Genetic mark-recapture analysis of winter faecal pellets allows estimation of population size in Sage Grouse Centrocercus urophasianus

The Sage Grouse Centrocercus urophasianus is a species of conservation concern throughout its range in western North America. Since the 1950s, the high count of males at leks has been used as an index for monitoring populations. However, the relationship between this lek-count index and population size is unclear, and its reliability for assessing population trends has been questioned. We used non-invasive genetic mark-recapture analysis of faecal and feather samples to estimate pre-breeding population size for the Parachute-Piceance-Roan, a small, geographically isolated population of Sage Grouse in western Colorado, during two consecutive winters from 2012 to 2014. We estimated total pre-breeding population size as 335 (95% confidence interval (CI): 287–382) in the first winter and 745 (95% CI: 627–864) in the second, an approximate doubling in abundance between years. Although we also observed a large increase in the spring lek-count index between those years, high male count data poorly represented mark-recapture estimates of male abundance in each year. Our data suggest that lek counts are useful for detecting the direction and magnitude of large changes in Sage Grouse abundance over time but they may not reliably reflect small changes in abundance that may be relevant to small populations of conservation concern.     

利用红外线相机监测地表水对广西弄岗国家级自然保护区兽类分布的影响

广西弄岗国家级自然保护区属岩溶地貌,表土层薄,储水度低,地表水奇缺,动物可能因水源而改变其活动范围和规律。2006年3月—2007年6月和2010年10月—2011年5月,该实验利用红外线相机在兽类通往水源地之间,即兽径上(如足迹和粪便)进行兽类调查。共拍摄到兽类5目12科17属19种,包括国家一级保护动物黑叶猴(Trachypithecus francoisi)和熊猴(Macaca assamensis)。物种累积曲线95%置信区间重迭,相似性分析和非度量多维标度显示两种微生境出没物种的差异较小,然而,差异物种占整体记录的42%,可见岩溶地区水资源极其珍贵。中、短期保护建议包括加强水源点的巡护、防止偷猎、限制滥抽地下水,以及考虑整合呈岛屿状的陇呼、弄岗及陇山地区,以加强保护大面积生境的连贯性,并加速恢复山峰间已遭破坏的圆洼谷地的原生树林。     

On the Sampling Method for Grand Canonical Monte Carlo Simulations

Abstract

A bulk Lennard-Jones fluid was simulated using the grand canonical Monte Carlo method. Three different sampling methods were used in the transition matrix, namely the Metropolis, Barker and a third novel method. While it can be shown that the Metropolis method will give the most accurate ensemble averages in the limit of an infinitely long run, the new method termed “Modified Barker Sampling” (MBS), is shown to be superior for the runs of practical length for the particular system studied.     

Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath

Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of freedom in the molecule to environment temperature, like dihedrals in generalized coordinates or nonhydrogen atoms in Cartesian coordinate. After applying to ALA dipeptide model, we find that this modified molecular dynamics greatly enhances the sampling behavior in the conformational space and provides more information about the state-to-state transition, while conventional molecular dynamics fails to do so. Moreover, from the results of 16 independent 100?ns simulations by the new method, it shows that trpzip2 has one-half chances to reach the naive state in all the trajectories, which is greatly higher than conventional molecular dynamics. Such an improvement would provide a potential way for searching the conformational space or predicting the most stable states of peptides and proteins.     

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin’s exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate–aromatic interactions including CH–π and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to β-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.     

