David L. Swofford's research while affiliated with Florida Museum of Natural History and other places

Publications (70)

Article
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BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrat...
Preprint
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Motivation: The coalescent model is now widely accepted as a necessary component for phylogenetic inference from genome-scale data. However, because model-based analysis under the coalescent is computationally prohibitive, a variety of inferential frameworks and corresponding algorithms have been proposed for estimation of species-level phylogenies...
Article
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Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each...
Article
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Phylogeographic analysis can be described as the study of the geological and climatological processes that have produced contemporary geographic distributions of populations and species. Here, we attempt to understand how the dynamic process of landscape change on Madagascar has shaped the distribution of a targeted clade of mouse lemurs (genus Mic...
Article
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Abstract A fern from the French Pyrenees-×Cystocarpium roskamianum-is a recently formed intergeneric hybrid between parental lineages that diverged from each other approximately 60 million years ago (mya; 95% highest posterior density: 40.2-76.2 mya). This is an extraordinarily deep hybridization event, roughly akin to an elephant hybridizing with...
Article
Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors. Marginal likelihoods can be estimated using newer methods...
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
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##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
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Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these appro...
Article
Because horizontal gene transfer can confound the recovery of the largely prokaryotic tree of life (ToL), most genome-based techniques seek to eliminate horizontal signal from ToL analyses, commonly by sieving out incongruent genes and data. This approach greatly limits the number of gene families analysed to a subset thought to be representative o...
Article
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Here we provide a detailed comparative analysis across the candidate X-Inactivation Center (XIC) region and the XIST locus in the genomes of six primates and three mammalian outgroup species. Since lemurs and other strepsirrhine primates represent the sister lineage to all other primates, this analysis focuses on lemurs to reconstruct the ancestral...
Article
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Inosine monophosphate dehydrogenase (IMPDH) catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinct catalytic residues. How did Nature construct suc...
Data
Simulations of the Thr Pathway with Glu431 Treated MM. Methods as described in Figure S1 (1.75 MB TIF)
Data
Phylogenetic Tree of IMPDH and GMPR The unrooted tree was inferred with MrBayes (including posterior probabilities) [49]. Organism names are followed by their sequence accession codes. IMPDH, GMPR1, and GMPR2 refer to members of InterPro accession codes IPR005990, IPR005993, and IPR005994, respectively. (4.39 MB TIF)
Data
Optimization of the Wang-Landau Metadynamics Conditions In order to optimize the Wang-Landau metadynamics conditions, three setups with the final Gaussian heights 1.0 kcal/mol, 0.06 kcal/mol, and 0.01 kcal/mol were executed. The 1.0 kcal/mol simulation yielded a result with large uncertainties and gave the free energy barrier of 14 kcal/mol at the...
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Phylogenetic Analysis Detailed description of the derivation of Figure S4. (101 KB PDF)
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Experimental Estimation of the Contribution of the Thr Pathway Assuming that E431Q mutation disables the Thr pathway, but has no effect on the pH dependence of the Arg pathway, then the pH-rate profile of the wild-type enzyme is described by: where Ka = 10−7.6 as determined from the pH dependence of E431Q. The pH-rate profile of the wild-type enz...
Article
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Unlabelled: A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulation...
Article
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Almost all studies that estimate phylogenies from DNA sequence data under the maximum-likelihood (ML) criterion employ an approximate approach. Most commonly, model parameters are estimated on some initial phylogenetic estimate derived using a rapid method (neighbor-joining or parsimony). Parameters are then held constant during a tree search, and...
Article
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Although long-branch attraction (LBA) is frequently cited as the cause of anomalous phylogenetic groupings, few examples of LBA involving real sequence data are known. We have found several cases of probable LBA by analyzing subsamples from an alignment of 18S rDNA sequences for 133 metazoans. In one example, maximum parsimony analysis of sequences...
Article
This unit provides a general description of reconstructing evolutionary trees using PAUP* 4.0. The protocol takes users through an example analysis of mitochondrial DNA sequence data using the parsimony and the likelihood criteria to infer optimal trees. The protocol also discusses searching options available in PAUP* and demonstrates how to import...
Chapter
Taxonomists currently recognize seven species and three subspecies in the genus Micropterus, Based on variation in meristic characters, allozymes, and mtDNA, two subspecies are clearly distinct from one another and warrant elevation to species status. Micropterus salmoides floridanus should now be recognized as the Florida bass M. floridanus, and M...
Book
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence o...
Article
The Bayesian Methods in Phylogenetics symposium was held as part of Evolution 2001 in Knoxville, TN, USA, from 26 to 30 June 2001.
