Combining animal movements and behavioural data to detect behavioural states

Animal movement paths show variation in space caused by qualitative shifts in behaviours. I present a method that (1) uses both movement path data and ancillary sensor data to detect natural breakpoints in animal behaviour and (2) groups these segments into different behavioural states. The method can also combine analyses of different path segments or paths from different individuals. It does not assume any underlying movement mechanism. I give an example with simulated data. I also show the effects of random variation, # of states and # of segments on this method. I present a case study of a fisher movement path spanning 8 days, which shows four distinct behavioural states divided into 28 path segments when only turning angles and speed were considered. When accelerometer data were added, the analysis shows seven distinct behavioural states divided into 41 path segments.     

High‐severity fire corroborated in historical dry forests of the western United States: response to Fulé et al.

Accurate assessment of changing fire regimes is important, since climatic change and people may be promoting more wildfires. Government wildland fire policies and restoration programmes in dry western US forests are based on the hypothesis that high‐severity fire was rare in historical fire regimes, modern fire severity is unnaturally high and restoration efforts should focus primarily on thinning forests to eliminate high‐severity fire. Using General Land Office (GLO) survey data over large dry‐forest landscapes, we showed that the proportion of historical forest affected by high‐severity fire was not insignificant, fire severity has not increased as a proportion of total fire area and large areas of dense forest were present historically (Williams & Baker, Global Ecology and Biogeography, 21 , 1042–1052, 2012; W&B). In response, Fulé et al. (Global Ecology and Biogeography, 2013, doi: 10.1111/geb.12136; FE) suggest that our inferences are unsupported and land management based on our research could be damaging to native ecosystems. Here, we show that the concerns of FE are unfounded. Their criticism comes from misquoting W&B, mistaking W&B's methods, misusing evidence (e.g. from Aldo Leopold) and missing substantial available evidence. We also update corroboration for the extensive historical high‐severity fire shown by W&B. We suggest that restoration programmes are misdirected in seeking to reduce all high‐severity fire in dry forests, given findings from spatially extensive GLO data and other sources.     

随机森林算法基本思想及其在生态学中的应用——以云南松分布模拟为例

通常来讲,生态学者对于解释生态关系、描述格局和过程、进行空间或时间预测比较感兴趣。这些工作可以通过模拟输出值(响应)与一些特征值(即解释变量)的关系来实现。然而,生态数据模拟遇到了挑战,这是因为响应变量和预测变量可能是连续变量或离散变量。需要解释的生态关系通常是非线性的,并且解释变量之间具有复杂的相互作用关系。响应变量和解释变量存在缺失值并不是不常有的现象,奇异值也经常出现在生态数据中。此外,生态学者通常希望生态模型即要易于建立又易要于解释。通常是利用多种统计方法来分析处理各种各样情景中出现的独特的生态问题,这些模型包括(多元)逻辑回归、线性模型、生存模型、方差分析等等。随机森林是一个可以处理所有这些问题的有效方法。随机森林可以用来做分类、聚类、回归和生存分析、评估变量的重要性、检测数据中的奇异值、对缺失数据进行插补等。鉴于随机森林本身在算法上的优势,将就随机森林在生态学中的应用进行总结,对建模过程进行概述,并以云南松分布模拟研究为例,对其主要功能特点进行案例展示。通过对随机森林的一般术语、概念和建模思想进行介绍,有利于读者掌握本方法的应用本质,可以预见随机森林在生态学研究中将得到更多的应用和发展。     

天宝岩自然保护区长苞铁杉混交林粗木质残体蓄水能力研究

选择天宝岩国家级自然保护区内4种不同长苞铁杉混交林(A~D)粗木质残体(CWD)为研究对象,采用自然风干法与室内浸泡法对不同类型(倒木、枯立木、树桩)和不同腐烂程度(Ⅰ~Ⅴ级,腐烂由轻到重)CWD的蓄水能力进行测定分析和对比研究。结果显示:(1)CWD有效拦蓄量在不同长苞铁杉混交林下表现为:长苞铁杉+石栎+马尾松混交林(B,14.21t/hm2)长苞铁杉+甜槠+青冈混交林(C,7.78t/hm2)长苞铁杉+青冈+深山含笑混交林(D,6.99t/hm2)长苞铁杉+猴头杜鹃混交林(A,4.74t/hm2),而在各CWD类型下表现为:倒木(19.579t/hm2)枯立木(8.494t/hm2)树桩(5.661t/hm2)。(2)各长苞铁杉混交林CWD的蓄水量和蓄水速率在蓄水过程中都表现为BDCA,而在脱水过程中都表现为BCAD。(3)不同腐烂等级的CWD按其蓄水量、蓄水速率和脱水速率大小排列皆为:Ⅱ级Ⅵ级Ⅲ级Ⅴ级Ⅰ级。研究表明:CWD蓄水量的大小差异与群落类型、腐烂等级、CWD本身持水性等因素有关,其蓄水和脱水的速率与其持水量、蓄积量以及腐烂等级之间也存在密切的联系;CWD的自然持水率随腐烂等级增加呈增加趋势,而且腐烂等级越高CWD蓄水速率变化也越明显,CWD腐烂等级对其蓄水能力影响较大;倒木具有较好的持水能力,并在蓄积量上远大于树桩和枯立木,对降雨有较强的实际拦截能力。     

