Major radiations in the evolution of Caviid rodents: reconciling fossils, ghost lineages, and relaxed molecular clocks

BACKGROUND

Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America ("eocardiids").

RESULTS

A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (referred here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates.

CONCLUSIONS

The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone.

A Middle Jurassic abelisaurid from Patagonia and the early diversification of theropod dinosaurs

Abelisaurids are a clade of large, bizarre predatory dinosaurs, most notable for their high, short skulls and extremely reduced forelimbs. They were common in Gondwana during the Cretaceous, but exceedingly rare in the Northern Hemisphere. The oldest definitive abelisaurids so far come from the late Early Cretaceous of South America and Africa, and the early evolutionary history of the clade is still poorly known. Here, we report a new abelisaurid from the Middle Jurassic of Patagonia, Eoabelisaurus mefi gen. et sp. nov., which predates the so far oldest known secure member of this lineage by more than 40 Myr. The almost complete skeleton reveals the earliest evolutionary stages of the distinctive features of abelisaurids, such as the modification of the forelimb, which started with a reduction of the distal elements. The find underlines the explosive radiation of theropod dinosaurs in the Middle Jurassic and indicates an unexpected diversity of ceratosaurs at that time. The apparent endemism of abelisauroids to southern Gondwana during Pangean times might be due to the presence of a large, central Gondwanan desert. This indicates that, apart from continent-scale geography, aspects such as regional geography and climate are important to reconstruct the biogeographical history of Mesozoic vertebrates.

A Middle Jurassic heterodontosaurid dinosaur from Patagonia and the evolution of heterodontosaurids

Heterodontosauridae is a morphologically divergent group of dinosaurs that has recently been interpreted as one of the most basal clades of Ornithischia. Heterodontosaurid remains were previously known from the Early Jurassic of southern Africa, but recent discoveries and studies have significantly increased the geographical and temporal range for this clade. Here, we report a new ornithischian dinosaur from the Middle Jurassic Cañadón Asfalto Formation in central Patagonia, Argentina. This new taxon, Manidens condorensis gen. et sp. nov., includes well-preserved craniomandibular and postcranial remains and represents the only diagnostic ornithischian specimen yet discovered in the Jurassic of South America so far. Derived features of its anatomy indicate that Manidens belongs to Heterodontosauridae, as the sister taxon of Heterodontosaurus and other South African heterodontosaurids. The presence of posterior dentary teeth with high crowns but lacking extensive wear facets in Manidens suggests that this form represents an intermediate stage in the development of the remarkable adaptations to herbivory described for Heterodontosaurus. The dentition of Manidens condorensis also has autapomorphies, such as asymmetrically arranged denticles in posterior teeth and a mesially projected denticle in the posteriormost teeth. At an estimated total length of 60-75 cm, Manidens furthermore confirms the small size of basal heterodontosaurids.

A new sauropodomorph dinosaur from the Early Jurassic of Patagonia and the origin and evolution of the sauropod-type sacrum

BACKGROUND

The origin of sauropod dinosaurs is one of the major landmarks of dinosaur evolution but is still poorly understood. This drastic transformation involved major skeletal modifications, including a shift from the small and gracile condition of primitive sauropodomorphs to the gigantic and quadrupedal condition of sauropods. Recent findings in the Late Triassic-Early Jurassic of Gondwana provide critical evidence to understand the origin and early evolution of sauropods.

METHODOLOGY/PRINCIPAL FINDINGS

A new sauropodomorph dinosaur, Leonerasaurus taquetrensis gen. et sp. nov., is described from the Las Leoneras Formation of Central Patagonia (Argentina). The new taxon is diagnosed by the presence of anterior unserrated teeth with a low spoon-shaped crown, amphicoelous and acamerate vertebral centra, four sacral vertebrae, and humeral deltopectoral crest low and medially deflected along its distal half. The phylogenetic analysis depicts Leonerasaurus as one of the closest outgroups of Sauropoda, being the sister taxon of a clade of large bodied taxa composed of Melanorosaurus and Sauropoda.

