Tracy A. Heath's research while affiliated with Iowa State University and other places

Publications (38)

Article
Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical datasets may contain a mix of precisel...
Preprint
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Gene-flow processes such as hybridization and introgression play important roles in shaping diversity across the tree of life. Recent studies extending birth-death models have made it possible to investigate patterns of reticulation in a macroevolutionary context. These models allow for different macroevolutionary patterns of gene flow events that...
Preprint
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Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow ( e.g ., introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic m...
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Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species-specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are kn...
Article
Myriad branches in the tree of life are intertwined through ecological relationships. Biologists have long hypothesized that intimate symbioses between lineages can influence diversification patterns to the extent that it leaves a topological imprint on the phylogenetic trees of interacting clades. Over the past few decades, cophylogenetic methods...
Article
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Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major c...
Preprint
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In 2020 and 2021, the COVID-19 pandemic led to an abrupt overhaul of many academic practices, including the transition of scientific events, such as workshops, to a fully virtual format. We describe our experiences organizing and teaching online-only statistical phylogenetics workshops and the lessons we learned along the way. We found that online...
Article
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The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers polli...
Article
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1. Cophylogenetic methods describe discordance between non‐independent phylogenies. 2. Simulation is necessary for testing cophylogenetic methods, but few simulators exist that are capable of generating data under explicit and biologically meaningful models. 3. We present an R package, treeducken , for simulating host‐symbiont evolution and gene tr...
Preprint
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Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data---while accounting for uncertainty in the ages of fossil specimens---in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical datasets may contain a mix of preci...
Preprint
Full-text available
Interactions between plants and their animal pollinators can shape processes of divergence and gene flow within associated lineages. For example, in the obligate mutualism between figs ( Ficus ) and fig pollinator wasps (family Agaonidae), each wasp species typically pollinates a single fig species, potentially reinforcing reproductive isolation am...
Article
Paederinae is one of the most diverse subfamilies among rove beetles, yet their evolutionary history remains poorly understood. This is attributed to the limited number of phylogenetic studies, which either sought answers at a shallower taxonomic level or included limited taxon sampling. Especially problematic is the position of the rare Neotropica...
Article
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New Zealand is a globally significant hotspot for seabird diversity, but the sparse fossil record for most seabird lineages has impeded our understanding of how and when this hotspot developed. Here, we describe multiple exceptionally well-preserved specimens of a new species of penguin from tightly dated (3.36-3.06 Ma) Pliocene deposits in New Zea...
Article
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Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates bas...
Article
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The fig and pollinator wasp obligate mutualism is diverse (∼750 described species), ecologically important, and ancient (∼80 Ma). Once thought to be an example of strict one‐to‐one cospeciation, current thinking suggests genera of pollinator wasps codiversify with corresponding sections of figs, but the degree to which cospeciation or other process...
Preprint
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The fig and pollinator wasp obligate mutualism is diverse (~750 described species), ecologically important, and ancient (~80-90 Ma), providing model systems for generating and testing many questions in evolution and ecology. Once thought to be a prime example of strict one-to-one cospeciation, current thinking suggests that genera of pollinator was...
Article
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A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting “birth” as branching speciation, “death” as extinction, and “sampling” as fossil preservation and recovery, this model – also referred to as the fossilized birth-death (FBD) model – gives rise to phylogenetic trees on extant and fo...
Article
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Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the evolutionary relationships among organisms, whereas phylodynamic approaches reveal the underlying diversification processes that lead to the observed relationships. These two fields have many practical applications in disciplines...
Chapter
Bayesian phylogenetic inference aims to estimate the evolutionary relationships among different lineages (species, populations, gene families, viral strains, etc.) in a model-based statistical framework that uses the likelihood function for parameter estimates. In recent years, evolutionary models for Bayesian analysis have grown in number and comp...
Article
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Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also...
Article
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The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describ...
Article
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Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed...
Article
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The total evidence approach to divergence-time dating uses molecular and morphological data of extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describin...
Article
Full-text available
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software...
Article
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There is an emerging consensus that undergraduate biology education in the United States is at a crucial juncture, especially as we acknowledge the need to train a new generation of scientists to meet looming environmental and health crises. Digital resources for biology now available online provide an opportunity to transform biology curricula to...
Article
Significance Divergence time estimation on an absolute timescale requires external calibration information, which typically is derived from the fossil record. The common practice in Bayesian divergence time estimation involves applying calibration densities to individual nodes. Often, these priors are arbitrarily chosen and specified yet have an ex...
Article
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Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generaliz...
Conference Paper
We present a substantially improved and parallelized version of DPPDiv, a software tool for estimating species divergence times and lineage-specific substitution rates on a fixed tree topology. The improvement is achieved by integrating the DPPDiv code with the Phylogenetic Likelihood Library (PLL), a fast, optimized, and parallelized collection of...
Article
In Bayesian divergence time estimation methods, incorporating calibrating information from the fossil record is commonly done by assigning prior densities to ancestral nodes in the tree. Calibration prior densities are typically parametric distributions offset by minimum age estimates provided by the fossil record. Specification of the parameters o...
Article
We introduce a new model for relaxing the assumption of a strict molecular clock for use as a prior in Bayesian methods for divergence time estimation. Lineage-specific rates of substitution are modeled using a Dirichlet process prior (DPP), a type of stochastic process that assumes lineages of a phylogenetic tree are distributed into distinct rate...
Article
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Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phyloge- netic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focuse...
Article
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We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring “tree islands” (sets of topologically related trees among larger sets of near-optimal trees), for comparing sets of trees obtained from bootstrapp...
Article
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Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of...