Reconciling estimates of the contemporary North American carbon balance among terrestrial biosphere models,atmospheric inversions,and a new approach for estimating net ecosystem exchange from inventory‐based data

We develop an approach for estimating net ecosystem exchange (NEE) using inventory‐based information over North America (NA) for a recent 7‐year period (ca. 2000–2006). The approach notably retains information on the spatial distribution of NEE, or the vertical exchange between land and atmosphere of all non‐fossil fuel sources and sinks of CO₂, while accounting for lateral transfers of forest and crop products as well as their eventual emissions. The total NEE estimate of a ?327 ± 252 TgC yr^?1 sink for NA was driven primarily by CO₂ uptake in the Forest Lands sector (?248 TgC yr^?1), largely in the Northwest and Southeast regions of the US, and in the Crop Lands sector (?297 TgC yr^?1), predominantly in the Midwest US states. These sinks are counteracted by the carbon source estimated for the Other Lands sector (+218 TgC yr^?1), where much of the forest and crop products are assumed to be returned to the atmosphere (through livestock and human consumption). The ecosystems of Mexico are estimated to be a small net source (+18 TgC yr^?1) due to land use change between 1993 and 2002. We compare these inventory‐based estimates with results from a suite of terrestrial biosphere and atmospheric inversion models, where the mean continental‐scale NEE estimate for each ensemble is ?511 TgC yr^?1 and ?931 TgC yr^?1, respectively. In the modeling approaches, all sectors, including Other Lands, were generally estimated to be a carbon sink, driven in part by assumed CO₂ fertilization and/or lack of consideration of carbon sources from disturbances and product emissions. Additional fluxes not measured by the inventories, although highly uncertain, could add an additional ?239 TgC yr^?1 to the inventory‐based NA sink estimate, thus suggesting some convergence with the modeling approaches.     

The function and structural influence of selective relaxed constraint at functional intracellular loop3 of 5-HT1A serotonin-1 receptor family

Serotonin (5-HT) and its receptors have been involved in critical signal transduction mechanism and deregulation implicated in mood-related disorders. 5-HT activities are mediated through a family of transmembrane spanning serotonin receptors. Both within the family and species, 5-HT receptor protein sequence diversity and 7-transmembrane structural homogeneity have long been intriguing. In this study, we have analyzed the codon site constraint in 5-HT1 subclass receptors from 13 orthologous mammalian mRNA coding sequence. Further, the study was extended to computationally investigate the impact of non-synonymous sites with respect to function and structural significance through sequence homology algorithm and molecular dynamics simulation (MDS). Codon sites with significant posterior probability were observed in 5-HT_1A, 5‐HT_1B and 5-HT_1D receptor indicating variations in site constraint within the 5‐HT1 sub-class genes. In 5-HT_1A receptor, seven sites were detected at the functional intracellular loop₃ (ICL₃) with higher substitution rate through Codeml program. Sequence homology algorithm identifies that these sites were functionally tolerant within the mammals representing a selectively relaxed constraint at this domain. On the other hand, the root mean square deviation (rmsd) values from MDS suggest differences in structural conformation of ICL₃ models among the species. Specifically, the human ICL₃ model fluctuation was comparatively more stable than other species. Hence, we argue that these sites may have varying influence in G-proteins coupling and activation of effectors systems through downstream interacting accessory proteins of cell among the species. However, further experimental studies are required to elucidate the precise role and the seeming difference of these sites in 5-HT receptors between species.     

Bryophyte Species Diversity in Secondary Forests Dominated by the Introduced Species Spathodea campanulata Beauv. in Puerto Rico

The introduced tree species Spathodea campanulata (Bignoniaceae) forms novel forests in Puerto Rico, these having emerged after the abandonment of fields in the mid‐20th century and resulting in forests with a new species composition. We assessed bryophyte species richness in these novel forests and sought correlations with geological substrate, past land use, forest edge and patch area, forest structure, elevation, microhabitat diversity, tree species richness, and microclimatic conditions. Transects were established (edge and forest interior) in nine moist forest patches dominated by Spathodea in north‐central Puerto Rico. These Spathodea forest patches ranged from 0.6 to 9 ha. ANOVA, Chi‐square, correlation, and cluster analyses were used in data analyses. We found 57 bryophyte species. There was a significant difference in bryophyte richness among patches. Those on karst exhibited highest bryophyte richness due to microhabitat diversity, past land use, and shorter hydroperiods. Alluvial sites scored lowest in bryophyte species richness, and forest structure was important for bryophyte communities on these sites. Significant differences in temperature, relative humidity, and light intensity were observed between edge and forest interior. These appeared important for establishing bryophyte species cover but not richness and composition. Microhabitat diversity, patch area, and forest age were more related to bryophyte species richness than elevation, exposed edge, and tree species richness, regardless of geologic substrate. Collectively, Spathodea patches were similar to mature forests on the Island with respect to bryophyte species richness and composition. Novel Spathodea forests have conservation value due to their habitat suitability for bryophyte communities.