Weighting against homoplasy improves phylogenetic analysis of morphological data sets

Is the Current Systematic Subdivision of the Subfamily Neanurinae (Collembola, Neanuridae) Still Valid? Testing the Monophyly and Phylogenetic Relationships of Currently Established Tribes of the Neanurinae

The subfamily Neanurinae is the largest in the family, with almost 800 described species. These springtails differ significantly from all other Collembola in their morphology, behaviour, and natural habitats. A systematic division of the Neanurinae into tribes was proposed more than 30 years ago by Cassagnau (1989), but it has not yet been tested using cladistic methods. Recent studies, both phylogenetic analyses of individual tribes or genera and descriptions of new taxa, suggest that the currently recognised tribes may not be monophyletic. The phylogenetic relationships among major lineages of the Neanurinae were explored by analysing a dataset of 101 discrete morphological characters. Bayesian and maximum parsimony analyses yielded similar tree topologies. The relationships among the Neanurinae were not resolved in any of the analyses, except for the support for the monophyly of the tribe Lobellini. The results indicate that the taxonomic characters used in the classification of Neanurinae are shared among members of the different tribes, which may have resulted in a classification with little phylogenetic basis. The article discusses the phylogenetic significance of morphological characters, including those recognised as key to the evolution and history of Neanurinae.

Bayesian tip-dated phylogeny and biogeography of Cissampelideae (Menispermaceae): Mitigating the effects of homoplastic morphological characters

The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.

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.

Insights from the first phylogenomic analysis of flat wasps (Hymenoptera, Bethylidae) reveal two new subfamilies

Despite significant advances in alpha level taxonomy in the past few decades, the higher-level phylogeny of flat wasps (Hymenoptera, Bethylidae) remains poorly explored. Herein we provide the first phylogenomic assessment of the family based on data from ultraconserved elements for 96 species in 61 genera of the family, with material from 29 countries and all biogeographic regions. Dataset cutoffs including ultraconserved element loci recovered for 50 and 70% of terminals resulted in matrices with 1513 and 451 loci, which were analysed in both parsimony and maximum likelihood frameworks. We also provide the first analyses of divergence dating for the family based on the calibration of 12 nodes. All analyses recovered the Bethylidae as a monophyletic group and estimated the origin of the family at around 143 Ma. The results suggest that all extant subfamilies had already diversified by the Late Cretaceous. All topologies suggest that Glenosema and Chilepyris form a clade separate from other Scleroderminae; owing to the morphological distinctiveness of each genus, we propose that they are accommodated in two new subfamilies, Glenoseminae subf. nov. and Chilepyrinae subf. nov. The monotypic sclerodermine genus Galodoxa was consistently recovered within Epyrinae and is transferred to the latter subfamily.

Early evolution of the ecdysozoan body plan

Extant ecdysozoans (moulting animals) are represented by a great variety of soft-bodied or articulated organisms that may or may not have appendages. However, controversies remain about the vermiform nature (i.e. elongated and tubular) of their ancestral body plan. We describe here Beretella spinosa gen. et sp. nov. a tiny (maximal length 3 mm) ecdysozoan from the lowermost Cambrian, Yanjiahe Formation, South China, characterized by an unusual sack-like appearance, single opening, and spiny ornament. Beretella spinosa gen. et sp. nov has no equivalent among animals, except Saccorhytus coronarius, also from the basal Cambrian. Phylogenetic analyses resolve both fossil species as a sister group (Saccorhytida) to all known Ecdysozoa, thus suggesting that ancestral ecdysozoans may have been non-vermiform animals. Saccorhytids are likely to represent an early off-shot along the stem-line Ecdysozoa. Although it became extinct during the Cambrian, this animal lineage provides precious insight into the early evolution of Ecdysozoa and the nature of the earliest representatives of the group.

Measuring homoplasy I: comprehensive measures of maximum and minimum cost under parsimony across discrete cost matrix character types

Here, we propose, prove mathematically and discuss maximum and minimum measures of maximum parsimony evolution across 12 discrete phylogenetic character types, classified across 4467 morphological and molecular datasets. Covered character types are: constant, binary symmetric, multistate unordered (non-additive) symmetric, multistate linear ordered symmetric, multistate non-linear ordered symmetric, binary irreversible, multistate irreversible, binary Dollo, multistate Dollo, multistate custom symmetric, binary custom asymmetric and multistate custom asymmetric characters. We summarize published solutions and provide and prove a range of new formulae for the algebraic calculation of minimum (m), maximum (g) and maximum possible (gmax) character cost for applicable character types. Algorithms for exhaustive calculation of m, g and gmax applicable to all classified character types (within computational limits on the numbers of taxa and states) are also provided. The general algorithmic solution for minimum steps (m) is identical to a minimum spanning tree on the state graph or minimum weight spanning arborescence on the state digraph. Algorithmic solutions for character g and gmax are based on matrix mathematics equivalent to optimization on the star tree, respectively for given state frequencies and all possible state frequencies meeting specified numbers of taxa and states. We show that maximizing possible cost (gmax) with given transition costs can be equivalent to maximizing, across all possible state frequency combinations, the lowest implied cost of state transitions if any one state is ancestral on the star tree, via the solution of systems of linear equations. The methods we present, implemented in the Claddis R package, extend to a comprehensive range, the fundamental character types for which homoplasy may be measured under parsimony using m, g and gmax, including extra cost (h), consistency index (ci), retention index (ri) or indices based thereon.

Exploring the effects of weighting against homoplasy in genealogies of palaeontological phylogenetic matrices

Although simulations have shown that implied weighting (IW) outperforms equal weighting (EW) in phylogenetic parsimony analyses, weighting against homoplasy lacks extensive usage in palaeontology. Iterative modifications of several phylogenetic matrices in the last decades resulted in extensive genealogies of datasets that allow the evaluation of differences in the stability of results for alternative character weighting methods directly on empirical data. Each generation was compared against the most recent generation in each genealogy because it is assumed that it is the most comprehensive (higher sampling), revised (fewer misscorings) and complete (lower amount of missing data) matrix of the genealogy. The analyses were conducted on six different genealogies under EW and IW and extended implied weighting (EIW) with a range of concavity constant values (k) between 3 and 30. Pairwise comparisons between trees were conducted using Robinson-Foulds distances normalized by the total number of groups, distortion coefficient, subtree pruning and regrafting moves, and the proportional sum of group dissimilarities. The results consistently show that IW and EIW produce results more similar to those of the last dataset than EW in the vast majority of genealogies and for all comparative measures. This is significant because almost all of these matrices were originally analysed only under EW. Implied weighting and EIW do not outperform each other unambiguously. Euclidean distances based on a principal components analysis of the comparative measures show that different ranges of k-values retrieve the most similar results to the last generation in different genealogies. There is a significant positive linear correlation between the optimal k-values and the number of terminals of the last generations. This could be employed to inform about the range of k-values to be used in phylogenetic analyses based on matrix size but with the caveat that this emergent relationship still relies on a low sample size of genealogies.

Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification

Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.

A camouflaged diversity: taxonomic revision of the thorny lacewing subfamily Symphrasinae (Neuroptera, Rhachiberothidae)

Species of the thorny lacewing subfamily Symphrasinae (Neuroptera: Rhachiberothidae) are revised. Prior to this work, 42 species were known in the genera Anchieta Navás, 1909, Plega Navás, 1928, and Trichoscelia Westwood, 1852. Herein, the number of species is increased to 60, 23 of which are newly described. Species previously known are redescribed, and their taxonomic status is revised. Keys, diagnoses, and high-resolution images for all species are presented. The distribution range of Anchieta is now known from Costa Rica to southern Brazil with a total of 11 species, of which three are newly described. The genus Plega is known from southwestern United States to southern Brazil and includes 28 species of which 14 are described as new. Moreover, the genus Trichoscelia occurs from central and southern Mexico to Argentina, with a total of 21 species, of which six are herein newly described. A phylogenetic analysis of Symphrasinae based on morphological characters recovered the three symphrasine genera as monophyletic, with Anchieta sister to Plega + Trichoscelia. The three genera are newly diagnosed based on a cladistic framework. Within the genus Anchieta, bee-mimicking species comprise a monophyletic group, while wasp-mimicking species form a laddered sequence to that lineage. Within Plega, three lineages are recovered, the first mostly composed of South and Mesoamerican species, the second with species predominantly from Central America and central and southern Mexico, and a third clade encompassing species mostly from central and northern Mexico and southwestern United States. By contrast, relationships between species of Trichoscelia were poorly resolved because of a simplified and conserved morphology of this group.

Hwiccewyrm trispiculum gen. et sp. nov., a new leptopleuronine procolophonid from the Late Triassic of southwest England

The fissure fill localities of southwest England and South Wales are well-known for preserving rich assemblages of predominantly small-bodied Late Triassic to Early Jurassic tetrapods, but many aspects of these assemblages remain contentious. The age of the Late Triassic fissures is disputed, with some lines of argument suggesting a latest Triassic (Rhaetian) age, whereas other evidence suggests they may be as old as Carnian. The fissures have been hypothesized by some workers to have formed on an archipelago, with island effects invoked to explain aspects of the assemblages such as the abundance of small-bodied species. Procolophonids were a successful group of Triassic parareptiles, best known from Early to early Late Triassic assemblages, but have only recently been described from one of the fissure fill sites (Ruthin) based upon fragmentary remains. Here, we describe new procolophonid specimens from another fissure (Cromhall) that represent at least six individuals of different sizes, with much of the skeleton represented including well-preserved skull material. The Cromhall procolophonid shows strong similarities to Late Triassic procolophonids from Scotland, Brazil and North America, but both autapomorphies and a unique character combination demonstrate that it represents a new species, which we name as Hwiccewyrm trispiculum gen. et sp. nov. Phylogenetic analysis places Hwiccewyrm in a derived clade within Leptopleuroninae, together with Leptopleuron, Hypsognathus, and Soturnia. The largest specimens of Hwiccewyrm demonstrate a body size that is similar to Leptopleuron and Hypsognathus, supporting other recent work that has questioned the insular dwarfism hypothesis for the fissure fill assemblages.

The largest freshwater odontocete: A South Asian river dolphin relative from the proto-Amazonia

Several dolphin lineages have independently invaded freshwater systems. Among these, the evolution of the South Asian river dolphin Platanista and its relatives (Platanistidae) remains virtually unknown as fossils are scarce. Here, we describe Pebanista yacuruna gen. et sp. nov., a dolphin from the Miocene proto-Amazonia of Peru, recovered in phylogenies as the closest relative of Platanista. Morphological characters such as an elongated rostrum and large supraorbital crests, along with ecological interpretations, indicate that this odontocete was fully adapted to fresh waters. Pebanista constitutes the largest freshwater odontocete known, with an estimated body length of 3 meters, highlighting the ample resource availability and biotic diversity in the region, during the Early to Middle Miocene. The finding of Pebanista in proto-Amazonian layers attests that platanistids ventured into freshwater ecosystems not only in South Asia but also in South America, before the modern Amazon River dolphin, during a crucial moment for the Amazonian evolution.

Position of Polyclithrum within Gyrodactylidae (Monogenoidea): incongruences between morphological and molecular phylogenies

This study aimed to enhance our understanding in monogenoid evolution by using morphological and molecular data to determine kinship relationships between species and changes in morphological structures over time. We focused on variations in characteristics among the organisms of the family Gyrodactylidae, concentrating on the phylogenetic position of Polyclithrum with other genera in the family. We collected specimens of Polyclithrum from the striped mullet, Mugil cephalus and Swingleus, and Fundulotrema specimens from mummichog Fundulus heteroclitus in estuarine systems of South Carolina, United States. In addition, we analyzed them and other genera (including e.g., Mormyrogyrodactylus, Gyrodactyloides, and Macrogyrodactylus) using both morphological and molecular (18S rDNA) approaches. We performed phylogenetic trees based on Maximum Parsymony, Maximum Likelihood and Bayesian Inference, and constructed a character morphological matrix by Parsimony Reconstruction of Ancestral Character States method. Our results suggest a homoplastic origin with evolutionary convergences in characters, revealing that there is inconsistency between our data and previously published works based solely on morphological structures of the group. The homoplasy scenario found in Gyrodactylidae can be a result of the limited set of putative homologous morphological features. However, differences between the phylogenies based on morphology and those based on molecular data may arise from both databases. While morphology remains essential in understanding the evolution of this group, molecular data, otherwise, provide a less biased source of information for constructing phylogenetic hypotheses. Combining these data facilitates a better comprehension of the homologous status of morphological features and to understand Gyrodactylidae evolutionary history.

3D atlas of tinamou (Neornithes: Tinamidae) pectoral morphology: Implications for reconstructing the ancestral neornithine flight apparatus

Palaeognathae, the extant avian clade comprising the flightless ratites and flight-capable tinamous (Tinamidae), is the sister group to all other living birds, and recent phylogenetic studies illustrate that tinamous are phylogenetically nested within a paraphyletic assemblage of ratites. As the only extant palaeognaths that have retained the ability to fly, tinamous may provide key information on the nature of the flight apparatus of ancestral crown palaeognaths-and, in turn, crown birds-as well as insight into convergent modifications to the wing apparatus among extant ratite lineages. To reveal new information about the musculoskeletal anatomy of tinamous and facilitate development of computational biomechanical models of tinamou wing function, we generated a three-dimensional musculoskeletal model of the flight apparatus of the extant Andean tinamou (Nothoprocta pentlandii) using diffusible iodine-based contrast-enhanced computed tomography (diceCT). Origins and insertions of the pectoral flight musculature of N. pentlandii are generally consistent with those of other extant volant birds specialized for burst flight, and the entire suite of presumed ancestral neornithine flight muscles are present in N. pentlandii with the exception of the biceps slip. The pectoralis and supracoracoideus muscles are robust, similar to the condition in other extant burst-flying birds such as many extant Galliformes. Contrary to the condition in most extant Neognathae (the sister clade to Palaeognathae), the insertion of the pronator superficialis has a greater distal extent than the pronator profundus, although most other anatomical observations are broadly consistent with the conditions observed in extant neognaths. This work will help form a basis for future comparative studies of the avian musculoskeletal system, with implications for reconstructing the flight apparatus of ancestral crown birds and clarifying musculoskeletal modifications underlying the convergent origins of ratite flightlessness.

