Long‐distance call evolution in the Felidae: effects of body weight,habitat, and phylogeny

Long‐distance calls used for mate attraction and territorial spacing are distinctive signals in the felid vocal repertoire. Their evolution is subject to natural and sexual selection, as well as various constraints. Body size is an important morphological constraint, with the scaling of the spectral characteristics of a species' vocalizations with its body size being established for several vertebrate groups. Alternatively, the structure of long‐distance calls may have been optimized for transmission in species' habitats (acoustic adaptation hypothesis). The present study assessed whether the mean dominant frequency of long‐distance calls in the Felidae (approximately 70% of all species incorporated) is influenced by the species' body size and/or conforms to the acoustic adaptation hypothesis. After controlling for phylogenetic relationships, we found a significant correlation between mean dominant frequency of a taxon's long‐distance calls and conditions for sound transmission in its habitat type (‘open/heterogeneous’ versus ‘dense’), although no significant influence of body size. Taxa living in more open habitat types have long‐distance calls with significantly lower mean dominant frequencies than those living in dense habitats. The result obtained in the present analysis is fairly robust against random removal of single or few taxa from the data, and also against the use of different branch‐length transformation models in phylogenetic regression. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 487–500.     

Compartments in a marine food web associated with phylogeny, body mass, and habitat structure

A long-standing question in community ecology is whether food webs are organized in compartments, where species within the same compartment interact frequently among themselves, but show fewer interactions with species from other compartments. Finding evidence for this community organization is important since compartmentalization may strongly affect food web robustness to perturbation. However, few studies have found unequivocal evidence of compartments, and none has quantified the suite of mechanisms generating such a structure. Here, we combine computational tools from the physics of complex networks with phylogenetic statistical methods to show that a large marine food web is organized in compartments, and that body size, phylogeny, and spatial structure are jointly associated with such a compartmentalized structure. Sharks account for the majority of predatory interactions within their compartments. Phylogenetically closely related shark species tend to occupy different compartments and have divergent trophic levels, suggesting that competition may play an important role structuring some of these compartments. Current overfishing of sharks has the potential to change the structural properties, which might eventually affect the stability of the food web.     

Rates of molecular evolution in tree ferns are associated with body size,environmental temperature,and biological productivity

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population‐level factors to better understand the processes affecting the tempo of evolution at the molecular level.     

Diets and trophic‐guild structure of a diverse fish assemblage in Chesapeake Bay,U.S.A.

Dietary habits and trophic‐guild structure were examined in a fish assemblage (47 species) of the Chesapeake Bay estuary, U.S.A., using 10 years of data from >25 000 fish stomachs. The assemblage was comprised of 10 statistically significant trophic guilds that were principally differentiated by the relative amounts of Mysida, Bivalvia, Polychaeta, Teleostei and other Crustacea in the diets. These guilds were broadly aggregated into five trophic categories: piscivores, zooplanktivores, benthivores, crustacivores and miscellaneous consumers. Food web structure was largely dictated by gradients in habitat (benthic to pelagic) and prey size. Size classes within piscivorous species were more likely to be classified into different guilds, reflecting stronger dietary changes through ontogeny relative to benthivores and other guilds. Relative to predator species and predator size, the month of sampling had negligible effects on dietary differences within the assemblage. A majority of sampled fishes derived most of their nutrition from non‐pelagic prey sources, suggesting a strong coupling of fish production to benthic and demersal food resources. Mysida (predominantly the opossum shrimp Neomysis americana) contributed substantially to the diets of over 25% of the sampled predator groups, indicating that this species is a critical, but underappreciated, node in the Chesapeake Bay food web.     

Enhanced Mutation Rate,Relaxed Selection,and the “Domino Effect” are associated with Gene Loss in Blattabacterium,A Cockroach Endosymbiont

Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511 and 645 kb. We found that 200 of the 566 analyzed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically inherited gut symbionts. Third, we found evidence of epistatic interactions among genes leading to a “domino effect” of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont.     

