Derived Character States Research Articles

Revision of the Schistura cincticauda species group (Teleostei, Nemacheilidae) using molecular and morphological markers

To approach the taxonomy of large and complex animal groups it is of advantage to focus on species groups with shared derived character state. We investigate the composition, morphological characteristics and relationships of and within the Schistura cincticauda species group, whose members are small freshwater fishes that inhabit streams and rivers in eastern Myanmar and western and southern Thailand. A phylogenetic analysis using molecular genetic markers demonstrated the monophyly of this group; a combined genetic and morphological analysis revealed the inclusion of at least twelve species. They share the presence of a pair of black marks on the lower lip, one on each side of the median interruption (these marks may be reduced to few melanophores or even missing in some individuals). Additionally, all species share a small body size (max. 60 mm SL), an incomplete lateral line reaching at most to vertical through anal-fin base, and the absence of sexual dimorphism. Each of the 12 species is diagnosed by a unique combination of character states in fin ray numbers, anus position, presence/absence of an axillary pelvic lobe, and colour pattern. The distribution areas of several species overlap and five cases of syntopic occurrence are known. Five unnamed species are described herein.

Evolution of Thoracosphaeroideae (Peridiniales, Dinophyceae) and a case of atavism in taxonomically clarified Chimonodinium lomnickii var. wierzejskii from the Polish Tatra Mountains

ABSTRACT Character evolution in calcareous dinophytes and their relatives is poorly understood at present, particularly regarding the transformations of the epitheca. The precise taxonomic identity of Chimonodinium lomnickii var. (≡ Peridinium) wierzejskii is unclear, but two different arrangements of the epithecal plate pattern have been reported. We studied dinophyte material collected across Central Europe, including the type localities of Peridinium wierzejskii (Polish Tatra) and Peridinium lomnickii var. punctulatum (Berlin), and investigated the morphology of eight monoclonal strains in detail. We further obtained rRNA sequences of the strains, including 27 new GenBank entries, for a molecular phylogenetic study using a representative taxon sample of the Thoracosphaeroideae. Five ITS ribotypes could be distinguished in Chimonodinium, but neither the distribution nor morphological differentiation seems to correlate with these ribotypes. An evolutionary transformation of the epitheca is inferred from the phylogenetic tree, with the predominant plate pattern found in C. lomnickii var. wierzejskii exemplifying the derived character state. However, the rare epithecal plate pattern of C. lomnickii var. wierzejskii represents the ancestral character state today found in, for example, Peridinium and Scrippsiella. This is an indication of an atavism, of which only very few cases are known from the microbial domain. The name Peridinium wierzejskii is taxonomically clarified by epitypification. HIGHLIGHTS • Rare documentation of atavism in the microbial domain• Deep morphology of strain established from type locality• Molecular phylogenetics inferred from concatenated rRNA sequence data

Ichthyosaurs from the Upper Triassic (Carnian–Norian) of the New Siberian Islands, Russian Arctic, and their implications for the evolution of the ichthyosaurian basicranium and vertebral column

ABSTRACTThe first ichthyosaurian specimens discovered from the Upper Triassic of the Russian Arctic (Kotelny Island, New Siberian Islands) are described herein. They include the remains of large- to small-bodied ichthyosaurians originating from six stratigraphic levels spanning the lower Carnian to middle Norian. The material is mostly represented by isolated vertebrae and ribs, which are not possible to accurately diagnose, but also includes specimens comprising associated vertebrae and a fragmentary skeleton that preserves cranial remains (parabasisphenoid, fragmentary quadrate, partial mandible and hyoids). Based on vertebral and rib morphology, we identify the specimens as representatives of the following taxonomic groups: large-bodied shastasaurids, medium-sized indeterminate ichthyosaurians with a single rib facet in the presacral centra, and small euichthyosaurians with double rib facets present throughout the presacral vertebrae that likely represent toretocnemids and/or basal parvipelvians. In addition, the cranial and mandibular remains preserved in one of the specimens, ZIN PH 5/250, were studied using micro-computed tomography. Its mandible is highly similar to that of toretocnemids, whereas the parabasisphenoid demonstrates a peculiar combination of both plesiomorphic and derived character states, providing the first detailed data on this cranial element in a Late Triassic ichthyosaurian. Furthermore, the specimen also demonstrates a distinctive condition of rib articulation in the anteriormost presacral (cervical) vertebrae, which together with other features allows for the erection of a new taxon – Auroroborealia incognita gen. et sp. nov. Although the phylogenetic position of this taxon is uncertain due to its fragmentary nature, its anatomy, indicating toretocnemid or parvipelvian affinities, further supports the previously hypothesised sister-group relationships between these two clades. The morphology of the parabasisphenoid and vertebral column of the new taxon is discussed in broader contexts of the patterns of evolution of these skeletal regions in ichthyosaurs.