The rise of macropredatory pliosaurids near the Early-Middle Jurassic transition

The emergence of gigantic pliosaurid plesiosaurs reshaped the trophic structure of Mesozoic marine ecosystems, and established an  ~ 80 million-year (Ma) dynasty of macropredatory marine reptiles. However, the timescale of their 'defining' trait evolution is incompletely understood because the fossil record of gigantic pliosaurids is scarce prior to the late-Middle Jurassic (Callovian),  ~ 165.3 Ma. Here, we pinpoint the appearance of large body size and robust dentitions to early-Middle Jurassic (Bajocian) pliosaurids from northeastern France and Switzerland. These specimens include a new genus that sheds light on the nascent diversification of macropredatory pliosaurids occurring shortly after the Early-Middle Jurassic transition, around  ~ 171 Ma. Furthermore, our multivariate assessment of dental character states shows that the first gigantic pliosaurids occupied different morphospace from coeval large-bodied rhomaleosaurid plesiosaurs, which were dominant in the Early Jurassic but declined during the mid-Jurassic, possibly facilitating the radiation and subsequent ecomorph acme of pliosaurids. Finally, we posit that while the emergence of macropredatory pliosaurids was apparently coordinated with regional faunal turnover in the epeiric basins of Europe, it paralleled a globally protracted extinction of other higher trophic-level marine reptiles that was not completed until after the earliest-Late Jurassic,  ~ 161.5 Ma.

A New Chengjiang Worm Sheds Light on the Radiation and Disparity in Early Priapulida

The vast majority of early Paleozoic ecdysozoan worms are often resolved as stem-group Priapulida based on resemblances with the rare modern representatives of the group, such as the structure of the introvert and the number and distribution of scalids (a spiny cuticular outgrowth) and pharyngeal teeth. In Priapulida, both scalids and teeth create symmetry patterns, and three major diagnostic features are generally used to define the group: 25 longitudinal rows of scalids (five-fold symmetry), 8 scalids around the first introvert circle and the pentagonal arrangement of pharyngeal teeth. Here we describe Ercaivermis sparios gen. et sp. nov., a new priapulid from the early Cambrian Chengjiang Lagerstätte, characterized by an annulated trunk lacking a sclerotized ornament, four pairs of anal hooks and 16 longitudinal rows of scalids along its introvert and eight scalids around each introvert circle, giving the animal an unusual octoradial symmetry. Cladistic analyses resolve Ercaivermis as a stem-group priapulid. Ercaivermis also suggests that several biradial symmetry patterns (e.g., pentagonal, octagonal) expressed in the cuticular ornament, may have co-existed among early Cambrian priapulids and that the pentaradial mode may have become rapidly dominant during the course of evolution, possibly via the standardization of patterning, i.e., the natural selection of one symmetry type over others.

Outside the pattern: Evolution of the genital asymmetry in Saicinae (Hemiptera: Heteroptera: Reduviidae)

Despite genital structures in insects being consistently important as systematic and taxonomy evidence, within assassin bugs (Heteroptera, Reduviidae) at least, the male and female genitalic structures of several subfamilies are poorly or totally unknown. The genital structure is mostly symmetric within Saicinae genera, but male genital asymmetry has been recorded in Gallobelgicus, Polytoxus, and recently Pseudosaica. The subfamily has been considered as closely related to Emesinae and Visayanocorinae but this hypothesis has never been tested using a comprehensive taxa sampling, being a constraint to test morphological traits changes or exploring characters' evolution hypotheses. Here, we compiled a morphological data set of 170 characters that includes external morphological characters and genitalia of both sexes of Saicinae which was analyzed cladistically including 55 terminals, comprising 16 genera (64% of the generic diversity), 43 species of Saicinae and 12 outgroups. Saicinae was recovered as polyphyletic, Saicireta correntina is recovered as sister-species of Empicoris armatus + Collartida (Emesinae), Oncerotrachelus, Carayonia (Visayanocorinae), and the Clade Saicinae sensu stricto. Carayonia orientalis is recovered as sister-species of Saicinae sensu stricto. Ancestral state reconstruction of symmetry of the male genitalia shows an ancestor with symmetric male genitalia, two independent emergences of asymmetrical male genitalia within Saicinae sensu stricto, and the asymmetrical endosomal sclerites appearing before the other asymmetric traits.

All quiet on the western front? The evolutionary history of monogeneans (Dactylogyridae: Cichlidogyrus, Onchobdella) infecting a West and Central African tribe of cichlid fishes (Chromidotilapiini)

Owing to the largely unexplored diversity of metazoan parasites, their speciation mechanisms and the circumstances under which such speciation occurs - in allopatry or sympatry - remain vastly understudied. Cichlids and their monogenean flatworm parasites have previously served as a study system for macroevolutionary processes, e.g., for the role of East African host radiations on parasite communities. Here, we investigate the diversity and evolution of the poorly explored monogeneans infecting a West and Central African lineage of cichlid fishes: Chromidotilapiini, which is the most species-rich tribe of cichlids in this region. We screened gills of 149 host specimens (27 species) from natural history collections and measured systematically informative characters of the sclerotised attachment and reproductive organs of the parasites. Ten monogenean species (Dactylogyridae: Cichlidogyrus and Onchobdella) were found, eight of which are newly described and one redescribed herein. The phylogenetic positions of chromidotilapiines-infecting species of Cichlidogyrus were inferred through a parsimony analysis of the morphological characters. Furthermore, we employed machine learning algorithms to detect morphological features associated with the main lineages of Cichlidogyrus. Although the results of these experimental algorithms remain inconclusive, the parsimony analysis indicates that West and Central African lineages of Cichlidogyrus and Onchobdella are monophyletic, unlike the paraphyletic host lineages. Several instances of host sharing suggest occurrences of intra-host speciation (sympatry) and host switching (allopatry). Some morphological variation was recorded that may also indicate the presence of species complexes. We conclude that collection material can provide important insights on parasite evolution despite the lack of well-preserved DNA material.

