Intracoastal shipping drives patterns of regional population expansion by an invasive marine invertebrate

Understanding the factors contributing to expansion of nonnative populations is a critical step toward accurate risk assessment and effective management of biological invasions. Nevertheless, few studies have attempted explicitly to test hypotheses regarding factors driving invasive spread by seeking correlations between patterns of vector movement and patterns of genetic connectivity. Herein, we describe such an attempt for the invasive tunicate Styela clava in the northeastern Pacific. We utilized microsatellite data to estimate gene flow between samples collected throughout the known range of S. clava in the region, and assessed correlation of these estimates with patterns of intracoastal commercial vessel traffic. Our results suggest that recent shipping patterns have contributed to the contemporary distribution of genetic variation. However, the analysis also indicates that other factors—including a complex invasion history and the influence of other vectors—have partially obscured genetic patterns associated with intracoastal population expansion.     

MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.     

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.     

Preliminary analysis of mitochondrial DNA variation in a southern feeding group of eastern North Pacific gray whales

Although the majority of eastern North Pacific(ENP) gray whales migrate to feeding grounds inthe Bering and Chukchi Seas, some terminate themigration in more southerly areas such asBritish Columbia (BC). Long-term sightingstudies in Clayoquot Sound (CS), BC, indicatethat approximately 35–50 individuals exhibitlong-term fidelity to this site. To determinethe sex composition (based on genetic sexing)of CS gray whales and to assess whethermatrilineal site-fidelity occurs in CS, wecollected skin biopsy samples from 16 CSindividuals (`residents') and 41 samples fromother areas (representative of the overallpopulation in the ENP: `non-residents'). Atotal of 27 polymorphic sites defined 24haploytpes among the 57 samples sequenced forHV1 of the mtDNA control region. Thenucleotide and haplotype diversities of thesesamples were 0.017 (SE = 0.0012) and 0.94(SE = 0.0019), respectively. Neighbor-joininganalysis revealed five lineages each of whichcontained haplotypes that were observed in bothresidents and non-residents. Residents did notdiffer significantly from non-residents, and nosignificant sex-ratio bias was found. Thesedata suggest a level of diversity that isinconsistent with a severe historicalbottleneck, and given the available samplesize, do not indicate matrilineally directedfidelity to Clayoquot Sound.     

Grazing by the intertidal fish Anoplarchus purpurescens upon a distasteful polychaete worm

Synopsis Cirratulid worms are common inhabitants of the central California rocky intertidal zone and appear to offer a potentially rich source of food for intertidal fishes. However, analyses of stomach contents revealed that they do not appear in the diets of the commonest intertidal fishes. Apparently only one species, the eel blenny Anoplarchus purpurescens, feeds on cirratulids in significant amounts.Feeding experiments employing local intertidal fishes showed that the common intertidal cirratulid, Cirriformia luxuriosa, is distasteful to most of the fishes. Only two species ate its tentacles, and only A. purpurescens consistently ate large quantities. We propose that C. luxuriosa possesses a predation-deterring chemical similar to that reported in C. spirabrancha, although A. purpurescens apparently has been able to circumvent this anti-predator mechanism.The ability of A. purpurescens to eat Cirriformia tentacles allows it to tap a seemingly little-used food source, and thus may decrease competition between A. purpurescens and other intertidal fishes. This feeding relationship also represents a possible example of coevolution between a predator and its prey.     

Mouse models of human single gene disorders. I: Nontransgenic mice.

Mouse models of human genetic disorders provide a valuable resource for investigating the pathogenesis of genetic disease and for testing potential therapies. The high degree of resolution of linkage mapping in the mouse allows mutant phenotypes to be mapped precisely which, combined with the accurate definition of areas of homology between the mouse and human genomes, greatly facilitates the identification of mouse models. We describe here mouse models of human single gene disorders dividing them into three categories depending on the information available; phenotypic similarities, comparative mapping and identification of the underlying genetic lesion.     

Interpretation of global differences in plant calorific values

Summary Calorific values for the vegetative tissues of a group of perennial desert and arid woodland plants ranged from 3,191 to 5,375 calories per gram, oven dry weight. These span the range of comparable values reported earlier for plants in other environments, and reflect variety in adaptations to dry environments. Tissues with low values had high ash percentages, and contain significant amounts of low-energy oxalate salts. To interpret differences in calorific values for plants, one must understand: 1) the significance of calorific values in plant energetics, 2) the functions of compounds responsible for high and low values, and 3) the relative rates of metabolism and dry matter production for those plants.