Ontogenetic changes in the postcranial skeleton of Mussaurus patagonicus (Dinosauria, Sauropodomorpha) and their impact on the phylogenetic relationships of early sauropodomorphs

Early sauropodomorphs were diverse in Gondwana, being particularly well represented in South America. Mussaurus patagonicus is one of the best-known non-sauropod sauropodomorphs that inhabited the Southern Hemisphere. Its importance relies on its phylogenetic position close to Sauropoda and also because it is known from a well-represented ontogenetic series, including embryos, neonate and late immature skeletons, which are particularly scarce among sauropodomorphs. In this regard, Mussaurus represents an excellent opportunity to explore anatomical and palaeobiological constraints during the ontogeny of early stages of the evolution of the group. We present the osteology of the postcranial skeleton of immature specimens of Mussaurus, highlighting the main anatomical changes that occurred during its ontogeny. The phylogenetic position of this taxon based on mature specimens is evaluated through a parsimony analysis, corroborating its position as closer to Sauropoda than most other early sauropodomorphs. Immature stages of this taxon were also evaluated phylogenetically, showing an overall phylogenetic signal that positioned them closer to the root of Sauropodomorpha than the mature specimens. However, the cranial and some postcranial anatomical partitions of neonates and late immature specimens have different phylogenetic signals, showing derived traits present in Sauropoda and related taxa (and supporting the hypothesis of paedomorphic evolution in certain regions of the skeleton). Our analysis shows that most of the appendicular apomorphies in Mussaurus appear late in ontogeny, whereas axial characters (in particular for OS 1), including those of the skull and the presacral vertebrae, show derived character states early in ontogeny that are congruent with the phylogenetic position of mature specimens. Ontogenetic series of other sauropodomorph species, however, are required to test if this pattern applies to the entire group.

Osteology and relationships of Revueltosaurus callenderi (Archosauria: Suchia) from the Upper Triassic (Norian) Chinle Formation of Petrified Forest National Park, Arizona, United States.

Once known solely from dental material and thought to represent an early ornithischian dinosaur, the early‐diverging pseudosuchian Revueltosaurus callenderi is described from a minimum of 12 skeletons from a monodominant bonebed in the upper part of the Chinle Formation of Arizona. This material includes nearly the entire skeleton and possesses a combination of plesiomorphic and derived character states that help clarify ingroup relationships within Pseudosuchia. A phylogenetic analysis recovers R. callenderi in a clade with Aetosauria and Acaenasuchus geoffreyi that is named Aetosauriformes. Key autapomorphies of R. callenderi include a skull that is longer than the femur, a complete carapace of dermal armor including paramedian and lateral rows, as well as ventral osteoderms, and a tail end sheathed in bone. Histology of the femur and associated osteoderms demonstrate that R. callenderi was slow growing and that the individuals from the bonebed were not young juveniles but had not ceased growing. A review of other material assigned to Revueltosaurus concludes that the genus cannot be adequately diagnosed based on the type materials of the three assigned species and that only R. callenderi can be confidently referred to Revueltosaurus.

The distribution of the recessus orbitalis across flatfishes (order: Pleuronectiformes).

The recessus orbitalis is an accessory organ of flatfishes functioning in the protrusion of the eyes. This character, along with cranial asymmetry and a forward insertion of the dorsal fin, have been considered synapomorphies for the Pleuronectiformes. New dissections and examination of images taken in the wild show that the recessus orbitalis is present in all representatives of Pleuronectoidei examined but is absent in the single species of Psettoidei dissected. Psettoidei, the most primitive pleuronectiform lineage, contains three recognized species; thus, the absence of the recessus orbitalis in this whole lineage is unclear without further dissections. Ancestral character estimation at the family level for the recessus orbitalis indicates that the recessus orbitalis was likely absent in the common ancestor of Pleuronectiformes but was most likely present in the common ancestor of the Pleuronectoidei. Given that so few species of flatfishes have been assessed for the recessus orbitalis to date, additional characterization of the distribution of the recessus orbitalis across flatfishes will further inform what states this character may have and if it is a synapomorphy of Pleuronectiformes or simply a derived character state of Pleuronectoidei.