First cladistic analysis of Toxotarsinae (Diptera: Calliphoridae), with insights on the evolution of the group and on the transformation series of some historically controversial characters

Toxotarsinae is a subfamily of Calliphoridae (Diptera: Calyptratae: Oestroidea) with 11 species currently distributed in three genera: Neta Shannon, 1926, Sarconesia Bigot, 1857, and Toxotarsus Macquart, 1851. All known species are endemic to South America, mostly restricted to areas with cooler temperatures-like high elevation areas of the Andean Cordillera-and lowlands and coastal regions in the subtropical and temperate parts of the continent. The classification of the subfamily has been somewhat controversial, with eleven, mostly monotypic nominal genera established to accommodate its species, mostly due to distinct interpretations of certain controversial characters by different authors. To provide a sound basis for a generic classification, we performed the first study aimed to understand the transformation series of those controversial characters and character states under a phylogenetic framework. Our maximum parsimony analyses, under both equal and implied weighting of characters and including all currently known species in the subfamily, retrieved two main clades of Toxotarsinae: the roraima group, composed of Sarconesia roraima (Townsend, 1935), Neta chilensis (Walker, 1836), and S. magellanica (Le Guillou, 1842), and the splendida group, composed of the remaining species of the subfamily. The position of S. magellanica varied, but the species was mostly recovered within the roraima group except in the analyses under implied weighting with k values between 1 and 6. Our results, which include an explicit interpretation of the transformation series associated with some characters and character states commonly used in Toxotarsinae systematics, suggest that both Sarconesia and Neta, along with other genera proposed in the past for species of the subfamily such as Sarconesiomima Lopes & Albuquerque, 1955, Chlorobrachycoma Townsend, 1918, Sarconesiopsis Townsend, 1918, and Roraimomusca Townsend, 1935, previously suggested to be synonyms of Sarconesia, do not properly reflect the evolution of lineages in the subfamily and should not be considered as valid nominal genera. Toxotarsus was the only genus consistently recovered as monophyletic and, based on the phylogenetic relationships recovered herein, we suggest including all known Toxotarsinae within this genus, with the roraima and splendida clades treated as species-groups. Finally, we discuss the characters commonly used to delimit the taxa subordinated to Toxotarsinae, such as the length of the first flagellomere, the position of the rays of the arista relative to the pedicel, the extension of the plumosity of the arista, and the number of postsutural acrostichal setae.

Revisiting the phylogeny of the family Miridae (Heteroptera: Cimicomorpha), with updated insights into its origin and life history evolution

Heteroptera is one of the most successfully adapted groups on Earth and can be observed in almost every environment. Within the evolution of heteropteran insects, Miridae show remarkable diversity (>11,700 spp.), accounting for a quarter of all Heteroptera. However, their phylogeny is still unclear, and no plausible theory for the driving force of their diversification has been established. In this work, we provide new suggestions for the phylogeny of Miridae using a larger dataset than previous studies. In addition, we suggest an alternative evolutionary history based on newly calibrated divergence dates for Miridae and its subordinate groups, and present probable factors of the family's success in terms of species diversity. The entire dataset comprises 16 outgroups and 188 ingroup taxa including all seven known subfamilies and 37 out of 45 known tribes. Each species is aligned as 3,577bp with six molecular loci (COI, 16S rRNA, 18S rRNA, 28S rRNA D3 region, H2A, and H3A). Among the molecular markers, we are the first to test histone genes (H2A, H3A) in Miridae. Our results raise the following points about phylogenetic relationships: i) The earliest group to diverge from Miridae was Monaloniini (Bryocorinae). ii) Bryocorinae and Cylapinae are polyphyletic, Deraeocorinae and Orthotylinae also rendered as non-monophyletic group. iii) Termatophylini and Coridromiini separated from Deraeocorinae and Orthotylinae respectively. iv) Four large tribes, Orthotylini, Phylini, Deraeocorini and Mirini are non-monophyletic. The results from our ancestral state reconstruction and divergence date estimation suggest the following: i) Miridae first diverged during the Late Jurassic (approx. 163.4 Mya), and the divergence dates of most subfamilies and tribes overlap with angiosperm radiation, which perhaps synergized their diversification. ii) Ancestral reconstruction results for Miridae reveal it to be predominantly phytophagous and diverge to oligophagy mainly in plant-tissue habitats, which could have allowed the mirids to select optimal tactics as plant-dwellers. iii) The common ancestor of Miridae originated among plant-dwellers mainly on Eudicots, and that tendency was largely maintained, but sporadic host shifts also occurred.

Phylogenetic relationships in Hybosoridae (Coleoptera: Scarabaeoidea)

Hybosoridae comprise five extant subfamilies (Anaidinae, Ceratocanthinae, Hybosorinae, Liparochrinae and Pachyplectrinae). The phylogenetics of Anaidinae and Ceratocanthinae have been analysed previously. This is the first thorough analysis with greater representation of the entire family, especially regarding Hybosorinae. The present study tested the monophyly of Hybosoridae; the monophyly and relationships of its subfamilies and among the genera; and the ‘incertae sedis’ placement of the hybosorid genera Borrochrus and Daimothoracodes and of Orubesa, currently assigned to Scarabaeidae. The matrix consisted of 111 morphological characters and 76 taxa. The monophyly of Hybosoridae and three subfamilies (Anaidinae, Ceratocanthinae and Liparochrinae) was supported. Few changes were necessary to recover the monophyly of Hybosorinae and Pachyplectrinae: Brenskea is transferred from Pachyplectrinae to Hybosorinae, and Borrochrus and Daimothoracodes are allocated to Pachyplectrinae. Hybosorinae include two paraphyletic genera: Apalonychus and Hybosorus. To recover their monophyly, two monotypic genera were synonymized: Hapalonychoides is now a junior subjective synonym of Apalonychus (Apalonychus similis comb. nov.) and Hybosoroides a junior subjective synonym of Hybosorus (Hybosorus alluaudi comb. nov.). Orubesa is more closely related to Ochodaeidae than to Hybosoridae.

A New Genus and Two New Species of Fireflies from South America (Lampyridae: Lampyrinae: Photinini)

Lampyridae taxonomy has traditionally relied on a few characters now deemed to be highly homoplastic, and their classification—especially at the genus level—is yet to be consolidated based on rigorous phylogenetic analyses. Recent studies highlighted the value of genitalic trait variation in the evolution in Lampyridae, particularly for the rich and poorly known South American Photinini fauna. Here, we describe a new genus, with a new species from the Cerrado and another one from the Atlantic Forest. Phylogenetic analyses based on Bayesian and Maximum Parsimony approaches recovered these two species as sister to each other, which we place here in Zoiudo gen. nov. Males of this new lineage of fireflies are overall strikingly similar to Photinus Laporte 1833, but can be readily distinguished by traits heretofore neglected, including the structure of tibial spurs and many genitalic traits. Instead, Zoiudo gen. nov. is strongly supported as sister to Ybytyramoan Silveira and Mermudes, 2014, supported by eight synapomorphies, the most conspicuous being the sternum VIII with lateral margins divergent up to basal 1/5, then convergent posteriorly, and the rudimentary ventral plate of phallus. Our study confirms the value of extensive character and taxon sampling towards a revised classification of Photinini taxa and highlights the need for a continued sampling and protection of South American biomes.

