Competition and community structure in diurnal arboreal geckos (genus Phelsuma) in the Indian Ocean

In this study, we investigate community structure in day geckos (genus Phelsuma ) in the Indian Ocean. Much of what we know about communities of diurnal arboreal lizards comes from studies of Caribbean Anolis . Phelsuma in the Indian Ocean are ecologically similar to Anolis but not closely related. Using field observations and an experiment, we test three hypotheses for Phelsuma communities, all derived from work on Anolis : (1) Phelsuma species richness will be correlated with the diversity of available perches, (2) sympatric species will partition their habitat use, shifting their habitat use depending on which other species of Phelsuma are present, and (3) experimentally removing individuals of one species will lead to changes in the microhabitat use and/or abundance of sympatric congeners. We find support for all three hypotheses. We also describe some unique aspects of Phelsuma communities, such as partitioning of palm vs. non-palm trees. This study identifies some potentially general features of diurnal arboreal lizard communities, and suggests that some aspects of community assembly might be repeatable.     

Trophic supplements to intraguild predation

Intraguild predation (IGP) is a dominant community module in terrestrial food webs that occurs when multiple consumers feed both on each other and on a shared prey. This specific form of omnivory is common in terrestrial communities and is of particular interest for conservation biology and biological control given its potential to disrupt management of threatened or pest species. Extensive theory exists to describe the dynamics of three-species IGP, but these models have largely overlooked the potential for other, exterior interactions, to alter the dynamics within the IGP module. We investigated how three forms of feeding outside of the IGP module by intraguild predators (i.e. trophic supplementation) affect the dynamics of the predators (both IG predator and IG prey) and their shared resource. Specifically, we examined how the provision of a constant donor-controlled resource, the availability of an alternative prey species, and predator plant-feeding affect the dynamics of IGP models. All three forms of trophic supplements modified the basic expectations of IGP theory in two important ways, and their effects were similar. First, coexistence was possible without the IG prey being a superior competitor for the original shared resource if the IG prey could effectively exploit one of the types of trophic supplements. However, supplements to the IG predator restricted the potential for coexistence. Second, supplements to the IG prey ameliorated the disruptive effects of the IG predator on the suppression of the shared resource, promoting effective control of the resource in the presence of both predators. Consideration of these three forms of trophic supplementation, all well documented in natural communities, adds substantial realism and predictive power to intraguild predation theory.     

Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom

A common pattern found in phylogeny-based empirical studies of diversification is a decrease in the rate of lineage accumulation toward the present. This early-burst pattern of cladogenesis is often interpreted as a signal of adaptive radiation or density-dependent processes of diversification. However, incomplete taxonomic sampling is also known to artifactually produce patterns of rapid initial diversification. The Monte Carlo constant rates (MCCR) test, based upon Pybus and Harvey's gamma (γ)-statistic, is commonly used to accommodate incomplete sampling, but this test assumes that missing taxa have been randomly pruned from the phylogeny. Here we use simulations to show that preferentially sampling disparate lineages within a clade can produce severely inflated type-I error rates of the MCCR test, especially when taxon sampling drops below 75%. We first propose two corrections for the standard MCCR test, the proportionally deeper splits that assumes missing taxa are more likely to be recently diverged, and the deepest splits only MCCR that assumes that all missing taxa are the youngest lineages in the clade, and assess their statistical properties. We then extend these two tests into a generalized form that allows the degree of nonrandom sampling (NRS)to be controlled by a scaling parameter, α. This generalized test is then applied to two recent studies. This new test allows systematists to account for nonrandom taxonomic sampling when assessing temporal patterns of lineage diversification in empirical trees. Given the dramatic affect NRS can have on the behavior of the MCCR test, we argue that evaluating the sensitivity of this test to NRS should become the norm when investigating patterns of cladogenesis in incompletely sampled phylogenies.     

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking.     

Rift Valley Fever Virus Strain MP-12 Enters Mammalian Host Cells via Caveola-Mediated Endocytosis

Rift Valley fever virus (RVFV) is a zoonotic pathogen capable of causing serious morbidity and mortality in both humans and livestock. The lack of efficient countermeasure strategies, the potential for dispersion into new regions, and the pathogenesis in humans and livestock make RVFV a serious public health concern. The receptors, cellular factors, and entry pathways used by RVFV and other members of the family Bunyaviridae remain largely uncharacterized. Here we provide evidence that RVFV strain MP-12 uses dynamin-dependent caveola-mediated endocytosis for cell entry. Caveolae are lipid raft domains composed of caveolin (the main structural component), cholesterol, and sphingolipids. Caveola-mediated endocytosis is responsible for the uptake of a wide variety of host ligands, as well as bacteria, bacterial toxins, and a number of viruses. To determine the cellular entry mechanism of RVFV, we used small-molecule inhibitors, RNA interference (RNAi), and dominant negative (DN) protein expression to inhibit the major mammalian cell endocytic pathways. Inhibitors and RNAi specific for macropinocytosis and clathrin-mediated endocytosis had no effect on RVFV infection. In contrast, inhibitors of caveola-mediated endocytosis, and RNAi targeted to caveolin-1 and dynamin, drastically reduced RVFV infection in multiple cell lines. Expression of DN caveolin-1 also reduced RVFV infection significantly, while expression of DN EPS15, a protein required for the assembly of clathrin-coated pits, and DN PAK-1, an obligate mediator of macropinocytosis, had no significant impact on RVFV infection. These results together suggest that the primary mechanism of RVFV MP-12 uptake is dynamin-dependent, caveolin-1-mediated endocytosis.     

New postcranial fossils of Australopithecus afarensis from Hadar, Ethiopia (1990-2007)

Renewed fieldwork at Hadar, Ethiopia, from 1990 to 2007, by a team based at the Institute of Human Origins, Arizona State University, resulted in the recovery of 49 new postcranial fossils attributed to Australopithecus afarensis. These fossils include elements from both the upper and lower limbs as well as the axial skeleton, and increase the sample size of previously known elements for A. afarensis. The expanded Hadar sample provides evidence of multiple new individuals that are intermediate in size between the smallest and largest individuals previously documented, and so support the hypothesis that a single dimorphic species is represented. Consideration of the functional anatomy of the new fossils supports the hypothesis that no functional or behavioral differences need to be invoked to explain the morphological variation between large and small A. afarensis individuals. Several specimens provide important new data about this species, including new vertebrae supporting the hypothesis that A. afarensis may have had a more human-like thoracic form than previously appreciated, with an invaginated thoracic vertebral column. A distal pollical phalanx confirms the presence of a human-like flexor pollicis longus muscle in A. afarensis. The new fossils include the first complete fourth metatarsal known for A. afarensis. This specimen exhibits the dorsoplantarly expanded base, axial torsion and domed head typical of humans, revealing the presence of human-like permanent longitudinal and transverse arches and extension of the metatarsophalangeal joints as in human-like heel-off during gait. The new Hadar postcranial fossils provide a more complete picture of postcranial functional anatomy, and individual and temporal variation within this sample. They provide the basis for further in-depth analyses of the behavioral and evolutionary significance of A. afarensis anatomy, and greater insight into the biology and evolution of these early hominins.