CONCLUSIONS/SIGNIFICANCE

The dental and postcranial anatomy of Leonerasaurus supports its close affinities with basal sauropods. Despite the small size and plesiomorphic skeletal anatomy of Leonerasaurus, the four vertebrae that compose its sacrum resemble that of the large-bodied primitive sauropods. This shows that the appearance of the sauropod-type of sacrum predated the marked increase in body size that characterizes the origins of sauropods, rejecting a causal explanation and evolutionary linkage between this sacral configuration and body size. Alternative phylogenetic placements of Leonerasaurus as a basal anchisaurian imply a convergent acquisition of the sauropod-type sacrum in the new small-bodied taxon, also rejecting an evolutionary dependence of sacral configuration and body size in sauropodomorphs. This and other recent discoveries are showing that the characteristic sauropod body plan evolved gradually, with a step-wise pattern of character appearance.

Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes

The development of distinct regions in the amniote vertebral column results from somite formation and Hox gene expression, with the adult morphology displaying remarkable variation among lineages. Mammalian regionalization is reportedly very conservative or even constrained, but there has been no study investigating vertebral count variation across Amniota as a whole, undermining attempts to understand the phylogenetic, ecological, and developmental factors affecting vertebral column variation. Here, we show that the mammalian (synapsid) and reptilian lineages show early in their evolutionary histories clear divergences in axial developmental plasticity, in terms of both regionalization and meristic change, with basal synapsids sharing the conserved axial configuration of crown mammals, and basal reptiles demonstrating the plasticity of extant taxa. We conducted a comprehensive survey of presacral vertebral counts across 436 recent and extinct amniote taxa. Vertebral counts were mapped onto a generalized amniote phylogeny as well as individual ingroup trees, and ancestral states were reconstructed by using squared-change parsimony. We also calculated the relationship between presacral and cervical numbers to infer the relative influence of homeotic effects and meristic changes and found no correlation between somitogenesis and Hox-mediated regionalization. Although conservatism in presacral numbers characterized early synapsid lineages, in some cases reptiles and synapsids exhibit the same developmental innovations in response to similar selective pressures. Conversely, increases in body mass are not coupled with meristic or homeotic changes, but mostly occur in concert with postembryonic somatic growth. Our study highlights the importance of fossils in large-scale investigations of evolutionary developmental processes.

A bizarre Cretaceous theropod dinosaur from Patagonia and the evolution of Gondwanan dromaeosaurids

Fossils of a predatory dinosaur provide novel information about the evolution of unenlagiines, a poorly known group of dromaeosaurid theropods from Gondwana. The new dinosaur is the largest dromaeosaurid yet discovered in the Southern Hemisphere and depicts bizarre cranial and postcranial features. Its long and low snout bears numerous, small-sized conical teeth, a condition resembling spinosaurid theropods. Its short forearms depart from the characteristically long-armed condition of all dromaeosaurids and their close avian relatives. The new discovery amplifies the range of morphological disparity among unenlagiines, demonstrating that by the end of the Cretaceous this clade included large, short-armed forms alongside crow-sized, long-armed, possibly flying representatives. The new dinosaur is the youngest record of dromaeosaurids from Gondwana and represents a previously unrecognized lineage of large predators in Late Cretaceous dinosaur faunas mainly dominated by abelisaurid theropods.

Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses

Severe acute respiratory syndrome (SARS) is a novel human illness caused by a previously unrecognized coronavirus (CoV) termed SARS-CoV. There are conflicting reports on the animal reservoir of SARS-CoV. Many of the groups that argue carnivores are the original reservoir of SARS-CoV use a phylogeny to support their argument. However, the phylogenies in these studies often lack outgroup and rooting criteria necessary to determine the origins of SARS-CoV. Recently, SARS-CoV has been isolated from various species of Chiroptera from China (e.g., Rhinolophus sinicus) thus leading to reconsideration of the original reservoir of SARS-CoV. We evaluated the hypothesis that SARS-CoV isolated from Chiroptera are the original zoonotic source for SARS-CoV by sampling SARS-CoV and non-SARS-CoV from diverse hosts including Chiroptera, as well as carnivores, artiodactyls, rodents, birds and humans. Regardless of alignment parameters, optimality criteria, or isolate sampling, the resulting phylogenies clearly show that the SARS-CoV was transmitted to small carnivores well after the epidemic of SARS in humans that began in late 2002. The SARS-CoV isolates from small carnivores in Shenzhen markets form a terminal clade that emerged recently from within the radiation of human SARS-CoV. There is evidence of subsequent exchange of SARS-CoV between humans and carnivores. In addition SARS-CoV was transmitted independently from humans to farmed pigs (Sus scrofa). The position of SARS-CoV isolates from Chiroptera are basal to the SARS-CoV clade isolated from humans and carnivores. Although sequence data indicate that Chiroptera are a good candidate for the original reservoir of SARS-CoV, the structural biology of the spike protein of SARS-CoV isolated from Chiroptera suggests that these viruses are not able to interact with the human variant of the receptor of SARS-CoV, angiotensin-converting enzyme 2 (ACE2). In SARS-CoV we study, both visually and statistically, labile genomic fragments and, putative key mutations of the spike protein that may be associated with host shifts. We display host shifts and candidate mutations on trees projected in virtual globes depicting the spread of SARS-CoV. These results suggest that more sampling of coronaviruses from diverse hosts, especially Chiroptera, carnivores and primates, will be required to understand the genomic and biochemical evolution of coronaviruses, including SARS-CoV. © The Willi Hennig Society 2008.

A basal dromaeosaurid and size evolution preceding avian flight

Fossil evidence for changes in dinosaurs near the lineage leading to birds and the origin of flight has been sparse. A dinosaur from Mongolia represents the basal divergence within Dromaeosauridae. The taxon's small body size and phylogenetic position imply that extreme miniaturization was ancestral for Paraves (the clade including Avialae, Troodontidae, and Dromaeosauridae), phylogenetically earlier than where flight evolution is strongly inferred. In contrast to the sustained small body sizes among avialans throughout the Cretaceous Period, the two dinosaurian lineages most closely related to birds, dromaeosaurids and troodontids, underwent four independent events of gigantism, and in some lineages size increased by nearly three orders of magnitude. Thus, change in theropod body size leading to flight's origin was not unidirectional.

On Divide-and-Conquer Strategies for Parsimony Analysis of Large Data Sets: Rec-I-DCM3 versus TNT

Roshan et al. recently described a "divide-and-conquer" technique for parsimony analysis of large data sets, Rec-I-DCM3, and stated that it compares very favorably to results using the program TNT. Their technique is based on selecting subsets of taxa to create reduced data sets or subproblems, finding most-parsimonious trees for each reduced data set, recombining all parts together, and then performing global TBR swapping on the combined tree. Here, we contrast this approach to sectorial searches, a divide-and-conquer algorithm implemented in TNT. This algorithm also uses a guide tree to create subproblems, with the first-pass state sets of the nodes that join the selected sectors with the rest of the topology; this allows exact length calculations for the entire topology (that is, any solution N steps shorter than the original, for the reduced subproblem, must also be N steps shorter for the entire topology). We show here that, for sectors of similar size analyzed with the same search algorithms, subdividing data sets with sectorial searches produces better results than subdividing with Rec-I-DCM3. Roshan et al.'s claim that Rec-I-DCM3 outperforms the techniques in TNT was caused by a poor experimental design and algorithmic settings used for the runs in TNT. In particular, for finding trees at or very close to the minimum known length of the analyzed data sets, TNT clearly outperforms Rec-I-DCM3. Finally, we show that the performance of Rec-I-DCM3 is bound by the efficiency of TBR implementation for the complete data set, as this method behaves (after some number of iterations) as a technique for cyclic perturbations and improvements more than as a divide-and-conquer strategy.