First Phylogeny of Pseudolychnuris Reveals Its Polyphyly and a Staggering Case of Convergence at the Andean Paramos (Lampyridae: Lampyrini)

South America is likely the cradle of several New World firefly lineages but remains largely understudied. Despite several advances in firefly systematics in the Neotropical region, the Andean region has been largely unstudied for over a century. The Colombian Páramos are a critically threatened biodiversity hotspot that houses several endemic species, including the firefly genus Pseudolychnuris, with two species-P. vittata and P. suturalis. Here, by analyzing the phylogenetic relationships of Pseudolychnuris, we found that this genus is polyphyletic. Pseudolychnuris vittata and P. suturalis were found to be distantly related despite the striking similarity in outline and color pattern of males and females. We redescribe Pseudolychnuris and its type species P. vittata. Moreover, we revalidate Alychnus Kirsch, 1865 stat. rev. to accommodate A. suturaliscomb. nov., also redescribed here. We provide updated distribution maps and report field observations for both monotypic genera. Since adults visit flowers and interact with pollen and nectar, Pseudolychnuris and Alychnus may be occasional pollinators of Andean-endemic plants, a phenomenon previously neglected. Our findings reveal an interesting case of convergence between Pseudolychnuris and Alychnus-probably associated with life in the Páramos-and shed light on character evolution in the Photinini lineage of fireflies.

Redescription, taxonomic revaluation and phylogenetic affinities of Proterochampsa nodosa (Archosauriformes: Proterochampsidae) from the early Late Triassic of the Candelaria Sequence (Santa Maria Supersequence)

Proterochampsidae are a group of predatory, putatively semi-aquatic, archosauriforms endemic to the Middle and Upper Triassic strata of Argentina and Brazil (Ischigualasto Formation and Santa Maria Supersequence). Here, the Brazilian species Proterochampsa nodosa from the Candelária Sequence (Santa Maria Supersequence of the Paraná Basin) is revisited with a detailed description, phylogenetic analysis and taxonomic revaluation. Through the application of computed tomographic scans, we were able to reveal part of the previously hidden morphology of its mandible and palate. We also discuss further differences between P. nodosa and P. barrionuevoi. The new phylogenetic analysis bolsters the monophyly of Proterochampsidae, the genus Proterochampsa and its position as the basalmost proterochampsid taxon in the clade.

Taxonomy and phylogenetic analysis of the South American genus

The systematics of Philodromidae is far from complete, especially for the Neotropical genera. Among these, Petrichus Simon, 1886 is a poorly known genus restricted to arid and semi-arid environments of South America. In this work, we performed a total-evidence analysis to assess the phylogenetic relationships of Petrichus and revised the taxonomy. Petrichus is monophyletic and closer to Titanebo and the New World Ebo. Within Petrichus, two clades are obtained: the Eremean Clade, containing five species displaying a Neotropical distribution; and the Patagonian Clade, with the seven species inhabiting southern South America. Our results also support a previous hypothesis on the phylogenetic relationships within Philodromidae. Thanatini is monophyletic and includes Fageia and Berlandiella, although this is not statistically supported, whereas Philodromini emerges as paraphyletic. We propose Philodromini be expanded to contain all genera having eyes on tubercles analysed in this work plus the closely related Halodromus, whereas the circumscription of Thanatini should await future phylogenetic analyses with new evidence. As for taxonomic proposals, we synonymise Bacillocnemis Mello-Leitão, 1938 with Petrichus, Petrichus ornatus Schiapelli & Gerschman, 1942 and P. luteus (Nicolet, 1849) with P. junior (Nicolet, 1849), P. lancearius Simon, 1905 with P. tullgreni Simon, 1902; we transfer P. corticinus Mello-Leitão, 1944 to Misumenoides Pickard-Cambridge, 1900 (Thomisidae); and P. fuliginosus (Nicolet, 1849), P. cinereus Tullgren, 1901, P. sordidus Tullgren, 1901 and P. zonatus Tullgren, 1901 are regarded as nomina dubia. In total, 13 species are recognised for the genus, of which four are new (described by Griotti & Grismado): P. spira, from western Argentina, P. patagoniensis, from south-western Argentina, P. roigjunenti, from Argentina and Chile and P. eremicus, from north-central Chile. ZooBank: http://zoobank.org/References/1220255e-6431-45c2-adfe-ed58d1f89b17

Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes

A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multimarker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58 of 137 species and characterize major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data for 136 of 137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters not only can mask phylogenetic signals, but also are key for characterizing species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterizations.

The evolution of biramous appendages revealed by a carapace-bearing Cambrian arthropod

Biramous appendages are a common feature among modern marine arthropods that evolved deep in arthropod phylogeny. The branched appendage of Cambrian arthropods has long been considered as the ancient biramous limb, sparking numerous investigations on its origin and evolution. Here, we report a new arthropod, Erratus sperare gen. et sp. nov., from the Lower Cambrian (Stage 3, 520 Ma) Chengjiang biota of Yunnan, China, with unique trunk appendages formed of lateral anomalocaridid-type flaps and ventral subconical endopods. These appendages represent an intermediate stage of biramous limb evolution, i.e. from 'two pairs of flap appendages' in radiodonts to 'flap + endopod' in Erratus, to 'exopod + endopod' in the rest of carapace-bearing arthropods that populate the basal region of the upper-stem lineage arthropods (deuteropods). The new species occupies a phylogenetic position at the first node closer to deuteropods than to radiodonts, and therefore pinpoints the earliest occurrence of the endopod within Deuteropoda. The primitive endopod is weakly sclerotized, and has unspecialized segments without endites or claw. The findings might support previous claims that the outer branch of the biramous limb of fossil marine arthropods, such as trilobites, is not a true exopod, but is instead a modified exite. This article is part of the theme issue 'The impact of Chinese palaeontology on evolutionary research'.

Protocol combining tree-based Maximum Parsimony and web-like Phylogenetic Networks analyses to investigate reticulate human evolution

Our protocol combines Maximum Parsimony and Phylogenetic Networks approaches to understand the phylogenetic relationships and evolutionary processes of hominin species that might have shared inheritance from multiple ancestors. By addressing the questions of pattern and process in human phylogeny, the protocol can be used to clarify the taxonomic definition(s) of diverse hominin groups and ascertain whether or not the mode of evolution of genus Homo is reticulate. Using high quality and informative phenotypic data sets is necessary to yield meaningful results. For complete details on the use and execution of this protocol, please refer to Caparros and Prat (2021).

