Phylogeny of snakes (Serpentes): Combining morphological and molecular data in likelihood,Bayesian and parsimony analyses

Abstract

The phylogeny of living and fossil snakes is assessed using likelihood and parsimony approaches and a dataset combining 263 morphological characters with mitochondrial (2693 bp) and nuclear (1092 bp) gene sequences. The ‘no common mechanism’ (NCMr) and ‘Markovian’ (Mkv) models were employed for the morphological partition in likelihood analyses; likelihood scores in the NCMr model were more closely correlated with parsimony tree lengths. Both models accorded relatively less weight to the molecular data than did parsimony, with the effect being milder in the NCMr model. Partitioned branch and likelihood support values indicate that the mtDNA and nuclear gene partitions agree more closely with each other than with morphology. Despite differences between data partitions in phylogenetic signal, analytic models, and relative weighting, the parsimony and likelihood analyses all retrieved the following widely accepted groups: scolecophidians, alethinophidians, cylindrophiines, macrostomatans (sensu lato) and caenophidians. Anilius alone emerged as the most basal alethinophidian; the combined analyses resulted in a novel and stable position of uropeltines and cylindrophiines as the second‐most basal clade of alethinophidians. The limbed marine pachyophiids, along with Dinilysia and Wonambi, were always basal to all living snakes. Other results stable in all combined analyses include: Xenopeltis and Loxocemus were sister taxa (fide morphology) but clustered with pythonines (fide molecules), and Ungaliophis clustered with a boine‐erycine clade (fide molecules). Tropidophis remains enigmatic; it emerges as a basal alethinophidian in the parsimony analyses (fide molecules) but a derived form in the likelihood analyses (fide morphology), largely due to the different relative weighting accorded to data partitions.     

Effects of grouping and fighting on the reproductive tracts of male white-footed mice (Peromyscus leucopus)

Summary Adult, male white-footed mice (Peromyscus leucopus) were subjected to a variety of social situations ranging from isolation during the 20 day experimental period to constant contact with both females and other adult males. Contacts included grouping (three or four males per cage) and exposure to fighters (once daily for 20 minutes). The following measurements were recorded: weights of the body, testes, epididymides, vesicular glands, vesicular gland tissue (wet and dry), seminal fluid of the vesicular gland, adrenal glands, and baculum; spermatozoan reserves of the testes and epididymides. Grouping significantly affected both the weight and spermatozoan reserves of the testes and epididymides, as well as both the tissue and seminal fluid weight of the vesicular glands. The results suggested a graded effect of all treatments on the reproductive tract. In order of magnitude of the associated response, from none to greatest, the treatments may be ranked as follows: pairing with females, isolating, handling, fighting, and grouping. All reproductive parameters measured showed this general ranking, suggesting that the response to the various treatments was similar and differed only quantitatively. The results further suggested decreased secretion of LH and testosterone, although measurements of testosterone did not substantiate this conclusion. The lack of significant effects of grouping on adrenal gland weights strengthened the argument that adrenal involvement is not a necessary adjunct to the suppression of the reproductive tract in groupedPeromyscus, but the adrenal may be involved if contacts between males result in overt fighting.     

High‐throughput analysis of vocalizations reveals sex‐specific changes in Fmr1 mutant pups

There have been several reports that individuals with Fragile X syndrome (FXS) and animal models of FXS have communication deficits. The present study utilized two different call classification taxonomies to examine the sex‐specificity of ultrasonic vocalization (USV) production on postnatal day (PD8) in the FVB strain of Fmr1 knockout (KO) mice. One classification protocol requires the investigator to score each call by hand, while the other protocol uses an automated algorithm. Results using the hand‐scoring protocol indicated that male Fmr1 KO mice exhibited longer calls (P = .03) than wild types on PD8. Male KOs also produced fewer complex, composite, downward, short and two‐syllable call‐types, as well as more frequency steps and chevron call‐types. Female heterozygotes exhibited no significant changes in acoustic or temporal aspects of calls, yet showed significant changes in call‐type production proportions across two different classification taxonomies (P < .001). They exhibited increased production of harmonic and frequency steps calls, as well as fewer chevron, downward and short calls. According to the second high‐throughput analysis, female heterozygotes produced significantly fewer single‐type and more multiple‐type syllables, unlike male KOs that showed no changes in these aspects of syllable production. Finally, we correlated both scoring methods and found a high level of correlation between the two methods. These results contribute further knowledge of sex differences in USV calling behavior for Fmr1 heterozygote and KO mice and provide a foundation for the use of high‐throughput analysis of neonatal USVs.     

Changing estuaries and impacts on juvenile salmon: A systematic review

Estuaries are productive ecosystems providing important habitat for a diversity of species, yet they also experience intense levels of anthropogenic development. To inform decision‐making, it is essential to understand the pathways of impacts of particular human activities, especially those that affect species such as salmon, which have high ecological, social‐cultural and economic values. Salmon systems provide an opportunity to build from the substantial body of research on responses to estuary developments and take stock of what is known. We conducted a systematic English‐language literature review on the responses of juvenile salmon to anthropogenic activities in estuaries and nearshore areas asking: what has been studied, where are the major knowledge gaps and how do stressors affect salmon? We found a substantial body of research (n = 167 studies; 1,369 comparative tests) to help understand responses of juvenile salmon to 24 activities and their 14 stressors. Across studies, 82% of the research was conducted in the eastern Pacific (Oregon and Washington, USA and British Columbia, Canada) showing a limited geographical scope. Using a semiquantitative approach to summarize the literature, including a weight‐of‐evidence metric, we found a range of results from low to moderate–high confidence in the consequences of the stressors. For example, we found moderate–high confidence in the negative impacts of pollutants and sea lice and moderate confidence in negative impacts from connectivity loss and changes in flow. Our results suggest that overall, multiple anthropogenic activities cause negative impacts across ecological scales. However, our results also reveal knowledge gaps resulting from minimal research on particular species (e.g. sockeye salmon), regions (e.g. Atlantic) or stressors (e.g. entrainment) that would be expedient areas for future research. With estuaries acting as a nexus of biological and societal importance and hotspots of ongoing development, the insights gained here can contribute to informed decision‐making.     

