GAPS: STATISTICAL PHYLOGEOGRAPHY OF HYDROTHERMAL VENT INVERTEBRATES
The invertebrate animals endemic to deep‐sea hydrothermal vents are distributed intermittently along relatively linear oceanic ridge axes. A one‐dimensional stepping‐stone model, therefore, provides a reasonable starting hypothesis of population structure for these species. Nevertheless, population genetic studies of many species from eastern Pacific vents did not detect the expected signatures of isolation‐by‐distance (IBD). Instead, distinct patterns of geographical subdivision have been attributed to the unique dispersal modes of individual species, topographical discontinuities of the ridge axes, nonequilibrium metapopulation scenarios and cryptic species. Here, we reexamined these inferences in light of expectations generated by computer simulations of a one‐dimensional stepping‐stone model. We evaluated whether the previously inferred subdivisions are statistically robust to an alternative explanation that continuous stepping‐stone migration has occurred along the ridge axes but discontinuities in the sampling design (gaps) have generated the apparent disjunctions. We found that previous inferences about barriers to gene flow (vicariance) were supported in many cases, but that failures to detect evidence for IBD could be explained by low statistical power associated with the sampling effort. The simulation approaches presented here might be useful for testing the significance of inferred phylogeographic gaps in other species.
1425122
Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes.
We present an expanded data set of 50 unlinked autosomal noncoding regions, resequenced in samples of Hausa from Cameroon, Italians, and Chinese. We use these data to make inferences about human demographic history by using a technique that combines multiple aspects of genetic data, including levels of polymorphism, the allele frequency spectrum, and linkage disequilibrium. We explore an extensive range of demographic parameters and demonstrate that our method of combining multiple aspects of the data results in a significant reduction of the compatible parameter space. In agreement with previous reports, we find that the Hausa data are compatible with demographic equilibrium as well as a set of recent population expansion models. In contrast to the Hausa, when multiple aspects of the data are considered jointly, the non-Africans depart from an equilibrium model of constant population size and are compatible with a range of simple bottleneck models, including a 50-90% reduction in effective population size occurring some time after the appearance of modern humans in Africa 160,000-120,000 years ago.
503065
Statistical evaluation of alternative models of human evolution
An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species ≈141 thousand years ago (Kya), an exit out-of-Africa ≈51 Kya, and a recent colonization of the Americas ≈10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.
56156011
Infering population history with DIY ABC: a user-friendly approach to Approximate Bayesian Computation
Department of Epidemiology and Public Health, Imperial College, St Mary’s Campus Norfolk Place, London W2 1PG, U.K. Centre de Biologie et de Gestion des Populations,INRA, Campus International de Baillarguet, CS 30016 Montferriersur-Lez, 34988 Saint-Gély-du-Fesc Cedex, France School of Biological Sciences, Lyle Building, The University of Reading Whiteknights, Reading RG6 6AS, UK CEREMADE, Université Paris-Dauphine, Place Delattre de Tassigny, 75775 Paris cedex 16, France INRIA Saclay, Projet select, Université Paris-Sud, Laboratoire de Mathématiques (Bât. 425), 91400 Orsay, France f UMR 1301 I.B.S.V. INRA-UNSA-CNRS. 400 Route des Chappes. BP 167 06903 Sophia Antipolis cedex. France
16789449
Molecular evidence of a peripatric origin for two sympatric species of field crickets (Gryllus rubens and G. texensis) revealed from coalescent simulations and population genetic tests
Species pairs that differ primarily in characters involved in mating interactions and are largely sympatric raise intriguing questions about the mode of speciation. When species divergence is relatively recent, the footprint of the demographic history during speciation might be preserved and used to reconstruct the biogeography of species divergence. In this study, patterns of genetic variation were examined throughout the geographical range of two cryptic sister taxa of field crickets, Gryllus texensis and G. rubens; mitochondrial cytochrome oxidase I (COI) was sequenced in 365 individuals sampled from 48 localities. Despite significant molecular divergence between the species, they were not reciprocally monophyletic. We devised several analyses to statistically explore what historical processes might have given rise to this genealogical structure. The analyses indicated that the biogeographical pattern of genetic variation does not support a model of recent gene flow between species. Instead, coalescent simulations suggested that the genealogical structure within G. texensis, namely a deep split between two geographically overlapping clades, reflects historical substructure within G. texensis. Additional tests that consider the concentration of G. rubens haplotypes in one of the two G. texensis genetic clusters suggest a model of speciation in which G. rubens was derived from one lineage of a geographically subdivided ancestor. These results indicate that, despite the contemporary sympatry of G. texensis and G. rubens, the data are indicative of an peripatric origin in which G. rubens was derived from one of the two historical partitions in the species currently recognized as G. texensis. This proposed model of species divergence suggests how the interplay of geography and selection may give rise to new species, although this requires testing with multilocus data. Specifically, the model highlights how that geographical partitioning of ancestral variation in the past may augment the selectively driven divergence of characters involved in the reproductive isolation of the species today.
