W.C. Wheeler

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• PhD
• Professor at American Museum of Natural History

Phylogenetic analysis strives to construct graphs, such as trees or networks, that encapsulate the historical structure of a set of terminal taxa. This process is based on comparative character data and an optimality criterion by which these graphs are evaluated. Whether there is structure in the data or not, phylogenetic analytical methods will pr...

Phylogenetic minimum description length (PMDL) is proposed as an optimality criterion for phylogenetic analysis. PMDL is based on algorithmic (Kolmogorov) information and the minimum description length principle. This criterion generates natural weighting functions (i.e. not being externally specified) for a diversity of phylogenetic graph, data an...

Anuran larvae are characterized by an extensive array of specialized oral structures that allow them to both graze on substrates and suspension feed with great efficiency. Diversity in these feeding structures accounts for significant diversity of anurans. Herein we describe an astonishing novel buccopharyngeal morphology in six larvae of ‘sand-eat...

A phylogenetic graph search relies on a large number of highly parameterized search procedures (e.g. branch‐swapping, perturbation, simulated annealing, genetic algorithm). These procedures vary in effectiveness over datasets and at alternative points in analytical pipelines. The multi‐armed bandit problem is applied to phylogenetic graph searching...

We present Phylogenetic Graph ( PhyG ), an open‐source, phylogenetic search tool for diverse data types and graphs, including softwired and hardwired networks, in addition to trees. This allows for analysis of horizontal transfer and hybridization scenarios, as well as the necessary vertical inheritance of trees. PhyG is the successor to POY5 in pe...

Scinax is the most species-rich genus of Neotropical treefrogs, with 129 currently recognized species divided between two major clades, the S. catharinae and S. ruber clades. The S. catharinae clade includes 52 species currently placed in the S. perpusillus and S. catharinae groups, whereas the S. ruber clade is composed of 77 species, 13 of which...

An algorithm is described for the optimization of character data (e.g. qualitative, nucleic acid sequence) on softwired phylogenetic networks. The algorithm presented here is an extension of those developed for trees under the parsimony criterion and can form the basis for phylogenetic network search procedures. Although the problem is (in general)...

The treatment of inapplicable characters has proved especially vexing to systematists. Investigators have wrestled with alternative coding scenarios to capture both the presence and absence of a feature, and its variation when present, in a reasonable manner. Three basic issues have presented themselves: (i) impossible states at internal nodes; (ii...

Oval frogs (Elachistocleis) have a broad geographic distribution covering nearly all of South America and parts of Central America. They also have a large inter- and intraspecific variation of the few morphological characters commonly used as diagnostic traits among species of the genus. Based on molecular data, we provide the most complete phyloge...

We performed a comparative analysis of human and 12 non-human primates to identify sequence variations in known cancer genes. We identified 395 human-specific fixed non-silent substitutions that emerged during evolution of human. Using bioinformatics analyses for functional consequences, we identified a number of substitutions that are predicted to...

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arac...

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arac...

Phylogenetic graph structures used in empirical and theoretical analysis have expanded beyond trees to more general directed acyclic graphs including networks and forests. Several methods to reconcile multiple such graphs are presented and discussed here, extending existing consensus and supertree techniques to form a set of phylogenetic supergraph...

The distance Wagner procedure of Farris (American Naturalist, 1972, 106, 645), in its original or random addition sequence form, is a rapid method of tree construction. The original formulation did not allow for refinement of tree hypotheses via common trajectory search operations (e.g. SPR, TBR). Here, the distance Wagner method is extended to all...

True toads of the genus Rhinella are among the most common and diverse group of Neotropical anurans. These toads are widely distributed throughout South America, inhabiting a great diversity of environments and ecoregions. Currently, however, the genus is defined solely on the basis of molecular characters, and it lacks a proper diagnosis. Although...

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree top...

Humans have an increased incidence of epithelial neoplasia compared to non-human primates. We performed a comparative analysis of 21 non-human primate genomes and 54 ancient human genomes to identify variations in known cancer genes that may explain this difference. We identified 299 human-specific fixed non-silent single nucleotide polymorphisms....

In this paper we present a phylogenetic analysis of the treefrogs of the Boana pulchella Group with the goals of (1) providing a rigorous test its monophyly; (2) providing a test of relationships supported in previous studies; and (3) exploring the relationships of the several species not included in previous analyses. The analyses included more th...

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecul...

Background: Given a binary tree [Formula: see text] of n leaves, each leaf labeled by a string of length at most k, and a binary string alignment function ⊗, an implied alignment can be generated to describe the alignment of a dynamic homology for [Formula: see text]. This is done by first decorating each node of [Formula: see text] with an alignm...

Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. This group of arthropods appeared early in the fossil record, with the oldest unambiguous fossils dating to the Silurian. Due to the inaccessibility of some small-bodied lineages, few phylogenetic...

A statistical framework to infer areas of endemism from geographic distributions is proposed. This novel method is based on hidden Markov random fields (HMRFs), a type of undirected graph model commonly used in computer vision. This framework assumes areas of endemism are the states of the hidden layer of the model, whereas taxon distributions are...

The new genus and species Myrmecicultor chihuahuensis Ramírez, Grismado, and Ubick is described and proposed as the type of the new family, Myrmecicultoridae Ramírez, Grismado, and Ubick. The species is ecribellate, with entelegyne genitalia, two tarsal claws, without claw tufts, and the males have a retrolateral palpal tibial apophysis. Some morph...

The general problem of representing collections of trees as a single graph has led to many tree summary techniques. Many consensus approaches take sets of trees (either inferred as separate gene trees or gleaned from the posterior of a Bayesian analysis) and produce a single “best” tree. In scenarios where horizontal gene transfer or hybridization...

Here, we define a sequence file format that allows for multi‐character elements (FASTC). The format is derived from the FASTA format and the custom alphabet format of POY4/5. The format is more general than either of these formats and can represent a broad variety of sequence‐type data. This format should be useful for analyses involving datasets e...

Phylogenetic methods offer a promising advance for the historical study of language and cultural relationships. Applications to date, however, have been hampered by traditional approaches dependent on unfalsifiable authority statements: in this regard, historical linguistics remains in a similar position to evolutionary biology prior to the cladist...

Gladiator Frogs (Boana) is a Neotropical group comprised of 92 species sorted into seven species groups. Herein, we present a phylogeny of the Boana semilineata species group, including all valid nominal species currently or suspected to be assigned to it- many sequenced for the first time. Parsimony and maximum likelihood analyses of two genes (16...

Non‐equilibrium dynamics and non‐neutral processes, such as trait‐dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential non‐equilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework....

We present a molecular phylogenetic analysis of the hylid tribe Hylini, with the goals of testing the monophyly of the genera Du- ellmanohyla, Isthmohyla, and Ptychohyla and providing a discussion on the monophyly of Bromeliohyla, Charadrahyla, Ecnomiohyla, Exerodonta, Megastomatohyla, and Sarcohyla. Our results indicate the paraphyly of Ptychohyla...

Heteroptera, the true bugs, are part of the largest clade of non-holometabolous insects, the Hemiptera, and include > 42 000 described species in about 90 families. Despite progress in resolving phylogenetic relationships between and within infraorders since the first combined morphological and molecular analysis published in 1993 (29 taxa, 669 bp,...

In our recent publication (Sharma et al., 2017), we tested the hypothesis that eggs attached to the legs of male Podoctidae (Opiliones, Laniatores) constituted a case of paternal care, using molecular sequence data in tandem with multiple sequence alignments to test the prediction that sequences of the eggs and the adults that carried them would in...

Peloso et al. (2015: PELOSO) published a comprehensive phylogenetic study of the frog family Microhylidae, which resulted in the discovery that several taxa were not monophyletic. To remedy this, a series of nomenclatural changes were proposed (several generic synonymies and two new subfamilies named). A recent study published in this journal by Sc...

We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups....

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...

This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).

Indo-Pacific members of the speciose and morphologically confusing group of Camponotus ants that resemble C. maculatus (FABRICIUS, 1782) have recently been the subject of a molecular phylogeny, and that analysis is used here as guidance to update the taxonomy of the Micronesian species. It is now known that Micronesian and some Melanesian specimens...

Willi Hennig (1913–76), founder of phylogenetic systematics, revolutionised our understanding of the relationships among species and their natural classification. An expert on Diptera and fossil insects, Hennig's ideas were applicable to all organisms. He wrote about the science of taxonomy or systematics, refining and promoting discussion of the p...

A new practice in systematics, “semaphoront” coding, treats developmental stages as terminals, and it derives from Hennig's concept of the same name. Semaphoront coding has been implemented recently by Lamsdell and Selden (BMC Evol. Biol., 2013, 13:98) and Wolfe and Hegna (Cladistics, 2014, 30:366) in an effort to understand the relationships of fo...

Scorpions (order Scorpiones) are unusual among arthropods, both for the extreme heteronomy of their bauplan and for the high gene family turnover exhibited in their genomes. These phenomena appear to be correlated, as two scorpion species have been shown to possess nearly twice the number of Hox genes present in most arthropods. Segmentally offset...

Two commonly used heuristic approaches to the generalized tree alignment problem are compared in the context of phylogenetic analysis of DNA sequence data. These approaches, multiple sequence alignment + phylogenetic tree reconstruction (MSA+TR) and direct optimization (DO), are alternative heuristic procedures used to approach the nested NP-Hard o...

