Phylogenetic estimation has largely come to rely on explicitly model-based methods. This approach requires that a model be chosen and choice justified. To date, justification been accomplished through use of likelihood-ratio tests (LRTs) assess the relative fit nested series reversible models. While this certainly represents an important advance over arbitrary selection, best models may not always provide most reliable phylogenetic estimates for finite real data sets, where all available are...

▪ Abstract Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render necessary, briefly nucleotide-based attempt to capture relevant features of evolutionary processes, methods have been applied phylogenetics: likelihood-ratio tests, AIC, BIC,...

Secondary structure models are an important step for aligning sequences, understanding probabilities of nucleotide substitutions, and evaluating the reliability phylogenetic reconstructions. A set conserved sequence motifs is derived from comparative analysis 184 invertebrate vertebrate taxa (including many same genera, families, orders) with reference to a secondary model domain III animal mitochondrial small subunit (12S) ribosomal RNA. template presented assist drawing. Our similar...

We investigated evolutionary relationships among deuterostome subgroups by obtaining nearly complete large-subunit ribosomal RNA (LSU rRNA)-gene sequences for 14 deuterostomes and 3 protostomes small-subunit (SSU) rRNA-gene five of these animals. With the addition previously published sequences, we compared 28 taxa using three different data sets only, SSU combined LSU + SSU) under minimum evolution (with LogDet distances), maximum likelihood, parsimony optimality criteria. Additionally,...

Mice of the Peromyscus aztecus species group occur at mid to high elevations in several mountain ranges highlands Middle America (Mexico and Central America), a region endemicity. We examined biogeography this by conducting phylogenetic analyses 668 bp mitochondrial cytochrome b (cyt b) gene. Phylogenetic under both parsimony likelihood frameworks produced same topologies, but estimates nodal support were artificially weighted analyses. This difference is attributed inability optimize branch...

We examine the evolution of mesic forest ecosystems in Pacific Northwest North America using a statistical phylogeography approach four animal and two plant lineages. Three priori hypotheses, which explain disjunction ecosystem with either recent dispersal or ancient vicariance, are tested phylogenetic coalescent methods. find strong support three amphibian lineages (Ascaphus spp., Dicampton Plethodon vandykei P. idahoensis) for deep divergence between coastal inland populations, as...

Resolving the interrelationships of three major extant lineages vertebrates (hagfishes, lampreys, and gnathostomes) is a particularly important issue in evolution, because basal resolution critically influences our understanding primitive vertebrate characters. A consensus has emerged over last 20 years that lampreys are sister group to gnathostomes hagfishes represent an ancient, lineage. This hypothesis essentially displaced classical monophyly cyclostomes (lampreys plus hagfishes). To...

Abstract Models that posit speciation in the face of gene flow are replacing classical views hybridization is rare between animal species. We use a multilocus approach to examine history and two species chipmunks ( Tamias ruficaudus T. amoenus ). Previous studies have shown these occupy different ecological niches distinct genital bone morphologies, yet appear be incompletely isolated reproductively multiple areas sympatry. compared data from four sequenced nuclear loci seven microsatellite...

The phylogeography of Sumichrast's harvest mouse (Reithrodontomys sumichrasti) was examined through maximum-likelihood and parsimony analyses 1,130 bp mitochondrial Cytochrome b sequence data from 43 individuals. this Middle American highland forest-dwelling species compared to that previously published for the codistributed Aztec deer complex (Peromyscus aztecus/Peromyscus hylocetes complex) in order test competing hypotheses concerted versus independent responses forms past climatic...

We examine the evolution of mesic forest ecosystems in Pacific Northwest North America using a statistical phylogeography approach four animal and two plant lineages. Three priori hypotheses, which explain disjunction ecosystem with either recent dispersal or ancient vicariance, are tested phylogenetic coalescent methods. find strong support three amphibian lineages (Ascaphus spp., Dicampton Plethodon vandykei P. idahoensis) for deep divergence between coastal inland populations, as...

