Robustness of a meta-network to alternative habitat loss scenarios

Studying how habitat loss affects the tolerance of ecological networks to species extinction (i.e. their robustness) is key for our understanding of the influence of human activities on natural ecosystems. With networks typically occurring as local interaction networks interconnected in space (a meta-network), we may ask how the loss of specific habitat fragments affects the overall robustness of the meta-network. To address this question, for an empirical meta-network of plants, herbivores and natural enemies we simulated the removal of habitat fragments in increasing and decreasing order of area, age and connectivity for plant extinction and the secondary extinction of herbivores, natural enemies and their interactions. Meta-network robustness was characterized as the area under the curve of remnant species or interactions at the end of a fragment removal sequence. To pinpoint the effects of fragment area, age and connectivity, respectively, we compared the observed robustness for each removal scenario against that of a random sequence. The meta-network was more robust to the loss of old (i.e. long-fragmented), large, connected fragments than of young (i.e. recently fragmented), small, isolated fragments. Thus, young, small, isolated fragments may be particularly important to the conservation of species and interactions, while contrary to our expectations larger, more connected fragments contribute little to meta-network robustness. Our findings highlight the importance of young, small, isolated fragments as sources of species and interactions unique to the regional level. These effects may largely result from an unpaid extinction debt, whereby younger fragments are likely to lose species over time. Yet, there may also be more long-lasting effects from cultivated lands (e.g. water, fertilizers and restricted cattle grazing) and network complexity in small, isolated fragments. Such fragments may sustain important biological diversity in fragmented landscapes, but maintaining their conservation value may depend on adequate restoration strategies.     

Integrated analysis of ceRNA network and tumor-infiltrating immune cells in esophageal cancer

Background: Esophageal cancer (ESCA) is one of the most commonly diagnosed cancers in the world. Tumor immune microenvironment is closely related to tumor prognosis. The present study aimed at analyzing the competing endogenous RNA (ceRNA) network and tumor-infiltrating immune cells in ESCA.Methods: The expression profiles of mRNAs, lncRNAs, and miRNAs were downloaded from the Cancer Genome Atlas database. A ceRNA network was established based on the differentially expressed RNAs by Cytoscape. CIBERSORT was applied to estimate the proportion of immune cells in ESCA. Prognosis-associated genes and immune cells were applied to establish prognostic models basing on Lasso and multivariate Cox analyses. The survival curves were constructed with Kaplan–Meier method. The predictive efficacy of the prognostic models was evaluated by the receiver operating characteristic (ROC) curves.Results: The differentially expressed mRNAs, lncRNAs, and miRNAs were identified. We constructed the ceRNA network including 23 lncRNAs, 19 miRNAs, and 147 mRNAs. Five key molecules (HMGB3, HOXC8, HSPA1B, KLHL15, and RUNX3) were identified from the ceRNA network and five significant immune cells (plasma cells, T cells follicular helper, monocytes, dendritic cells activated, and neutrophils) were selected via CIBERSORT. The ROC curves based on key genes and significant immune cells all showed good sensitivity (AUC of 3-year survival: 0.739, AUC of 5-year survival: 0.899, AUC of 3-year survival: 0.824, AUC of 5-year survival: 0.876). There was certain correlation between five immune cells and five key molecules.Conclusion: The present study provides an effective bioinformatics basis for exploring the potential biomarkers of ESCA and predicting its prognosis.     

不同身体质量指数人群肠道菌群结构及共存网络解析

[背景] 人体能量稳态失衡表现为体重过轻、超重和肥胖,肠道菌群与人体能量稳态的维持有关,但不同身体质量指数（Body Mass Index,BMI）人群的肠道菌群特征仍需进一步探究。[目的] 基于美国肠道计划公开数据库,解析4类BMI人群肠道菌群的特征,并探究4类BMI人群肠道菌群共存网络特征及差异,为基于肠道菌群来干预肥胖及体重过轻等不健康状态提供新的理论依据。[方法] 从美国肠道计划数据集中筛选具有BMI信息的肠道菌群样本,并根据世界卫生组织规定的BMI划分标准将筛选后的样本分为4类：体重过轻（BMI<18.5 kg/m²）,正常体重（18.5 kg/m²2）,超重（25 kg/m²2）,肥胖（BMI>30 kg/m²）;通过计算和比较肠道菌群的α多样性和β多样性探究4类BMI人群肠道菌群的整体结构特征及差异;通过多元线性回归模型对不同BMI分类与肠道菌群进行相关性分析,并且将地域、年龄、性别因素作为混杂因素加入到模型中进行校正;采用SparCC分别计算4类BMI人群肠道菌群中菌属相关性,并分别构建肠道菌群共存网络。[结果] 经过Wilcoxon秩和检验,发现体重过轻、超重、肥胖人群的肠道菌群α多样性都显著低于正常体重人群;β多样性分析结果表明4类BMI人群肠道菌群的整体结构存在显著差异;4类BMI人群肠道中厚壁菌门（Firmicutes）和拟杆菌门（Bacteroidetes）的相对含量无显著差异;通过MaAsLin分析,并且将地域、年龄、性别因素作为混杂因素加入到模型中进行校正,共得到49个与BMI类型显著相关的物种;4类BMI人群肠道菌群共存网络的拓扑结构具有一定差异,体重过轻和正常体重人群肠道菌群共存网络的复杂度较高,超重和肥胖人群肠道菌群共存网络的复杂度较低。[结论] 4类BMI人群肠道菌群的多样性、整体结构和共存网络间均存在差异。     

