A new scanilepiform from the Lower Triassic of northern Gansu Province,China, and phylogenetic relationships of non‐teleostean Actinopterygii

A new scanilepiform, Beishanichthys brevicaudalis gen. et sp. nov. , is named and described based on fossils from the Lower Triassic lake deposits exposed in Beishan area, Gansu Province, China. The discovery documents a new record of this group, which is significantly older than other known scanilepiforms from China, and is slightly younger than Evenkia from the Lowest Triassic of Central Siberia. Although the Beishan beds were previously interpreted as Late Permian in age, based on megaplant fossils, this new discovery supports the reinterpretation of the deposits as Early Triassic in age, based on vertebrate fossils from the same locality and horizon. Phylogenetic analysis was conducted to resolve the relationships of Scanilepiformes with other actinopterygian clades, and the inter‐relationships within Scanilepiformes. Contrary to previous thought that scanilepiforms are closely related to the Amiidae, the phylogenetic results of this study recognize the Scanilepiformes as stem‐group neopterygians. Relationships of the Scanilepiformes and Australosomus with other neopterygians remain unresolved. With a characteristic long‐based dorsal fin, scanilepiforms represent a small group that emerged in Early Triassic freshwater environments, inhabited Eurasia and North America during the Middle–Late Triassic, briefly invaded the marine environment by the Late Triassic in Europe, and became extinct at the end of Triassic. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 595–612.     

Phylogenetic relationships and biogeography of midwife toads (Discoglossidae: Alytes)

Aim To devise a robust phylogenetic hypothesis for midwife toads (Alytes: Anura: Discoglossidae) and to discuss its implications for the reconstruction of the biogeographical history of the group. Location Western Palearctic. Methods Analysis of sequences of mitochondrial DNA (cytochrome b and 16S RNA, 861 bp) and 29 characters of cranial osteology of all species and subspecies within Alytes. Results Phylogenetic analyses support a sister group relationship between Alytes dickhilleni and A. muletensis, and of this clade with A. maurus. The monophyly of A. obstetricans is controversial; in particular, the phylogenetic position of A. obstetricans almogavarii is uncertain. The estimated dates for the cladogenetic events within Alytes are congruent with those derived from independent analyses (allozymes), except for the differentiation of A. o. almogavarii and the split between A. dickhilleni and A. muletensis. Main conclusions The phylogeny based on the analysis of morphological and mtDNA data differs from previous hypotheses in the positions of A. o. almogavarii and A. maurus. Events associated with the radiation of Alytes are the formation of large inland saline lakes in Iberia c. 16 Ma and the 11 ° C dramatic decrease in average annual temperature during the Middle–Late Badenian transition c. 14–13.5 Ma (A.cisternasii vs. the ancestor of the remaining clades), the structuring of the Neo‐Pyrenees and the reopening of the Betic Strait c. 10–8 Ma(A. o. almogavarii vs. A. obstetricans and vs. the subgenus Baleaphryne), the opening of the Gibraltar Strait at the end of the Messinian Salinity Crisis at c. 5.3 Ma (A. maurus vs. the ancestor of the A. dickhilleni A. muletensis clade) and a transmarine colonization event at c. 3 Ma (the ancestor of A. muletensis vs. A. dickhilleni). Following the new hypothesis, A. maurus, previously considered a subspecies of A. obstetricans, deserves species status. Second, A. o. almogavarii is a well‐differentiated lineage that was isolated from other A. obstetricans more than c. 5 Ma, but later lost its genetic and specific identity following secondary contact, hybridization and introgression with the main stock. The presence of a marked morphological and genetic diversity within A. obstetricans renders reconstruction of the evolutionary history of the genus more complicated than previously appreciated.     