Article
As maximum-likelihood approaches to the study of molecular systematics and evolution become both more flexible and more accessible, the importance of understanding the statistical properties of parameter estimation becomes critical. Using variation in NADH-2 sequences for 40 species of requiem sharks, we illustrate that estimates of rate heterogene...
Article
Steel demonstrated that the maximum-likelihood function for a phylogenetic tree may have multiple local maxima. If this phenomenon were general, it would compromise the applicability of maximum likelihood as an optimality criterion for phylogenetic trees. In several simulation studies reported on in this paper, the true tree, and other trees of ver...
Article
Phylogenies that include long, unbranched lineages can be difficult to reconstruct. This is because long-branch taxa (such as rapidly evolving species) may share character states by chance more often than more closely related taxa share derived character states through common ancestry. Despite Kim's warning that added taxa can decrease accuracy, so...
Article
We have developed a rapid parsimony method for reconstructing ancestral nucleotide states that allows calculation of initial branch lengths that are good approximations to optimal maximum-likelihood estimates under several commonly used substitution models. Use of these approximate branch lengths (rather than fixed arbitrary values) as starting poi...
Article
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NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of se...
Article
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The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed t...
Article
We provide three simple examples demonstrating that Wheeler and Nixon's method of recoding “stepmatrix’ characters can fail to yield most parsimonious reconstructions of character evolution under specified cost (transformation-weight) schemes. These examples variously indicate undercounting or overcounting of tree lengths due to an inappropriate as...
Article
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The monophyly of Rodentia has repeatedly been challenged based on several studies of molecular sequence data. Most recently, D''Erchia et al. (1996) analyzed complete mtDNA sequences of 16 mammals and concluded that rodents are not monophyletic. We have reanalyzed these data using maximum-likelihood methods. We use two methods to test for significa...
Article
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Isozyme electrophoresis was used to assess genetic variation in potoos (Nyctibiidae), a distinctive Neotropical family of caprimulgiform nightbirds. Interspecific levels of genetic differentiation among potoos are extremely high (range of Nei's D = 0.191-1.172) and are comparable to intergeneric levels of differentiation in other bird families. In...
Article
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A morphological and allozymic examination of variation in the Etheostoma squamiceps complex led to the discovery of five previously unrecognized species and brings the total number of described species in the subgenus Catonotus to 17. Each of the 10 species in the E. squamiceps complex has a unique second dorsal-fin pattern on the breeding male and...
Article
The problem of assigning optimal character states to the hypothetical ancestors of an evolutionary tree under the Wagner parsimony criterion is examined. A proof is provided for the correctness of Farris's well-known, but previously unproven, algorithm for solving this problem. However, the solution is not, in general, unique, and Farris's method o...
Article
Most workers attempting to infer evolutionary trees from polymorphic data using established parsimony procedures either have ignored frequency information entirely or have tolerated “optimal” solutions that hypothesize ancestors that cannot possibly exist in the space of the original frequencies. We describe a new method for inferring evolutionary...
Article
Etheostoma whipplei and E. radiosum are closely related to one another but show no evidence of intergradation. The two species are distributed allopatrically over most of their ranges, but overlap slightly in the Ouachita River system and possibly in the Red River system. Only one mixed collection of the two species was examined during this study,...
Article
Darters feed on small benthic organisms, primarily insects, and evolutionarily have become increasingly small and benthic; most species are less than 80 mm in standard length. Constraints on decreasing body size include living in midwater and territoriality. Lineages of darters have arisen as new habitats were invaded. Consequently, members of diff...
Article
Full-text available
The salt marsh greenhead, Tabanus nigrovittatus (Diptera Tabanidae), long suspected of being composed of several cryptic species, has been examined by starch gel electrophoresis of enzymes. Adult flies from four localities in New Jersey were separable into two genetically distinct species, based on three fixed locus differences. Total length was si...
Article
BIOSYS-1 is a FORTRAN IV program designed to aid biochemical population geneticists and systematists in the analysis of electrophoretically detectable allelic variation. It can be used to compute allele frequencies and genetic variability measures, to test for deviation of genotype frequencies from Hardy-Weinberg expectations, to calculate F-statis...

Citations

... For example, there are fast NJ implementations suitable for hundreds of thousands of sequences [Wheeler, 2009]. Similarly, BEAGLE provides a fast implementation of the likelihood computation [Ayres et al., 2012[Ayres et al., , 2019. Nevertheless, asymptotically, NJ remains the algorithmic bottleneck of Dodonaphy with O(n 3 ). ...