The Bio3D packages for structural bioinformatics

Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ .     

Strategic Habitat Conservation for Beach Mice: Estimating Management Scenario Efficiencies

The Perdido Key beach mouse (Peromyscus polionotus trissyllepsis), Choctawhatchee beach mouse (P. p. allophrys), and St. Andrew beach mouse (P. p. peninsularis) are 3 federally endangered subspecies that inhabit coastal dunes of Alabama and Florida, USA. Conservation opportunities for these subspecies are limited and costly. Consequently, well-targeted efforts are required to achieve their downlisting criteria. To aid the development of targeted management scenarios that are designed to achieve downlisting criteria, we developed a Bayesian network model that uses habitat characteristics to predict the probability of beach mouse presence at a 30-m resolution across a portion of the Florida Panhandle. We then designed alternative management scenarios for a variety of habitat conditions for coastal dunes. Finally, we estimated how much area is needed to achieve the established downlisting criterion (i.e., habitat objective) and the amount of effort needed to achieve the habitat objective (i.e., management efficiency). The results suggest that after 7 years of post-storm recolonization, habitat objectives were met for Perdido Key (within its Florida critical habitat) and Choctawhatchee beach mice. The St. Andrew beach mouse required 5.14 km² of additional critical habitat to be protected and occupied. The St. Andrew beach mouse habitat objective might be achieved by first restoring protected critical habitat to good dune conditions and then protecting or restoring the unprotected critical habitat with the highest predicted probability of beach mouse presence. This scenario provided a 28% increase in management efficiency compared to a scenario that randomly protected or restored undeveloped unprotected critical habitat. In total, when coupled with established downlisting criteria, these quantitative and spatial decision support tools could provide insight into how much habitat is available, how much more is needed, and targeted conservation or restoration efforts that might efficiently achieve habitat objectives. © 2020 The Wildlife Society.     

Socially Defined Subpopulations Reveal Demographic Variation in a Giraffe Metapopulation

Populations are typically defined as spatially contiguous sets of individuals, but large populations of social species can be composed of discrete social communities that often overlap in space. Masai giraffes (Giraffa camelopardalis tippelskirchi) of Tanzania live in distinct social subpopulations that overlap spatially, enabling us to simultaneously explore environmental and social factors correlated with demographic variation in a metapopulation of >1,400 adult females and calves. We considered statistically distinct communities in the social network as subpopulations and tested for variation among the 10 subpopulations in adult female survival, calf survival, and reproductive rate (calf-to-adult female ratio). We then related variation in demographic rates among subpopulations to differences in vegetation, soil type, proximity to 2 types of human settlements, local giraffe population density, and social metrics of relationship strength and exclusivity among adult females. We did not find any among-subpopulation effects on adult female survival, suggesting adult female survival is buffered against environmental heterogeneity among subpopulations. Variation in calf demographic rates among subpopulations were correlated with vegetation, soils, anthropogenic factors, and giraffe population density but not with adult female relationship metrics, despite substantial spatial overlap. Subpopulations with more dense bushlands in their ranges had lower calf survival probabilities, and those closer to human settlements had higher reproductive rates, possibly because of spatial gradients in natural predation. Reproductive rates were higher in subpopulations with more volcanic soils, and calf survival probabilities were greater in subpopulations with higher local adult female densities, possibly related to higher-quality habitat associated with fertile soils or lower predation risk, or to greater competitive ability. The variation in fitness among subpopulations suggests that giraffes do not move unhindered among resource patches to equalize reproductive success, as expected according to an ideal free distribution. The differences in calf survival and reproductive rates could rather indicate intercommunity differences in competitive ability, perception, learning, or experience. Our approach of comparing demography among spatially overlapping yet distinct socially defined subpopulations provides a biologically meaningful way to quantify environmental and social factors influencing fine-scale demographic variation for social species. © 2021 The Wildlife Society.