6487847
Stability Predicts Genetic Diversity in the Brazilian Atlantic Forest Hotspot
Biodiversity hotspots, representing regions with high species endemism and conservation threat, have been mapped globally. Yet, biodiversity distribution data from within hotspots are too sparse for effective conservation in the face of rapid environmental change. Using frogs as indicators, ecological niche models under paleoclimates, and simultaneous Bayesian analyses of multispecies molecular data, we compare alternative hypotheses of assemblage-scale response to late Quaternary climate change. This reveals a hotspot within the Brazilian Atlantic forest hotspot. We show that the southern Atlantic forest was climatically unstable relative to the central region, which served as a large climatic refugium for neotropical species in the late Pleistocene. This sets new priorities for conservation in Brazil and establishes a validated approach to biodiversity prediction in other understudied, species-rich regions.
205834605
Phylogeography's past, present, and future: 10 years after Avise, 2000.
Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of "likelihood-free" approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology.
9897442
Arctic‐Alpine Distributions—Metapopulations on a Continental Scale?
Cold‐adapted species in the Northern Hemisphere frequently show arctic‐alpine discontinuous ranges at high latitudes and on mountains farther south, but area connectivity through current and historical gene flow remains unclear. We used the coalescent‐based program IMa (Isolation with Migration—analytic) to test for migration among disjunct European areas of arctic‐alpine wolf spiders of the Pardosa saltuaria group. Mitochondrial (ND1) and nuclear (ITS1, 5.8S rDNA, ITS2) markers were analyzed simultaneously. Gene flow was unidirectional from Scandinavia to the Alps and the Carpathians, complex with respect to intermediate relict areas in central Europe, and very limited in outlying areas in the Balkans and Pyrenees. Population connectivity may have been greater during glacial events that might alternatively account for the inferred arctic‐alpine links. A simulation study under various demographic histories (using a new module in the Mesquite package, which models episodic migration) showed that the empirical results are equally consistent with moderate levels of ongoing (continuous) migration or, alternatively, with strong migration bursts at the last glacial maximum but not at earlier times. Habitat connectivity was probably maximal during glacial events, illustrating the potential influence of ecology and life history on organismal responses to past climatic change.
86232076
Phylogenetic relationships in the iguanid lizard genus Liolaemus: multiple origins of viviparous reproduction and evidence for recurring Andean vicariance and dispersal
Phylogenetic relationships within the iguanid lizard genus Liolaemus are investigated using 1710 aligned base positions (785 phylogenetically informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COL Sixty new sequences ranging in length from 1736 to 1754 bases are compared with four previously reported sequences. Liolaemus species form two well-supported monophyletic groups of subgeneric status, Liolaemus and Eulaemus. These subgenera appear to have separated at least 12.6 million years ago based on the amount of molecular evolutionary divergence between them. Hypotheses that species occurring in the Andes, west of the Andes, and east of the Andes, each comprise distinct monophyletic groups are independently rejected statistically. The shortest estimate of phylogeny suggests mat Liolaemus originated either in the Andes or the eastern lowlands. Numerous evolutionary shifts have occurred between the Andes, and the eastern and western lowlands, suggesting recurring vicariance and dispersal. Species occurring at high elevations or high latitudes usually have viviparous reproduction. Depending on whether parity mode is considered reversible in Liolaemus, the most parsimonious reconstruction supports at least six independent origins of viviparity or at least three gains followed by three losses of viviparity among die 60 Liolaemus lineages examined.
198152256
PHYLOGENY AND PHYLOGEOGRAPHY OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE): EVIDENCE FOR INTROGRESSION AND INCOMPLETE LINEAGE SORTING
Abstract Although mitochondrial DNA markers have several properties that make them suitable for phylogeographic studies, they are not free of difficulties. Phylogeographic inferences within and between closely related species can be mislead by introgression and retention of ancestral polymorphism. Here we combine different phylogenetic, phylogeographic, and population genetic methods to extract the maximum information from the Liolaemus darwinii complex. We estimate the phylogeographic structure of L. darwinii across most of its distributional range, and we then estimate relationships between L. darwinii and the syntopic species L. laurenti and L. grosseorum. Our results suggest that range expansion of these lineages brought them into secondary contact in areas where they are presently in syntopy. Here we present the first evidence for introgression in lizards from temperate South America (of L. darwinii mitochondrial DNA into L. laurenti and L. grosseorum), and for incomplete lineage sorting (between L. darwinii and L. laurenti). We show that a combination of methods can provide additional support for inferences derived from any single method and thus provide more robust interpretations and narrow the range of plausible hypotheses about mechanisms and processes of divergence. Additional studies are needed in this group of lizards and in other codistributed groups to determine if Pleistocene climatic changes could be a general factor influencing the evolutionary history of a regional biota.
