Passerines may be sufficiently plastic to track temperature‐mediated shifts in optimum lay date

Projecting the fates of populations under climate change is one of global change biology's foremost challenges. Here, we seek to identify the contributions that temperature‐mediated local adaptation and plasticity make to spatial variation in nesting phenology, a phenotypic trait showing strong responses to warming. We apply a mixed modeling framework to a Britain‐wide spatiotemporal dataset comprising >100 000 records of first egg dates from four single‐brooded passerine bird species. The average temperature during a specific time period (sliding window) strongly predicts spatiotemporal variation in lay date. All four species exhibit phenological plasticity, advancing lay date by 2–5 days °C^?1. The initiation of this sliding window is delayed further north, which may be a response to a photoperiod threshold. Using clinal trends in phenology and temperature, we are able to estimate the temperature sensitivity of selection on lay date (B), but our estimates are highly sensitive to the temporal position of the sliding window. If the sliding window is of fixed duration with a start date determined by photoperiod, we find B is tracked by phenotypic plasticity. If, instead, we allow the start and duration of the sliding window to change with latitude, we find plasticity does not track B, although in this case, at odds with theoretical expectations, our estimates of B differ across latitude vs. longitude. We argue that a model combining photoperiod and mean temperature is most consistent with current understanding of phenological cues in passerines, the results from which suggest that each species could respond to projected increases in spring temperatures through plasticity alone. However, our estimates of B require further validation.     

Biocomplexity in Coupled Natural–Human Systems: A Multidimensional Framework

As defined by Ascher, biocomplexity results from a “multiplicity of interconnected relationships and levels.” However, no integrative framework yet exists to facilitate the application of this concept to coupled human–natural systems. Indeed, the term “biocomplexity” is still used primarily as a creative and provocative metaphor. To help advance its utility, we present a framework that focuses on linkages among different disciplines that are often used in studies of coupled human–natural systems, including the ecological, physical, and socioeconomic sciences. The framework consists of three dimensions of complexity: spatial, organizational, and temporal. Spatial complexity increases as the focus changes from the type and number of the elements of spatial heterogeneity to an explicit configuration of the elements. Similarly, organizational complexity increases as the focus shifts from unconnected units to connectivity among functional units. Finally, temporal complexity increases as the current state of a system comes to rely more and more on past states, and therefore to reflect echoes, legacies, and evolving indirect effects of those states. This three-dimensional, conceptual volume of biocomplexity enables connections between models that derive from different disciplines to be drawn at an appropriate level of complexity for integration.     

行为的结构、刚性和多样性

有关动物行为的定义、结构和多样性是一个被长期忽视的研究领域。然而,动物行为多样性不仅是一个生物多样性基础理论问题,也与濒危动物的成功保护有关。本文定义了动物行为以及行为的刚性与弹性,探讨了行为表达的空间条件以及生境因素与行为多样性之间的关系。我们发现雌雄大熊猫个体在较大的活动空间里的发情行为表现的频次及活动频率显著地高于那些在较小的空间里的雌雄个体,说明活动空间对雄性或雌性大熊猫的发情行为有显著影响。圈养空间影响麋鹿的社会行为、通讯行为和聚群行为。圈养在小圈中的麋鹿没有出现同性聚群现象,当圈养麋鹿野放后即表现出这种现象。圈养环境中长大的动物个体由于缺乏行为的表达空间,仅仅表现出刚性大的行为,丧失了许多弹性大的行为,从而导致动物行为的多样性下降。对那些生活在开阔草原和荒漠上的野生有蹄类动物实施迁地保护时,必须考虑其逃逸空间,为那些动物建立自然保护区时,则必须考虑其迁移空间。此外,动物行为的多样性与生境元素有关。我们应当给圈养动物提供复杂而多样的环境,以增加圈养野生动物表达寻找食物、建立领域、筑巢和避开不利环境等行为的可能性,维持濒危个体的行为多样性。     

中日“防灾公园”和“城市防灾避险绿地”概念辨析

城市绿地是城市防灾避险体系中的重要载体,近些年城市防灾避险绿地的研究与建设逐渐受到重视。日本灾害频发,因此在防灾避险建设领域拥有较为丰富的经验和信息。在学习和借鉴中,中国的防灾避险研究与建设也在逐步发展。但目前从中日的相关研究来看,“防灾公园”“防灾据点”等概念的实际应用在两国之间存在着一定的差异。本文分析了中、日相关文献,辨析了“防灾公园”“防灾据点”等概念的定义及与“城市防灾避险绿地”的关系,细分了城市防灾避险绿地的类型。最后对中日两国防灾公园的概念定义和范围进行了对比,得到了日本“防灾公园”这一概念的实质更接近于中国“城市防灾避险绿地”这一概念的结论。     

A review of the occurrence of inter‐colony segregation of seabird foraging areas and the implications for marine environmental impact assessment

