Taran Grant

PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Abstract The known diversity of dart-poison frog species has grown from 70 in the 1960s to 247 at present, with no sign that the discovery of new species will wane in the foreseeable future. Although this growth in knowledge of the diversity of this group has been accompanied by detailed investigations of many aspects of the biology of dendrobatids, their phylogenetic relationships remain poorly understood. This study was designed to test hypotheses of dendrobatid diversification by combining new and prior genotypic and phenotypic evidence in a total evidence analysis. DNA sequences were sampled for five mitochondrial and six nuclear loci (approximately 6,100 base pairs [bp]; x¯ = 3,740 bp per terminal; total dataset composed of approximately 1.55 million bp), and 174 phenotypic characters were scored from adult and larval morphology, alkaloid profiles, and behavior. These data were combined with relevant published DNA sequences. Ingroup sampling targeted several previously unsampled species, including Aromobates nocturnus, which was hypothesized previously to be the sister of all other dendrobatids. Undescribed and problematic species were sampled from multiple localities when possible. The final dataset consisted of 414 terminals: 367 ingroup terminals of 156 species and 47 outgroup terminals of 46 species. Direct optimization parsimony analysis of the equally weighted evidence resulted in 25,872 optimal trees. Forty nodes collapse in the strict consensus, with all conflict restricted to conspecific terminals. Dendrobatids were recovered as monophyletic, and their sister group consisted of Crossodactylus, Hylodes, and Megaelosia, recognized herein as Hylodidae. Among outgroup taxa, Centrolenidae was found to be the sister group of all athesphatanurans except Hylidae, Leptodactyidae was polyphyletic, Thoropa was nested within Cycloramphidae, and Ceratophryinae was paraphyletic with respect to Telmatobiinae. Among dendrobatids, the monophyly and content of Mannophryne and Phyllobates were corroborated. Aromobates nocturnus and Colostethus saltuensis were found to be nested within Nephelobates, and Minyobates was paraphyletic and nested within Dendrobates. Colostethus was shown to be rampantly nonmonophyletic, with most species falling into two unrelated cis- and trans-Andean clades. A morphologically and behaviorally diverse clade of median lingual process-possessing species was discovered. In light of these findings and the growth in knowledge of the diversity of this large clade over the past 40 years, we propose a new, monophyletic taxonomy for dendrobatids, recognizing the inclusive clade as a superfamily (Dendrobatoidea) composed of two families (one of which is new), six subfamilies (three new), and 16 genera (four new). Although poisonous frogs did not form a monophyletic group, the three poisonous lineages are all confined to the revised family Dendrobatidae, in keeping with the traditional application of this name. We also propose changes to achieve a monophyletic higher-level taxonomy for the athesphatanuran outgroup taxa. Analysis of character evolution revealed multiple origins of phytotelm-breeding, parental provisioning of nutritive oocytes for larval consumption (larval oophagy), and endotrophy. Available evidence indicates that transport of tadpoles on the dorsum of parent nurse frogs—a dendrobatid synapomorphy—is carried out primitively by male nurse frogs, with three independent origins of female transport and five independent origins of biparental transport. Reproductive amplexus is optimally explained as having been lost in the most recent common ancestor of Dendrobatoidea, with cephalic amplexus arising independently three times.

Data exploration in phylogenetic inference: scientific, heuristic, or neither

The methods of data exploration have become the centerpiece of phylogenetic inference, but without the scientific importance of those methods having been identified. We examine in some detail the procedures and justifications of Wheelers sensitivity analysis and relative rate comparison (saturation analysis). In addition, we review methods designed to explore evidential decisiveness, clade stability, transformation series additivity, methodological concordance, sensitivity to prior probabilities (Bayesian analysis), skewness, computer‐intensive tests, long‐branch attraction, model assumptions (likelihood ratio test), sensitivity to amount of data, polymorphism, clade concordance index, character compatibility, partitioned analysis, spectral analysis, relative apparent synapomorphy analysis, and congruence with a “known” phylogeny. In our review, we consider a method to be scientific if it performs empirical tests, i.e., if it applies empirical data that could potentially refute the hypothesis of interest. Methods that do not perform tests, and therefore are not scientific, may nonetheless be heuristic in the scientific enterprise if they point to more weakly or ambiguously corroborated hypotheses, such propositions being more easily refuted than those that have been more severely tested and are more strongly corroborated. Based on common usage, data exploration in phylogenetics is accomplished by any method that performs sensitivity or quality analysis. Sensitivity analysis evaluates the responsiveness of results to variation or errors in parameter values and assumptions. Sensitivity analysis is generally interpreted as providing a measure of support, where conclusions that are insensitive (robust, stable) to perturbations are judged to be accurate, probable, or reliable. As an alternative to that verificationist concept, we define support objectively as the degree to which critical evidence refutes competing hypotheses. As such, degree of support is secondary to the scientific optimality criterion of maximizing explanatory power. Quality analyses purport to distinguish good, reliable, accurate data from bad, misleading, erroneous data, thereby assessing the ability of data to indicate the true phylogeny. Only the quality analysis of character compatibility can be judged scientific—and a weak test at that compared to character congruence. Methods judged to be heuristic include Bremer support, long‐branch extraction, and safe taxonomic reduction, and we underscore the great heuristic potential of a posteriori analysis of patterns of transformations on the total‐evidence cladogram. However, of the more than 20 kinds of data exploration methods evaluated, the vast majority is neither scientific nor heuristic. Given so little demonstrated cognitive worth, we conclude that undue emphasis has been placed on data exploration in phylogenetic inference, and we urge phylogeneticists to consider more carefully the relevance of the methods that they employ.