Redescription and Phylogenetic Assessment of ‘Prognathodon’ Stadtmani: Implications for Globidensini Monophyly and Character Homology in Mosasaurinae

ABSTRACT Prognathodon stadtmani was discovered in the Campanian portion of the Upper Cretaceous Mancos Shale in western Colorado in 1975. Following its original description almost two decades ago, more material of the holotype was prepared. Those new elements include a quadrate, often considered one of the most critical bones for understanding mosasaur systematics, portions of the skull roof, posterior mandible, and braincase. Prognathodon stadtmani exhibits a suite of features that include both derived character states observed in later mosasaurines and primitive features present in earlier members of the clade, such as Clidastes. Although the quadrate resembles those of Prognathodon and Globidens in some respects, it lacks fusion between the suprastapedial process and ascending tympanic rim observed in those taxa. I ran a series of phylogenetic analyses using parsimony and Bayesian inference to understand the relationships of this taxon. Regardless of character selection or methodology, ‘Prognathodon’ stadtmani was not found to be monophyletic with the rest of the genus Prognathodon. Depending on method, it was recovered as the sister taxon to the rest of Globidensini, the sister taxon to Mosasaurini + Globidens, or an early diverging mosasaurine outside of both Globidensini and Mosasaurini. Owing to these results, I assign the type to a new genus, Gnathomortis, gen. nov., yielding the species Gnathomortis stadtmani, comb. nov. Furthermore, the rest of the genus Prognathodon and the clade Globidensini more broadly were not consistently recovered as monophyletic. Many characters of the quadrate and the dentition that typically united those clades are optimized as homoplastic based on my resulting topologies.

Modeling the Evolution of Ceramic Traditions Through a Phylogenetic Analysis of the Chaînes Opératoires: the European Bronze Age as a Case Study

The chaines operatoires underlying the manufacture of objects are good proxies for studying social groups and how cultural traits are transmitted and modified through the learning process. With the rise of evolutionary archaeology, the evolution of ceramic vessels can be modeled by using cladistics to elaborate kinship relationships between different taxa on the basis of shared derived character states. Here the modeling applies to ceramic fashioning from the European Middle Bronze Age (France and the United Kingdom). The aim is to assess the nature of the evolution and the relationships between three main cultures—in southern England, Normandy, and in the center-west of France. The cladistics analysis highlights that the ceramic traditions largely result from a process of phylogenesis—a result of descent with modification from an ancestral assemblage—rooted in the Early Bronze Age, suggesting a common origin for the Trevisker/Deverel-Rimbury and French Atlantic technical traditions. On the other hand, the Norman appears to be related to the Duffaits tradition, but to the exclusion of the Trevisker/Deverel-Rimbury traditions. This study supports the theoretical premise that some technical sequences are more stable than others. The evolution of sequences requiring motor habits, such as shaping, stabilized fairly quickly, unlike the finishing operations that continued to diverge throughout the Bronze Age. This study suggests that cladistics based on the description of the ceramic material in terms of chaines operatoires is a useful tool for studying cultural change.

New remains of kollpaniine “condylarths” (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

The description of new specimens of kollpaniines “condylarths” from Tiupampa (early Palaeocene of Bolivia) represents a significant addition to the knowledge of the earliest fauna of South American ungulates. Several partial mandibles and maxillae of Molinodus suarezi and Simoclaenus sylvaticus are described. The morphology of the lower premolars of Molinodus, being associated to lower molars, is established and a previous referral of an isolated p4 is rejected. A maxilla of Simoclaenus reveals the morphology of the so far unknown P1-4 of this taxon and allows a discussion on the development of the protocone in Palaeocene “condylarths”. The subvertical maxilla-premaxilla suture and the vertical implantation of the P1/p1 confirm the shortness of the snout of Simoclaenus, whereas the procumbency of the p1 of Molinodus indicates a longer rostrum. The upper molars of Molinodus confirm the presence of a tendency to duplication of the protocone, which is regarded as the incipient development of a pseudohypocone. The various patterns of formation of a hypocone (or pseudohypocone) are considered and, among other South American Native Ungulates, a protocone-derived pseudohypocone (i.e. Molinodus-like) is hypothesized in Lamegoia, Raulvaccia, and notoungulates, whereas a postcingulum-derived, hypocone is present in didolodontids and litopterns.The new specimens confirm the conspicuous small size of the M1/m1 of Molinodus and Simoclaenus as compared to the M2/m2. Consequently, we examined the relative proportions of molars in these taxa as compared to a variety of extant and extinct euungulates. Their proportions were plotted into the ‘developmental’ morphospace based on the predictive mathematical model of Kavanagh et al. (2007) (Inhibitory Cascade Model, or IC model), which might explain a large part of the mammalian diversity in molar proportions. Based on the upper molars, the Tiupampa kollpaniines were retrieved in a separate area of the predicted morphospace with other North American “condylarths” with large M2; this departure is also consistent with previous results concerning the lower molars (large m2). These peculiar molar proportions were found distinct from many other mammals, and might represent clade-specific differences: the large size of both the upper and lower second molars relative to other molars thus possibly representing a derived character state shared by some “condylarths” and kollpaniines.