Systematic revision and phylogeny of Paragripopteryx Enderlein, 1909 (Plecoptera: Gripopterygidae)

Among the Neotropical gripopterygids, the genus Paragripopteryx occurs along the Brazilian Atlantic coast to Uruguay. Since its first recognition by Enderlein in 1909, the genus underwent a confusing taxonomic history with some combinations. In this study, we aim to revise Paragripopteryx and present the first morphology-based phylogeny for the genus. The analysis comprised 38 morphological characters and their respective states in 30 terminal taxa, including 13 Paragripopteryx species, two new species identified as belonging to Paragripopteryx, and 15 outgroup species, among which we can highlight 12 different South American genera and one Australian genus of Gripopterygidae. The cladistic analysis yielded a parsimonious tree for k = 3 (137 steps, consistency index = 0.445, and retention index = 0.591) where most Paragripopteryx are nested, except for Uruguayan Paragripopteryx munoai. We can then infer that in its current circumscription Paragripopteryx is polyphyletic. The following two species are described: Paragripopteryx dasalmas sp. nov. and Paragripopteryx ogum sp. nov. Paragripopteryx baratinii is designated as a nomen dubium. Additionally, we provide a key for species identification, updated geographical records, and illustrations for all species. As a corollary, our study gathers relevant morphological information that can help to better understand this genus and create foundations for the next steps.

Combined phylogeny and new classification of catsharks (Chondrichthyes: Elasmobranchii: Carcharhiniformes)

This is the first study to combine morphological and molecular characters to infer the phylogenetic relationships among catsharks. All currently valid genera classified in the family Scyliorhinidae s.l. and representatives of other carcharhinoid families plus one lamnoid and two orectoloboids were included as terminal taxa. A total of 143 morphological characters and 44 NADH2 sequences were analysed. Parsimony analyses under different weighting schemes and strengths were used to generate hypotheses of phylogenetic relationships. The phylogenetic analysis of 78 terminal taxa, using the combined dataset and weighting each column separately (SEP; k = 3) resulted in one most-parsimonious cladogram of 4441 steps with the greatest internal resolution of clades and strongest support. The main changes in nomenclature and classification are the revised definition and scope of Scyliorhinidae, Apristurus and Pentanchus and the revalidation of Atelomycteridae. The monophyly of Pentanchidae is supported, as is that of most catshark genera. Two new subfamilies of the family Pentanchidae are defined: Halaelurinae subfam. nov. and Galeinae subfam. nov. Our analysis emphasizes the relevance of morphological characters in the inference of evolutionary history of carcharhinoids and sheds light on the taxonomic status of some genera in need of further exploration.

Dactylogyridae 2022: a meta-analysis of phylogenetic studies and generic diagnoses of parasitic flatworms using published genetic and morphological data

Dactylogyridae is one of the most studied families of parasitic flatworms with more than 1000 species and 166 genera described to date including ecto- and endoparasites. Dactylogyrid monogeneans were suggested as model organisms for host-parasite macroevolutionary and biogeographical studies due to the scientific and economic importance of some of their host lineages. Consequently, an array of phylogenetic research into different dactylogyrid lineages has been produced over the past years but the last family-wide study was published 16 years ago. Here, we provide a meta-analysis of the phylogenetic relationships of Dactylogyridae including representatives of all genera with available molecular data (n=67). First, we investigate the systematic informativeness of morphological characters widely used to diagnose dactylogyrid genera through a parsimony analysis of the characters, character mapping, and phylogenetic comparative methods. Second, we provide an overview of the current state of the systematics of the family and its subfamilies, and summarise potentially poly- and paraphyletic genera. Third, we elaborate on the implications of taxonomic, citation, and confirmation bias in past studies. Fourth, we discuss host range, biogeographical, and freshwater-marine patterns. We found two well-supported macroclades which we assigned to the subfamilies Dactylogyrinae and Ancyrocephalinae. These subfamilies further include 16 well-supported clades with only a few synapomorphies that could be deduced from generic diagnoses in the literature. Furthermore, few morphological characters considered systematically informative at the genus level display a strong phylogenetic signal. However, the parsimony analysis suggests that these characters provide little information on the relationships between genera. We conclude that a strong taxonomic bias and low coverage of DNA sequences and regions limit knowledge on morphological and biogeographical evolutionary patterns that can be inferred from these results. We propose addressing potential citation and confirmation biases through a 'level playing field' multiple sequence alignment as provided by this study.

Haplocauda, a New Genus of Fireflies Endemic to the Amazon Rainforest (Coleoptera: Lampyridae)

Simple Summary

The Amazon Rainforest is still a frontier in the study of insect biodiversity, housing several species yet to be described and studied. Yet, its continuous deforestation urges scientists to study insect diversity there before it is too late. Here, we identified and described new species and a new genus of fireflies from the Amazon Rainforest. These new species are unique among other fireflies due to their unique abdominal morphology, supposed here to involve a clamping mechanism used during mating.

Abstract

Most firefly genera have poorly defined taxonomic boundaries, especially in the Neotropics, where they are more diverse and more difficult to identify. Recent advances that shed light on the diversity of fireflies in South America have focused mainly on Atlantic Rainforest taxa, whereas lampyrids in other biomes remained largely unstudied. We found three new firefly species endemic to the Amazon basin that share unique traits of the male abdomen where sternum VIII and the pygidium are modified and likely work as a copulation clamp. Here we test and confirm the hypothesis that these three species form a monophyletic lineage and propose Haplocaudagen. nov. to accommodate the three new species. Both maximum parsimony and probabilistic (Bayesian and maximum likelihood) phylogenetic analyses confirmed Haplocaudagen. nov. monophyly, and consistently recovered it as the sister group to Scissicauda, fireflies endemic to the Atlantic Rainforest that also feature a copulation clamp on abdominal segment VIII, although with a different configuration. We provide illustrations, diagnostic descriptions, and keys to species based on males and females. The three new species were sampled from different regions, and are likely allopatric, a common pattern among Amazonian taxa.