42493173
Congeneric phylogeography: hypothesizing species limits and evolutionary processes in Patagonian lizards of the Liolaemus boulengeri group (Squamata: Liolaemini)
In poorly known groups for which data are insufficient to develop biologically plausible model-based approaches to phylogeographical analyses, a ‘first hypotheses’ protocol is suggested as offering the best way to generate hypotheses for subsequent model-based tests. Preliminary hypotheses are formulated about species boundaries and population processes in three species complexes of the Liolaemus boulengeri group in the context of mtDNA ‘congeneric phylogeography’. The temperate South American Liolaemus provides a model with ancient and recent allopatric divergence across ecologically and geologically complex landscapes, incipient speciation, secondary contact, and discordance between molecular and morphological patterns of variation. Moderately dense sampling of widely distributed ‘inertial’ species in the Patagonian Steppe has revealed hidden genetic and probably species diversity, and also hinted at demographic and historical processes that may have shaped the histories of these taxa. Five of the seven focal species of the present study were paraphyletic for mtDNA genealogies, suggesting that they represent complexes of species, and nested clade phylogeographical analysis (NCPA) analyses suggest that different historical and demographic processes have shaped the observed patterns. Introgression and incomplete lineage sorting are hypothesized as being the cause of some of the observed paraphyly. Provisional delimitations of species are proposed and NCPA is used to generate hypotheses of population history, all of which are subject to further testing. Multi-faceted studies, involving phylogenetic assessments of independent molecular markers and morphological variation across codistributed taxa with estimates of niche breadths in a landscape context, will likely yield the most promising returns for cross-validation of hypotheses of population and speciation histories. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89, 241–275.
41094879
Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
The temperate South American lizard genus Liolaemus is the one of the most widely distributed and species-rich genera of lizards on earth. The genus is divided into two subgenera, Liolaemus sensu stricto (the ‘Chilean group’) and Eulaemus (the ‘Argentino group’), a division that is supported by recent molecular and morphological data. Owing to a lack of reliable fossil data, previous studies have been forced to use either global molecular clocks, a standardized mutation rate adopted from previous studies, or the use of geological events as calibration points. However, simulations indicate that these types of assumptions may result in less accurate estimates of divergence times when clock-like models or mutation rates are violated. We used a multilocus data set combined with a newly described fossil to provide the first calibrated phylogeny for the crown groups of the clade Eulaemus, and derive new fossil-calibrated substitution rates (with error) of both nuclear and mtDNA gene regions for Eulaemus specifically. Divergence date estimates for each of the crown groups and appropriate rate estimates will provide the foundation for understanding rates of speciation, historical biogeography, and phylogeographical history for various clades in one of the most diverse lizard genera in the poorly studied Patagonian region. 
 
 
 
© 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164, 825–835.
88227784
A critical review and systematic discussion of recent classification proposals for liolaemid lizards
We provide a critical review of a recent taxonomic revision of Chilean Liolaemus lizards (Iguania: Liolaemidae) by Pincheira-Donoso and Nunez (2005) and a recent paper (PincheiraDonoso et al. 2008), which proposed several new taxonomic and phylogenetic arrangements. We document fundamental problems with many of the proposed taxonomic revisions in both publications, which if followed, could lead to serious taxonomic confusion. In Pincheira-Donoso and Nunez (2005) a subgeneric classification is erected, which was produced by outdated methods (phenetic analyses), cannot be replicated (no matrix is presented), and is taxonomically untenable (some of the subgenera are nested within other subgenera). Most of the taxonomic groups that are proposed have been previously proposed, albeit differently constituted, yet often previous research is not given attribution; when findings are different, the research of others is either overlooked or dismissed without comment. The diagnoses of species and subspecies (including several newly proposed taxa) are often written in an authoritative manner (without supporting data or information), making them insufficient for distinguishing the focal taxon from others belonging to the same group, finally leading to uncertainty regarding the validity of several of the newly proposed taxa, combinations, or synonymies. We also describe less egregious errors of omission and commission. In Pincheira-Donoso et al. (2008), most of the proposals follow the Pincheira-Donoso and Nunez (2005) revisions, some species are allocated to groups without consistent cladistic support and other proposed relationships are based on incomplete evidence from other studies dismissing the limitations of the arrangement. Critical species are not identified in a list of material examined. Finally, Pincheira-Donoso et al. (2008) present a somewhat outdated and biased discussion of the relative value of using molecules or morphology in systematics. In light of these limitations, and in an effort to stabilize and prevent further taxonomic confusion, we provide an updated phylogenetic classification of the currently recognized lizards of the family Liolaemidae (Ctenoblepharys, Liolaemus, and Phymaturus), which is based on a consensus of studies published since the first phylogenetic major revision of the clade in 1995.
