Testing Geology with Biology: Plate Tectonics and the Diversification of Microhylid Frogs in the Papuan Region.

Studies of the Papuan region have provided fundamental insights into the evolutionary processes generating its exceptional biodiversity, but the influence of geological processes merits further study. Lying at the junction of five tectonic plates, this region has experienced a turbulent geological history that has not only produced towering mountains allowing elevational specialization and island archipelagos with varying degrees of isolation promoting vicariance, but also active margins where land masses have collided and been subsequently rifted apart creating a mosaic of intermixed terranes with vastly different geological histories. Asterophryine frogs are a hyperdiverse clade representing half the world's microhylid diversity (over 360 species) centered on New Guinea and its satellite islands. We show that vicariance facilitated by geological history explains this far and wide distribution of a clade that should have poor dispersal abilities. We recovered a mainland tectonic unit, the East Papua Composite Terrane (EPCT), as the center of origin for Asterophryinae and no fewer than 71 instances of what appear to be long-distance dispersal events, 29 of which are between mainland regions, with 42 from the mainland to the islands, some presently as far as 200 km away from source populations over open ocean. Furthermore, we find strong support for a "Slow and Steady" hypothesis for the formation of the northern margin of New Guinea by many separate accretion events during the Miocene, over other major geological alternatives, consistent with the 20 M year age of the clade and arrival via the EPCT. In addition, the historical biogeography of our frogs strongly supports an affiliation of the Louisiade Archipelago and Woodlark Island with the Owen Stanley Range on the EPCT, and the recent proximity of the large New Britain Island. Our results show that Asterophryinae did not have to repeatedly and independently disperse across large ocean barriers to the offshore islands, against the predictions of island biogeography theory, but that the current distribution can be explained through vicariance and short-distance oceanic dispersal as historical land connections disappeared and islands slowly became separated from each other. We show that islands have a life history, changing in distance from other land masses, with consequent opportunities for dispersal, isolation, and cladogenesis of their biotas. More broadly, we can begin to see how the geological history of the Papuan region can result in the rapid accumulation and staggering number of extant species.

Molecular and phylogenetic datasets for the Asterophryinae frogs of New Guinea with additional data on lifestyle, geography, and elevation.

The data provided here are related to the article "Resolving the Deep Phylogeny: Implications for Early Adaptive Radiation, Cryptic, and Present-day Ecological Diversity of Papuan Microhylid Frogs" [1]. The dataset is based on 233 tissue samples of the subfamily Asteroprhyinae, with representatives from all recognized genera, in addition to three outgroup taxa. The sequence dataset contains over 2400 characters per sample for five genes: three nuclear (Seventh in Absentia (SIA), Brain Derived Neurotrophic Factor (BDNF), Sodium Calcium Exchange subunit-1 (NXC-1)), and two mitochondrial loci (Cytochrome oxidase b (CYTB), and NADH dehydrogenase subunit 4 (ND4)); and is 99% complete. New primers were designed for all loci and accession numbers for the raw sequence data are provided. The sequences are used with geological time calibrations to produce time-calibrated Bayesian inference (BI) and Maximum Likelihood (ML) phylogenetic reconstructions using BEAST2 and IQ-TREE. Lifestyle data (arboreal, scansorial, terrestrial, fossorial, semi-aquatic) were collected from the literature and field notes and used to infer ancestral character states for each lineage. Collection location and elevation data were used to verify sites where multiple species or candidate species co-occur. All sequence data, alignments, and associated metadata (voucher specimen number, species identification, type locality status, global positioning system [GPS] coordinates, elevation, site with species list, and lifestyle) as well as the code to produce all analyses and figures are provided.

Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs.