Background: Many problems in comparative biology are, or are thought to be, best expressed as phylogenetic "networks" as opposed to trees. In trees, vertices may have only a single parent (ancestor), while networks allow for multiple parent vertices. There are two main interpretive types of networks, "softwired" and "hardwired." The parsimony cost...

At both global and local scales, mite harvestmen (Opiliones, Cyphophthalmi) have been shown to have achieved their current global distribution strictly through vicariance. However, the implicit low dispersal capability of this group does not explain how they expand their ranges and come to occupy enormous landmasses prior to rifting. To investigate...

Incongruence between morphological and molecular-based phylogenetic hypotheses has been reported across a wide range of taxa. Specifically, morphological and molecular hypotheses of squamate phylogeny have been consistently incongruent and have been notoriously difficult to reconcile. With the ever-rising popular view of the superiority of molecula...

Sand flies in the psychodid subfamily Phlebotominae carry important human pathogens in the trypanosomatid protozoan genus Leishmania (Cupolillo). Despite the fact that hundreds of sequences for this group are now publicly available, they constitute different sets of taxa and genetic markers. Integrating these data to construct a molecular phylogeny...

The segmental architecture of the arthropod head is one of the most controversial topics in the evolutionary developmental biology of arthropods. The deutocerebral (second) segment of the head is putatively homologous across Arthropoda, as inferred from the segmental distribution of the tripartite brain and the absence of Hox gene expression of thi...

The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fieldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed b...

Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) ge...

Ants that resemble Camponotus maculatus (Fabricius, 1782) present an opportunity to test the hypothesis that the origin of the Pacific island fauna was primarily New Guinea, the Philippines, and the Indo-Malay archipelago (collectively known as Ma-lesia). We sequenced two mitochondrial and four nuclear markers from 146 specimens from Pacific island...

The evolutionary success of the largest animal phylum, Arthropoda, has been attributed to tagmatization, the coordinated evolution of adjacent metameres to form morphologically and functionally distinct segmental regions called tagmata. Specification of regional identity is regulated by the Hox genes, of which 10 are inferred to be present in the a...

Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending to the Cambrian, and is sister to the remaining extant arthropods, the mandibulates. Attempts to resolve the internal phylogeny of chelicerates have achieved little consensus, due to marked discord in both morphological and molecular hypotheses of chelicer...

Introduction The practice of molecular dating is an essential tool for hypothesis testing in evolutionary biology. Vagaries of fossilization and taphonomic bias commonly engender high uncertainty in molecular dating in taxonomic groups wherein few fossils can be unambiguously assigned to phylogenetic nodes. A recent and novel implementation in mole...

Finding the optimal evolutionary history for a set of taxa is a challenging computational problem, even when restricting possible solutions to be "tree-like" and focusing on the maximum-parsimony optimality criterion. This has led to much work on using heuristic tree searches to find approximate solutions. We present an approach for finding exact o...

Specimens of Metasiro from its three known disjunct population centers in the southeastern US were examined and had a 769 bp fragement of the mitochondrial gene cytochrome c oxidase subunit I (COI) sequenced. These populations are located in the western panhandle of Florida and nearby areas of Georgia, in the Savannah River delta of South Carolina,...

We present POY version 5, an open source program for the phylogenetic analysis of diverse data types including qualitative, aligned sequences, unaligned sequences, genomic data, and user‐defined sequences. In addition to the maximum‐parsimony optimality criterion supported by POY 4, POY 5 supports several types of maximum likelihood as well as post...

Language origins and diversification are vital for mapping human history. Traditionally, the reconstruction of language trees has been based on cognate forms among related languages, with ancestral protolanguages inferred by individual investigators. Disagreement among competing authorities is typically extensive, without empirical grounds for reso...

sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecologi...

Abstract Scoring a given phylogenetic network is the first step that is required in searching for the best evolutionary framework for a given dataset. Using the principle of maximum parsimony, we can score phylogenetic networks based on the minimum number of state changes across a subset of edges of the network for each character that are required...

The monophyly of Mandibulata - the division of arthropods uniting pancrustaceans and myriapods - is consistent with several morphological characters, such as the presence of sensory appendages called antennae and the eponymous biting appendage, the mandible. Functional studies have demonstrated that the patterning of the mandible requires the activ...

Even as recent studies have focused on the construction of larger and more diverse datasets, the proper placement of the hymenopteran superfamilies remains controversial. In order to explore the implications of these new data, we here present the first direct optimization-sensitivity analysis of hymenopteran superfamilial relationships, based on a...