9793511
Lizards from the end of the world: phylogenetic relationships of the Liolaemus lineomaculatus section (Squamata: Iguania: Liolaemini).
The Liolaemus lineomaculatus section is a geographically widely distributed group of lizards from the Patagonian region of southern South America, and includes 18 described species representing the most southerly distributed Liolaemus taxa (the genus includes 228 species and extends from Tierra del Fuego north to south-central Peru). Despite high species diversity, the phylogenetic relationships of this section are unknown. In the present work we sampled all described species in the L. lineomaculatus section as well as currently undescribed candidate species to reconstruct the first complete phylogenetic hypothesis for the clade. Our data set included four anonymous nuclear loci, three nuclear protein-coding loci, and two mitochondrial genes. We compared results obtained with three different phylogenetic methods for the concatenated data set (Maximum Parsimony, Maximum Likelihood and Bayesian Inference) with a coalescent-based species tree approach (BEST), and recovered congruent, strongly-supported topological arrangements across all methods. We identified four main clades within the L. lineomaculatus section: the lineomaculatus, magellanicus, somuncurae, and kingii+archeforus groups, for which we estimated divergence times. We discuss the taxonomic implications of these results and how the future integration of phylogeographic, niche modeling and morphological approaches will allow testing biogeographical hypotheses in this clade.
9383096
How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia and their concordance with other codistributed taxa
Patagonia was shaped by a complex geological history, including the Miocene uplift of the Andes, followed by volcanism, marine introgressions, and extreme climatic oscillations during Pliocene–Pleistocene glaciation–deglaciation cycles. The distributional patterns and phylogenetic relationships of southern patagonian animals and plants were affected in different ways, and those imprints are reflected in the seven phylogeographic breaks and eight refugia that have been previously proposed. In this study, we estimated time‐calibrated phylogenetic/phylogeographic patterns in lizards of the Liolaemus lineomaculatus group and relate them to historical Miocene‐to‐Pleistocene events of Patagonia and the previously proposed phylogeographic patterns. Individuals from 51 localities were sequenced for the mitochondrial marker (cyt‐b) and a subsample of individuals from each mitochondrial lineage was sequenced for one nuclear (LDA12D) and one slow evolving mitochondrial gene (12S). Our analyses revealed strong phylogeographic structure among lineages and, in most cases, no signal of demographic changes through time. The lineomaculatus group is composed of three strongly supported clades (lineomaculatus, hatcheri and kolengh + silvanae), and divergence estimates suggested their origins associated with the oldest known Patagonian glaciation (7–5 Ma); subsequent diversification within the lineomaculatus clade coincided with the large Pliocene glaciations (~3.5 Ma). The lineomaculatus clade includes nine strongly genetically and geographically structured lineages, five of which are interpreted as candidate species. Our findings suggest that some Liolaemus lineages have persisted in situ, each of them in a different refugium, through several glaciation–deglaciation cycles without demographic fluctuations. We also summarize and update qualitative evidence of some shared phylogeographic breaks and refugia among plants, rodents and lizards.
82406808
Past and present taxonomy of the Liolaemus lineomaculatus section (Liolaemidae): is the morphological arrangement hypothesis valid?
