Effect of the presence of empty sites on the evolution of cooperation by costly punishment in spatial games

Cooperation and spiteful behavior are still evolutionary puzzles. Costly punishment, for which the game payoff is the same as that of spiteful behavior, is one mechanism for promoting the evolution of cooperation. A spatially structured population facilitates the evolution of either cooperation or spite/punishment if cooperation is linked explicitly or implicitly with spite/punishment; a cooperator cooperates with another cooperator and punishes/spites the other type of player. Different updating rules in the evolutionary game produce different evolutionary outcomes: with one updating rule—the score-dependent viability model, in which a player dies with a probability inversely proportional to the game score and the resulting unoccupied site is colonized by one player chosen randomly—the evolution of spite/punishment is promoted more than with the other updating rule—the score-dependent fertility model, in which, after a player dies randomly, the site is colonized by a player with a higher game score. If the population has empty sites, spiteful players or punishers should have less chance to interact with others and then spite/punish others. Thus the presence of empty sites would affect the evolutionary dynamics of spite/punishment. Here, we investigated whether the presence of empty sites discourages the evolution of spite/punishment in both a lattice-structured population and a completely mixing population where players interact with others randomly, especially when the score-dependent viability model is adopted. In the lattice-structured population adopting this viability model, the presence of empty sites promoted the evolution of cooperation and did not reduce the effect of spite/punishment. In the completely mixing population, the presence of empty sites did not promote evolution of cooperation by punishment. The evolutionary dynamics of the score-dependent viability model with empty sites were close to those of the score-dependent fertility model.     

How can the Yelkouan shearwater survive feral cat predation? A meta-population structure as a solution?

The Yelkouan shearwater, Puffinus yelkouan, is an endangered Mediterranean endemic species of burrowing petrel threatened by feral cats. The life-history parameters of a small population of Yelkouan shearwaters on the Mediterranean island, Port-Cros, were studied in conjunction with the diet of feral cats, to examine the birds’ vulnerability to introduced cats. Yelkouan shearwaters were the birds most frequently found in cat scats, with 431 ± 72 birds killed per year, and predation highest during the pre-laying period. A demographic model was created using data for P. yelkouan and for closely related shearwater species. Without cat predation, only two of four survival rate scenarios led to a mean growth rate (λ) ≥ 1. The model was constrained to have a stable population growth rate and used to predict predation scenarios compatible with the observed population stability, because the population under study has remained stable at around 180 pairs for at least 20 years despite feral cat predation. The results of assuming that the population is closed were inconsistent with the estimated mortalities due to feral cats, while it was possible to reconcile the observed numbers of breeding pairs with the observed mortalities due to cats by assuming that Port-Cros Island is a sink sustained by immigration. This illustrates that small colonies may need to be sustained by larger ones to avoid being driven to extinction. Unfortunately, the absence of a large geographic-scale ringing program makes the precise identification of the origin of the immigrants impossible in this case.     

Understanding gene essentiality by finely characterizing hubs in the yeast protein interaction network

The centrality-lethality rule, i.e., high-degree proteins or hubs tend to be more essential than low-degree proteins in the yeast protein interaction network, reveals that a protein’s central position indicates its important function, but whether and why hubs tend to be more essential have been heavily debated. Here, we integrated gene expression and functional module data to classify hubs into four types: non-co-expressed non-co-cluster hubs, non-co-expressed co-cluster hubs, co-expressed non-co-cluster hubs and co-expressed co-cluster hubs. We found that all the four hub types are more essential than non-hubs, but they also show different enrichments in essential proteins. Non-co-expressed non-co-cluster hubs play key role in organizing different modules formed by the other three hub types, but they are less important to the survival of the yeast cell. Among the four hub types, co-expressed co-cluster hubs, which likely correspond to the core components of stable protein complexes, are the most essential. These results demonstrated that our classification of hubs into four types could better improve the understanding of gene essentiality.     

BIODIVERSITY RESEARCH: Nestedness for different reasons: the distributions of birds,lizards and small mammals on islands of an inundated lake

Aim We examined whether the community compositions of birds, lizards and small mammals were nested in a fragmented landscape in the Thousand Island Lake, China. We also assessed whether the mechanisms influencing nestedness differed among these taxonomic groups. Location Thousand Island Lake, China. Methods Presence/absence matrices were compiled for birds (42 islands) and lizards (42 islands) using line‐transect methods, and for small mammals (14 islands) using live‐trapping methods from 2006 to 2009. Nestedness was analysed using BINMATNEST, and statistical significance was assessed using the conservative null model 3. We used Spearman rank correlations and partial Spearman rank correlations to examine associations of nestedness and habitat variables (area, isolation, habitat diversity and plant richness) as well as life‐history traits (body size, habitat specificity, geographical range size and area requirement) related to species extinction and immigration tendencies. Results The community compositions of birds, lizards and small mammals were all significantly nested, but the causal factors underlying nestedness differed among taxonomic groups. For birds, island area, habitat specificity and area requirement were significantly correlated with nestedness after controlling for other independent variables. For lizards, habitat heterogeneity was the single best correlate of nestedness. For small mammals, island area, habitat heterogeneity and habitat specificity were significantly correlated with nestedness. The nested patterns of birds, lizards and small mammals were not attributable to passive sampling or selective colonization. Main conclusions The processes influencing nested patterns differed among taxonomic groups. Nestedness of bird assemblages was driven by selective extinction, and lizard assemblage was caused by habitat nestedness, while nestedness of small mammals resulted from both selective extinction and habitat nestedness. Therefore, we should take taxonomic differences into account when analysing nestedness to develop conservation guidelines and refrain from using single taxa as surrogates for others.     