Three additional phyletic group types, “periphyletic,” “epiphyletic”, and “anaphyletic” (in addition to Hennigian mono-, para-, and polyphyletic) are defined in terms of trees and phylogenetic networks (trees with directed reticulate edges) via a generalization of the algorithmic definitions of Farris. These designations concern groups defined as m...

Aim Our aim was to elucidate the effect of mass extinctions on inferred crown ages of terrestrial clades endemic to ancient islands. We thereby assessed the potential for mass extinction events, such as the Zealandian marine incursion episode in the Oligocene, to skew the interpretation of the evolutionary history of clades of various sizes. Locat...

Spiny-backed tree frogs of the genus Osteocephalus are conspicuous components of the tropical wet forests of the Amazon and the Guiana Shield. Here, we revise the phylogenetic relationships of Osteocephalus and its sister group Tepuihyla, using up to 6134bp of DNA sequences of nine mitochondrial and one nuclear gene for 338 specimens from eight cou...

One of the most time-consuming aspects of Bayesian posterior probability analysis in the analysis of phylogenetic trees is the use of Metropolis-coupled Markov chain Monte Carlo (MC3) methods to determine relative posteriors and identify maximum a posteriori (MAP) trees. Here, analytical and numerical methods are presented to determine tree likelih...

The description of venation patterns in neotropical Vaccinieae has been problematic because of the lack of an operational definition. Moreover, the underlying homologies remain unknown across and within lineages, thus precluding the use of venation characters in phylogenetic analyses. Venation patterns are often obscured in herbarium and living spe...

The frog clade composed of the alsodid genera Alsodes + Eupsophus is the most species-rich of the Patagonian endemic frog clades, including nearly 31 of the slightly more than 50 species of that region. The biology of this group of frogs is poorly known, its taxonomy quite complex (particularly Alsodes), and its diversity in chromosome number strik...

Background A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The patterns that can be observed...

Background The inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpart is known as the multiple sequence alignment problem. There are various criteria and methods available to perform multiple sequen...

Species of the genus Pleurodema are relatively small, plump frogs that mostly occur in strong-seasonal and dry environments. The genus currently comprises 14 species distributed from Panama to southern Patagonia. Here we present a phylogenetic analysis of Pleurodema, including all described species and several outgroups. Our goals include testing i...

Although there has been a recent proliferation in maximum-likelihood (ML)-based tree estimation methods based on a fixed sequence alignment (MSA), little research has been done on incorporating indel information in this traditional framework. We show, using a simple model on a single character example, that a trivial alignment of a different form t...

We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonot...

Systematics: A Course of Lectures is designed for use in an advanced undergraduate or introductory graduate level course in systematics and is meant to present core systematic concepts and literature. The book covers topics such as the history of systematic thinking and fundamental concepts in the field including species concepts, homology, and hyp...

Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutio...

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Systematics: A Course of Lectures is designed for use in an advanced undergraduate or introductory graduate level course in systematics and is meant to present core systematic concepts and literature. The book covers topics such as the history of systematic thinking and fundamental concepts in the field including species concepts, homology, and hyp...

Farris (1983) stated that the rationale of the parsimony criterion was to minimize extra (i.e. non-minimal) steps. For traditional characters, this is equivalent to minimizing total steps (i.e. length). Under dynamic homology (sensu Wheeler, 2001), this identity is broken. Here, it is shown that extra steps (but not total) can be minimized triviall...

The first comprehensive analysis of higher-level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF-1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symp...

The Hymenoptera--ants, bees and wasps--represent one of the most successful but least understood insect radiations. We present the first comprehensive molecular study spanning the entire order Hymenoptera. It is based on approximately 7 kb of DNA sequence from 4 gene regions (18S, 28S, COI and EF-1α) for 116 species representing all superfamilies a...

Novel pathogens have the potential to become critical issues of national security, public health and economic welfare. As demonstrated by the response to Severe Acute Respiratory Syndrome (SARS) and influenza, genomic sequencing has become an important method for diagnosing agents of infectious disease. Despite the value of genomic sequences in cha...

Several commonly used support measures are discussed and described as either optimal or expected support. This distinction is based on whether the indices are based on a function of optimal and non-optimal hypotheses, or on the statistical expectation of clades. © The Willi Hennig Society 2010.

The leaf or monkey frogs of the hylid subfamily Phyllomedusinae are a unique group of charismatic anurans. We present a molecular phylogenetic analysis that includes 45 of the 60 species of phyllomedusines using up to 12 genes and intervening tRNAs. The aims were to gain a better understanding of the phylogenetic position of Phrynomedusa, test the...

We present POY version 4, an open source program for the phylogenetic analysis of morphological, prealigned sequence, unaligned sequence, and genomic data. POY allows phylogenetic inference when not only substitutions, but insertions, deletions, and rearrangement events are allowed (computed using the breakpoint or inversion distance). Compared wit...

A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however...