A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae)
AbstractAnolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species ofAnolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treat...
Source: Systematic Biology - February 27, 2017 Category: Biology Source Type: research
Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models
Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM ’s likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM...
Source: Systematic Biology - February 21, 2017 Category: Biology Source Type: research
An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution
Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associated with the rate of genome and sequence evolution. However, inference methodologies that analyze sequence and phenotypic data in a unified statistical framework are still scarce. Here, we present TraitRateProp, a probabilistic method that allows testing whether the rate of sequence evolution is associated wi...
Source: Systematic Biology - February 16, 2017 Category: Biology Source Type: research
PHRAPL: Phylogeographic Inference Using Approximate Likelihoods
We describe the method and test its performance in model selection and parameter estimation using simulated data. We also compare model probabilities estimated using our approximate likelihood method to those obtained using standard analytical likelihood. The method performs well under a wide range of scenarios, although this is sometimes contingent on sampling many loci. In most scenarios, as long as there are enough loci and if divergence among populations is sufficiently deep, PHRAPL can return the true model in nearly all simulated replicates. Parameter estimates from the method are also generally accurate in most case...
Source: Systematic Biology - February 16, 2017 Category: Biology Source Type: research
An Integrated Model of Phenotypic Trait Changes and Site-Specific Sequence Evolution
Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associated with the rate of genome and sequence evolution. However, inference methodologies that analyze sequence and phenotypic data in a unified statistical framework are still scarce. Here, we present TraitRateProp, a probabilistic method that allows testing whether the rate of sequence evolution is associated wi...
Source: Systematic Biology - February 16, 2017 Category: Biology Source Type: research
PHRAPL: Phylogeographic Inference Using Approximate Likelihoods
We describe the method and test its performance in model selection and parameter estimation using simulated data. We also compare model probabilities estimated using our approximate likelihood method to those obtained using standard analytical likelihood. The method performs well under a wide range of scenarios, although this is sometimes contingent on sampling many loci. In most scenarios, as long as there are enough loci and if divergence among populations is sufficiently deep, PHRAPL can return the true model in nearly all simulated replicates. Parameter estimates from the method are also generally accurate in most case...
Source: Systematic Biology - February 16, 2017 Category: Biology Source Type: research
A Poissonian Model of Indel Rate Variation for Phylogenetic Tree Inference
We describe a method to construct phylogeny estimates from a fixed alignment using neighbor joining. Using simulation studies, we show that ignoring indel rate variation may have a detrimental effect on the accuracy of the inferred phylogenies, and that our proposed method can sidestep this issue by inferring latent indel rate categories. We also show that our phylogenetic inference method may be more stable to taxa subsampling than methods that either ignore indels or indel rate variation. [evolutionary stochastic process; indel rate variation; Poisson indel process; TKF91.] (Source: Systematic Biology)
Source: Systematic Biology - February 16, 2017 Category: Biology Source Type: research
Erratum
Rojas D., Warsi O.M., D ávalos L.M. 2016. Bats (Chiroptera: Noctilionoidea) challenge a recent origin of extant neotropical diversity. Syst. Biol. 65(3):432–448. doi:10.1093/sysbio/syw011. (Source: Systematic Biology)
Source: Systematic Biology - February 13, 2017 Category: Biology Source Type: research
Erratum
D ávalos L.M., Velazco P.M., Warsi O.M., Smits P.D., Simmons N.B. 2014. Integrating incomplete fossils by isolating conflicting signal in saturated and non-independent morphological characters. Syst. Biol. 63:582–600. doi:10.1093/sysbio/syu022. (Source: Systematic Biology)
Source: Systematic Biology - February 13, 2017 Category: Biology Source Type: research
Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L.
AbstractSeveral well-documented evolutionary processes are known to cause conflict between species-level phylogenies and gene-level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridization and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several existing methods have dealt with these processes but none has yet been able to untangle all three at once. Here, we propose a stepwise method by which these processes can be discerned using information on genomic location coupled with coalescent simulations. In the first step,...
Source: Systematic Biology - February 8, 2017 Category: Biology Source Type: research
Using Genomic Location and Coalescent Simulation to Investigate Gene Tree Discordance in Medicago L.
AbstractSeveral well-documented evolutionary processes are known to cause conflict between species-level phylogenies and gene-level phylogenies. Three of the most challenging processes for species tree inference are incomplete lineage sorting, hybridization and gene duplication, which may result in unwarranted comparisons of paralogous genes. Several existing methods have dealt with these processes but none has yet been able to untangle all three at once. Here, we propose a stepwise method by which these processes can be discerned using information on genomic location coupled with coalescent simulations. In the first step,...
Source: Systematic Biology - February 8, 2017 Category: Biology Source Type: research
Age-Dependent and Lineage-Dependent Speciation and Extinction in the Imbalance of Phylogenetic Trees
It is known that phylogenetic trees are more imbalanced than expected from a birth –death model with constant rates of speciation and extinction, and also that imbalance can be better fit by allowing the rate of speciation to decrease as the age of the parent species increases. If imbalance is measured in more detail, at nodes within trees as a function of the number of species descended from the nodes, age-dependent models predict levels of imbalance comparable to real trees for small numbers of descendent species, but predicted imbalance approaches an asymptote not found in real trees as the number of descendent specie...
Source: Systematic Biology - February 7, 2017 Category: Biology Source Type: research
Can We “Future-Proof” Consensus Trees? †
AbstractConsensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the new source trees may begin to tell a different evolutionary story when restricted to the original set of taxa. However, if the new trees, restricted to the original set of taxa, were to agree exactly with the earlier trees, then we might hope that their consensus would either agree with or resolve the original consensus tree. In this article, we ask under what conditions consensus methods exist that are “future proof” in this sense. While we show ...
Source: Systematic Biology - February 7, 2017 Category: Biology Source Type: research
New Evidence from Linguistic Phylogenetics Identifies Limits to Punctuational Change
AbstractSince the early 1970s, biologists have debated whether evolution is punctuated by speciation events with bursts of cladogenetic changes, or whether evolution tends to be of a more gradual, anagenetic nature. A similar discussion among linguists has barely begun, but the present results suggest that there is also room for controversy over this issue in linguistics. The only previous study correlated the number of nodes in linguistic phylogenies with branch lengths and found support for punctuated equilibrium. We replicate this result for branch lengths, but find no support for punctuated equilibrium using a differen...
Source: Systematic Biology - January 31, 2017 Category: Biology Source Type: research