Twenty-one species of lizards are included in the southernmost clade of South America, the Liolaemus lineomaculatus section. There are two hypotheses of species-grouping within this section, one based on morphological similarities and the other based on molecular phylogenetic relationships; although discordant, both are in use. The ‘morphological arrangement hypothesis’, which sorts the species of the section in three groups, was proposed ∼30 years ago; however, despite taxonomic changes and almost doubling the species diversity of this section since then, the hypothesis has never been tested. Here, we (1) present an updated chronological review of taxonomic changes, species descriptions, morphological groups, and genetic clades proposed for the L. lineomaculatus section, and (2) evaluate the accuracy of the ‘morphological arrangement hypothesis’. We show that the traditional practice of classifying 11 of these species in two of the three traditional morphological groups of the section (Liolaemus kingii and Liolaemus archeforus), which is not supported by molecular data, is also not supported by morphological data, and therefore should be abandoned; we suggest referring to this group of species as the L. kingii group. We characterized the Liolaemus magellanicus group based on morphology, and extend the previously published morphological characteristics of the L. lineomaculatus group. Finally, we comment on future prospects for studies of sexual dimorphism and its possible ecological implications. This paper provides a critical synthesis of our understanding of the morphological and phylogenetic patterns within the L. lineomaculatus section and presents a useful framework for future tests of taxonomic hypotheses and physiological, behavioural, and evolutionary questions within this section.  © 2013 The Linnean Society of London
32432720
Multilocus phylogeny of the widely distributed South American lizard clade Eulaemus (Liolaemini, Liolaemus)
The lizard genus Liolaemus and different clades within it have been the focus of several recent phylogenetic studies mainly based on morphology and mtDNA. Although there is general consensus for recognizing two clades (subgenera) within the genus, [Liolaemus (sensu stricto) and Eulaemus], phylogenetic relationships within each subgenus remain difficult to elucidate, given incomplete taxonomic sampling and large discordance between published studies. Here, new phylogenetic relationships for the Eulaemus subgenus are proposed based on the largest molecular data set ever used for this clade, which includes 188 individuals and 14 loci representing different parts of the genome (mtDNA, anonymous nuclear loci and nuclear protein‐coding loci). This data set was analysed using two species tree approaches (*beast and MDC). Levels of discordance among methods were found, and with previously published studies, but results are robust enough to propose new phylogenetic hypotheses for the Eulaemus clade. Specifically well‐resolved and well‐supported novel hypotheses are provided within the lineomaculatus section, and we formally recognize the zullyae clade, the sarmientoi clade and the hatcheri group. We also resolve species relationships within the montanus section, and particularly within the melanops series. We found discordance between mitochondrial and nuclear trees and discussed alternative hypotheses for the lineomaculatus and montanus sections, as well as the challenge in resolving phylogenetic relationships for large clades in general.
12659871
Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment.
We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three fully resolved tree topologies that can be computed for four sequences. The three likelihoods are represented as one point inside an equilateral triangle. The triangle is partitioned in different regions. One region represents star-like evolution, three regions represent a well-resolved phylogeny, and three regions reflect the situation where it is difficult to distinguish between two of the three trees. The location of the likelihoods in the triangle defines the mode of sequence evolution. If n sequences are analyzed, then the likelihoods for each subset of four sequences are mapped onto the triangle. The resulting distribution of points shows whether the data are suitable for a phylogenetic reconstruction or not.
7969169
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
SUMMARY
TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers.


AVAILABILITY
http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).
8492361
Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae).
Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consists of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South American lizards of the Liolaemus darwinii species group and reconstructed a species tree with *BEAST, then compared the performance of this method under different sampling strategies of loci, individuals, and sequence lengths. We found an increase in the accuracy and precision of species trees with the number of loci, but for any number of loci, accuracy substantially decreased only when using only one individual per species or 25% of the full sequence length (∼ 147 bp). In addition, locus "informativeness" was an important factor in the accuracy/precision of species trees when using a few loci, but it became increasingly irrelevant with additional loci. Our empirical results combined with the previous simulation studies suggest that there is an optimal range of sampling effort of loci, individuals, and sequence lengths for a given speciation history and information content of the data. Future studies should be directed toward further assessment of other factors that can impact performance of species trees, including gene flow, locus "informativeness," tree shape, missing data, and errors in species delimitation.
85429017
Calibrating molecular estimates of substitution rates and divergence times in birds
Many evolutionary studies of birds rely on the estimation of molecular divergence times and substitution rates. In order to perform such analyses, it is necessary to incorporate some form of calibration information: a known substitution rate, radiometric ages of heterochronous sequences, or inferred ages of lineage splitting events. All three of these techniques have been employed in avian molecular studies, but their usage has not been entirely satisfactory. For example, the ‘traditional’ avian mitochondrial substitution rate of 2% per million years is frequently adopted without acknowledgement of the associated uncertainty. Similarly, fossil and biogeographic information is almost always converted into an errorless calibration point. In both cases, the resulting estimates of divergence times and substitution rates will be artificially precise, which has a considerable impact on hypothesis testing. In addition, using such a simplistic approach to calibration discards much of the information offered by the fossil record. A number of more sophisticated calibration methods have recently been introduced, culminating in the development of probability distribution-based calibrations. In this article, I discuss the use of this new class of methods and offer guidelines for choosing a calibration technique.
