Overcoming problems with the use of ratios as continuous characters for phylogenetic analyses

Exploring Phylogenetic Relationships of the Mecocephala Group (Hemiptera: Pentatomidae) Using Continuous and Discrete Characters, with Notes on Taxonomy

The Mecocephala group comprises about 50 species, restricted to the Neotropics and with the highest species richness in Neotropical South America. Several species use rice as host plants and their identification is facilitated by the presence of exaggerated head proportions and a unique male genitalic morphology. The taxonomy of the group has been extensively explored, but inferring its monophyly and especially its internal phylogenetic relationships has been challenging. Here, we inferred the phylogenetic relationships for the group assembling the most complete taxonomic sampling to date, analyzing discrete and continuous morphological characters through equal and implied weighted parsimony analyses. The monophyly of the group was recovered, but internal relationships varied slightly according to the dataset tested. Thus, we propose internal arrangements for the group and provide a formal description of the Mecocephala group, diagnoses for each genus, a dichotomous key to identify its genera, and illustrations of the morphological characters and type species.

What else is dentition telling us? A new specimen-level phylogeny of Mesotheriidae (Mammalia, Notoungulata)

Mesotheriidae (Panperissodactyla, Notoungulata) are an extinct clade (early Oligocene-Pleistocene) of small to medium-sized herbivorous mammals that were widely distributed in South America. Although two subfamilies traditionally have been recognized (Trachytheriinae and Mesotheriinae), recent cladistic analyses based on discrete characters have indicated that "Trachytheriinae" is a paraphyletic assemblage. Given the availability of a large number of specimens and the fact that dental characters are the most common characters used in mesotheriid phylogenies, we performed specimen-level cladistic analyses combining discrete, continuous and geometric morphometrics-based dental characters. The aim was to: (1) include new scored morphological characters to solve the phylogenetic relationships of Mesotheriidae; (2) compare the results of the upper and lower dentition analyses as different character partitions and in combination, to establish phylogenetic hypotheses; and (3) trace the evolution of dental traits. Phylogenetic analyses employing characters of associated upper and lower dentitions recovered one most parsimonious tree with Archaeohyracidae (outgroup) as the sister group of Pan-Mesotheriidae (= Mesotheriidae; converted clade name), this latter composed of trachytheriines (stem-mesotheriine) + Mesotheriinae (converted clade name). Within Mesotheriinae, we recovered two main lineages phylogenetically defined here as Bolivarini and Pampaini (new clade names). Analyses of isolated upper and lower dentition sub-datasets each resulted in one most parsimonious tree congruent with the associated dentition. Our study emphasizes the use of geometric morphometrics characters to resolve additional clades in phylogenetic analyses, provides information on the evolution of size and morphology of teeth, and exposes specimen assignment issues at a taxonomic level. The integration of osteological characters might be crucial to further understanding the evolution of Mesotheriidae.

Total-evidence phylogeny and evolutionary morphology of New World pitvipers (Serpentes: Viperidae: Crotalinae)

Crotalines (pitvipers) in the Americas are distributed from southern Canada to southern Argentina, and are represented by 13 genera and 163 species that constitute a monophyletic group. Their phylogenetic relationships have been assessed mostly based on DNA sequences, while morphological data have scarcely been used for phylogenetic inquiry. We present a total-evidence phylogeny of New World pitvipers, the most taxon/character comprehensive phylogeny to date. Our analysis includes all genera, morphological data from external morphology, cranial osteology and hemipenial morphology, and DNA sequences from mitochondrial and nuclear genes. We performed analyses with parsimony as an optimality criterion, using different schemes for character weighting. We evaluated the contribution of the different sources of characters to the phylogeny through analyses of reduced datasets and calculation of weighted homoplasy and retention indexes. We performed a morphological character analysis to identify synapomorphies for the main clades. In terms of biogeography, our results support a single colonization event of the Americas by pitvipers, and a cladogenetic event into a Neotropical clade and a North American/Neotropical clade. The results also shed light on the previously unstable position of some taxa, although they could not sufficiently resolve the position of Bothrops lojanus, which may lead to the paraphyly of either Bothrops or Bothrocophias. The morphological character analyses demonstrated that an important phylogenetic signal is contained in characters related to head scalation, the jaws and the dorsum of the skull, and allowed us to detect morphological convergences in external morphology associated with arboreality.