Developing a management procedure robust to uncertainty for southern bluefin tuna: a somewhat frustrating struggle to bridge the gap between ideals and reality

Fisheries management is conducted to achieve sustainable use of fishery resources, mainly through regulation of fishing activities. For almost a decade, the Commission for the Conservation of Southern Bluefin Tuna (CCSBT) struggled to reach agreement on a total allowable catch (TAC) for southern bluefin tuna (SBT) because of stock assessment uncertainties. To address this, in 2002 the CCSBT commenced development of a management procedure (MP), a pre-agreed set of rules to determine how the TAC will be adjusted as new monitoring data become available. The CCSBT Scientific Committee tested various candidate MPs using operating models which simulate fish population and fishery dynamics as well as incorporate process, observation, and model uncertainties. Candidate MPs were evaluated using performance measures related to the following management objectives: maximize catches, avoid stock collapse, and minimize interannual catch variation. Of the MPs explored, some relied solely on empirical data [i.e., adjusted TAC based on catch per unit effort (CPUE) trends], whereas others were more complicated, based on population models. In 2005, the CCSBT adopted a model-based MP that realized a moderate catch with low variability and avoided stock collapse. This MP struck a compromise between the risk-prone and risk-averse standpoints of the different stakeholders. However, despite this concerted scientific effort, the MP was not implemented because, shortly after its adoption, it became evident that historical catches may have been substantially underreported. This complication necessitates returning to near the beginning of the development process. MP approaches have various advantages and challenges to be explored further. However, it is essential to lessen human-introduced uncertainty (such as catch misreporting) by enhanced enforcement, and to increase management robustness to biological uncertainties by implementing MPs.     

Mark—Recapture Accurately Estimates Census for Tuatara,a Burrowing Reptile

Abstract: Estimates of population size are necessary for effective management of threatened and endangered species, but accurate estimation is often difficult when species are cryptic. We evaluated effectiveness of mark–recapture techniques using the Lincoln–Peterson estimator for predicting true census size of a population of tuatara (Sphenodon punctatus), a burrowing reptile that is a conservation priority in New Zealand. We found that Lincoln–Peterson estimates (NŇ = 85) were accurate for predicting the census size (N = 87) after only a 3-day mark–recapture survey. We recommend this method as a cost-effective way to accurately estimate population size for isolated, inaccessible tuatara populations, because it requires limited personnel, expertise, and time, and has low environmental impact on fragile sites.     

Phenotypic evolution in high‐elevation populations of western fence lizards (Sceloporus occidentalis) in the Sierra Nevada Mountains

Adaptive divergence in response to variable habitats, climates, and altitude is often accentuated along elevation gradients. We investigate phenotypic evolution in body size and coloration in the western fence lizard (Sceloporus occidentalis Baird & Girard, 1852) across elevation gradients in Yosemite National Park, California, situated in the Sierra Nevada mountains of Western North America. High‐elevation populations occurring above 2100 m a.s.l. are recognized as a separate subspecies (Sceloporus occidentalis taylori Camp, 1916), with a distinctive phenotype characterized by a large body size and extensive blue ventral pigmentation. We sampled S. occidentalis from across elevation gradients in Yosemite National Park, California, and collected phenotypic data (body size and ventral coloration measurements; 410 specimens) and mitochondrial DNA sequence data (complete NADH1 gene; 969 bp, 181 specimens) to infer phylogenetic relationships, and examine the genetic and phenotypic diversity among populations. Populations of S. occidentalis in Yosemite National Park follow Bergmann's rule and exhibit larger body sizes in colder, high‐elevation environments. The high‐elevation subspecies S. o. taylori is not monophyletic, and the mitochondrial DNA genealogy supports a model of convergent phenotypic evolution among high‐elevation populations belonging to different river drainages. The hypothesis that separate populations of S. occidentalis expanded up river drainages after the recession of glaciers is supported by population demographic analyses, and suggest that Bergmann's clines can evolve rapidly along elevation gradients. The distinctive high‐elevation phenotype that is attributable to S. o. taylori has evolved independently several times, and includes adaptive phenotypic changes associated with increases in body size and ventral coloration. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 630–641.     

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.     

Scaling of Size and Dimorphism in Primates I: Microevolution

I used a new quantitative genetics model to predict relationships between sex-specific body size and sex-specific relative variability when populations experience differences in relative intensity of sex-specific selection pressures—stronger selection on males or females—and direction of selection: increase or decrease in size. I combined Lande's (Evolution 34: 292–305) model for the response of sex-specific means to selection with a newly derived generalization of Bulmer's (Am. Nat. 105: 201–211) model for the response of relative variability to selection. I used this combined response model to predict correlations of sex-specific size and relative variability under various starting conditions, which one can compare to correlations between closely related primate populations. One can then compare predicted patterns of sex-specific selection pressures to social and ecological variables pertaining to those populations to identify likely forces producing microevolutionary change in sexual size dimorphism (SSD). I provide examples of this approach for populations representing three taxa: Papio anubis, Saguinus mystax, and Cercopithecus aethiops pygerythrus. Model results suggest that microevolutionary changes in SSD can result from greater selection acting on males or females, and that natural selection or natural and sexual selection combined, rather than sexual selection alone, may sometimes explain sex-specific selection differentials.