A phylogenetic analysis of the arachnid orders based on morphological characters

Morphological evidence for resolving relationships among arachnid orders was surveyed and assembled in a matrix comprising 59 euchelicerate genera (41 extant, 18 fossil) and 202 binary and unordered multistate characters. Parsimony analysis of extant genera recovered a monophyletic Arachnida with the topology (Palpigradi (Acaromorpha (Tetrapulmonata (Haplocnemata, Stomothecata nom. nov. )))), with Acaromorpha containing Ricinulei and Acari, Tetrapulmonata containing Araneae and Pedipalpi (Amblypygi, Uropygi), Haplocnemata (Pseudoscorpiones, Solifugae) and Stomothecata (Scorpiones, Opiliones). However, nodal support and results from exploratory implied weights analysis indicated that relationships among the five clades were effectively unresolved. Analysis of extant and fossil genera recovered a clade, Pantetrapulmonata nom nov. , with the topology (Trigonotarbida (Araneae (Haptopoda (Pedipalpi)))). Arachnida was recovered as monophyletic with the internal relationships (Stomothecata (Palpigradi, Acaromorpha (Haplocnemata, Pantetrapulmonata))). Nodal support and exploratory implied weights indicated that relationships among these five clades were effectively unresolved. Thus, some interordinal relationships were strongly and/or consistently supported by morphology, but arachnid phylogeny is unresolved at its deepest levels. Alternative hypotheses proposed in the recent literature were evaluated by constraining analyses to recover hypothesized clades, an exercise that often resulted in the collapse of otherwise well-supported clades. These results suggest that attempts to resolve specific nodes based on individual characters, lists of similarities, evolutionary scenarios, etc., are problematic, as they ignore broader impacts on homoplasy and analytical effects on non-target nodes.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 221–265.     

Housekeeping genes for phylogenetic analysis of eutherian relationships

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.     

The larval head morphology of Xyela sp. (Xyelidae, Hymenoptera) and its phylogenetic implications

Larval head structures of Xyela sp. are described in detail. The characters are compared to conditions found in larvae of other groups of Hymenoptera and Endopterygota. Like other symphytan larvae the immature stages of Xyelidae are mainly characterized by presumably plesiomorphic features of the head. The head sutures are well developed and all parts of the tentorium are present. The labrum is free and a complete set of labral muscles is present. The maxillae are in a retracted position. In contrast to other hymenopteran larvae Xyela possesses a clypeofrontal suture, a comparatively long antenna and three well‐developed antennal muscles. Apomorphic features of Xyela are the absence of muscles associated with the salivarium and the complete absence of Musculus craniocardinalis. A clade comprising Orussidae and Apocrita is supported by the unsegmented maxillary and labial palps and the absence of the lacinia. Six potential autapomorphies for the Hymenoptera were revealed: (1) the caudal tentorial apodeme, (2) the bifurcated tendon of Musculus craniomandibularus internus, (3) the lateral lobe of the cardo, (4) the origin of M. tentoriohypopharyngalis from the posterior head capsule, (5) the exceptionally strong prepharyngo‐pharyngeal longitudinal muscle and (6) the longitudinal muscle of the silk press. The maxillolabial complex, the vestigial M. craniocardinalis and a distinctly developed labio‐hypopharyngeal lobe bearing the opening of the salivary duct are potential synapomorphies of Hymenoptera and Mecopterida. The globular, orthognathous head capsule, the modified compound eyes, the occipital furrow and the X‐shaped tentorium are features with unclear polarity shared by Hymenoptera and Mecoptera.     

Untangling the contribution of characters to evolutionary relationships: a case study using fossils,morphology, and Genes

Given the importance of phylogenetic trees to understanding common ancestry and evolution, they are a necessary part of the undergraduate biology curriculum. However, a number of common misconceptions, such as reading across branch tips and understanding homoplasy, can pose difficulties in student understanding. Students also may take phylogenetic trees to be fact, instead of hypotheses. Below we outline a case study that we have used in upper-level undergraduate evolution and ichthyology courses that utilizes shark teeth (representing fossils), body characters, and mitochondrial genes. Students construct their own trees using freely available software, and are prompted to compare their trees with a series of questions. Finally, students explore homoplasy, polytomies, and trees as hypotheses during a class discussion period. This case study gives students practice with tree-thinking, as well as demonstrating that tree topology is reliant on which characters and tree-building algorithms are used.     