Transformation Series as an Ideographic Character Concept

An ideographic concept of character is indispensable to phylogenetic inference. Hennig proposed that characters be conceptualized as “transformation series”, a proposal that is firmly grounded in evolutionary theory and consistent with the method of inferring transformation events as evidence of phylogenetic propinquity. Nevertheless, that concept is usually overlooked or rejected in favor of others based on similarity. Here we explicate Hennigs definition of character as an ideographic concept in the science of phylogenetic systematics. As transformation series, characters are historical individuals akin to species and clades. As such, the related concept of homology refers to a historical identity relation and is not equivalent to or synonymous with synapomorphy. The distinction between primary and secondary homology is dismissed on the grounds that it conflates the concept of homology with the discovery operations used to detect instances of that concept. Although concern for character dependence is generally valid, it is often misplaced, focusing on functional or developmental correlation (both of which are irrelevant in phylogenetic systematics but may be valid in other fields) instead of the historical/transformational independence relevant to phylogenetic inference. As an ideographic science concerned with concrete objects and events (i.e. individuals), intensionally and extensionally defined properties are inconsistent with the individuation of characters for phylogenetic analysis, the utility of properties being limited to communicating results and facilitating future rounds of testing.

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.

Systematics of the Neotropical Genus Leptodactylus Fitzinger, 1826 (Anura: Leptodactylidae): Phylogeny, the Relevance of Non-molecular Evidence, and Species Accounts

Abstract. A phylogeny of the species-rich clade of the Neotropical frog genus Leptodactylus sensu stricto is presented on the basis of a total evidence analysis of molecular (mitochondrial and nuclear markers) and non-molecular (adult and larval morphological and behavioral characters) sampled from > 80% of the 75 currently recognized species. Our results support the monophyly of Leptodactylus sensu stricto, with Hydrolaetare placed as its sister group. The reciprocal monophyly of Hydrolaetare and Leptodactylus sensu stricto does not require that we consider Hydrolaetare as either a subgenus or synonym of Leptodactylus sensu lato. We recognize Leptodactylus sensu stricto, Hydrolaetare, Adenomera, and Lithodytes as valid monophyletic genera. Our results generally support the traditionally recognized Leptodactylus species groups, with exceptions involving only a few species that are easily accommodated without proposing new groups or significantly altering contents. The four groups form a pectinate tree, with the Leptodactylus fuscus group diverging first, followed by the L. pentadactylus group, which is sister to the L. latrans and L. melanonotus groups. To evaluate the impact of non-molecular evidence on our results, we compared our total evidence results with results obtained from analyses using only molecular data. Although non-molecular evidence comprised only 3.5% of the total evidence matrix, it had a strong impact on our total evidence results. Only one species group was monophyletic in the molecular-only analysis, and support differed in 86% of the 54 Leptodactylus clades that are shared by the results of the two analyses. Even though no non-molecular evidence was included for Hydrolaetare, exclusion of that data partition resulted in that genus being nested within Leptodactylus, demonstrating that the inclusion of a small amount of non-molecular evidence for a subset of species can alter not only the placement of those species, but also species that were not scored for those data. The evolution of several natural history and reproductive traits is considered in the light of our phylogenic framework. Invasion of rocky outcrops, larval oophagy, and use of underground reproductive chambers are restricted to species of the Leptodactylus fuscus and L. pentadactylus groups. In contrast, larval schooling, larval attendance, and more complex parental care are restricted to the L. latrans and L. melanonotus groups. Construction of foam nests is plesiomorphic in Leptodactylus but their placement varies extensively (e.g., underground chambers, surface of waterbodies, natural or excavated basins). Information on species synonymy, etymology, adult and larval morphology, advertisement call, and geographic distribution is summarized in species accounts for the 30 species of the Leptodactylus fuscus group, 17 species of the L. pentadactylus group, eight species of the L. latrans group, and 17 species of the L. melanonotus group, as well as the three species that are currently unassigned to any species group.

From conviction to anti-superfluity: old and new justifications of parsimony in phylogenetic inference

Traditional justifications of parsimony in phylogenetic inference assume a correspondence between character‐state similarity and steps (character transformation events). In addition to similarity, justifying arguments appeal to conviction, descriptive efficiency, ad hoc hypotheses of homoplasy and frequentist probability. Each of these rationales fails in so far as the arguments are incoherent or logically inconsistent with the ontological status of what is assumed and being explained historically. An ideographic justification of parsimony, where character‐states constitute transformation events, does, however, allow for a rational preference of most parsimonious phylogenetic hypotheses by invoking the anti‐superfluity principle (ASP). According to ASP, explanatory power is maximized by minimizing the number of transformation events required to explain the character‐states of the terminal taxa as hypotheses of homology, where the concept homology is restricted to just those inherited“things” shared by species. The empirical significance of this rationale is exemplified with the method of direct optimization, which can identify more parsimonious hypotheses than can be confirmed with an analysis of character‐state similarities.

