Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata

As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.     

Reconstructing pectoral appendicular muscle anatomy in fossil fish and tetrapods over the fins‐to‐limbs transition

The question of how tetrapod limbs evolved from fins is one of the great puzzles of evolutionary biology. While palaeontologists, developmental biologists, and geneticists have made great strides in explaining the origin and early evolution of limb skeletal structures, that of the muscles remains largely unknown. The main reason is the lack of consensus about appendicular muscle homology between the closest living relatives of early tetrapods: lobe‐finned fish and crown tetrapods. In the light of a recent study of these homologies, we re‐examined osteological correlates of muscle attachment in the pectoral girdle, humerus, radius, and ulna of early tetrapods and their close relatives. Twenty‐nine extinct and six extant sarcopterygians were included in a meta‐analysis using information from the literature and from original specimens, when possible. We analysed these osteological correlates using parsimony‐based character optimization in order to reconstruct muscle anatomy in ancestral lobe‐finned fish, tetrapodomorph fish, stem tetrapods, and crown tetrapods. Our synthesis revealed that many tetrapod shoulder muscles probably were already present in tetrapodomorph fish, while most of the more‐distal appendicular muscles either arose later from largely undifferentiated dorsal and ventral muscle masses or did not leave clear correlates of attachment in these taxa. Based on this review and meta‐analysis, we postulate a stepwise sequence of specific appendicular muscle acquisitions, splits, and fusions that led from the ancestral sarcopterygian pectoral fin to the ancestral tetrapod forelimb. This sequence largely agrees with previous hypotheses based on palaeontological and comparative work, but it is much more comprehensive in terms of both muscles and taxa. Combined with existing information about the skeletal system, our new synthesis helps to illuminate the genetic, developmental, morphological, functional, and ecological changes that were key components of the fins‐to‐limbs transition.     

The postcranial anatomy of Suminia getmanovi (Synapsida: Anomodontia), the earliest known arboreal tetrapod

The basal anomodont Suminia getmanovi Ivakhnenko, 1994 from the late Palaeozoic of Russia is highly specialized in its masticatory apparatus, and has been suggested to represent the earliest arboreal tetrapod in the fossil record. Its postcranial anatomy is described in detail for the first time, revealing a large number of autapomorphies for this small herbivore. These include a reduced number of presacral and therein dorsal vertebrae, an elongate neck, a long and possibly prehensile tail, a procoracoid with a notch at its ventromedial margin rather than a foramen, an iliac blade with a robust ridge at its anteromedial edge, a pubis with a puboischiadic fenestra and separate pubic foramen, and elongate limbs. Additional autapomorphic characters are displayed in the autopodium, which comprises about 40% of the entire limb length. These features include an enlarged, phalangiform distal carpal 1 and tarsal 1, a short and robust first metacarpal, a crescent‐shaped distal tarsal 4, and elongate penultimate phalangeal elements. The phylogenetic relationships of basal anomodonts are revisited using an expanded data set, with the addition of key taxa and several postcranial characters. Unlike dicynodonts, Suminia retained the plesiomorphic phalangeal formula for amniotes of 2‐3‐4‐5‐3 (manus) and 2‐3‐4‐5‐4 (pes). This pattern is achieved by the retention of disc‐like phalangeal elements between the proximal and penultimate phalanges in digits III, IV (manus and pes), and V (pes only). In light of the new material, Suminia can be recognized as the most complete basal anomodont, offering new insights into the early evolution of the group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 661–698.     

Variation in Discosauriscus austriacus (Makowsky, 1876) from the Lower Permian of the Boskovice Furrow (Czech Republic)

Two genera and four species of discosauriscids, Discosauriscus potamites, D. pulcherrimus, Letoverpeton austriacum and L. moravicum , have previously been described from the Boskovice Furrow in Moravia. These laxa were differentiated primarily on the basis of proportional differences of the skull together with other morphological characters.
Excavations at two localities in the Boskovice Furrow have produced new, relatively abundant, skeletal material. The specimens are preserved three-dimensionally. In order to evaluate the differences in skull proportions, 17 variable characters on 70 skulls were measured. Statistical analysis demonstrates the existence of several morphological trends in the shape of the skull. However, no trend permits the division of this set of specimens into two clearly differentiated groups. The morphological differences used previously to define genera and species seem to be incorrect. Pending the discovery of distinct morphological differences, the Moravian discosauriscids can be considered as belonging to only one taxon: Discosauriscus austriacus (Makowsky, 1876).     