2162532
Recurrent evolution of herbivory in small, cold-climate lizards: breaking the ecophysiological rules of reptilian herbivory.
Herbivory has evolved in many groups of vertebrates, but it is rare among both extinct and extant nonavian reptiles. Among squamate reptiles, (lizards, snakes, and their relatives), <2% of the >7,800 species are considered to be herbivorous, and herbivory is restricted to lizards. Here, we show that within a group of South American lizards (Liolaemidae, approximately 170 species), herbivory has evolved more frequently than in all other squamates combined and at a rate estimated to be >65 times faster. Furthermore, in contrast to other herbivorous lizards and to existing theory, most herbivorous liolaemids are small bodied and live in cool climates. Herbivory is generally thought to evolve only in reptile species that are large bodied, live in warm climates, and maintain high body temperatures. These three well known "rules" of herbivory are considered to form the bases of physiological constraints that explain the paucity of herbivorous reptile species. We suggest that the recurrent and paradoxical evolution of herbivory in liolaemids is explained by a combination of environmental conditions (promoting independent origins of herbivory in isolated cool-climate regions), ecophysiological constraints (requiring small body size in cool climates, yet high body temperatures for herbivores), and phylogenetic history. More generally, our study demonstrates how integrating information from ecophysiology and phylogeny can help to explain macroevolutionary trends.
15450879
DNA EVIDENCE FOR NONHYBRID ORIGINS OF PARTHENOGENESIS IN NATURAL POPULATIONS OF VERTEBRATES
Naturally occurring unisexual reproduction has been documented in less than 0.1% of all vertebrate species. Among vertebrates, true parthenogenesis is known only in squamate reptiles. In all vertebrate cases that have been carefully studied, the clonal or hemiclonal taxa have originated through hybridization between closely related sexual species. In contrast, parthenogenetic reproduction has arisen in invertebrates by a variety of mechanisms, including likely cases of “spontaneous” (nonhybrid) origin, a situation not currently documented in natural populations of vertebrates. Here, we present molecular data from the Neotropical night lizard genus Lepidophyma that provides evidence of independent nonhybrid origins for diploid unisexual populations of two species from Costa Rica and Panama. Our mitochondrial and nuclear phylogenies are congruent with respect to the unisexual taxa. Based on 14 microsatellite loci, heterozygosity (expected from a hybrid origin) is low in Lepidophyma reticulatum and completely absent in unisexual L. flavimaculatum. The unique value of this system will allow direct comparative studies between parthenogenetic and sexual lineages in vertebrates, with an enormous potential for this species to be a model system for understanding the mechanisms of nonhybrid parthenogenesis.
30112290
DEEP DIVERSIFICATION AND LONG‐TERM PERSISTENCE IN THE SOUTH AMERICAN ‘DRY DIAGONAL’: INTEGRATING CONTINENT‐WIDE PHYLOGEOGRAPHY AND DISTRIBUTION MODELING OF GECKOS
The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range‐wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American ‘dry diagonal’ biomes. Our approach couples traditional and model‐based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex. Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the ‘dry diagonal’ biomes. We recover extremely high genetic diversity and suggest that eight well‐supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low‐vagility species complexes, characterized by strong genetic structure and pre‐Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.
1021017
Bayesian Inference of Species Trees from Multilocus Data
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.
16379422
Phylogenomics and the reconstruction of the tree of life
As more complete genomes are sequenced, phylogenetic analysis is entering a new era — that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.
16084838
Bushes in the Tree of Life
A discussion of how homoplasy (the frequency of independently evolved characters) and the spacing of cladogenetic events limit our ability to reconstruct the tree of life using existing phylogenetic methods.
2365991
Trends, Rhythms, and Aberrations in Global Climate 65 Ma to Present
Since 65 million years ago (Ma), Earth's climate has undergone a significant and complex evolution, the finer details of which are now coming to light through investigations of deep-sea sediment cores. This evolution includes gradual trends of warming and cooling driven by tectonic processes on time scales of 105to 107 years, rhythmic or periodic cycles driven by orbital processes with 104- to 106-year cyclicity, and rare rapid aberrant shifts and extreme climate transients with durations of 103 to 105 years. Here, recent progress in defining the evolution of global climate over the Cenozoic Era is reviewed. We focus primarily on the periodic and anomalous components of variability over the early portion of this era, as constrained by the latest generation of deep-sea isotope records. We also consider how this improved perspective has led to the recognition of previously unforeseen mechanisms for altering climate.