Citations

... Morphological data can be combined with a molecular matrix either based on a few loci (generated with Sanger techniques) [49] or based on hundreds of loci (generated with nextgeneration sequencing techniques) [80]. A morphological clock is then integrated, along with several molecular clocks, taking into account rate and clock heterogeneity across the dataset. ...
... In F. rubiginosa, three cryptic species of Pleistodontes imperialis coexist in the same localities while retaining reproductive isolation (Sutton et al., 2017), with Wolbachia identified as the most likely candidate of post-zygotic reproductive isolation (Haine & Cook, 2005). Similarly, no hybridization was detected between pollinating-wasps of genus Pegoscapus in Panama (Satler et al., 2022). ...
... First, systematic studies are warranted for testing the accuracy of various phylogenetic methods. For example, simulation tools such as the one proposed by Dismukes and Heath [36] may be useful in performing these assessments using synthetically generated datasets. ...
... Paederinae is one of the largest subfamilies of rove beetles (Staphylinidae and Coleoptera), containing around 7600 described extant species in 225 genera worldwide [1,2]. The majority of the studies relating to this group have mainly been taxonomic, in particular descriptions of new species or generic revisions, phylogenetic studies concentrating mainly on the morphological characters of adults, and to a lesser extent on larval stages, and very Table 1. ...
... maxima) (Molbo et al., 2004;Wiebes, 1995). F. obtusifolia and F. popenoei are each pollinated by two cryptic fig wasp species that cannot be distinguished morphologically (Molbo et al., 2004;Satler et al., 2020). For each fig species, one of the cryptic pollinator species is much more common than the other, and the wasps are sister species (P. ...
... The humerus is often important in traditional systematic methods for identifying and classifying seabird taxa (e.g. Degrange et al., 2018;Thomas et al., 2020b), while conversely, the femur is not a typically informative bone within Procellariiformes (e.g. Mayr & Smith, 2012;Tennyson & Mannering, 2018) or Sphenisciformes (e.g. ...
... These priors are typically advocated by the so-called subjective Bayesian school, initiated by De Finetti (1974). These priors are not so often used in phylogenetics, with the important exception of soft fossil calibrations in molecular dating (see Yang and Rannala (2006); Chapter 5.1 [Pett and Heath 2020]). Uninformative, default or reference priors. ...
... and paleogeographic patterns (scenarios 1 and 2) rely on presence data that are incomplete and uncertain (Janvier and Blieck 1993), making it difficult to reject or support competition using these criteria. A taxon's range is based on whether it is preserved in a particular layer or a particular region; however, decreasing abundance of taxa can result in tails of stratigraphic and/or geographic ranges that are missed entirely due to incomplete sampling of a taxon (Weiss and Marshall 1999;Warnock et al. 2020). The chance of a taxon being preserved in the fossil record near the edges of its range (end or the beginning stratigraphically) are low (Weiss and Marshall 1999). ...
... Assigning fixed costs to each event with no objective justification has the potential to bias results and infer erroneous phylogenetic histories. A new generation of model-based methods relaxes the assumption that cospeciation is the main driver of coevolution and estimate relative rates of different processes directly from the data, overcoming the biases associated with parsimony-based methods [31]. ...
... Other extraction techniques tested on small-bodied low-input samples, for example using Chelex (e.g., Lienhard & Schäffer, 2019), may yield more DNA than the method used here, but this comparison remains to be tested. In extremely small-bodied specimens with low input DNA, whole genome amplification following DNA extraction has been successfully used to increase DNA yield for library preparation (e.g., Branstetter et al. 2017b;Satler et al., 2018). It would be beneficial to test multiple whole genome amplification protocols specifically targeting small-bodied and highly degraded museum specimens. ...