Clade support measures and their adequacy

In addition to hypothesis optimality, the evaluation of clade (group, edge, split, node) support is an important aspect of phylogenetic analysis. Here we clarify the logical relationship between support and optimality and formulate adequacy conditions for support measures. Support, S, and optimality, O, are both empirical knowledge claims about the strength of hypotheses, h1, h2, …hn, in relation to evidence, e, given background knowledge, b. Whereas optimality refers to the absolute strength of hypotheses, support refers to the relative strength of hypotheses. Consequently, support and optimality are logically related such that they vary in direct proportion to each other, S(h | e,b) ∝ O(h | e,b). Furthermore, in order for a support measure to be objective it must quantify support as a function of explanatory power. For example, Goodman–Bremer support and ratio of explanatory power (REP) support satisfy the adequacy requirement S(h | e,b) ∝ O(h | e,b) and calculate support as a function of explanatory power. As such, these are adequate measures of objective support. The equivalent measures for statistical optimality criteria are the likelihood ratio (or log‐likelihood difference) and likelihood difference support measures for maximum likelihood and the posterior probability ratio and posterior probability difference support measures for Bayesian inference. These statistical support measures satisfy the adequacy requirement S(h | e,b) ∝ O(h | e,b) and to that extent are internally consistent; however, they do not quantify support as a function of explanatory power and therefore are not measures of objective support. Neither the relative fit difference (RFD; relative GB support) nor any of the parsimony (bootstrap and jackknife character resampling) or statistical [bootstrap character resampling, Markov chain Monte Carlo (MCMC) clade frequencies] support measures based on clade frequencies satisfy the adequacy condition S(h | e,b) ∝ O(h | e,b) or calculate support as a function of explanatory power. As such, they are not adequate support measures.

Biological invasions and the acoustic niche: the effect of bullfrog calls on the acoustic signals of white-banded tree frogs.

Invasive species are known to affect native species in a variety of ways, but the effect of acoustic invaders has not been examined previously. We simulated an invasion of the acoustic niche by exposing calling native male white-banded tree frogs (Hypsiboas albomarginatus) to recorded invasive American bullfrog (Lithobates catesbeianus) calls. In response, tree frogs immediately shifted calls to significantly higher frequencies. In the post-stimulus period, they continued to use higher frequencies while also decreasing signal duration. Acoustic signals are the primary basis of mate selection in many anurans, suggesting that such changes could negatively affect the reproductive success of native species. The effects of bullfrog vocalizations on acoustic communities are expected to be especially severe due to their broad frequency band, which masks the calls of multiple species simultaneously.

Testing Methods: The Evaluation of Discovery Operations in Evolutionary Biology

Scientific discovery requires both abstract, theoretically defined concepts and discovery operations formed by sets of rules that permit the empirical detection of instances of those concepts. In this paper, I examine the ontological status of discovery operations and the tests employed to evaluate them in evolutionary biology. Attention is drawn to the distinction between nomothetic (universal, predictive) and ideographic (historical, retrodictive) discovery operations, and between complementary and exclusive discovery operations. Three types of tests of discovery operations are commonly employed in evolutionary biology. Theoretical tests aim to show that a discovery operation is inconsistent with accepted, well‐corroborated, empirical theories. Empirical tests evaluate the performance of competing discovery operations in terms of their results when applied to the same empirical data sets. Philosophical tests aim to show that an operation is inconsistent with logical and epistemological principles. Appropriately designed theoretical and philosophical tests of ideographic discovery operations may be scientifically valid. Empirical tests, however, are incapable of evaluating the scientific merits of competing discovery operations. Nonetheless, empirical comparisons (not tests) of competing discovery operations may provide insight into the ways discovery operations may be misleading and therefore may play an important role in stimulating critical debate and eventually establishing a scientifically optimal operation. In practice, theoretical and philosophical tests are often combined to test competing discovery operations as rigorously as possible.

Widespread Occurrence of the American Bullfrog, Lithobates catesbeianus (Shaw, 1802) (Anura: Ranidae), in Brazil

ABSTRACT. We report new records of Lithobates catesbeianus feral populations in Brazil. Data were based on fieldwork, natural history collection records, and literature and electronic database searches. Lithobates catesbeianus occurs in 130 municipalities of Brazil, including 55 presented for the first time in this work. Most records are from south and southeastern Brazil in the Atlantic Forest biome with climatic conditions that are favorable to the establishment of bullfrog populations. The wide and possibly expanding distribution of feral L. catesbeianus populations in Brazil poses a major conservation challenge and demands research on the invasion patterns.