22771974
Evolution of Thermal Physiology in Liolaemus Lizards: Adaptation, Phylogenetic Inertia, and Niche Tracking
Microevolutionary studies often find that complex quantitative characters are highly evolvable and adapted to the local environment, while macroevolutionary studies often show evidence of strong phylogenetic effects and stasis. In this contribution, we show how phylogenetic comparative methods can be used to test hypotheses that may help resolve this paradox. As a test case, we studied the interplay between adaptation and phylogenetic inertia on the thermobiology of 32 species of Liolaemus (Squamata: Liolaemidae), a genus of South American lizards living under diverse climatic conditions. Despite a strong phylogenetic effect in the preferred (selected) body temperature, we found clear evidence that this variable is adapted to local temperature and climate. After controlling for adaptation to the thermal environment, little influence of phylogeny was left. This indicates that the phylogenetic effect was not caused by a lag or slowness in adaptation but primarily by the distribution of the thermal environments on the phylogeny. This can be due to thermal niche tracking. In contrast, we found little or no evidence for adaptation to the thermal environment in either cooling or heating rates, critical thermal minimum, or body size.
9578762
Erosion of Lizard Diversity by Climate Change and Altered Thermal Niches
Demise of the Lizards Despite pessimistic forecasts from recent studies examining the effects of global climate change on species, and observed extinctions in local geographic areas, there is little evidence so far of global-scale extinctions. Sinervo et al. (p. 894; see the Perspective by Huey et al.) find that extinctions resulting from climate change are currently reducing global lizard diversity. Climate records during the past century were synthesized with detailed surveys of Mexican species at 200 sites over the past 30 years. Temperature change has been so rapid in this region that rates of adaptation have not kept pace with climate change. The models were then extended to all families of lizards at >1000 sites across the globe, and suggest that climate change-induced extinctions are currently affecting worldwide lizard assemblages. A historical record of lizard populations in Mexico is used to parameterize models that predict global effects of climate change. It is predicted that climate change will cause species extinctions and distributional shifts in coming decades, but data to validate these predictions are relatively scarce. Here, we compare recent and historical surveys for 48 Mexican lizard species at 200 sites. Since 1975, 12% of local populations have gone extinct. We verified physiological models of extinction risk with observed local extinctions and extended projections worldwide. Since 1975, we estimate that 4% of local populations have gone extinct worldwide, but by 2080 local extinctions are projected to reach 39% worldwide, and species extinctions may reach 20%. Global extinction projections were validated with local extinctions observed from 1975 to 2009 for regional biotas on four other continents, suggesting that lizards have already crossed a threshold for extinctions caused by climate change.
42957595
Chronology of the Late Cenozoic Patagonian glaciations and their correlation with biostratigraphic units of the Pampean region (Argentina)
The absolute chronology of the Patagonian glaciations is one of the most complete in the world and probably the best available for the Southern Hemisphere outside Antarctica. The oldest known Patagonian glaciations took place between approximately 7 and 5 Ma (Latest Miocene–Earliest Pliocene). A minimum of eight glaciations occurred in the Middle–Late Pliocene (Oxygen Isotopic Stages 54–82). The Great Patagonian Glaciations (GPG) developed between 1.168 and 1.016 Ma (OIS 30–34; Early Pleistocene). After the GPG, 14–16 cold (glacial/stadial) geoclimatic events intercalated with their corresponding warm (interglacial/interstadial) equivalents. Thirteen post-GPG moraines have been identified, some of the Early–Middle Pleistocene and others of the Last Glaciation (LG). The LG reached its maximum around 25,000 and ended nearly 16,000 calendar years ago (OIS 2; Late Pleistocene). Finally, two readvances (or stationary phases) took place during the Late Glacial (15,000–10,000 14 C years BP). During these glacial events, climatic and environmental changes had a great influence on the landscape and Patagonian/Pampean ecosystem development during the last 5 Myr. Loess/paleosol sequences probably developed in the Pampas along this period, as in northern China, though much more poorly preserved. The model of replacement of the terrestrial Pampean faunas since the LGM proposes the exchange of Patagonian for Brazilian species in the Holocene with megafauna extinction. If this model fits previous cycles as well, regional faunistic interchange would have taken place at least 14 times since the GPG and perhaps more than 50 times since the Early Pliocene. These mechanisms should be taken into consideration in the study of paleobiogeographical distribution, ecosystem displacements, and extinction processes since 5 Ma. The environmental impact of climatic changes also should be considered when analyzing the early peopling of Patagonia during Late Glacial times. q 2005 Elsevier Ltd. All rights reserved.
