遗传多样性上限假说所揭示的进化历程

作为生物进化的两个主流理论, 中性学说和现代达尔文进化理论相对系统地揭示了进化机理和历程, 但也都有缺陷, 比如对某些重大进化现象如遗传等距离和重叠位点(Overlap sites)的忽视, 对复杂性的视而不见, 对遗传多样性的片面解读, 以及与化石证据相悖等。遗传多样性上限假说(Maximum genetic diversity hypothesis, MGD)通过对遗传等距离现象的重新解读, 给出了复杂性的量化定义和可操作研究手段, 提出了重叠特征和遗传多样性具有上限等结论。它对人猿分类关系和现代人多地区起源的分子解读结论, 与独立的化石证据契合度较高, 重新肯定了中国在人类发展中的关键作用, 点出了流行分子结论的荒谬在于误用了极限距离。该理论同时对复杂性状和复杂疾病的遗传机制研究具有指导意义。文章对多种酵母、鱼类、灵长类的细胞色素c进行序列比对, 独立验证了MGD假说的部分论断, 并解释了重叠位点在遗传距离计算上的重要意义。MGD假说中的上限或最佳平衡概念, 与传统国学和中医阴阳中庸思想对宇宙基本规律的描述是一脉相承的。     

生态位理论在张家界市主要旅游景区评价中的应用

选择张家界市5个主要旅游景区作为研究对象、50种影响旅游景区发展的资源状态作为评价指标, 通过指标逐级合并处理, 在3个指标级别(Ⅰ、Ⅱ、Ⅲ级)上分析了生态位宽度和生态位重叠. 结果表明: 张家界市旅游景区生态位宽度受指标级别的影响显著(F=10.278, P=0.006), 而采用相对生态位宽度则不受指标级别的影响, 说明在旅游景区开发潜力评价中, 相对生态位宽度比绝对生态位宽度更具合理性; 从Ⅲ级指标到Ⅰ级指标, 旅游景区生态位重叠度值有增大趋势, 表明指标级别的选择会影响旅游景区间实际生态位重叠的评价. 随着评价指标的逐步细化, 当观测到的Pianka指数和采用Monte Carlo模拟的Pianka指数的差值达到显著水平时, 该指标级别可作为评价指标细化的最低标准, 模拟的生态位重叠值可作为旅游景区竞争评价的重要参考.     

ABCA1胞外第四环缺失突变体的构建及其抗砷性初步研究

目的：构建ABCA1细胞外第四环第1 479～1 597位氨基酸残基缺失的突变体。方法：采用重叠区扩增基因拼接法构建ABCA1第1 479～1 597位氨基酸残基缺失的突变体基因,并将其克隆至pcDNA3.1/V5-His/ABCA1重组载体上,脂质体法转染Hela细胞,激光共聚焦观察突变体定位,Cell Counting Kit-8(CCK-8)试剂盒检测其48h急性砷中毒后生存率的变化。结果：该突变体基因经DNA序列分析表明其具有正确的序列和阅读框。激光共聚焦证实其表达的蛋白仍然能正确定位在Hela细胞的细胞膜上。CCK-8结果显示转染重组质粒和突变体质粒的细胞在各种砷浓度下生存率都较空载体组高。结论：成功构建了ABCA1胞外第四环第1 479～1 597位氨基酸残基缺失的突变体,且其表达的蛋白仍然定位于细胞膜上,突变体仍然具有一定的抗砷性,提示ABCA1胞外第四环可能不是关键抗砷结构域。     

Resource partitioning in sympatric langurs and macaques in tropical rainforests of the central Western Ghats, south India