Climatic drivers of latitudinal variation in Late Triassic tetrapod diversity

The latitudinal biodiversity gradient (LBG), the increase in biodiversity from the poles to the equator, is one of the most widely recognized global macroecological patterns, yet its deep time evolution and drivers remain uncertain. The Late Triassic (237–201 Ma), a critical interval for the early evolution and radiation of modern tetrapod groups (e.g. crocodylomorphs, dinosaurs, mammaliamorphs), offers a unique opportunity to explore the palaeolatitudinal patterns of tetrapod diversity since it is extensively sampled spatially when compared with other pre‐Cenozoic intervals, particularly at lower palaeolatitudes. Here, we explore palaeolatitudinal patterns of Late Triassic tetrapod diversity by applying sampling standardization to comprehensive occurrence data from the Paleobiology Database (PBDB). We then use palaeoclimatic model simulations to explore the palaeoclimatic ranges occupied by major tetrapod groups, allowing insight into the influence of palaeoclimate on the palaeolatitudinal distribution of these groups. Our results show that Late Triassic tetrapods generally do not conform to a modern‐type LBG; instead, sampling‐standardized species richness is highest at mid‐palaeolatitudes. In contrast, the richness of pseudosuchians (crocodylians and their relatives) is highest at the palaeoequator, a pattern that is retained throughout their subsequent evolutionary history. Pseudosuchians generally occupied a more restricted range of palaeoclimatic conditions than other tetrapod groups, a condition analogous to modern day reptilian ectotherms, while avemetatarsalians (the archosaur group containing dinosaurs and pterosaurs) exhibit comparatively wider ranges, which is more similar to modern endotherms, such as birds and mammals, suggesting important implications for the evolution of thermal physiology in dinosaurs.     

Amphibian swimming traces from the Lower Permian of southern New Mexico

Fossilised traces of swimming amphibians, assigned to Batrachichnus delicatulus and Serpentichnus robledoensis igen. et isp. nov., are described from the Lower Permian of the Robledo Mountains, southern New Mexico. The B. delicatulus specimen is interpreted as a trackway of a small 'amphibian' (temnospondyl, nectridean, microsaur or juvenile embolomere) swimming straight ahead. S. robledoensis consists of repeated pes imprints separated by discontinuous, L-shaped imprints (body traces). It is interpreted as a trackway of an 'amphibian' swimming in a similar manner to the motion of a side-winding snake. The producer of S. robledoensis is more distinctive than in B. delicatulus , and is suggestive of the lysorophian Brachydectes . This is the first locomotory trace to be assigned to this 'amphibian' group.     

Biogeography of Triassic tetrapods: evidence for provincialism and driven sympatric cladogenesis in the early evolution of modern tetrapod lineages

Triassic tetrapods are of key importance in understanding their evolutionary history, because several tetrapod clades, including most of their modern lineages, first appeared or experienced their initial evolutionary radiation during this Period. In order to test previous palaeobiogeographical hypotheses of Triassic tetrapod faunas, tree reconciliation analyses (TRA) were performed with the aim of recovering biogeographical patterns based on phylogenetic signals provided by a composite tree of Middle and Late Triassic tetrapods. The TRA found significant evidence for the presence of different palaeobiogeographical patterns during the analysed time spans. First, a Pangaean distribution is observed during the Middle Triassic, in which several cosmopolitan tetrapod groups are found. During the early Late Triassic a strongly palaeolatitudinally influenced pattern is recovered, with some tetrapod lineages restricted to palaeolatitudinal belts. During the latest Triassic, Gondwanan territories were more closely related to each other than to Laurasian ones, with a distinct tetrapod fauna at low palaeolatitudes. Finally, more than 75 per cent of the cladogenetic events recorded in the tetrapod phylogeny occurred as sympatric splits or within-area vicariance, indicating that evolutionary processes at the regional level were the main drivers in the radiation of Middle and Late Triassic tetrapods and the early evolution of several modern tetrapod lineages.     

A new Lower Permian trematopid (Temnospondyli: Dissorophoidea) from Richards Spur,Oklahoma

A new trematopid amphibian, Acheloma dunni, is reported based on excellently preserved cranial and postcranial elements recovered from the Lower Permian fissure fill deposits of the Dolese Brothers Co. limestone quarry near Richards Spur, Oklahoma. The new taxon is characterized by lateral exposures of the palatine (l.e.p.) and ectopterygoid (l.e.e.), which are clearly visible externally and completely enclosed within the suborbital elements. This large, terrestrial carnivore may represent the top predator of the Richards Spur assemblage. A phylogenetic analysis including 12 taxa and 53 cranial characters yielded a single most parsimonious tree, placing Ach. dunni within the monophyletic Trematopidae as the sister taxon to Acheloma cumminsi. Furthermore, the analysis includes the enigmatic Ecolsonia and Actiobates within Trematopidae, forming a clade with the Upper Pennsylvanian Anconastes and the Lower Permian Tambachia. The study comprehensively analyses all valid and aberrant forms of Trematopidae. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 789–815.