Phylogenetic analysis of the family Megalopodidae (Coleoptera: Chrysomeloidea): better taxon-sampling facilitates detection of new relationships and new taxa

The systematics of Megalopodidae is not adequately known, in spite of it being a relatively small group of phytophagous beetles. The first phylogenetic analysis of Megalopodidae with a comprehensive generic representation (25 genera of 30 described, 10 subgenera and 77 species) is undertaken. A parsimony analysis under equal and implied weights was carried out based on 147 adult and larval morphological characters. Subfamilies Palophaginae and Zeugophorinae were recovered as monophyletic, by contrast with Megalopodinae, which proved to be paraphyletic. Atelederinae are proposed as a new subfamily. Also, three tribes and three subtribes within Megalopodinae are proposed: Leucasteini trib.n., Sphondyliini trib.n. and Megalopodini, the latter including Macrolophina subtrib.n., Temnaspidina subtrib.n. and Megalopodina. The genera Macrolopha, Kuilua, Poecilomorpha, Temnaspis, Antonaria, Agathomerus, Megalopus and Bothromegalopus were recovered as non-monophyletic. New delimitations of the polyphyletic genera Poecilomorpha and Macrolopha are proposed, Clythraxeloma is resurrected, and the subgenera of Agathomerus are suppressed. The following new combinations are proposed: Kuilua apicata (Fairmaire), K. nyassae (Jacoby), Poecilomorpha cribricollis (Pic), P. minuta (Pic), Clythraxeloma assamensis (Jacoby), C. bipartita (Lacordaeri), C. discolineata (Pic), C. downesii (Baly), C. gerstaeckeri (Westwood), C. laosensis (Pic), C. maculata (Pic), C. mouhoti (Baly), C. nigrocyanea (Motschulsky), C. pretiosa (Reineck), Temnaspis tricoloripes (Pic) and Barticaria faciatus (Dalman). Clythraxeloma cyanipennis Kraatz is a restored combination. Distribution patterns of Megalopodidae largely conform to the breakup of Gondwanaland, with its main clades having particular distributions: Andean-Australian (Palophaginae), Ethiopian (Leucasteini, Sphondyliini, and Macrolophina), Neotropical (Ateledrinae and Megalopodina) and Ethiopian-Oriental-Palaearctic (Temnaspidina the result of a secondary expansion. Zeugophorinae present a worldwide distribution, except for the Neotropical and Andean regions, which may be the result of geodispersal. The findings of the present study also shed light on groups with taxonomic issues, where phylogenetic analyses are strongly needed.

Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha)

The importance of morphology in the phylogenomic era has recently gained attention, but relatively few studies have combined both types of information when inferring phylogenetic relationships. Sanger sequencing legacy data can also be important for understanding evolutionary relationships. The possibility of combining genomic, morphological and Sanger data in one analysis seems compelling, permitting a more complete sampling and yielding a comprehensive view of the evolution of a group. Here we used these three data types to elucidate the systematics and evolution of the Dionycha, a highly diverse group of spiders relatively underrepresented in phylogenetic studies. The datasets were analyzed separately and combined under different inference methods, including a novel approach for analyzing morphological matrices with commonly used evolutionary models. We tested alternative hypotheses of relationships and performed simulations to investigate the accuracy of our findings. We provide a comprehensive and thorough phylogenetic hypothesis for Dionycha that can serve as a robust framework to test hypotheses about the evolution of key characters. We also show that morphological data might have a phylogenetic impact, even when massively outweighed by molecular data. Our approach to analyze morphological data may serve as an alternative to the proposed practice of arbitrarily partitioning, weighting, and choosing between parsimony and stochastic models. As a result of our findings, we propose Trachycosmidae new rank for a group of Australian genera formerly included in Trochanteriidae and Gallieniellidae, and consider Ammoxenidae as a junior synonym of Gnaphosidae. We restore the family rank for Prodidomidae, but transfer the subfamily Molycriinae to Gnaphosidae. Drassinella is transferred to Liocranidae, Donuea to Corinnidae, and Mahafalytenus to Viridasiidae.

A redescription of the Late Jurassic (Tithonian) turtle Uluops uluops and a new phylogenetic hypothesis of Paracryptodira

We study the Late Jurassic (Tithonian) turtle Uluops uluops using micro-computed tomography scans to investigate the cranial anatomy of paracryptodires, and provide new insights into the evolution of the internal carotid artery and facial nerve systems, as well as the phylogenetic relationships of this group. We demonstrate the presence of a canalis caroticus lateralis in Uluops uluops, the only pleurosternid for which a palatine artery canal can be confidently identified. Our phylogenetic analysis retrieves Uluops uluops as the earliest branching pleurosternid, Helochelydridae within Pleurosternidae, and Compsemydidae including Kallokibotion bajazidi within Baenidae, which suggests at least two independent losses of the palatine artery within paracryptodires. We expect future studies will provide additional insights into the evolution of the circulation system of paracryptodires, as well as clarifying relationships along the turtle stem.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s13358-021-00234-y.

Phylogeny of drepanosiphine aphids sensu lato (Hemiptera, Aphidoidea) inferred from molecular and morphological data

As the second largest and most diverse group in the superfamily Aphidoidea, the phylogeny of drepanosiphine aphids sensu lato (s.l.) is critical for discussing the evolution of aphids. However, the taxa composition and phylogenetic relationships of drepanosiphine aphids s.l. have not been fully elucidated to date. In this study, based on total-evidence analyses combining 4 molecular genes (3 mitochondrial, COI, tRNA-Leu/COII, and CytB; 1 nuclear, EF-1ɑ) and 64 morphological and biological characteristics, the phylogeny of this group was reconstructed for the first time at the subfamily level using different datasets, parsimonies and model-based methods. All of our phylogenetic inferences clearly indicated that the drepanosiphine aphids s.l. was not a monophyletic group and seemed to support the division of the drepanosiphine aphids s.l. into different groups classified at the subfamily level. Calaphidinae was also not a monophyletic group, and Saltusaphidinae was nested within this subfamily. Drepanosiphinae was not clustered with Chaitophorinae, which was inconsistent with the previous hypothesis of a close relationship between them, illustrating that their phylogeny remains controversial. Overall, some groups of drepanosiphine aphids s.l., including Phyllaphidinae, Macropodaphidinae, Pterastheniinae, Lizeriinae, Drepanosiphinae, Spicaphidinae, Saltusaphidinae, and Calaphidinae, clustered together and might constitute the actual drepanosiphine aphids s.l. To a certain extent, our results clarified the phylogenetic relationships among drepanosiphine aphids s.l. and confirmed their taxonomic status as subfamilies.

A putatively extinct higher taxon of Spirotrichea (Ciliophora) from the Lower Cretaceous of Brazil

Fossil microeukaryotes are key elements for understanding ancient ecosystems at microscopic level and improving the knowledge on the diversification of microbial life as a whole. We describe Palaeohypothrix bahiensis gen. et sp. nov., an exceptionally well-preserved Lower Cretaceous (Berriasian-Barremian; 145-125 Mya) amber-entrapped microeukaryote, identified as a spirotrich ciliate. The preservation of structures interpreted as the nuclear apparatus and remains of the ciliature revealed a novel ground plan, not found in modern Spirotrichea, thus representing a putatively extinct higher taxon lineage, viz. the Palaeohypotricha nov. tax. Based on cladistic analysis, the new taxon is hypothesized as phylogenetically related to the Protohypotrichia.

