Phylogenetic relationships based on morphological data and taxonomy of the genus Salvadora Baird & Girard, 1853 (Reptilia, Colubridae)

The genus Salvadora has not been subjected to a modern phylogenetic analysis. Described in 1853, its taxonomic history is complex and confusing. In this study, we evaluate the monophyly of the genus and present the first phylogenetic hypothesis based on an analysis of 66 qualitative and quantitative morphological characters of over 1000 specimens representing all described taxa across their entire distribution. Morphological characters were processed in Fast Morphology for subsequent phylogenetic analysis in PAUP under the maximum parsimony criterion. We obtained a single tree in which Salvadora appears as a monophyletic group with two clearly defined geographic species groups: a southern mexicana group and a northern grahamiae group. Based on our phylogenetic hypothesis, we evaluate the taxonomic status of all described taxa. Additionally, we include a diagnosis for all species, distribution maps, and an illustrated dichotomous taxonomic key of the genus.

Cladistic analysis and taxonomic review of the millipede tribe Arthrosolaenomeridini Hoffman, 1976 (Polydesmida: Chelodesmidae)

Chelodesmidae is one of the most diverse families belonging to the Polydesmida, comprising almost 800 described species distributed in 172 genera, 20 tribes and two subfamilies. Among the tribes within the Neotropical subfamily Chelodesminae, Arthrosolaenomeridini represents a very interesting group occurring in the Central-West region of Brazil. Currently the tribe contains three genera: Arthrosolaenomeris Schubart, 1943, Gangugia Schubart, 1947, and Angelodesmus Schubart, 1962. In this study, we conducted a cladistic analysis including 18 species of Arthrosolaenomeridini and 7 species of other associated Chelodesminae tribes as an outgroup. The matrix is composed of 64 morphological characters from which 39 are herein proposed for the first time. The data were analyzed under the parsimony criterion using TNT 1.5. Based on the results, Arthrosolaenomeridini was recovered as monophyletic with Macrocoxodesmini + Telonychopodini as sister group. Arthrosolaenomeris Schubart, 1943 and Gangugia Schubart, 1947 were recovered as monophyletics. The genus Angelodesmus Schubart, 1962 was recovered as paraphyletic and redefined as monotypic. The tribe is now composed of the genera Arthrosolaenomeris (6 spp.), Gangugia (6 spp.), Angelodesmus (monotypic), Abiliodesmus n. gen. (4 spp.) and Folcloredesmus n. gen. (monotypic). In addition, we conduct a taxonomic revision of the tribe Arthrosolaenomeridini providing detailed redescriptions, drawings, and distribution maps for all species and genera, including the two new genera and the ten new species proposed: Arthrosolaenomeris saci n. sp.; A. curupira n. sp.; A. caipora n. sp.; A. iara n. sp.; Gangugia boitata n. sp.; G. cuca n. sp.; G. boto n. sp.; G. mula n. sp.; Abiliodesmus mapinguari n. sp. and Folcloredesmus thomasi n. sp. Furthermore, we include an identification key to all the genera and species.

Tree-Building Algorithms and Philosophies

This chapter evaluates “quantitative cladistics” in detail, including the issues of fit, parsimony algorithms, and character weighting. Although systematists have long associated characters with taxa, the relationship between character data and “phylogeny” has not always been obvious. The ideas of Willi Hennig clarified this relationship, and the formalization of these concepts in a quantitative method, via the parsimony criterion, allowed for computer implementation of phylogenetic inference and the feasible solution of previously intractable problems. It is this computational capability that took the study of taxonomic relationships from an almost purely qualitative and speculative enterprise to one dominated by the use of computer software and “objective” methodologies. The chapter then discusses the use, advantages, and disadvantages of maximum likelihood and Bayesian techniques as alternative approaches to the application of parsimony.

Simultaneous equations modelling of communities with interacting species networks

To understand community assembly, ecologists have long sought to extract the signal of biotic interactions from species co-occurrence patterns. These efforts face multiple difficulties such as confounding environmental effects, confounding indirect interactions between multiple species and asymmetry of interactions. To address these problems, we propose Simultaneous Community Equations Modelling (SCEM) as a framework to explicitly account for asymmetric interaction networks in community models. SCEM uses a system of equations to model the occurrence of each species as a function of measured and unmeasured (latent) environmental predictors, and the occurrence of potentially all the other species in the community. Biotic interactions most supported by the data are identified using heuristic optimization of a parsimony criterion, implemented as a Genetic Algorithm. Extensive simulations show that SCEM can recover interaction network topologies in virtual communities. We present a software to implement SCEM and illustrate its application with a case study.

A new weevil genus from the highlands of China casts doubts on monophyly of Cotasteromimina (Coleoptera: Curculionidae, Molytinae)

We describe Zembrus perseus gen. et sp. nov., a new weevil from Yunnan, China. A single flightless male was sifted from under Rhododendron bush in the alpine zone of the Cangshan Mountain Range. The specimen’s appearance suggests affinities to the molytine subtribe Cotasteromimina, which currently comprises six named species in four genera distributed between Japan, the Andaman Islands, Borneo and the Philippines. To test the species’ phylogenetic affinities, we analysed 73 morphological characters of adult specimens of 23 molytine and one rooting species. Besides Z. perseus, the ingroup includes four named species, each representing a named genus of Cotasteromimina, and two other, likely closely related unnamed species. Phylogenetic analysis using the parsimony criterion and four character-weighting and/or ordering strategies consistently failed to detect a clade of Cotasteromimina, either with or without Z. perseus. The most parsimonious trees are inconsistent, the bootstrap consensus trees are almost entirely unresolved, and previously published DNA data are phylogenetically indecisive. We conclude that either adult morphological characters constitute an inadequate data source to test monophyly of Cotasteromimina or that the subtribe is not monophyletic or both. We illustrate the relevant adult structures of Z. perseus and most of the in- and out-group taxa used in the analysis.