Signal and preference divergence among populations of the non‐endemic basal Lake Malawi cichlid fish Astatotilapia calliptera (Perciformes: Cichlidae)

In Lake Malawi and Lake Victoria, cichlid fishes have diversified into hundreds of species, many reproductively isolated by mate choice. Territorial males tend to be more aggressive to similar‐coloured males, facilitating coexistence of divergent colour morphs or species. Behavioural mate choice and aggression biases of species and allopatric populations of specialized rocky shore cichlids are influenced by divergent signals such as male colour. Believed to be basal to the Lake Malawi haplochromine radiation, and inhabiting shallow weedy areas of the lake and neighbouring water bodies, Astatotilapia calliptera also shows allopatric variation in colour. Here, it is demonstrated that such signal divergence is associated with tendencies of females to mate with males of their own population and also for males to preferentially attack males of their own population, indicating that preference divergence related to signal divergence in allopatry may have operated throughout the adaptive radiation of the Malawian cichlids. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 180–188.     

PATERNITY PROTECTION CAN PROVIDE A KICK‐START FOR THE EVOLUTION OF MALE‐ONLY PARENTAL CARE

Sperm competition and uncertainty of paternity hamper the evolution of male parental care. Thus, maternal care predominates in most taxa. What if males can, however, limit cuckoldry by guarding the eggs postmating? Here, we show that this provides a reason to reconsider an old and nowadays rather discredited hypothesis: that external fertilization is associated with male care because the parent who releases its gametes first can depart leaving the other in a “cruel bind,” having to care for the offspring. In our model, protection of paternity provides an additional incentive for the male to stay associated with its young. When we then assume that offspring survive better if guarded, paternity protection proves enough to kick‐start the evolution of male‐only parental care from a scenario with no care. This fits with data from fishes, where male‐only care is associated with external fertilization, whereas female‐only care almost always evolves after an initial transition to internal fertilization. Our model unifies disparate hypotheses regarding parental care roles and provides support for the idea that care roles can be influenced by sex differences in selection to be physically close to the offspring, including selection that is initially not based on offspring survival.     

UNDERSTANDING PROMISCUITY: WHEN IS SEEKING ADDITIONAL MATES BETTER THAN GUARDING AN ALREADY FOUND ONE?

Paternity protection and the acquisition of multiple mates select for different traits. The consensus from theoretical work is that mate‐guarding intensifies with an increasing male bias in the adult sex ratio (ASR). A male bias can thus lead to male monogamy if guarding takes up the entire male time budget. Given that either female‐ or male‐biased ASRs are possible, why is promiscuity clearly much more common than male monogamy? We address this question with two models, differing in whether males can assess temporal cues of female fertility. Our results confirm the importance of the ASR: guarding durations increase with decreasing female availability and increasing number of male competitors. However, several factors prevent the mating system from switching to male monogamy as soon as the ASR becomes male biased. Inefficient guarding, incomplete last male sperm precedence, any mechanism that allows sperm to fertilize eggs after the male's departure, and (in some cases) the unfeasibility of precopulatory guarding all help explain cases where promiscuity exists on its own or alongside temporally limited mate‐guarding. Shortening the window of fertilization shifts guarding time budgets from the postcopulatory to the precopulatory stage.     

GENETIC ANALYSIS OF MATE DISCRIMINATION IN DROSOPHILA SIMULANS

Courtship is an elaborate behavior that conveys information about the identity of animal species and suitability of individual males as mates. In Drosophila, there is extensive evidence that females are capable of evaluating and comparing male courtships, and accepting or rejecting males as mates. These relatively simple responses minimize random sexual encounters involving subpar conspecific males and heterospecific males, and over generations can potentially select novel physical and behavioral traits. Despite its evolutionary and behavioral significance, little is still known about the genes involved in mating choice and how choices for novel males and females arise during evolution. Drosophila simulans and Drosophila sechellia are two recently diverged species of Drosophila in which females have a preference for conspecific males. Here we analyzed a total of 1748 F2 hybrid females between these two species and found a small number of dominant genes controlling the preference for D. simulans males. We also mapped two redundant X‐linked loci of mating choice, Macho‐XA and Macho‐XB, and show that neither one is required for female attractiveness. Together, our results reveal part of the genetic architecture that allows D. simulans females to recognize, mate, and successfully generate progenies with D. simulans males.