The microhylid frogs of the New Guinea region are the largest and most ecologically diverse subfamily (Asterophryinae) of one of the largest anuran families in the world and can live in communities of up to 20 species. While there has been recent progress in resolving the phylogenetic relationships of Asterophryinae, significant uncertainties remain, impeding further progress in understanding the evolution of microhabitat use, parental care, and life history variation in this group. In particular, the early divergences at the base of the tree remain unclear; as does the monophyly of some genera; and recent studies have discovered that species with wide geographic distribution are instead cryptic species complexes. In this study, we fortified geographic sampling of the largest previous phylogenetic effort by sequencing an additional 62 taxa and increased data quality and quantity by adding new layers of data vetting and by filling in previously incomplete loci to the five gene dataset (2 mitochondrial, 3 nuclear protein-coding genes) to obtain a dataset that is now 99% complete in over 2400 characters for 233 samples (205 taxa) of Asterophryinae and 3 outgroup taxa, and analyzed microhabitat use data for these taxa from field data and data collected from the literature. Importantly, our sampling includes complete community complements at 19 sites as well as representatives at over 80 sites across New Guinea and its offshore islands. We present a highly resolved molecular phylogeny which, for the first time, has over 95% of nodes supported (84% highly supported) whether using Maximum Likelihood or Bayesian Inference, allowing clarification of all genera (whether monophyletic or clearly not), their sister genera relationships, as well as an age estimate for the Asterophryinae at approximately 20MYA. Early generic diversification occurring between 17 and 12 MYA gave rise to a surprising diversity of about 18 genera as well as the 5 putative microhabitat types. Our tree reveals extensive cryptic diversity calling any widespread taxa into doubt, and clearly demonstrates that complex multispecies communities of Asterophryinae are ecologically diverse, are numerous, and of ancient origin across New Guinea. We discuss the implications of our phylogeny for explaining the explosive diversification of Asterophryinae as the result of adaptive radiation, niche conservatism, and non-adaptive radiation.

Molecular phylogenetics and dating of the problematic New Guinea microhylid frogs (Amphibia: Anura) reveals elevated speciation rates and need for taxonomic reclassification.

Asterophryinae is a large monophyletic subfamily of Anurans containing over 300 species distributed across one of the world's most geologically active areas - New Guinea and its satellite islands, Australia and the Philippines. The tremendous ecological and morphological diversity of this clade, with apparent specializations for burrowing, terrestrial, semi-aquatic, and arboreal lifestyle, suggests an evolutionary process of adaptive radiation. Despite this spectacular diversity, this and many other questions of evolutionary processes have received little formal study because until now the phylogeny of this spececies-rich clade has remained uncertain. Here we reconstruct a phylogeny for Asterophryinae with greatly increased taxon and genetic sampling relative to prior studies. We use Maximum Likelihood and Bayesian Inference methods to produce the most robust and comprehensive phylogeny to date containing 155 species using 3 nuclear and 2 mitochondrial loci. We also perform a time calibration analysis to estimate the age of the clade. We find support for the monophyly of Asterophryinae as well as need for taxonomic reclassification of several genera. Furthermore, we find increased rates of speciation across the clade supporting the hypothesis of rapid radiation. Lastly, we found that adding taxa to the analysis produced more robust phylogenetic results over adding loci.

Adaptive evolution in locomotor performance: How selective pressures and functional relationships produce diversity.

Despite the complexity of nature, most comparative studies of phenotypic evolution consider selective pressures in isolation. When competing pressures operate on the same system, it is commonly expected that trade-offs will occur that will limit the evolution of phenotypic diversity, however, it is possible that interactions among selective pressures may promote diversity instead. We explored the evolution of locomotor performance in lizards in relation to possible selective pressures using the Ornstein-Uhlenbeck process. Here, we show that a combination of selection based on foraging mode and predator escape is required to explain variation in performance phenotypes. Surprisingly, habitat use contributed little explanatory power. We find that it is possible to evolve very different abilities in performance which were previously thought to be tightly correlated, supporting a growing literature that explores the many-to-one mapping of morphological design. Although we generally find the expected trade-off between maximal exertion and speed, this relationship surprisingly disappears when species experience selection for both performance types. We conclude that functional integration need not limit adaptive potential, and that an integrative approach considering multiple major influences on a phenotype allows a more complete understanding of adaptation and the evolution of diversity.