In order to have confidence in model-based phylogenetic analysis, the model of nucleotide substitution adopted must be selected a statistically rigorous manner. Several model-selection methods are applicable maximum likelihood (ML) including hierarchical likelihood-ratio test (hLRT), Akaike information criterion (AIC), Bayesian (BIC), and decision theory (DT), but their performance relative empirical data has not been investigated thoroughly. this study, we use 250 sets obtained from...

The conservation status of most plant species is currently unknown, despite the fundamental role plants in ecosystem health. To facilitate costly process assessment, we developed a predictive protocol using machine-learning approach to predict over 150,000 land species. Our study uses open-source geographic, environmental, and morphological trait data, making this largest assessment risk date only global for plants. results indicate that large number unassessed are likely at identify several...

An often-expressed concern regarding the use ofmaximum likelihoodandothermodelbased methods in phylogenetic analysis is that assumedmodels are too simple, violating known aspects of sequence evolution several ways (e.g., Sanderson and Kim, 2000). For example,we know sites do not truly evolve independently, substitution process completely homogeneous across through time, simple stochastic models fail to adequately represent complexity nucleotide process. Many advances have been made an effort...

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance morphological, chromosomal, allozyme, other DNA data sets. Because these genes physically linked the nonrecombining genome, they necessarily share same history. Phylogenetic analysis cyt gene recovers well-corroborated relationships, generally with strong support. None methods that we...

Tailed frogs are distributed in high-gradient streams within the disjunct mesic forests of Pacific North-west and represent basal lineage anurans. We sequenced 1530 nucleotides mitochondrial cytochrome b NADH dehydrogenase subunit two genes from 23 populations used parsimony, maximum-likelihood, nested-clade analyses to estimate relationships among infer evolutionary processes. found divergent haplotype clades corresponding with land Rocky Mountain coastal separated by up 0.133 substitutions...

As the number of molecular studies continues to grow, so does problem how analyze multiple data sets. The importance this is indicated by flurry recent papers (reviewed de Queiroz et alv 1995) addressing philosophical and practical considerations facing systematists fortunate enough have several pertinent sets on hand. Perhaps most rigorous treatment was that Bull al. (1993), who argued against combining when there demonstrable heterogeneity among different in processes governing character...

Almost all studies that estimate phylogenies from DNA sequence data under the maximum-likelihood (ML) criterion employ an approximate approach. Most commonly, model parameters are estimated on some initial phylogenetic derived using a rapid method (neighbor-joining or parsimony). Parameters then held constant during tree search, and ideally, procedure is repeated until convergence achieved. However, effectiveness of this approximation has not been formally assessed, in part because doing so...

Abstract Several theoretical studies have demonstrated the importance of accounting for coalescent stochasticity in phylogeographical studies, however, there are few empirical examples that do so context explicit hypothesis testing. Here, we provide an example from Idaho giant salamander ( Dicamptodon aterrimus ) using 118 mtDNA sequences, nearly 2 kb length. This species is endemic to mesic forests northern and central Idaho, several a priori hypotheses been erected based both on...

Mesic forests in the North American Pacific Northwest occur two disjunct areas: along coastal and Cascade ranges of Oregon, Washington, British Columbia as well Northern Rocky Mountains Idaho, Montana, Columbia. Over 150 species or complexes have populations each area, a priori hypotheses based on phytogeography geology potentially explain disjunction via either dispersal vicariance. Here, we test these salamander complex Plethodon vandykei P. idahoensis by collecting genetic data (669 bp...

The causes and consequences of rapid radiations are major unresolved issues in evolutionary biology. This is part because phylogeny estimation confounded by processes such as stochastic lineage sorting hybridization. Because these expected to be heterogeneous across the genome, comparison among marker classes may provide a means disentangling elements. Here we use introns from nuclear-encoded reproductive protein genes resistant introgression estimate western chipmunks (Tamias: subgenus:...