An Eocene Bunodont South American Native Ungulate (Didolodontidae) from the Lumbrera Formation, Salta Province, Argentina

The extinct South American native ungulates are widely known as a particular evolutionary experiment of mammalian herbivory. Among their representatives, forms with bunodont dentition have received little attention, being usually regarded as primitive and placed in the paraphyletic order “Condylarthra”. Here we describe a new Didolodontidae Saltaodus sirolli gen. et sp. nov. from the Eocene of Lumbrera Formation (Santa Barbara Subgroup) near San Antonio de los Cobres, Salta Province, Argentina. Saltaodus is represented by a small left dentary with a canine alveolus and a brachydont dentition, with p1-2, the roots of p3 and p4-m2. The jaw is broken mesial to the canine alveolus, which is circular and mesially projected. There is only one root for p1 and p2. The specimen has some similarity with North American archaic ungulates but more resembles South American bunodont ungulates. In contrast to Kollpaniinae, Saltaodus presents more separate, slender and higher cusps with well-developed cristids; the talonid basin is wide and not filled by the base of the hypoconid or the distal wall of the metaconid. Several derived character states as compared to Kollpaniinae, such as the more molarized p4, with a clear difference between trigonid and talonid, molars with a talonid equal to or wider than the trigonid, and well separated hypoconid, hypoconulid and entoconid, allow the placement of Saltaodus among Didolodontidae. Saltaodus represents one of the few known small didolodontids (< 5 kg) from the lower latitudes of South America.

Scanning the Hyocephalidae: details of their external morphology with respect to phylogenetic relationships within Eutrichophora (Hemiptera: Heteroptera)

Abstract Hyocephalidae (Hemiptera: Heteroptera: Pentatomomorpha) is a small family of true bugs containing two genera and three species endemic to Australia. For the first time, we examine here selected structures of their external morphology using scanning electron microscopy – the external structures associated with the metathoracic and dorsoabdominal scent glands, the strainer organ on the sternite III, as well as the trichobothrial pattern and ultrastructure. The following character states are confirmed (i, ii, iii) or newly recognised (iv, v) as autapomorphies of Hyocephalidae: i) apically projected scimitar-shaped peritreme of the metathoracic scent glands; ii) presence of a strainer organ on sternite III in both sexes; iii) trichobothria on sternite V placed immediately ventrad of spiracle, iv) trichobothria on each of abdominal segments III–VII all grouped together within a common trichome, and v) presence of crocus-like structures within the trichome. Of particular interest is the presence of a shallow open bothrium (type B) surrounded by a trichome in Hyocephalidae, a probably derived character state shared with Pyrrhocoroidea and most Lygaeoidea, while Stenocephalidae (previously considered to be closely related to Hyocephalidae and used here for comparison) and the remaining Coreoidea possess a recessed bothrium of type A2, lacking the trichome. The morphology of trichobothria in Hyocephalidae may thus suggest either their closer relationship to Lygaeoidea + Pyrrhocoroidea than to Coreoidea, or a parallel evolution of the open bothrium with trichome in Eutrichophora. We highlight the importance of Hyocephalidae for a better understanding of the phylogeny of Eutrichophora and the urgent need to obtain phylogenomic data for future research. A taxonomic catalogue of Hyocephalidae is supplemented. The neotype designation for Hyocephalus aprugnus Bergroth, 1906 made by ŠTYS (1964) and supported by GRANT &amp; ŠTYS (1970) is found invalid.