Multiple trade‐offs regulate the effects of woody plant removal on biodiversity and ecosystem functions in global rangelands

Woody plant encroachment is a major land management issue. Woody removal often aims to restore the original grassy ecosystem, but few studies have assessed the role of woody removal on ecosystem functions and biodiversity at global scales. We collected data from 140 global studies and evaluated how different woody plant removal methods affected biodiversity (plant and animal diversity) and ecosystem functions (plant production, hydrological function, soil carbon) across global rangelands. Our results indicate that the impact of removal is strongly context dependent, varying with the specific response variable, removal method, and traits of the target species. Over all treatments, woody plant removal increased grass biomass and total groundstorey diversity. Physical and chemical removal methods increased grass biomass and total groundstorey biomass (i.e., non‐woody plants, including grass biomass), but burning reduced animal diversity. The impact of different treatment methods declined with time since removal, particularly for total groundstorey biomass. Removing pyramid‐shaped woody plants increased total groundstorey biomass and hydrological function but reduced total groundstorey diversity. Environmental context (e.g., aridity and soil texture) indirectly controlled the effect of removal on biomass and biodiversity by influencing plant traits such as plant shape, allelopathic, or roots types. Our study demonstrates that a one‐size‐fits‐all approach to woody plant removal is not appropriate, and that consideration of woody plant identity, removal method, and environmental context is critical for optimizing removal outcomes. Applying this knowledge is fundamental for maintaining diverse and functional rangeland ecosystems as we move toward a drier and more variable climate.     

Grazing and productivity alter individual grass size dynamics in semi-arid woodlands

The spatial arrangement of perennial vegetation is critical for ecosystem function in drylands. While much is known about how vegetation patches respond to grazing and abiotic conditions, the size dynamics of individual plants is mostly limited to theoretical studies. We measured the size distribution (mean, variance, skewness) and density of individual grasses, and grass species composition at 451 sites spanning a range of grazing intensities across three broad vegetation communities in semi-arid eastern Australia. We assessed the relative role of grazing by livestock (cattle and sheep), native (kangaroos) and introduced (rabbits) free ranging herbivores, and several environmental measures (productivity, diversity, composition and groundstorey plant cover) on the size distribution and density of individual grasses. We found mean grass size and density were more sensitive to shifts in grazing intensity and environmental conditions than size variance or the frequency of the smallest individuals (skewness), and shifts were mostly driven by site productivity and cattle and kangaroo grazing. Sheep grazing only reduced mean grass size, and rabbit grazing had no consistent effects. Importantly, we found that site productivity and species composition altered the impacts of grazing on grass density and size distribution. For example, increasing cattle grazing led to larger grasses in low productivity sites. It also led to larger, denser, more variable-sized grasses among grass species from sites with finer soil texture. Increasing kangaroo grazing led to smaller, denser individuals among grass species from sites with coarse soil texture. At high diversity sites kangaroo grazing led to denser, more homogenised grass sizes with a lower frequency of small individuals. Understanding the in situ response of individual plant sizes gives us insights into the processes driving shifts in perennial vegetation patchiness, improving our ability to predict how the spatial arrangement of ecosystems might change under global change scenarios.     

Glutaminyl‐tRNA Synthetase from Pseudomonas aeruginosa: Characterization,structure, and development as a screening platform

Pseudomonas aeruginosa has a high potential for developing resistance to multiple antibiotics. The gene (glnS) encoding glutaminyl‐tRNA synthetase (GlnRS) from P. aeruginosa was cloned and the resulting protein characterized. GlnRS was kinetically evaluated and the K_M and k_cat^obs, governing interactions with tRNA, were 1.0 μM and 0.15 s^?1, respectively. The crystal structure of the α₂ form of P. aeruginosa GlnRS was solved to 1.9 Å resolution. The amino acid sequence and structure of P. aeruginosa GlnRS were analyzed and compared to that of GlnRS from Escherichia coli. Amino acids that interact with ATP, glutamine, and tRNA are well conserved and structure overlays indicate that both GlnRS proteins conform to a similar three‐dimensional structure. GlnRS was developed into a screening platform using scintillation proximity assay technology and used to screen ~2,000 chemical compounds. Three inhibitory compounds were identified and analyzed for enzymatic inhibition as well as minimum inhibitory concentrations against clinically relevant bacterial strains. Two of the compounds, BM02E04 and BM04H03, were selected for further studies. These compounds displayed broad‐spectrum antibacterial activity and exhibited moderate inhibitory activity against mutant efflux deficient strains of P. aeruginosa and E. coli. Growth of wild‐type strains was unaffected, indicating that efflux was likely responsible for the lack of sensitivity. The global mode of action was determined using time‐kill kinetics. BM04H03 did not inhibit the growth of human cell cultures at any concentration and BM02E04 only inhibit cultures at the highest concentration tested (400 μg/ml). In conclusion, GlnRS from P. aeruginosa is shown to have a structure similar to that of E. coli GlnRS and two natural product compounds were identified as inhibitors of P. aeruginosa GlnRS with the potential for utility as lead candidates in antibacterial drug development in a time of increased antibiotic resistance.