24660156
Neogene paleoenvironmental and paleoclimatic change in southern temperate ecosystems - a southern perspective.
Recently, a greatly increased number of macrofossil and pollen analytical records from Australasia and southern South America has permitted, for the first time, a comprehensive overview of past vegetation and climate change in southern temperate ecosystems. While the course of Neogene climatic change has been comparable to that of the temperate northern hemisphere, a distinctive southern hemisphere vegetation has evolved, not primarily because of its common Gondwana origin, but as a consequence of the minor amplitude of Quaternary change, absence of large ice sheets, and failure of full-glacial environments to persist through interglacials.
5682280
Estimating Species Trees Using Multiple-Allele DNA Sequence Data
Abstract Several techniques, such as concatenation and consensus methods, are available for combining data from multiple loci to produce a single statement of phylogenetic relationships. However, when multiple alleles are sampled from individual species, it becomes more challenging to estimate relationships at the level of species, either because concatenation becomes inappropriate due to conflicts among individual gene trees, or because the species from which multiple alleles have been sampled may not form monophyletic groups in the estimated tree. We propose a Bayesian hierarchical model to reconstruct species trees from multipleallele, multilocus sequence data, building on a recently proposed method for estimating species trees from single allele multilocus data. A two-step Markov Chain Monte Carlo (MCMC) algorithm is adopted to estimate the posterior distribution of the species tree. The model is applied to estimate the posterior distribution of species trees for two multiple-allele datasets—yeast (Saccharomyces) and birds (Manacus—manakins). The estimates of the species trees using our method are consistent with those inferred from other methods and genetic markers, but in contrast to other species tree methods, it provides credible regions for the species tree. The Bayesian approach described here provides a powerful framework for statistical testing and integration of population genetics and phylogenetics.
3724099
Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes.
Phylogenetic relationships and taxonomic distinctiveness of closely related species and subspecies are most accurately inferred from data derived from multiple independent loci. Here, we apply several approaches for understanding species-level relationships using data from 18 nuclear DNA loci and 1 mitochondrial DNA locus within currently described species and subspecies of Sistrurus rattlesnakes. Collectively, these methods provide evidence that a currently described species, the massasauga rattlesnake (Sistrurus catenatus), consists of two well-supported clades, one composed of the two western subspecies (S. c. tergeminus and S. c. edwardsii) and the other the eastern subspecies (S. c. catenatus). Within pigmy rattlesnakes (S. miliarius), however, there is not strong support across methods for any particular grouping at the subspecific level. Monophyly based tests for taxonomic distinctiveness show evidence for distinctiveness of all subspecies but this support is strongest by far for the S. c. catenatus clade. Because support for the distinctiveness of S. c. catenatus is both strong and consistent across methods, and due to its morphological distinctiveness and allopatric distribution, we suggest that this subspecies be elevated to full species status, which has significant conservation implications. Finally, most divergence time estimates based upon a fossil-calibrated species tree are > 50% younger than those from a concatenated gene tree analysis and suggest that an active period of speciation within Sistrurus occurred within the late Pliocene/Pleistocene eras.
8237525
Gene tree discordance, phylogenetic inference and the multispecies coalescent.
The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories.
10601318
The study of structured populations — new hope for a difficult and divided science
Natural populations, including those of humans, have complex geographies and histories. Studying how they evolve is difficult, but it is possible with population-based DNA sequence data. However, the study of structured populations is divided by two distinct schools of thought and analysis. The phylogeographic approach is fundamentally graphical and begins with a gene-tree estimate. By contrast, the more traditional approach of using summary statistics is fundamentally mathematical. Both approaches have limitations, but there is promise in newer probabilistic methods that offer the flexibility and data exploitation of the phylogeographic approach in an explicitly model-based mathematical framework.
1399144
Coalescent genealogy samplers: windows into population history.
Coalescent genealogy samplers attempt to estimate past qualities of a population, such as its size, growth rate, patterns of gene flow or time of divergence from another population, based on samples of molecular data. Genealogy samplers are increasingly popular because of their potential to disentangle complex population histories. In the last decade they have been widely applied to systems ranging from humans to viruses. Findings include detection of unexpected reproductive inequality in fish, new estimates of historical whale abundance, exoneration of humans for the prehistoric decline of bison and inference of a selective sweep on the human Y chromosome. This review summarizes available genealogy-sampler software, including data requirements and limitations on the use of each program.