Jeet Sukumaran

DendroPy: a Python library for phylogenetic computing

UNLABELLED DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPys data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. AVAILABILITY The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

Evolutionary and Biogeographic Origins of High Tropical Diversity in Old World Frogs (Ranidae)

Differences in species richness between regions are ultimately explained by patterns of speciation, extinction, and biogeographic dispersal. Yet, few studies have considered the role of all three processes in generating the high biodiversity of tropical regions. A recent study of a speciose group of predominately New World frogs (Hylidae) showed that their low diversity in temperate regions was associated with relatively recent colonization of these regions, rather than latitudinal differences in diversification rates (rates of speciation-extinction). Here, we perform parallel analyses on the most species-rich group of Old World frogs (Ranidae; ∼1300 species) to determine if similar processes drive the latitudinal diversity gradient. We estimate a time-calibrated phytogeny for 390 ranid species and use this phytogeny to analyze patterns of biogeography and diversification rates. As in hylids, we find a strong relationship between the timing of colonization of each region and its current diversity, with recent colonization of temperate regions from tropical regions. Diversification rates are similar in tropical and temperate clades, suggesting that neither accelerated tropical speciation rates nor greater temperate extinction rates explain high tropical diversity in this group. Instead, these results show the importance of historical biogeography in explaining high species richness in both the New World and Old World tropics.

Multispecies coalescent delimits structure, not species

Significance Despite its widespread application to the species delimitation problem, our study demonstrates that what the multispecies coalescent actually delimits is structure. The current implementations of species delimitation under the multispecies coalescent do not provide any way for distinguishing between structure due to population-level processes and that due to species boundaries. The overinflation of species due to the misidentification of general genetic structure for species boundaries has profound implications for our understanding of the generation and dynamics of biodiversity, because any ecological or evolutionary studies that rely on species as their fundamental units will be impacted, as well as the very existence of this biodiversity, because conservation planning is undermined due to isolated populations incorrectly being treated as distinct species. The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent. We show that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries. Because of the misidentification of population structure as putative species, our work raises questions about the practice of genome-based species discovery, with cascading consequences in other fields. Specifically, all fields that rely on species as units of analysis, from conservation biology to studies of macroevolutionary dynamics, will be impacted by inflated estimates of the number of species, especially as genomic resources provide unprecedented power for detecting increasingly finer-scaled genetic structure under the multispecies coalescent. As such, our work also represents a general call for systematic study to reconsider a reliance on genomic data alone. Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.

A Justification for Reporting the Majority-Rule Consensus Tree in Bayesian Phylogenetics

This is an electronic version of an article published in Systematic Biology [Holder, Mark T., Jeet Sukumaran, and Paul O. Lewis. A justification for reporting majority-rule consensus tree in Bayesian phylogenetics. Systematic Biology, 57(5):814{821, 2008.] Systematic Biology is available online at informaworld http://dx.doi.org/10.1080/10635150802422308

Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion?

Southeast Asias widespread species offer unique opportunities to explore the effects of geographical barriers to dispersal on patterns of vertebrate lineage diversification. We analyzed mitochondrial gene sequences (16S rDNA) from a geographically widespread sample of 266 Southeast Asian tree frogs, including 244 individuals of Polypedates leucomystax and its close relatives. Our expectation was that lineages on island archipelagos would exhibit more substantial geographic structure, corresponding to the geological history of terrestrial connectivity in this region, compared to the Asian mainland. Contrary to predictions, we found evidence of numerous highly divergent lineages from a limited area on the Asian mainland, but fewer lineages with shallower divergences throughout oceanic islands of the Philippines and Indonesia. Surprisingly and in numerous instances, lineages in the archipelagos span distinct biogeographical provinces. Phylogeographic analyses identified four major haplotype clades; summary statistics, mismatch distributions, and Bayesian coalescent inference of demography provide support for recent range expansion, population growth, and/or admixture in the Philippine and some Sulawesi populations. We speculate that the current range of P. leucomystax in Southeast Asia is much larger now than in the recent past. Conversion of forested areas to monoculture agriculture and transportation of agricultural products between islands may have facilitated unprecedented population and range expansion in P. leucomystax throughout thousands of islands in the Philippine and Indonesian archipelagos.

EVIDENCE FOR CLIMATE‐DRIVEN DIVERSIFICATION? A CAUTION FOR INTERPRETING ABC INFERENCES OF SIMULTANEOUS HISTORICAL EVENTS

Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co‐distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea‐level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation‐based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene‐driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence‐time parameters.

NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata

Abstract In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.

Phylogenetic relationships of Ansonia from Southeast Asia inferred from mitochondrial DNA sequences: Systematic and biogeographic implications (Anura: Bufonidae)

We investigated the phylogenetic relationships and estimated the history of species diversification and biogeography in the bufonid genus Ansonia from Southeast Asia, a unique organism with tadpoles adapted to life in strong currents chiefly in montane regions and also in lowland rainforests. We estimated phylogenetic relationships among 32 named and unnamed taxa using 2461bp sequences of the mitochondrial 12S rRNA, tRNA(val), and 16S rRNA genes with equally-weighted parsimony, maximum likelihood, and Bayesian methods of inference. Monophyletic clades of Southeast Asian members of the genus Ansonia are well-supported, allowing for the interpretation of general biogeographic conclusions. The genus is divided into two major clades. One of these contains two reciprocally monophyletic subclades, one from the Malay Peninsula and Thailand and the other from Borneo. The other major clade primarily consists of Bornean taxa but also includes a monophyletic group of two Philippine species and a single peninsular Malaysian species. We estimated absolute divergence times using Bayesian methods with external calibration points to reconstruct the relative timing of faunal exchange between the major landmasses of Southeast Asia.

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model Choice By Simulation-Trained Discriminant Analysis

Current statistical biogeographical analysis methods are limited in the ways ecology can be related to the processes of diversification and geographical range evolution, requiring conflation of geography and ecology, and/or assuming ecologies that are uniform across all lineages and invariant in time. This precludes the possibility of studying a broad class of macroevolutionary biogeographical theories that relate geographical and species histories through lineage-specific ecological and evolutionary dynamics, such as taxon cycle theory. Here we present a new model that generates phylogenies under a complex of superpositioned geographical range evolution, trait evolution, and diversification processes that can communicate with each other. We present a likelihood-free method of inference under our model using discriminant analysis of principal components of summary statistics calculated on phylogenies, with the discriminant functions trained on data generated by simulations under our model. This approach of model selection by classification of empirical data with respect to data generated under training models is shown to be efficient, robust, and performs well over a broad range of parameter space defined by the relative rates of dispersal, trait evolution, and diversification processes. We apply our method to a case study of the taxon cycle, that is testing for habitat and trophic level constraints in the dispersal regimes of the Wallacean avifaunal radiation.

Neutral Models of Microbiome Evolution.

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.