Modeling the No-Show of Patients to Exam Appointments of Computed Tomography

Background: No-shows of patients have negative impacts on healthcare systems, such as resources’ underutilization, efficiency loss, and cost increase. Predicting no-show is key to develop strategies that counteract its effects. In this paper, we propose a model to predict the no-show of ambulatory patients to exam appointments of computed tomography at the Radiology department of a large Brazilian public hospital.Methods: We carried out a retrospective study on 8,382 appointments made to computed tomography (CT) exams between January and December 2017. Penalized logistic regression and multivariate logistic regression were used to model the influence of 15 candidate variables on patients’ no-show. The predictive capabilities of the models were evaluated analyzing the Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC).Results: The no-show rate in computerized tomography exams appointments was 6.65%. The two models performed similarly in terms of AUC. The penalized logistic regression model was selected using the parsimony criterion, with 8 of the 15 variables analyzed appearing as significant. One of the variables included in the model (number of exams scheduled in previous year) had not been previously reported in the related literature.Conclusions: Our findings may be used to guide the development of strategies to reduce the no-show of patients to exam appointments.

Phylogenetic analysis of the subfamily Prodidominae (Arachnida: Araneae: Gnaphosidae)

Prodidominae was recently re-established as a subfamily of Gnaphosidae, comprising 316 species placed in 33 genera. In this study, we conduct a cladistic analysis including 59 species of Prodidominae and 32 outgroup species. The matrix is composed of 291 morphological characters and the data are analysed under the parsimony criterion, using differing weighting regimes. Prodidominae is not recovered as monophyletic, because Anagrina did not arise within the subfamily. Cryptotoerithus, Molycria, Myandra, Nomindra, Wesmaldra and Wydundra arise to form a clade. Thus, we re-establish Molycriinae as a distinct subfamily in Gnaphosidae, sister to Prodidominae. We redefine the limits of Prodidominae to include the genera Austrodomus, Brasilomma, Caudalia, Chileomma, Chileuma, Chilongius, Eleleis, Indiani, Katumbea, Lygromma, Lygrommatoides, Moreno, Namundra, Neozimiris, Nopyllus, Paracymbiomma, Plutonodomus, Prodidomus, Purcelliana, Theuma, Theumella, Tivodrassus, Tricongius, Zimirina and Zimiris. Species of these genera share the presence of anterior lateral spinnerets with pyriform gland spigots associated with patches of long setae and the presence of a large protrusion between coxae IV with erect setae and unsclerotized margins. In addition, we propose three new synonymies: Oltacloea as a junior synonym of Tricongius, and Prodida as junior synonym of Prodidomus. Lygromma ybyguara is transferred to Tricongius.

The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

ABSTRACTSpecimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

Phylogenetic position of Echeveria heterosepala (Crassulaceae): a rare species with diagnostic characters of Pachyphytum

<p><strong>Background: </strong><em>Echeveria</em> and <em>Pachyphytum</em> are two closely related Neotropical genera in the Crassulaceae. Several species in <em>Echeveria</em> possess characters cited as diagnostic for <em>Pachyphytum</em> such as a clearly defined stem, a nectary scale on the inner face of petals and as inflorescence a scorpioid cyme or cincinnus. <em>Pachyphytum</em> has been identified as monophyletic while <em>Echeveria</em> as polyphyletic in previous molecular phylogenetic analysess.</p><p><strong>Hypothesis: </strong>The objective of this paper is to identify the phylogenetic position of a rare species with restricted distribution in <em>Echeveria</em>, <em>E. heterosepala</em> that possesses the diagnostic characters of <em>Pachyphytum</em> to better understand the generic limits between these two genera. We expect this species to be closely related to <em>Pachyphytum</em>.</p><p><strong>Methods</strong>: Bayesian inference and Maximum Likelihood analyses were carried out using 47 taxa, including as ingroup, species of <em>Echeveria, Graptopetalum, Lenophyllum, Pachyphytum, Sedum</em>, <em>Thompsonella</em> and <em>Villadia</em> and as outgroup, species in<em> Dudleya</em>. Analyses were conducted based on plastid (<em>rpl16, trnL-F</em>) and nuclear (ETS, ITS) markers. Ancestral character reconstruction was carried out under a parsimony criterion based on the molecular trees retrieved by the phylogenetic analyses. Four morphological characters were considered: defined stem, type of inflorescence, nectary scale in petals and position of sepals.</p><strong>Results</strong>: Accessions of <em>E</em>. <em>heterosepala</em> were retrieved in a well-supported clade group comprising exclusively <em>Echeveria</em> species. Therefore this species belongs to <em>Echeveria</em> although possessing characters similar to <em>Pachyphytum</em> and moreover it was not identified closely related to this genus. None of the traits considered have taxonomic importance. The node at the <em>Pachyphytum</em> clade identified unambiguous character states such as stem present, straight sepals, nectary scale on petals, however these character states were identified in the rest of the clades as well. Remarkably, the monophyly of <em>Pachyphytum</em> was corroborated, while <em>Echeveria</em> remains poorly understood.