In a competitive sympatric association, coexisting species may try to reduce interspecific interactions as well as competition for similar resources by several ecological and behavioral practices. We studied resource utilization of three sympatric primate species namely, lion-tailed macaques (Macaca silenus), bonnet macaques (M. radiata) and Hanuman langurs (Semnopithecus entellus) in a tropical rainforest of the central Western Ghats, south India. We studied resource use, tree-height use, foraging height, substrate use when consuming animal prey and interspecific interactions. The results revealed that across the year, there was very limited niche overlap in diet between each species-pair. Each primate species largely depended on different plant species or different plant parts and phenophases from shared plant species. Primate species used different heights for foraging, and the two macaque species searched different substrates when foraging on animal prey. We also recorded season-wise resource abundance for the resources shared by these three primate species. While there was low dietary overlap during the dry season (a period of relatively low resource abundance), there was high dietary overlap between the two macaque species during the wet season (a period of high resource abundance for the shared resources). We observed only a few interspecific interactions. None of these were agonistic, even during the period of high niche overlap. This suggests that the sympatric primate species in this region are characterized by little or no contest competition. Unlike in some other regions of the Western Ghats, the lack of interspecific feeding competition appears to allow these primates, especially the macaques, to remain sympatric year-round.     

Foraging ecology and niche overlap in pygmy (Kogia breviceps) and dwarf (Kogia sima) sperm whales from waters of the U.S. mid‐Atlantic coast

A complementary approach of stomach content and stable isotope analyses was used to characterize the foraging ecology and evaluate niche overlap between pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales stranded on the U.S. mid‐Atlantic coast between 1998 and 2011. Food habits analysis demonstrated both species were primarily teuthophagous, with 35 species of cephalopods, and 2 species of mesopelagic fishes represented in their overall diets. Pianka's Index of niche overlap suggested high overlap between whale diets (O_n = 0.92), with squids from the families Histioteuthidae, Cranchidae, and Ommastrephidae serving as primary prey. Pygmy sperm whales consumed slightly larger prey sizes (mean mantle length [ML] = 10.8 cm) than dwarf sperm whales (mean ML = 7.8 cm). Mean prey sizes consumed by pygmy sperm whales increased with growth, but showed no trend in dwarf sperm whales. Significant differences were not detected in δ¹⁵N and δ¹³C values of muscle tissues from pygmy (10.8‰ ± 0.5‰, ?17.1‰ ± 0.6‰), and dwarf sperm whales (10.7‰ ± 0.5‰, ?17.0‰ ± 0.4‰), respectively. Isotopic niche widths also did not differ significantly and dietary overlap was high between the two species. Results suggest the feeding ecologies of the pygmy and dwarf sperm whales are similar and both species occupy equivalent trophic niches in the region.     

Testing the stages model in the adaptive radiation of cichlid fishes in East African Lake Tanganyika

Adaptive radiation (AR) is a key process in the origin of organismal diversity. However, the evolution of trait disparity in connection with ecological specialization is still poorly understood. Available models for vertebrate ARs predict that diversification occurs in the form of temporal stages driven by different selective forces. Here, we investigate the AR of cichlid fishes in East African Lake Tanganyika and use macroevolutionary model fitting to evaluate whether diversification happened in temporal stages. Six trait complexes, for which we also provide evidence of their adaptiveness, are analysed with comparative methods: body shape, pharyngeal jaw shape, gill raker traits, gut length, brain weight and body coloration. Overall, we do not find strong evidence for the ‘stages model’ of AR. However, our results suggest that trophic traits diversify earlier than traits implicated in macrohabitat adaptation and that sexual communication traits (i.e. coloration) diversify late in the radiation.     

Social organization,survival, and dispersal of cape foxes (Vulpes chama) in South Africa