The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters

The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as "Ocadia" kehreri and "Ocadia" messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.

Sinomacrops bondei, a new anurognathid pterosaur from the Jurassic of China and comments on the group

Anurognathids are an elusive group of diminutive, potentially arboreal pterosaurs. Even though their monophyly has been well-supported, their intrarelationships have been obscure, and their phylogenetic placement even more. In the present work, we present a new genus and species from the Middle-Late Jurassic Tiaojishan Formation, the third nominal anurognathid species from the Jurassic of China. The new species provides new information concerning morphological diversity for the group. Furthermore, we provide a new phylogenetic analysis incorporating into a single data set characters from diverging phylogenetic proposals. Our results place them as the sister-group of Darwinoptera + Pterodactyloidea, as basal members of the Monofenestrata.

The phylogenetic relationships of neosuchian crocodiles and their implications for the convergent evolution of the longirostrine condition

Since their origin in the Late Triassic, crocodylomorphs have had a long history of evolutionary change. Numerous studies examined their phylogeny, but none have attempted to unify their morphological characters into a single, combined dataset. Following a comprehensive review of published character sets, we present a new dataset for the crocodylomorph clade Neosuchia consisting of 569 morphological characters for 112 taxa. For the first time in crocodylian phylogenetic studies, quantitative variation was treated as continuous data (82 characters). To provide the best estimate of neosuchian relationships, and to investigate the origins of longirostry, these data were analysed using a variety of approaches. Our results show that equally weighted parsimony and Bayesian methods cluster unrelated longirostrine forms together, producing a topology that conflicts strongly with their stratigraphic distributions. By contrast, applying extended implied weighting improves stratigraphic congruence and removes longirostrine clustering. The resulting topologies resolve the major neosuchian clades, confirming several recent hypotheses regarding the phylogenetic placements of particular species (e.g. Baryphracta deponiae as a member of Diplocynodontinae) and groups (e.g. Tethysuchia as non-eusuchian neosuchians). The longirostrine condition arose at least three times independently by modification of the maxilla and premaxilla, accompanied by skull roof changes unique to each longirostrine clade.

The taxonomy and phylogeny of Diopecephalus kochi (Wagner, 1837) and ‘Germanodactylus rhamphastinus’ (Wagner, 1851)

The Solnhofen pterosaurs Pterodactylus antiquus, Aerodactylus scolopaciceps, Diopecephalus kochi, Germanodactylus cristatus and Germanodactylus rhamphastinus all have complicated taxonomic histories. Species originally placed in the genus Pterodactylus, such as Aerodactylus scolopaciceps, Ardeadactylus longicollum, Cycnorhamphus suevicus and Germanodactylus cristatus possess apomorphies not observed in the type species of Pterodactylus, and consequently have been placed in new genera. The affinities of another Solnhofen pterosaur previously placed in Pterodactylus, Diopecephalus kochi, are less clear. It has been proposed that D. kochi is a juvenile specimen of Pterodactylus antiquus, or perhaps ‘Germanodactylus rhamphastinus’ specimens are mature examples of D. kochi. Furthermore, studies have suggested that ‘Germanodactylus rhamphastinus’ is not congeneric with the type species of Germanodactylus. Geometric morphometric analysis of prepubes and a cladistic analysis of the Pterosauria elucidate plesiomorphic and apomorphic conditions for basal Jurassic pterodactyloids. Germanodactylus is found to be a monotypic genus and Pterodactylus, Diopecephalus, and ‘G. rhamphastinus’ are found as distinct taxa belonging in individual genera, diagnosable using a combination of characters. Thus, Diopecephalus kochi is not demonstrated to be congeneric with Germanodactylus or Pterodactylus and is maintained as a valid taxon. ‘G. rhamphastinus’ is readily distinguishable from other Solnhofen pterosaur taxa, and a new genus is erected for its reception.