Uncertainty in the Age of Fossils and the Stratigraphic Fit to Phylogenies

The ages of first appearance of fossil taxa in the stratigraphic record are inherently associated to an interval of error or uncertainty, rather than being precise point estimates. Contrasting this temporal information with topologies of phylogenetic relationships is relevant to many aspects of evolutionary studies. Several indices have been proposed to compare the ages of first appearance of fossil taxa and phylogenies. For computing most of these indices, the ages of first appearance of fossil taxa are currently used as point estimates, ignoring their associated errors or uncertainties. The effect of age uncertainty on measures of stratigraphic fit to phylogenies is explored here for two indices based on the extension of ghost lineages (MSM* and GER). A solution based on randomization of the ages of terminal taxa is implemented, resulting in a range of possible values for measures of stratigraphic fit to phylogenies, rather than in a precise but arbitrary stratigraphic fit value. Sample cases show that ignoring the age uncertainty of fossil taxa can produce misleading results when comparing the stratigraphic fit of competing phylogenetic hypotheses. Empirical test cases of alternative phylogenies of two dinosaur groups are analyzed through the randomization procedure proposed here.

An Unusual Marine Crocodyliform from the Jurassic-Cretaceous Boundary of Patagonia

Remains of the marine crocodyliform Dakosaurus andiniensis from western South America reveal a lineage that drastically deviated from the skull morphology that characterizes marine crocodyliforms. The snout and lower jaw are extremely robust, short, and high and only bear a few large teeth with serrated edges (resembling those of some terrestrial carnivorous archosaurs). This unusual morphology contrasts with the long and gracile snout and lower jaws bearing numerous teeth, which are present in the closest relatives of D. andiniensis (and interpreted as indicating feeding on small fish or mollusks). Thus, the morphological diversity of pelagic marine crocodyliforms was wider than had been thought.

Empirical problems of the hierarchical likelihood ratio test for model selection

Advocates of maximum likelihood (ML) approaches to phylogenetics commonly cite as one of their primary advantages the use of objective statistical criteria for model selection. Currently, a particular implementation of the likelihood ratio test (LRT) is the most commonly used model-selection criterion in phylogenetics. This approach requires the choice of a starting point and a parameter addition (or removal) sequence that can affect all ML inferences (i.e., topology, model, and all evolutionary parameters). Here, several alternative starting points and parameter sequences are tested in empirical data sets to assess their influence on model selection and optimal topology. In the studied data sets, varying model-selection protocols leads to selection of different models that, in some cases, lead to different ML trees. Given the sensitivity of the LRT, some possible solutions to model selection (within the hypothesis testing approach) are outlined, and alternative model-selection criteria are discussed. Some of the suggested alternatives seem to lack these problems, although their behavior and adequacy for phylogenetics needs to be further explored.

New evidence on deinonychosaurian dinosaurs from the Late Cretaceous of Patagonia

Most of what is known about the evolution of deinonychosaurs (that is, the group of theropods most closely related to birds) is based on discoveries from North America and Asia. Except for Unenlagia comahuensis and some fragmentary remains from northern Africa, no other evidence was available on deinonychosaurian diversity in Gondwana. Here we report a new, Late Cretaceous member of the clade, Neuquenraptor argentinus gen. et sp. nov., representing uncontroversial evidence of a deinonychosaurian theropod in the Southern Hemisphere. The new discovery demonstrates that Cretaceous theropod faunas from the southern continents shared greater similarity with those of the northern landmasses than previously thought. Available evidence suggests that deinonychosaurians were probably distributed worldwide at least by the beginning of the Cretaceous period. The phylogenetic position of the new deinonychosaur, as well as other Patagonian coelurosaurian theropods, is compatible with a vicariance model of diversification for some groups of Gondwanan and Laurasian dinosaurs.