Comprehensive phenotypic phylogenetic analysis supports the monophyly of stromateiform fishes (Teleostei: Percomorphacea)

More than half the ray-finned fishes and about one-quarter of all living vertebrates belong to Percomorphacea. Among its 30 orders, Stromateiformes encompass 77 species in 16 genera and six families. Stromateiform monophyly has never been tested using morphology, and it has been rejected by molecular analyses. This comprehensive revision of Stromateiformes includes all its valid genera of all percomorph families previously aligned with the order. We sampled 207 phenotypic characters in 66 terminal taxa representing 14 orders and 46 acanthopterygian families. This dataset significantly surpasses all previous phenotype-based phylogenies of Stromateiformes, which analysed only a fraction of these characters. Stromateiformes is recovered as monophyletic, supported by eight unequivocal synapomorphies. Amarsipidae is the sister group of all other Stromateiformes (= Stromateoidei). Centrolophidae is paraphyletic, with three of its genera allocated into an early-diverging clade and the other four appearing as successive sister groups to a lineage containing the remaining stromateiforms. All other stromateoid families are monophyletic, with the following cladistic arrangement: (Nomeidae (Stromateidae (Tetragonuridae, Ariommatidae))). Our analysis convincingly refutes recent molecular phylogenetic interpretations that fail to recover a monophyletic Stromateiformes. These findings call into question large-scale conclusions of percomorph relationships and trait evolution based solely on molecular data.

Phylogenetic analysis of a new morphological dataset elucidates the evolutionary history of Crocodylia and resolves the long-standing gharial problem

First appearing in the latest Cretaceous, Crocodylia is a clade of semi-aquatic, predatory reptiles, defined by the last common ancestor of extant alligators, caimans, crocodiles, and gharials. Despite large strides in resolving crocodylian interrelationships over the last three decades, several outstanding problems persist in crocodylian systematics. Most notably, there has been persistent discordance between morphological and molecular datasets surrounding the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. Whereas molecular data consistently support a sister taxon relationship, in which they are more closely related to crocodylids than to alligatorids, morphological data indicate that Gavialis is the sister taxon to all other extant crocodylians. Here we present a new morphological dataset for Crocodylia based on a critical reappraisal of published crocodylian character data matrices and extensive firsthand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs scored for 330 characters) and includes a new, illustrated character list with modifications to the construction and scoring of characters, and 46 novel characters. Under a maximum parsimony framework, our analyses robustly recover Gavialis as more closely related to Tomistoma than to other extant crocodylians for the first time based on morphology alone. This result is recovered regardless of the weighting strategy and treatment of quantitative characters. However, analyses using continuous characters and extended implied weighting (with high k-values) produced the most resolved, well-supported, and stratigraphically congruent topologies overall. Resolution of the gharial problem reveals that: (1) several gavialoids lack plesiomorphic features that formerly drew them towards the stem of Crocodylia; and (2) more widespread similarities occur between species traditionally divided into tomistomines and gavialoids, with these interpreted here as homology rather than homoplasy. There remains significant temporal incongruence regarding the inferred divergence timing of the extant gharials, indicating that several putative gavialids ('thoracosaurs') are incorrectly placed and require future re-appraisal. New alligatoroid interrelationships include: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) the recovery of the early Paleogene South American taxon Eocaiman as a 'basal' alligatoroid; and (3) the paraphyly of the Cenozoic European taxon Diplocynodon. Among crocodyloids, notable results include modifications to the taxonomic content of Mekosuchinae, including biogeographic affinities of this clade with latest Cretaceous-early Paleogene Asian crocodyloids. In light of our new results, we provide a comprehensive review of the evolutionary and biogeographic history of Crocodylia, which included multiple instances of transoceanic and continental dispersal.

Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family-level relationships

In recent years, the use of extensive molecular and morphological datasets has clarified the phylogenetic relationships among the orders of complex thalloid liverworts (Marchantiidae). However, previous studies excluded extinct taxa; thereby, undersampling the actual taxonomic diversity of the group. Here, we conducted a total-evidence analysis of Marchantiidae incorporating fossils. The combined dataset consisted of 11 genes-sampled from the nuclear, mitochondrial and plastid genomes-and 128 morphological characters. Sixty-two species, representing all classes and orders within Marchantiophyta and genera within Marchantiidae were included in the analyses. Six fossils were scored from literature: two assigned to the outgroup (Metzgeriothallus sharonae and Pallaviciniites sandaolingensis) and four to the ingroup (Marchantites cyathodoides, M. huolinhensis, Ricciopsis ferganica and R. sandaolingensis). Tree searches were conducted using parsimony as the optimality criterion. Clade sensitivity was assessed across a wide range of weighting regimes. Also, we evaluated the influence of fossils on the inferred topologies and branch support. Our results were congruent with previously inferred clades above the order level: Neohodgsoniales was sister to a clade formed by Sphaerocarpales and Marchantiales. However, relationships among families within Marchantiales contradicted recent studies. For instance, a clade consisting of Monosoleniaceae, Wiesnerellaceae and Targioniaceae was sister to the morphologically simple taxa instead of being nested within them as in previous studies. Novel synapomorphies were found for several clades within Marchantiales. Outgroup fossils were more influential than Marchantiidae fossils on overall topologies and branch support values. Except for a single weighting scheme, sampling continuous characters and down-weighting characters improved fossil stability. Ultimately, our results challenge the widespread notion that bryophyte fossils are problematic for phylogenetic inference.

Phylogenetic Signal and Bias in Paleontology

An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.

Morphology-based cladistics splinters the century-old dichotomy of the pied harvestmen (Arachnida: Gonyleptoidea: Cosmetidae)

The cosmetids are conspicuous harvestmen, remarkably diverse in size, shape and colour. However, the effectiveness of all these morphological traits for diagnosing groups is scarcely explored in the literature. Since the early 20th century, the family Cosmetidae has been divided into two subfamilies, Cosmetinae and Discosomaticinae, and there has been no further effort to delimit additional or alternative subfamilial groups.

In this analysis, we aim to test the issue of the basal dichotomy of Cosmetinae and Discosomaticinae. Thus, we propose a more comprehensive phylogenetic analysis using both parsimony and Bayesian approach, comprising 103 terminals of Cosmetidae, plus seven outgroup terminals scored for 130 morphological characters. Discosomaticinae is revisited and all its species were included in our matrix. To offer a real challenge to the monophyly of Discosomaticinae, members of 36 genera of Cosmetinae have also been scored. Our results support neither Cosmetinae nor Discosomaticinae sensu Pickard-Cambridge/Roewer as monophyletic groups. We found that Cosmetidae may be organized into a few major clades, which are here diagnosed. Accordingly, taxonomic changes in the arrangement of the family are introduced: description of one new tribe, five new subfamilies and revalidation of a sixth, description of three new genera, and proposition of synonymies, transfers and revalidations at generic level.

Bayesian Morphological Clock versus Parsimony: An insight into the relationships and dispersal events of postvacuum Cricetidae (Rodentia, Mammalia)

Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only datasets. Herein, we present a morphological dataset for a group of cricetid rodents to which we apply an array of methods fairly new in palaeontology that can be used by palaeontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated and non-calibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our dataset, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes and diversification in cricetids.