A comparative study of activity levels in larval anurans and response to the presence of different predators

Activity level is a key behavioral trait in many animals whichmediates a trade-off between finding food and avoiding predation.Optimal activity level will therefore depend on environment,and plasticity in response may increase fitness (if an organismencounters multiple environments in a lifetime). One groupin which activity level, and its relationship to foraging andpredation risk, has been well studied is larval anurans. Anuransinhabit a range of distinct freshwater aquatic community typesthat are created by differences in pond permanency and toppredator. Species segregate across these pond types and thereforetadpoles from different species encounter different selection regimes. I hypothesized that species from different pond typeswould therefore differ in activity behavior, and in plasticityof this behavior. I tested this in a phylogenetic frameworkto consider the evolution of plasticity in anurans diversifyinginto different pond types. Time spent active was quantifiedfor larvae of each of 13 anuran species (from three taxonomicfamilies) in four conditions: when no predator was present,and in the non-lethal presence of a dragonfly, newt, or fishpredator. Species nested within pond type by taxonomic familydiffered significantly in time spent active. A significant interaction between predator treatment and taxonomic familywas also observed. A phylogenetic analysis of change in behaviorrevealed strong positive correlations in evolution of thesebehaviors and suggests constraints on the ability of larvalanurans to independently modify activity levels in the presenceversus absence of predators.     

A new choristodere (Reptilia: Diapsida) from the Lower Cretaceous of western Liaoning Province, China, and phylogenetic relationships of Monjurosuchidae

The publication of the scientific name Monjurosuchus splendens in 1940 documented the first tetrapod fossil of the later world-renowned Jehol Biota. For more than half a century since this discovery, however, Monjurosuchus has remained as a monotypic genus of the family Monjurosuchidae, and the relationships of the family with choristoderes have not been correctly recognized until quite recently. In this paper, a new monjurosuchid is named and described based on a nearly complete skull and postcranial skeleton from the Early Cretaceous Chiufotang Formation exposed near Chaoyang, western Liaoning Province, China. This new material documents the first occurrence of monjurosuchid choristoderes outside the type Lingyuan area, and extends the geological range of the family from the Yixian Formation to the younger Chiufotang Formation. Cladistic analyses were conducted with inclusion of monjurosuchids, and the results support the placement of the family Monjurosuchidae as a primitive clade outside the Neochoristodera. A new classification scheme is proposed for choristoderes on the basis of the recovered phylogenetic framework of the group.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 427–444.     

Osteology and myology of the cephalic region and pectoral girdle of the Chinese catfish Cranoglanis bouderius,with a discussion on the autapomorphies and phylogenetic relationships of the Cranoglanididae (Teleostei: Siluriformes)

The cephalic and pectoral girdle structures of the Chinese catfish Cranoglanis bouderius are described and compared with those of other catfishes as the foundation for an analysis on the Cranoglanididae autapomorphies and also for a discussion on the phylogenetic relationships between the cranoglanidids and the other catfishes. Our observations and comparisons indicate that cranoglanidids are defined, at least, by four autapomorphies, namely: 1) the cartilages associated with the mandibular barbels are broad, somewhat circular; 2) epioccipital with a well-developed posterodorsal process, which presents a large, deep, circular posterior concavity; 3) a well-defined, deep, anteroposteriorly elongated concavity formed by both the frontal and the lateral ethmoid to receive the anteromedial surface of the metapterygoid; 4) the adductor mandibulae A3" is dorsally divided into two bundles and partially inserted on the posterior portion of the primordial ligament. With respect to the phylogenetic relationships of the Cranoglanididae, this study strongly suggests that these fishes are probably closely related to the Ariidae and the Claroteidae.     

A comparative analysis of predator-induced plasticity in larval Triturus newts

Species that occupy similar habitats are expected to show convergent phenotypes. If habitats are defined by the presence of predators, then traits that modify vulnerability to predation, including predator-induced phenotypic plasticity, should be similar within habitats. We tested this idea using larvae of six syntopic newt species belonging to the two Triturus clades. Behavioural plasticity induced by odonate predators was strongly dissimilar between the two main clades but similar within them. Morphological plasticity was variable among species, even between one pair of closely related species. A predation experiment tested whether differences between clades could be caused by differences in body size. Size-specific vulnerability differed between newts in the small-bodied and large-bodied clades, indicating that similar predators may affect the two clades differently. The results showed both similarity and dissimilarity in predator-induced phenotypic plasticity in syntopic larval newts although theory suggests that divergence is unlikely in such ecologically similar species.     