Understanding the determinants of species’ distributions is a fundamental aim in ecology and a prerequisite for conservation but is particularly challenging in the marine environment. Advances in bio‐logging technology have resulted in a rapid increase in studies of seabird movement and distribution in recent years. Multi‐colony studies examining the effects of intra‐ and inter‐colony competition on distribution have found that several species exhibit inter‐colony segregation of foraging areas, rather than overlapping distributions. These findings are timely given the increasing rate of human exploitation of marine resources and the need to make robust assessments of likely impacts of proposed marine developments on biodiversity. Here we review the occurrence of foraging area segregation reported by published tracking studies in relation to the density‐dependent hinterland (DDH) model, which predicts that segregation occurs in response to inter‐colony competition, itself a function of colony size, distance from the colony and prey distribution. We found that inter‐colony foraging area segregation occurred in 79% of 39 studies. The frequency of occurrence was similar across the four seabird orders for which data were available, and included species with both smaller (10–100 km) and larger (100–1000 km) foraging ranges. Many predictions of the DDH model were confirmed, with examples of segregation in response to high levels of inter‐colony competition related to colony size and proximity, and enclosed landform restricting the extent of available habitat. Moreover, as predicted by the DDH model, inter‐colony overlap tended to occur where birds aggregated in highly productive areas, often remote from all colonies. The apparent prevalence of inter‐colony foraging segregation has important implications for assessment of impacts of marine development on protected seabird colonies. If a development area is accessible from multiple colonies, it may impact those colonies much more asymmetrically than previously supposed. Current impact assessment approaches that do not consider spatial inter‐colony segregation will therefore be subject to error. We recommend the collection of tracking data from multiple colonies and modelling of inter‐colony interactions to predict colony‐specific distributions.     

人为干扰对武汉市城市绿地鸟类群落结构的影响

城市绿地生态系统是城市景观的重要组成部分,具有重要的生态与文化价值。鸟类是城市绿地生态系统的指示类群,研究人类活动对鸟类资源的影响能够为城市生态景观的建设与维护提供重要理论依据。本研究于2021年10月至2022年5月,采用样线法对武汉市不同干扰强度的城市绿地内林鸟群落进行调查。共记录到鸟类11目34科100种,其中国家二级重点保护鸟类9种,在物种组成上以雀形目为主(76种,占调查到总鸟种数的76%),在居留型上以留鸟为主(42种,42%),在区系上主要属于东洋界(45种,45%)。繁殖季鸟类物种数高于非繁殖季,主要是由于夏候鸟和旅鸟的增加导致。在不同干扰强度中,重度干扰斑块的平均鸟类个体数最多,轻度干扰斑块的鸟类物种丰富度、多样性指数和均匀度指数最高,而中度干扰斑块的鸟类个体数、物种丰富度、多样性指数和均匀度指数均为最低,且繁殖季和非繁殖季鸟类群落结构在不同人为干扰强度中的格局未发生变化。综上所述,武汉市城市绿地的鸟类多样性较为丰富,随着干扰强度增加,鸟类多样性出现非线性差异,揭示了人为干扰与自然干扰对生态影响的差异;在面积狭小、破碎化严重的斑块中,人为干扰可能有利于城市绿地鸟类多样性的维持。     

参数序列比对算法研究

序列比对是生物信息学中的一项重要任务,通过序列比对可以发现生物序列中的功能、结构和进化的信息。序列比对结果的生物学意义与所选择的匹配、不匹配、插入和删除以及空隙的罚分函数密切相关。现介绍一种参数序列比对方法,该方法把最佳比对作为权值和罚分的函数,可以系统地得到参数的选择对最佳比对结果的影响。然后将其应用于RNA序列比对,分析不同的参数选择对序列比对结果的影响。最后指出参数序列比对算法的应用以及未来的发展方向。     

Structural analysis based on state-space modeling.

A new method has been developed to compute the probability that each amino acid in a protein sequence is in a particular secondary structural element. Each of these probabilities is computed using the entire sequence and a set of predefined structural class models. This set of structural classes is patterned after Jane Richardson''s taxonomy for the domains of globular proteins. For each structural class considered, a mathematical model is constructed to represent constraints on the pattern of secondary structural elements characteristic of that class. These are stochastic models having discrete state spaces (referred to as hidden Markov models by researchers in signal processing and automatic speech recognition). Each model is a mathematical generator of amino acid sequences; the sequence under consideration is modeled as having been generated by one model in the set of candidates. The probability that each model generated the given sequence is computed using a filtering algorithm. The protein is then classified as belonging to the structural class having the most probable model. The secondary structure of the sequence is then analyzed using a "smoothing" algorithm that is optimal for that structural class model. For each residue position in the sequence, the smoother computes the probability that the residue is contained within each of the defined secondary structural elements of the model. This method has two important advantages: (1) the probability of each residue being in each of the modeled secondary structural elements is computed using the totality of the amino acid sequence, and (2) these probabilities are consistent with prior knowledge of realizable domain folds as encoded in each model. As an example of the method''s utility, we present its application to flavodoxin, a prototypical alpha/beta protein having a central beta-sheet, and to thioredoxin, which belongs to a similar structural class but shares no significant sequence similarity.     

基于混沌理论的蛋白质序列特性的研究

蛋白质序列特性的研究对于蛋白质的结构及功能具有重要意义。该文为了研究蛋白质序列是否具有混沌行为,先将蛋白质序列通过氨基酸电子离子相互作用势(electron interaction potential,EIIP)转化为时间序列,再根据混沌理论对其进行相空间重构,利用去偏自相关系数,经典G-P算法确定系统的时间延迟t和嵌入维数m,系统的最大Lyapunov指数则用改进的最大Lyapunov指数计算方法计算,其结果绝大多数为正,从而确认了蛋白质时间序列的混沌行为,并对特例进行了说明。