April M. Wright

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data.

Despite the introduction of likelihood-based methods for estimating phylogenetic trees from phenotypic data, parsimony remains the most widely-used optimality criterion for building trees from discrete morphological data. However, it has been known for decades that there are regions of solution space in which parsimony is a poor estimator of tree topology. Numerous software implementations of likelihood-based models for the estimation of phylogeny from discrete morphological data exist, especially for the Mk model of discrete character evolution. Here we explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, we describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity.

Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors

The Mk model was developed for estimating phylogenetic trees from discrete morphological data, whether for living or fossil taxa. Like any model, the Mk model makes a number of assumptions. One assumption is that transitions between character states are symmetric (i.e., the probability of changing from 0 to 1 is the same as 1 to 0). However, some characters in a data matrix may not satisfy this assumption. Here, we test methods for relaxing this assumption in a Bayesian context. Using empirical data sets, we perform model fitting to illustrate cases in which modeling asymmetric transition rates among characters is preferable to the standard Mk model. We use simulated data sets to demonstrate that choosing the best-fit model of transition-state symmetry can improve model fit and phylogenetic estimation.

Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states

Changes in parity mode between egg-laying (oviparity) and live-bearing (viviparity) have occurred repeatedly throughout vertebrate evolution. Oviparity is the ancestral amniote state, and viviparity has evolved many times independently within amniotes (especially in lizards and snakes), with possibly a few reversions to oviparity. In amniotes, the shelled egg is considered a complex structure that is unlikely to re-evolve if lost (i.e., it is an example of Dollos Principle). However, a recent ancestral state reconstruction analysis concluded that viviparity was the ancestral state of squamate reptiles (lizards and snakes), and that oviparity re-evolved from viviparity many times throughout the evolutionary history of squamates. Here, we re-evaluate support for this provocative conclusion by testing the sensitivity of the analysis to model assumptions and estimates of squamate phylogeny. We found that the models and methods used for parity mode reconstruction are highly sensitive to the specific estimate of phylogeny used, and that the point estimate of phylogeny used to suggest that viviparity is the root state of the squamate tree is far from an optimal phylogenetic solution. The ancestral state reconstructions are also highly sensitive to model choice and specific values of model parameters. A method that is designed to account for biases in taxon sampling actually accentuates, rather than lessens, those biases with respect to ancestral state reconstructions. In contrast to recent conclusions from the same data set, we find that ancestral state reconstruction analyses provide highly equivocal support for the number and direction of transitions between oviparity and viviparity in squamates. Moreover, the reconstructions of ancestral parity state are highly dependent on the assumptions of each model. We conclude that the common ancestor of squamates was oviparous, and subsequent evolutionary transitions to viviparity were common, but reversals to oviparity were rare. The three putative reversals to oviparity with the strongest phylogenetic support occurred in the snakes Eryx jayakari and Lachesis, and the lizard, Liolaemus calchaqui. Our results emphasize that because the conclusions of ancestral state reconstruction studies are often highly sensitive to the methods and assumptions of analysis, researchers should carefully consider this sensitivity when evaluating alternative hypotheses of character-state evolution.

Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria).

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.

Inferring node dates from tip dates in fossil Canidae: the importance of tree priors

Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.

Shared Escovopsis parasites between leaf-cutting and non-leaf-cutting ants in the higher attine fungus-growing ant symbiosis