A pug-nosed crocodyliform from the Late Cretaceous of Madagascar

Although the image of crocodyliforms as 'unchanged living fossils' is naive, several morphological features of the group are thought to have varied only within narrow limits during the course of evolution. These include an elongate snout with an array of conical teeth, a dorsoventrally flattened skull and a posteriorly positioned jaw articulation, which provides a powerful bite force. Here we report an exquisitely preserved specimen of a new taxon from the Late Cretaceous of Madagascar that deviates profoundly from this Bauplan, possessing an extremely blunt snout, a tall, rounded skull, an anteriorly shifted jaw joint and clove-shaped, multicusped teeth reminiscent of those of some ornithischian dinosaurs. This last feature implies that the diet of the new taxon may have been predominantly if not exclusively herbivorous. A close relationship with notosuchid crocodyliforms, particularly Uruguaysuchus (Late Cretaceous, Uruguay) is suggested by several shared derived features; this supports a biogeographical hypothesis that Madagascar and South America were linked during the Late Cretaceous.

Embryotoxic effects of sodium arsenite and sodium arsenate on mouse embryos in culture

Embryotoxic effects of two inorganic arsenic compounds, sodium arsenite (Asi) and sodium arsenate (Asa), on the development of mouse embryos during early organogenesis were studied using the whole embryo culture technique. Embryos with three to five somites exposed to 1-40 microM Asi or to 10-400 microM Asa were cultured for 48 hours and their development was compared with that of control embryos. Asi proved to be teratogenic between 3 and 4 microM and embryolethal at higher concentrations; Asa had similar activity but at concentrations ten times higher than for Asi. Both compounds produced a growth retardation and a similar pattern of defects. Growth retardation was indicated by a statistically significant reduction in crown-rump length, head length, and yolk sac diameter. Abnormal embryos were characterized by hypoplasia of the prosencephalon with open neural tube, hydropericardium, somite abnormalities, and failure of development of limb buds and sensory placodes. These results confirm that both Asa and Asi are embryotoxic compounds and that the Asi activity occurs at concentrations ten times lower than for Asa. Our results suggest that in humans both of these compounds may be involved in part of "unaccountable" early abortions and malformations claimed to be due to the toxicity of heavy metals.

The inferior colliculus of the mouse. A Nissl and Golgi study

Serial sections of cell- and fiber-stained and Golgi-impregnated material from adult mice were used to study the cytoarchitectonics, fiber and neuronal architecture of the inferior colliculus. The size of the cells, the pattern of dendritic branching, and the appearance of the neuropil were the features used to delineate the three main regions of the auditory tectum: the central mass of cells or central nucleus, the cortex, and the paracentral nuclei. The central nucleus contains two major cell types: the bipolar cells, which are the most abundant, and the multipolar cells. The dendrites of the bipolar cells are oriented in the same direction and the afferent axons of the lateral lemniscus run along them, contributing to form fibrodendritic strips: the laminae of the central nucleus. The orientation of these laminae differs in the various parts of the central nucleus and delineates four subdivisions. In these four subdivisions, the laminae maintain the same relative position throughout the anteroposterior axis of the central nucleus, but they stop abruptly at the periphery of the nucleus. The cortex surrounds the central nucleus dorsally and caudally. The lamination in four layers concentric to the surface, the increasing gradient of size from the periphery to the deep tissue, the existence of two major types of cells, stellate and pyramidal, permit this structure to be considered as a true cortex. The paracentral nuclei are scattered around the central nucleus. The commissural nucleus is composed of cells with a simple dendritic branching pattern perpendicular or parallel to the fibers of the intercollicular commissure. The dorsomedial and ventrolateral nuclei are characterized by the presence of large multipolar cells. The nucleus of the rostral pole, distinct from the anterior pole of the central nucleus, is composed of small and medium-sized multipolar cells. The lateral nucleus appears as an extension of the dorsal cortex with only two or three layers of cells. The neuronal organization in the central nucleus appears similar in the mouse and in the cat, suggesting an identical processing of auditory information in the two species. Our results seem to establish definitely the cortical nature of the sheet of cells covering the central nucleus.