Flower and fruit anatomy of Cordia nodosa Lam. and Varronia bonplandii Desv. (Cordiaceae, Boraginales) with phylogenetic implications

Despite their ecological importance and wide distribution, Cordiaceae have not been subject to detailed anatomical study yet. We examined flower and fruit anatomies of Cordia nodosa and Varronia bonplandii (using paraffin sectioning and light microscopy) in comparison with other woody members of Boraginales. The internal architecture of the superior bicarpellate ovary resulted from the development of secondary septa including apical, basal and false septa, as reported also from other Boraginales. Novel characters of Cordiaceae were identified such as an extensive tissue surrounding the gynoecium of C. nodosa and a lignified cap on top of the endocarp in V. bonplandii. Fruits containing a single seed may have originated several times independently in Cordiaceae deriving from the four-seeded condition present today in most other non-capsular Boraginales. Distyly of V. bonplandii does not appear genetically fixed but may result from different ecological conditions. Hemianatropous ovules are now considered the derived character state in Cordiaceae, originating from anatropous ovules present in other Boraginales. Studies like this improve the knowledge about generative organs in general and identify phylogenetically informative characters. However, better knowledge of functional morphology and ecological importance regarding many traits identified require further investigations on the diversity of Cordiaceae.

The Biochemistry and Evolution of the Dinoflagellate Nucleus.

Dinoflagellates are known to possess a highly aberrant nucleus—the so-called dinokaryon—that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones—the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.

Bone histology of Azendohsaurus laaroussii: Implications for the evolution of thermometabolism in Archosauromorpha

AbstractThis paper is aimed at constraining the phylogenetic frame of the acquisition of endothermy by Archosauromorpha. We analyzed the bone histology of Azendohsaurus laaroussii. Stylopodial and zeugopodial bones show three tissue types: (1) avascular lamellar zonal bone formed at low growth rates; (2) a scaffold of parallel-fibered bone containing either small primary osteons or simple vascular canals; and (3) fibrolamellar bone formed at high growth rates. We used quantitative histology to infer the thermometabolic regime of this taxon. We define endothermy as the presence of any mechanism of nonshivering thermogenesis that increases both body temperature and resting metabolic rate. Thus, estimating the resting metabolic rate of an extinct organism may be a good proxy to infer its thermometabolic regime (endothermy vs. ectothermy). High resting metabolic rates have been shown to be primitive for the clade Prolacerta–Archosauriformes. Therefore, we inferred the resting metabolic rates of A. laaroussii, a sister group of this clade, and of 14 extinct related taxa, using phylogenetic eigenvector maps. All the inferences obtained are included in the range of variation of resting metabolic rates measured in mammals and birds, so we can reasonably assume that all these taxa (including Azendohsaurus) were endotherms. A parsimony optimization of the presence of endothermy on a phylogenetic tree of tetrapods shows that this derived character state was acquired by the last common ancestor of the clade Azendohsaurus–Archosauriformes and that there is a reversion in Crocodylia.

Morpho-functional analysis of the explosive defensive system of basal bombardier beetles (Carabidae: Paussinae: Metriini)

Bombardier beetles, belonging to the carabid subfamilies Paussinae and Brachininae, are famous for their unique ability to explosively discharge a hot spray of quinones from their pygidial glands when threatened. The paussine tribe Metriini is broadly acknowledged as the most basal group of bombardiers. In order to complement the available information on the chemical substances and the primitive discharging mechanism of Metriini, we provide a detailed morpho-functional analysis of the explosive defensive system of Metrius contractus Eschscholtz, 1829 and Sinometrius turnai Wrase and J. Schmidt, 2006, representatives of the two genera in this tribe. We use dissections, histology, scanning electron microscopy (SEM), and focused ion beam microscopy (FIB/SEM) to describe and illustrate various levels of anatomical complexity. FIB/SEM microscopy is used to analyse ultrastructural features of the cellular regions, replacing the classical transmission electron microscopy (TEM). Compared to other Paussinae tribes, Metriini lacks the typical flange of Coanda, the elytral fold used to direct the defensive secretions forward, but has a similar arrangement of internal components. We find that the internal components of the explosive defensive system, including the secretory lobes, collecting duct, reservoir chamber, valve, reaction chamber, accessory chamber and accessory glands, are only slightly different between Metrius Eschscholtz, 1829 and Sinometrius Wrase and J. Schmidt, 2006. The accessory chamber to the reaction chamber is a unique, derived character state common to all Paussinae examined and therefore represents a clear apomorphy of the Paussinae. We use the same microscopy techniques as used in a recent publication on the Brachininae, to compare the defensive systems of Metriini and Brachininae. We find a lack of morphological similarity at the ultrastructural level, suggesting that the bombarding mechanism may have evolved independently in the Paussinae and the Brachininae, perhaps in response to different ecological pressures.