Detecting Adaptive Evolution in Phylogenetic Comparative Analysis Using the Ornstein-Uhlenbeck Model.

Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multiple selective optima and hypotheses with rate variation within and across lineages. The statistical performance of these sophisticated models has received relatively little systematic attention, however. We conducted an extensive simulation study to quantify the statistical properties of a class of models toward the simpler end of the spectrum that model phenotypic evolution using Ornstein-Uhlenbeck processes. We focused on identifying where, how, and why these methods break down so that users can apply them with greater understanding of their strengths and weaknesses. Our analysis identifies three key determinants of performance: a discriminability ratio, a signal-to-noise ratio, and the number of taxa sampled. Interestingly, we find that model-selection power can be high even in regions that were previously thought to be difficult, such as when tree size is small. On the other hand, we find that model parameters are in many circumstances difficult to estimate accurately, indicating a relative paucity of information in the data relative to these parameters. Nevertheless, we note that accurate model selection is often possible when parameters are only weakly identified. Our results have implications for more sophisticated methods inasmuch as the latter are generalizations of the case we study.

Running for your life or running for your dinner: what drives fiber-type evolution in lizard locomotor muscles?

Despite its role in whole-animal performance, the adaptation of muscle physiology related to terrestrial locomotion remains underexplored. We tested evolutionary models based on predator escape and foraging strategies of lizards to assess whether fiber-type composition of a leg muscle is adaptive for behavior. The best-fitting model for fast-twitch fiber-type evolution was one based on predator-escape strategy, while the foraging-mode model fared poorly (Akaike Information Criterion with small sample size correction; DeltaAICc=29.7). According to the predator-escape model, lizards relying on sprints to avoid predators are predicted to have relatively higher proportions of fast glycolytic (FG) fibers (70%), while cryptic lizards are predicted to have relatively higher fast oxidative glycolytic (FOG) fiber proportions (77%). This pattern suggests an evolutionary trend toward greater FG (FOG) fiber composition among lizards that specialize in sprinting (crypsis). The best-fitting model for slow-twitch fibers had a single optimum, suggesting a common selective pressure across these lizards. The second-best model explaining slow-twitch fiber-type evolution was Brownian motion (DeltaAICc=0.80), indicating some support for neutral evolution. We find evidence suggesting that different fiber types occurring in the same muscle can evolve under different evolutionary pressures.

Sexual dimorphism and adaptive radiation in Anolis lizards.

Sexual dimorphism is widespread and substantial throughout the animal world. It is surprising, then, that such a pervasive source of biological diversity has not been integrated into studies of adaptive radiation, despite extensive and growing attention to both phenomena. Rather, most studies of adaptive radiation either group individuals without regard to sex or focus solely on one sex. Here we show that sexual differences contribute substantially to the ecomorphological diversity produced by the adaptive radiations of West Indian Anolis lizards: within anole species, males and females occupy mostly non-overlapping parts of morphological space; the overall extent of sexual variation is large relative to interspecific variation; and the degree of variation depends on ecological type. Thus, when sexual dimorphism in ecologically relevant traits is substantial, ignoring its contribution may significantly underestimate the adaptive component of evolutionary radiation. Conversely, if sexual dimorphism and interspecific divergence are alternative means of ecological diversification, then the degree of sexual dimorphism may be negatively related to the extent of adaptive radiation.

Vive le difference! Sexual dimorphism and adaptive patterns in lizards of the genus Anolis.