Fungus-gardening (attine) ants grow fungus for food in protected gardens, which contain beneficial, auxiliary microbes, but also microbes harmful to gardens. Among these potentially pathogenic microorganisms, the most consistently isolated are fungi in the genus Escovopsis, which are thought to co-evolve with ants and their cultivar in a tripartite model. To test clade-to-clade correspondence between Escovopsis and ants in the higher attine symbiosis (including leaf-cutting and non-leaf-cutting ants), we amassed a geographically comprehensive collection of Escovopsis from Mexico to southern Brazil, and reconstructed the corresponding Escovopsis phylogeny. Contrary to previous analyses reporting phylogenetic divergence between Escovopsis from leafcutters and Trachymyrmex ants (non-leafcutter), we found no evidence for such specialization; rather, gardens from leafcutters and non-leafcutters genera can sometimes be infected by closely related strains of Escovopsis, suggesting switches at higher phylogenetic levels than previously reported within the higher attine symbiosis. Analyses identified rare Escovopsis strains that might represent biogeographically restricted endemic species. Phylogenetic patterns correspond to morphological variation of vesicle type (hyphal structures supporting spore-bearing cells), separating Escovopsis with phylogenetically derived cylindrical vesicles from ancestral Escovopsis with globose vesicles. The new phylogenetic insights provide an improved basis for future taxonomic and ecological studies of Escovopsis.

Long-branch attraction and the phylogeny of true water bugs (Hemiptera: Nepomorpha) as estimated from mitochondrial genomes

BackgroundMost previous studies of morphological and molecular data have consistently supported the monophyly of the true water bugs (Hemiptera: Nepomorpha). An exception is a recent study by Hua et al. (BMC Evol Biol 9: 134, 2009) based on nine nepomorphan mitochondrial genomes. In the analysis of Hua et al. (BMC Evol Biol 9: 134, 2009), the water bugs in the group Pleoidea formed the sister group to a clade that consisted of Nepomorpha (the remaining true water bugs) + Leptopodomorpha (shore bugs) + Cimicomorpha (assassin bugs and relatives) + Pentatomomorpha (stink bugs and relatives), thereby suggesting that fully aquatic hemipterans evolved independently at least twice. Based on these results, Hua et al. (BMC Evol Biol 9: 134, 2009) elevated the Pleoidea to a new infraorder, the Plemorpha.ResultsOur reanalysis suggests that the lack of support for the monophyly of the true water bugs (including Pleoidea) by Hua et al. (BMC Evol Biol 9: 134, 2009) likely resulted from inadequate taxon sampling. In particular, long-branch attraction (LBA) between the distant outgroup taxa and Pleoidea, as well as LBA among taxa in the ingroup, made Nepomorpha appear to be polyphyletic. We used three complementary strategies to test and alleviate the effects of LBA: (1) the removal of distant outgroups from the analysis; (2) the addition of closely related outgroups; and (3) the addition of a mitochondrial genome from a second family of Pleoidea. We also performed likelihood-ratio tests to examine the support for monophyly of Nepomorpha with different combinations of taxa included in the analysis. Furthermore, we found that specimens of Helotrephes sp. were misidentified as Paraplea frontalis (Fieber, 1844) by Hua et al. (BMC Evol Biol 9: 134, 2009).ConclusionsAll analyses that included the addition of more taxa significantly and consistently supported the placement of Pleoidea within the Nepomorpha (i.e., supported the monophyly of the traditional true water bugs). Our analyses further support a close relationship between Notonectoidea and Pleoidea within Nepomorpha, and the superfamilies Nepoidea, Ochteroidea, Naucoroidea, and Pleoidea are resolved as monophyletic in all trees with strong support. Our results also confirmed that monophyly of Nepomorpha clearly is not refuted by the mitochondrial genome data.

Ground truthing tip-dating methods using fossil Canidae reveals major differences in performance

Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using Beast 2.1.3 and MrBayes 3.2.5. We find that for key nodes (Canis, ~3.2 Ma, Caninae ~11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death, and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic vs. non-mechanistic) and their applicability to fossil datasets.

Editor's note on ‘Putting fossils in trees’ special issue

This special feature has its origins with a 2014 symposium organized by myself and my co-editors David W. Bapst, Graeme T. Lloyd and Nicholas J. Matzke at the Society for Vertebrate Paleontology meetings in Berlin, Germany. In the years prior to 2014, there had been several interesting and important