We monitored 20 cape foxes (Vulpes chama) to determine the social organization, survival, and dispersal of this species on two sites in South Africa from 2005 to 2008. Cape foxes were socially monogamous and territorial, with annual home ranges of mated pairs (n = 8) overlapping 80% on average, compared to a mean overlap of 3% between foxes in adjacent ranges. At least 2 pairs remained associated for >1 breeding season, and both sexes exhibited strong site fidelity, as home ranges in consecutive years overlapped 58–98%. Members of mated pairs never foraged together, however they used the same or nearby (<100 m apart) day rests 81% of the time when pups were 0–4 months of age, but only 28% of the time during other months of the year. Dispersal was male biased, as all juvenile males (n = 6) dispersed when 9–11.5 months old, whereas 3 of 4 juvenile females remained philopatric as either breeders or non-breeding associates. At least 6 foxes bred as yearlings (3 F, 3 M), indicating cape foxes have high reproductive potential. Two adult females maintained their territories after their mates died, whereas two adult males dispersed soon after their mates died, indicating cape foxes likely have a female-based social organization. Annual survival was 0.64, and predation from larger carnivores, primarily black-backed jackals (Canis mesomelas), was responsible for 71% of mortalities. Our results provided empirical support for previous hypotheses regarding the relationship between body size and life-history patterns in Canidae, as several ecological parameters of cape foxes were similar to that of other small (<6 kg) canid species, especially Vulpes species inhabiting arid and semi-arid environments.     

Historical contingency in species interactions: towards niche‐based predictions

The way species affect one another in ecological communities often depends on the order of species arrival. The magnitude of such historical contingency, known as priority effects, varies across species and environments, but this variation has proven difficult to predict, presenting a major challenge in understanding species interactions and consequences for community structure and function. Here, we argue that improved predictions can be achieved by decomposing species' niches into three components: overlap, impact and requirement. Based on classic theories of community assembly, three hypotheses that emphasise related, but distinct influences of the niche components are proposed: priority effects are stronger among species with higher resource use overlap; species that impact the environment to a greater extent exert stronger priority effects; and species whose growth rate is more sensitive to changes in the environment experience stronger priority effects. Using nectar‐inhabiting microorganisms as a model system, we present evidence that these hypotheses complement the conventional hypothesis that focuses on the role of environmental harshness, and show that niches can be twice as predictive when separated into components. Taken together, our hypotheses provide a basis for developing a general framework within which the magnitude of historical contingency in species interactions can be predicted.     

A feature selection method for classification within functional genomics experiments based on the proportional overlapping score

Background

Microarray technology, as well as other functional genomics experiments, allow simultaneous measurements of thousands of genes within each sample. Both the prediction accuracy and interpretability of a classifier could be enhanced by performing the classification based only on selected discriminative genes. We propose a statistical method for selecting genes based on overlapping analysis of expression data across classes. This method results in a novel measure, called proportional overlapping score (POS), of a feature’s relevance to a classification task.

Results

We apply POS, along‐with four widely used gene selection methods, to several benchmark gene expression datasets. The experimental results of classification error rates computed using the Random Forest, k Nearest Neighbor and Support Vector Machine classifiers show that POS achieves a better performance.

Conclusions

A novel gene selection method, POS, is proposed. POS analyzes the expressions overlap across classes taking into account the proportions of overlapping samples. It robustly defines a mask for each gene that allows it to minimize the effect of expression outliers. The constructed masks along‐with a novel gene score are exploited to produce the selected subset of genes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-274) contains supplementary material, which is available to authorized users.     

Interspecies and intraspecies interactions in social amoebae

The stable co‐existence of individuals of different genotypes and reproductive division of labour within heterogeneous groups are issues of fundamental interest from the viewpoint of evolution. Cellular slime moulds are convenient organisms in which to address both issues. Strains of a species co‐occur, as do different species; social groups are often genetically heterogeneous. Intra‐ and interspecies 1 : 1 mixes of wild isolates of Dictyostelium giganteum and D. purpureum form chimaeric aggregates, following which they segregate to varying extents. Intraspecies aggregates develop in concert and give rise to chimaeric fruiting bodies that usually contain more spores (reproductives) of one component than the other. Reproductive skew and variance in the proportion of reproductives are positively correlated. Interspecies aggregates exhibit almost complete sorting; most spores in a fruiting body come from a single species. Between strains, somatic compatibility correlates weakly with sexual compatibility. It is highest within clones, lower between strains of a species and lowest between strains of different species. Trade‐offs among fitness‐related traits (between compatible strains), sorting out (between incompatible strains) and avoidance (between species) appear to lie behind coexistence.