... For example, when the multispecies coalescent is used as the basis for inference of a phylogenetic network from multilocus DNA sequence data, an inheritance parameter γ e is used to represent the proportional contribution of the parental lineage represented by arc e to the lineage that descends from the reticulation vertex. As an alternative to use of algorithms for constrained optimization, transformations of parameters may be applied to allow application of faster, better-performing numerical algorithms for unconstrained parameter estimation (see, e.g., the approach of Peng et al. (2021)). ...
... The diversity and efficiency of the modern wood-decomposer pathways lagged behind evolution of wood itself [96]. Four wood-decay innovations are thought to have emerged much after the evolution of wood, in order of emergence: (i) the enzymatic pathway key to white rot fungi which breaks down lignin [11]; (ii) the less metabolically expensive chelator-mediated Fenton pathway in which free radicals modify lignin, allowing brown rot fungi to access other carbon polymers [97][98][99]; (iii) the modification of invertebrate gut symbiosis [100]; and (iv) the origin of fungus-farming insects [91]. ...
... The geographic distribution of M. lehilahytsara is uniquely suited for this purpose. It is the only mouse lemur species found in isolated Central Highland forest patches Yoder et al., 2016) as well as in the humid rainforests along the escarpment of Madagascar's east coast (Radespiel et al., 2012;Blanco et al., 2017). It is also found in the rainforests of northeastern Madagascar, as the formerly recognized M. mittermeieri was recently recommended as a junior synonym of M. lehilahytsara based on both morphological (Schüßler et al., 2020a) and molecular evidence . ...
... The RB algorithm estimates substitution models alongside the phylogeny without the need for a priori selection. The parameter for the proportion of invariable sites (+I) was not estimated given its correlation with the +Γ parameter, resulting in inadequate models when both +Γ and +I are included (Sullivan et al., 1999;Mayrose et al., 2005). Given that the dataset focused on intraspecific diversification, we did not assume the substitution rate to vary substantially throughout the tree and, as a result, we used a strict clock model with lognormally distributed priors (mean = 1, SD = 1.25) for all partitions and a coalescent constant population tree prior. ...
... Pairwise, genetic distance between accessions was calculated based on the minimum evolution evolutionary distance coefficient [48] using IRAP and REMAP data, and the correction between two distance matrices was statistically tested by using the mantel test. The ability of IRAP and REMAP markers to reveal genetic relationships among all the Ae. ...
... A database in GraphPad Prism version 8.0.0 for Windows was designed for the data obtained; a comparative analysis (Mann-Whitney U test, t Student) was performed to determine if there was any signi cant difference between groups. Gene frequencies, summary of genetic variation parameters, and deviations from Hardy-Weinberg equilibrium were determined by using the BIOSYS-1 program [21]. ...
... A broad geographic, molecular assessment to supplement existing morphological information is needed to assess validity of the two remaining subspecies of E. radiosum. W E redescribe and recognize Etheostoma cyanorum as a valid species, separate from Etheostoma radiosum (Orangebelly Darter; Moore and Rigney, 1952;Collette, 1965;Matthews and Gelwick, 1988), within the larger Etheostoma whipplei (Redfin Darter) species complex, or clade (Retzer et al., 1986;Lang and Mayden, 2006;Near et al., 2011). We review its taxonomic history and recent treatments, supplement and reevaluate previous morphological data, and add molecular genetic data supporting specific recognition. ...
... Zhao et al., 2020). Our results contribute to a growing scientific consensus around the validity of M. floridanus as a distinct species (Kassler et al., 2002;Near et al., 2003;Near & Kim, 2021 perch (Stepien et al., 2015), suggesting that the timing of population divergence in this geographic locale can vary across fish taxa. ...
... Rufous Potoo is the smallest potoo (21-25 cm) and is restricted to the Amazon lowlands, from western Amazonia east to the Rio Tapajós (Cohn-Haft 1999, Solano-Ugalde 2011. Molecular studies revealed that N. bracteatus represents the oldest lineage in the family (Brumfield et al. 1997, Braun & Huddleston 2009, Costa 2014, White et al. 2017 and, due to its unique morphological and behavioural characteristics, a monotypic genus Phyllaemulor has been erected to accommodate the species (Costa et al. 2018). Despite being the only understorey potoo (Ingels et al. 2008, Cleere 2010, which might make N. bracteatus easier to observe, its breeding ecology is poorly known, and few published data are available on even basic aspects of the species' natural history (Cohn-Haft 1999, Cleere 2010, Solano-Ugalde 2011. ...