Osteology and myology of the cephalic region and pectoral girdle of Erethistes pusillus, comparison with other erethistids, and comments on the synapomorphies and phylogenetic relationships of the Erethistidae (Teleostei: Siluriformes)

The cephalic and pectoral girdle structures of the erethistid Erethistes pusillus (Erethistinae) are described and compared with those of another species of the subfamily Erethistinae, namely Hara filamentosa , and of the single species of the subfamily Continae, Conta conta , as well as of several other catfishes, as the foundation for a discussion on the synapomorphies and phylogenetic position of the Erethistidae. The observations and comparisons support de Pinna's phylogenetic hypothesis, according to which the Erethistidae is the sister‐group of the Aspredinidae, with the clade formed by these two families being the sister‐group of the Sisoridae sensu stricto . In addition, the observations and comparisons pointed out a new, additional character to diagnose the family Erethistidae, namely: mesocoracoid arch deeply bifurcated dorsally.     

Evolution of morphology and locomotor performance in anurans: relationships with microhabitat diversification

The relationships between morphology, performance, behavior and ecology provide evidence for multiple and complex phenotypic adaptations. The anuran body plan, for example, is evolutionarily conserved and shows clear specializations to jumping performance back at least to the early Jurassic. However, there are instances of more recent adaptation to habit diversity in the post‐cranial skeleton, including relative limb length. The present study tested adaptive models of morphological evolution in anurans associated with the diversity of microhabitat use (semi‐aquatic arboreal, fossorial, torrent, and terrestrial) in species of anuran amphibians from Brazil and Australia. We use phylogenetic comparative methods to determine which evolutionary models, including Brownian motion (BM) and Ornstein‐Uhlenbeck (OU) are consistent with morphological variation observed across anuran species. Furthermore, this study investigated the relationship of maximum distance jumped as a function of components of morphological variables and microhabitat use. We found there are multiple optima of limb lengths associated to different microhabitats with a trend of increasing hindlimbs in torrent, arboreal, semi‐aquatic whereas fossorial and terrestrial species evolve toward optima with shorter hindlimbs. Moreover, arboreal, semi‐aquatic and torrent anurans have higher jumping performance and longer hindlimbs, when compared to terrestrial and fossorial species. We corroborate the hypothesis that evolutionary modifications of overall limb morphology have been important in the diversification of locomotor performance along the anuran phylogeny. Such evolutionary changes converged in different phylogenetic groups adapted to similar microhabitat use in two different zoogeographical regions.     

Adapting generalized frequency coding to use colour spectra in the determination of phylogenetic relationships: an example with hummingbirds

We introduce a methodology to perform phylogenetic analyses on bird taxa using parsimony based on plumage colour characters obtained as spectra. The generalized frequency coding method was adapted to transform continuous colour spectral data into discrete variables. As an example of the application of the methodology, we analysed two species of the hummingbird genus Campylopterus and all species of the genera Anthracothorax and Eulampis , which occur in South and Central America and the Caribbean islands. The genus Topaza was used as an outgroup because of its basal position within the hummingbirds. The results were mostly in accordance with both traditional morphological as well as molecular analyses indicating that there is phylogenetic information in plumage colours measured in an integral and objective way and that the new method is appropriate for phylogenetic analyses at this lower taxonomic level.     

Head capsule characters in the Hymenoptera and their phylogenetic implications

The head capsule of a taxon sample of three outgroup and 86 ingroup taxa is examined for characters of possible phylogenetic significance within Hymenoptera. 21 morphological characters are illustrated and scored, and their character evolution explored by mapping them onto a phylogeny recently produced from a large morphological data set. Many of the characters are informative and display unambiguous changes. Most of the character support demonstrated is supportive at the superfamily or family level. In contrast, only few characters corroborate deeper nodes in the phylogeny of Hymenoptera.