A revision of the Heatherellidae (Parasitiformes: Mesostigmata) with a new genus and two new species from Australasia.

The discovery of a new genus of Heatherellidae in New Zealand has led us to revise this enigmatic family and its constituent genera. Aheatherella n. gen., based on A. mira n. sp. from the North Island of New Zealand, lacks some of the derived character states that link the Australian Heatherella, most notably the lack of sexual dimorphism in the dorsal shields and in the presence of peritremes in adult Aheatherella. Heatherella osleri n. sp. is described from New South Wales, extending the distribution of this genus beyond Queensland. New collection records of H. callimaulos and a key to the genera and species of the family are provided. We propose that the Heatherellidae-previously placed in its own cohort outside the Gamasina-are best considered a superfamily of gamasine mites within the subcohort Epicriiae.

First Species of Oreoeudesis from Rwanda, with Description of Suboreon subgen. nov. (Coleoptera: Staphylinidae)

The Afrotropical genus Oreoeudesis Franz was previously known to occur in Tanzania, Kenya and Cameroon. A new species, Oreoeudesis ruandensis sp. nov. is described on the basis of a material coming from Rwanda. Differences in cephalic, pronotal, mesonotal and genital structures justify placing the new species in a separate subgenus, Suboreon subgen. nov. Morphological structures of O. ruandensis, especially the large composite eyes and fully developed wings, seem to be plesiomorphic as compared to derived character states in the previously known, microphthalmous or anophthalmous and wingless species.

Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions

BackgroundPhylogenetic comparative methods allow us to test evolutionary hypotheses without the benefit of an extensive fossil record. These methods, however, make simplifying assumptions, among them that clades are always increasing or stable in diversity, an assumption we know to be false. This study simulates hypothetical clades to test whether the Binary State Speciation and Extinction (BiSSE) method can be used to correctly detect relative differences in diversification rate between ancestral and derived character states even as net diversification rates are declining overall. We simulate clades with declining but positive diversification rates, as well those in which speciation rates decline below extinction rates so that they are losing richness for part of their history. We run these analyses both with simulated symmetric and asymmetric speciation rates to test whether BiSSE can be used to detect them correctly.ResultsFor simulations with a neutral character, the fit for a BiSSE model with a neutral character is better than alternative models so long as net diversification rates remain positive. Once net diversification rates become negative, the BiSSE model with the greatest likelihood often has a non-neutral character, even though there is no such character in the simulation. BiSSE’s usefulness in detecting real asymmetry in speciation rates improves with clade age, even well after net diversification rates have become negative.ConclusionsBiSSE is most useful in analyzing clades of intermediate age, before they have reached peak diversity and gone into decline. After this point, users of BiSSE risk incorrectly inferring differential evolutionary rates when none exist. Fortunately, most studies using BiSSE and similar models focus on rapid, recent diversifications, and are less likely to encounter the biases BiSSE models are subject to for older clades. For extant groups that were once more diverse than now, however, caution should be taken in inferring past diversification patterns without fossil data.

Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data.

Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (Mkparsinf), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices.

New information on the cranial morphology of Avimimus (Theropoda: Oviraptorosauria)

ABSTRACTThe cranial morphology of the oviraptorosaurian Avimimus portentosus is described based on a new specimen, one that includes bones such as the nasal and the jugal, which had not been available or only incompletely preserved previously. The left and right nasals are fused together as in oviraptorids. Morphology of the jugal, which is not fused with the quadratojugal, and the postorbital indicate that the infratemporal fenestra is completely separate from the orbit, not confluent with the latter, as inferred previously. The left and right dentaries are fused together without a trace of suture. Such newly available information indicates that the skull of Avimimus is not as ‘avian’-like as inferred in previous studies. Rather, it shows a mixture of plesiomorphic and derived character states observed in Oviraptorosauria, consistent with an intermediate phylogenetic position of this dinosaur between Early Cretaceous basal oviraptorosaurians and the diverse clade of Caenagnathoidea.