Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards.

-Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A.

The Expected Behaviors of Posterior Predictive Tests and Their Unexpected Interpretation.

Poor fit between models of sequence or trait evolution and empirical data is known to cause biases and lead to spurious conclusions about evolutionary patterns and processes. Bayesian posterior prediction is a flexible and intuitive approach for detecting such cases of poor fit. However, the expected behavior of posterior predictive tests has never been characterized for evolutionary models, which is critical for their proper interpretation.

Testing concordance and conflict in spatial replication of landscape genetics inferences.

The degree to which landscape genetics findings can be extrapolated to different areas of a species range is poorly understood. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses with a total of 119 individuals in five areas within the Sierra Nevada mountain range.

Temperate Zone Isolation by Climate: An Extension of Janzen's 1967 Hypothesis.

AbstractOne of the most stunning patterns of the distribution of life on Earth is the latitudinal biodiversity gradient. In an influential article, Janzen (1967) predicted that tropical mountains are more effective migration barriers than temperate mountains of the same elevation, because annual temperature variation in the tropics is lower. A great deal of research has demonstrated that the mechanism envisioned by Janzen operates at broad latitudinal scales.

Biogeographic inferences across spatial and evolutionary scales.

The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species.

The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization.

Hybridization between diverging lineages is associated with the generation and loss of species diversity, introgression, adaptation, and changes in reproductive mode, but it is unknown when and why it results in these divergent outcomes. We estimate a comprehensive evolutionary network for the largest group of unisexual vertebrates and use it to understand the evolutionary outcomes of hybridization. Our results show that rates of introgression between species decrease with time since divergence and suggest that species must attain a threshold of evolutionary divergence before hybridization results in transitions to unisexuality.

On the Need for New Measures of Phylogenomic Support.

The scale of data sets used to infer phylogenies has grown dramatically in the last decades, providing researchers with an enormous amount of information with which to draw inferences about evolutionary history. However, standard approaches to assessing confidence in those inferences (e.g.

Genomic differentiation in an endemic Philippine genus (Aves: ) owing to geographical isolation on recently disassociated islands.

Phylogeographical studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation but remains relatively undocumented, perhaps because the current episode of island isolation started in relatively recent times. We investigated inter- and intra-island population structure in a Philippine endemic bird genus () to determine whether genetic differentiation has evolved during the recent period of isolation.

Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis.

Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages.

A New Diploid Parthenogenetic Whiptail Lizard from Sonora, Mexico, Is the "Missing Link" in the Evolutionary Transition to Polyploidy.

AbstractTransitions between sexual and unisexual reproductive modes have significant consequences for the evolutionary trajectories of species. These transitions have occurred numerous times in vertebrates and are frequently mediated by hybridization events. Triploid unisexual vertebrates are thought to arise through hybridization between individuals of a diploid unisexual lineage and a sexual species, although additional evidence that confirms this mechanism is needed in numerous groups.

A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins.

Living turtles are characterized by extraordinarily low species diversity given their age. The clade's extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that, together, represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times.

Properties of Markov Chain Monte Carlo Performance across Many Empirical Alignments.

Nearly all current Bayesian phylogenetic applications rely on Markov chain Monte Carlo (MCMC) methods to approximate the posterior distribution for trees and other parameters of the model. These approximations are only reliable if Markov chains adequately converge and sample from the joint posterior distribution. Although several studies of phylogenetic MCMC convergence exist, these have focused on simulated data sets or select empirical examples.

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny.

Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated?

A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci.

Complex patterns of hybridization and introgression across evolutionary timescales in Mexican whiptail lizards (Aspidoscelis).

Identifying patterns of introgression across the tree of life is foundational to understanding general mechanisms that govern the impacts of gene flow on the speciation process. There are few vertebrate groups in which hybridization is associated with as large a diversity of outcomes as in North American whiptail lizards (Aspidoscelis). Of particular interest is that hybridization among divergent whiptail species has repeatedly led to the formation of unisexual (parthenogenetic) lineages.

Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation.

A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios.

Revised classification of the righteye flounders (Teleostei: Pleuronectidae) based on multilocus phylogeny with complete taxon sampling.

Members of the family Pleuronectidae are common representatives of the marine benthic fauna inhabiting northern regions of the Atlantic and Pacific oceans. The most recent comprehensive classification of the family, based entirely on morphological synapomorphies, recognized five subfamilies, 23 genera, and 61 extant species. However, several subsequent molecular studies have shown that many synapomorphic characters discovered in the morphological study might represent homoplasies, thereby questioning the reliance on these characters with the warning that they may provide misleading information for testing other morphology-based evolutionary hypotheses.

Variation Across Mitochondrial Gene Trees Provides Evidence for Systematic Error: How Much Gene Tree Variation Is Biological?

The use of large genomic data sets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological vs.

The Behavior of Metropolis-Coupled Markov Chains When Sampling Rugged Phylogenetic Distributions.

Bayesian phylogenetic inference relies on the use of Markov chain Monte Carlo (MCMC) to provide numerical approximations of high-dimensional integrals and estimate posterior probabilities. However, MCMC performs poorly when posteriors are very rugged (i.e.

Molecular phylogeny and divergence of the map turtles (Emydidae: Graptemys).

The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies.

P3: Phylogenetic Posterior Prediction in RevBayes.

Tests of absolute model fit are crucial in model-based inference because poorly structured models can lead to biased parameter estimates. In Bayesian inference, posterior predictive simulations can be used to test absolute model fit. However, such tests have not been commonly practiced in phylogenetic inference due to a lack of convenient and flexible software.

Impact of Model Violations on the Inference of Species Boundaries Under the Multispecies Coalescent.

The use of genetic data for identifying species-level lineages across the tree of life has received increasing attention in the field of systematics over the past decade. The multispecies coalescent model provides a framework for understanding the process of lineage divergence and has become widely adopted for delimiting species. However, because these studies lack an explicit assessment of model fit, in many cases, the accuracy of the inferred species boundaries are unknown.

Bayes Factors Unmask Highly Variable Information Content, Bias, and Extreme Influence in Phylogenomic Analyses.

As the application of genomic data in phylogenetics has become routine, a number of cases have arisen where alternative data sets strongly support conflicting conclusions. This sensitivity to analytical decisions has prevented firm resolution of some of the most recalcitrant nodes in the tree of life. To better understand the causes and nature of this sensitivity, we analyzed several phylogenomic data sets using an alternative measure of topological support (the Bayes factor) that both demonstrates and averts several limitations of more frequently employed support measures (such as Markov chain Monte Carlo estimates of posterior probabilities).