Multi‐scale effects of habitat structure and landscape context on a vertebrate with limited dispersal ability (the brown‐throated sloth,Bradypus variegatus)

As human population, food consumption, and demand for forest products continue to rise over the next century, the pressures of land‐use change on biodiversity are projected to intensify. In tropical regions, countryside habitats that retain abundant tree cover and structurally complex canopies may complement protected areas by providing suitable habitats and landscape connectivity for a significant portion of the native biota. Species with low dispersal capabilities are among the most at risk of extinction as a consequence of land‐use change. We assessed how the spatial distribution of the brown‐throated sloth (Bradypus variegatus), a model species for a vertebrate with limited dispersal ability, is shaped by differences in habitat structure and landscape patterns of countryside habitats in north‐central Costa Rica using a multi‐scale framework. We quantified the influence of local habitat characteristics and landscape context on sloth occurrence using mixed‐effects logistic regression models. We recorded 27 sloths within countryside habitats and found that both local and landscape factors significantly influenced their spatial distribution. Locally, sloths favored structurally complex habitats, with greater canopy cover and variation in tree height and basal area. At the landscape scale, sloths demonstrated a preference for habitats with high proportions of forest and nearby large tracts of forest. Although mixed‐use areas and tree plantations are not substitutes for protected forests, our results suggest they provide important supplemental habitats for sloths. To promote the conservation and long‐term viability of sloth populations in the tropical countryside, we recommend that land managers retain structurally complex vegetation and large patches of native habitat.     

Metabolites related to gut bacterial metabolism,peroxisome proliferator‐activated receptor‐alpha activation,and insulin sensitivity are associated with physical function in functionally‐limited older adults

Identification of mechanisms underlying physical function will be important for addressing the growing challenge that health care will face with physical disablement in the expanding aging population. Therefore, the goals of the current study were to use metabolic profiling to provide insight into biologic mechanisms that may underlie physical function by examining the association between baseline and the 6‐month change in serum mass spectrometry‐obtained amino acids, fatty acids, and acylcarnitines with baseline and the 6‐month change in muscle strength (leg press one repetition maximum divided by total lean mass, LP/Lean), lower extremity function [short physical performance battery (SPPB)], and mobility (400 m gait speed, 400‐m), in response to 6 months of a combined resistance exercise and nutritional supplementation (whey protein or placebo) intervention in functionally‐limited older adults (SPPB ≤ 10; 70–85 years, N = 73). Metabolites related to gut bacterial metabolism (cinnamoylglycine, phenol sulfate, p‐cresol sulfate, 3‐indoxyl sulfate, serotonin, N‐methylproline, hydrocinnamate, dimethylglycine, trans‐urocanate, valerate) that are altered in response to peroxisome proliferator‐activated receptor‐alpha (PPAR‐α) activation (α‐hydroxyisocaproate, α‐hydroxyisovalerate, 2‐hydroxy‐3‐methylvalerate, indolelactate, serotonin, 2‐hydroxypalmitate, glutarylcarnitine, isobutyrylcarnitine, cinnamoylglycine) and that are related to insulin sensitivity (monounsaturated fatty acids: 5‐dodecenoate, myristoleate, palmitoleate; γ‐glutamylamino acids: γ‐glutamylglutamine, γ‐glutamylalanine, γ‐glutamylmethionine, γ‐glutamyltyrosine; branched‐chain amino acids: leucine, isoleucine, valine) were associated with function at baseline, with the 6‐month change in function or were identified in backward elimination regression predictive models. Collectively, these data suggest that gut microbial metabolism, PPAR‐α activation, and insulin sensitivity may be involved in mechanisms that underlie physical function in functionally‐limited older adults.     

Down‐regulation of BnDA1, whose gene locus is associated with the seeds weight,improves the seeds weight and organ size in Brassica napus

Brassica napus L. is an important oil crop worldwide and is the main raw material for biofuel. Seed weight and seed size are the main contributors to seed yield. DA1 (DA means big in Chinese) is an ubiquitin receptor and negatively regulates seed size. Down‐regulation of AtDA1 in Arabidopsis leads to larger seeds and organs by increasing cell proliferation in integuments. In this study, BnDA1 was down‐regulated in B. napus by over expressed of AtDA1^R358K, which is a functional deficiency of DA1 with an arginine‐to‐lysine mutation at the 358th amino acid. The results showed that the biomass and size of the seeds, cotyledons, leaves, flowers and siliques of transgenic plants all increased significantly. In particular, the 1000 seed weight increased 21.23% and the seed yield per plant increased 13.22% in field condition. The transgenic plants had no negative traits related to yield. The candidate gene association analysis demonstrated that the BnDA1 locus was contributed to the seeds weight. Therefore, our study showed that regulation of DA1 in B. napus can increase the seed yield and biomass, and DA1 is a promising target for crop improvement.