The repeated, convergent evolution of body shape and microhabitat use in Greater Antillean lizards of the genus Anolis (anoles) provides compelling evidence of the importance of microhabitat specialization in shaping morphology. Interestingly, sexual dimorphism is also extensive, with males and females differing in body size as well as in shape. It is important to note that the components of shape analyzed in these studies is related to locomotion and are size-adjusted, including: relative limb and body lengths and mass of the body. Numbers of lamellae were also used and these do not vary with size. Furthermore, dimorphism in both size and shape differs by habitat type. Thus, does functionally-relevant sexual dimorphism imply that one sex is the "ecological" sex, with the other being maladapted to it's environment? Alternatively, sexual dimorphism may interact with adaptive diversification. Different classes of individuals within a species may act as separate ecological units if they play ecologically different roles. Here, I reanalyze a data set of morphological data for 15 species of Puerto Rican and Jamaican Anolis, which represent two largely independent adaptive radiations of lizards. I test for concordance between size and shape dimorphism and microhabitat (ecomorph) type, and for "parallel" patterns of sexual dimorphism among species. I integrate these results and, in the light of previous research, evaluate the relative influence that larger-scale ecological patterns have on sexual dimorphism, as well as the influence of sexual dimorphism on community structuring. I conclude that the presence of ecologically-relevant dimorphism may in fact increase the adaptive diversity present within a community.

Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution.

Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on the Ornstein-Uhlenbeck (OU) process, first proposed by Hansen. Ornstein-Uhlenbeck models incorporate both selection and drift and are thus qualitatively different from, and more general than, pure drift models based on Brownian motion. Most importantly, OU models possess selective optima that formalize the notion of adaptive zone. In this article, we develop the method for one quantitative character, discuss interpretations of its parameters, and provide code implementing the method. Our approach allows us to translate hypotheses regarding adaptation in different selective regimes into explicit models, to test the models against data using maximum-likelihood-based model selection techniques, and to infer details of the evolutionary process. We illustrate the method using two worked examples. Relative to existing approaches, the direct modeling approach we demonstrate allows one to explore more detailed hypotheses and to utilize more of the information content of comparative data sets than existing methods. Moreover, the use of a model selection framework to simultaneously compare a variety of hypotheses advances our ability to assess alternative evolutionary explanations.

TESTING FOR UNEQUAL AMOUNTS OF EVOLUTION IN A CONTINUOUS CHARACTER ON DIFFERENT BRANCHES OF A PHYLOGENETIC TREE USING LINEAR AND SQUARED-CHANGE PARSIMONY: AN EXAMPLE USING LESSER ANTILLEAN ANOLIS LIZARDS.

Although a large body of work investigating tests of correlated evolution of two continuous characters exists, hypotheses such as character displacement are really tests of whether substantial evolutionary change has occurred on a particular branch or branches of the phylogenetic tree. In this study, we present a methodology for testing such a hypothesis using ancestral character state reconstruction and simulation. Furthermore, we suggest how to investigate the robustness of the hypothesis test by varying the reconstruction methods or simulation parameters. As a case study, we tested a hypothesis of character displacement in body size of Caribbean Anolis lizards. We compared squared-change, weighted squared-change, and linear parsimony reconstruction methods, gradual Brownian motion and speciational models of evolution, and several resolution methods for linear parsimony. We used ancestor reconstruction methods to infer the amount of body size evolution, and tested whether evolutionary change in body size was greater on branches of the phylogenetic tree in which a transition from occupying a single-species island to a two-species island occurred. Simulations were used to generate null distributions of reconstructed body size change. The hypothesis of character displacement was tested using Wilcoxon Rank-Sums. When tested against simulated null distributions, all of the reconstruction methods resulted in more significant P-values than when standard statistical tables were used. These results confirm that P-values for tests using ancestor reconstruction methods should be assessed via simulation rather than from standard statistical tables. Linear parsimony can produce an infinite number of most parsimonious reconstructions in continuous characters. We present an example of assessing the robustness of our statistical test by exploring the sample space of possible resolutions. We compare ACCTRAN and DELTRAN resolutions of ambiguous character reconstructions in linear parsimony to the most and least conservative resolutions for our particular hypothesis.