Epigenetics for ecologists

There is now mounting evidence that heritable variation in ecologically relevant traits can be generated through a suite of epigenetic mechanisms, even in the absence of genetic variation. Moreover, recent studies indicate that epigenetic variation in natural populations can be independent from genetic variation, and that in some cases environmentally induced epigenetic changes may be inherited by future generations. These novel findings are potentially highly relevant to ecologists because they could significantly improve our understanding of the mechanisms underlying natural phenotypic variation and the responses of organisms to environmental change. To understand the full significance of epigenetic processes, however, it is imperative to study them in an ecological context. Ecologists should therefore start using a combination of experimental approaches borrowed from ecological genetics, novel techniques to analyse and manipulate epigenetic variation, and genomic tools, to investigate the extent and structure of epigenetic variation within and among natural populations, as well as the interrelations between epigenetic variation, phenotypic variation and ecological interactions.     

Lightning-caused disturbance in the Peruvian Amazon

We surveyed seven lightning strike sites in the northern Peruvian Amazon. An average of 17.3 trees were damaged per strike; large trees (> 60 cm diameter) were disproportionately affected. The results contribute to a growing body of evidence that lightning is an important agent of disturbance pantropically. Abstract in Spanish is available with online material.     

Parasitoids as model organisms for ecologists

This paper introduces the special issue of this journal, which is devoted to parasitoid ecology. We provide a brief review of the role that parasitoids have played in research in population, community, and behavioral ecology and speculate on their future importance to the subject. Received: January 11, 1999 / Accepted: January 19, 1999     

Demystifying computer science for molecular ecologists

In this age of data‐driven science and high‐throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long‐standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373–389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context‐specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade‐offs that are not obvious to the uninitiated.     

Useful surrogates of soil texture for plant ecologists from airborne gamma‐ray detection

Plant ecologists require spatial information on functional soil properties but are often faced with soil classifications that are not directly interpretable or useful for statistical models. Sand and clay content are important soil properties because they indicate soil water‐holding capacity and nutrient content, yet these data are not available for much of the landscape. Remotely sensed soil radiometric data offer promise for developing statistical models of functional soil properties applicable over large areas. Here, we build models linking radiometric data for an area of 40,000 km² with soil physicochemical data collected over a period of 30 years and demonstrate a strong relationship between gamma radiometric potassium (⁴⁰K), thorium (²³²Th), and soil sand and clay content. Our models showed predictive performance of 43% with internal cross‐validation (to held‐out data) and ~30% for external validation to an independent test dataset. This work contributes to broader availability and uptake of remote sensing products for explaining patterns in plant distribution and performance across landscapes.     

基于随机森林的不同径级树木死亡影响因子研究

树木死亡是多种因素共同作用的结果,然而不同径级的林木,导致其死亡的原因是否相同尚不明确。以坝上地区小叶杨为对象,于2016-2017年调查了100块20m×20m样地。以林木胸径、林木相对断面积、林龄、林分密度、不同土层土壤含水量和土壤容重等11个因子为输入变量,运用随机森林算法分别不同径级建立树木死亡模型,分析各因子对不同径级树木死亡的影响大小,并得到关键影响因子的阈值。结果表明：依据不同径级树木死亡与影响因子的相关性不同,可将林木径级划分为 < 10cm、10-25cm、 > 25cm;胸径 < 10cm时,林木相对断面积对树木死亡的影响最大,当0.23 < 林木相对断面积 < 0.43时,树木死亡率最低;胸径为10-25cm时,密度对树木死亡的影响最大,当密度 > 600株/hm²时,树木死亡率随着密度的增加明显上升;胸径 > 25cm时,20-60cm土壤水分和林分断面积对树木死亡的影响最大且相近,当20-60cm土壤质量含水量 > 5%时,树木死亡率明显下降;基于随机森林算法建立的树木死亡模型可以解释树木死亡70%-90%的变异,具有一定的预测优势和应用价值,可为坝上地区树木死亡预测和防护林的经营管护提供参考。     

What plant ecologists can learn from zoology

Biology, like all sciences, is increasingly compartmentalized. This helps us to interact more easily with fellow specialists, but also tends to shield us from useful cross-fertilization with other fields. For example, plant and animal ecologists have established largely distinct research traditions over the years. Botanists studying population ecology, interspecific competition, and ecological and evolutionary aspects of sexual reproduction can benefit by importing more of the conceptual advances occurring in zoology (and vice versa). Botanists working on plant-animal interactions have a similar opportunity to shed light on their questions by learning more about the animals. For example, botanists studying pollination may be unaware of some modern advances in animal physiology and behaviour which undermine a typological view of pollination systems. Similarly, botanists studying loss of seeds to granivores may be unaware of details of animal behaviour that can cause granivores to benefit the plants in surprising ways. These examples illustrate how improved communication with zoology can enrich plant ecology. To remove barriers to communication we suggest some individual and collective actions that plant ecologists can take.     

A statistical explanation of MaxEnt for ecologists

MaxEnt is a program for modelling species distributions from presence‐only species records. This paper is written for ecologists and describes the MaxEnt model from a statistical perspective, making explicit links between the structure of the model, decisions required in producing a modelled distribution, and knowledge about the species and the data that might affect those decisions. To begin we discuss the characteristics of presence‐only data, highlighting implications for modelling distributions. We particularly focus on the problems of sample bias and lack of information on species prevalence. The keystone of the paper is a new statistical explanation of MaxEnt which shows that the model minimizes the relative entropy between two probability densities (one estimated from the presence data and one, from the landscape) defined in covariate space. For many users, this viewpoint is likely to be a more accessible way to understand the model than previous ones that rely on machine learning concepts. We then step through a detailed explanation of MaxEnt describing key components (e.g. covariates and features, and definition of the landscape extent), the mechanics of model fitting (e.g. feature selection, constraints and regularization) and outputs. Using case studies for a Banksia species native to south‐west Australia and a riverine fish, we fit models and interpret them, exploring why certain choices affect the result and what this means. The fish example illustrates use of the model with vector data for linear river segments rather than raster (gridded) data. Appropriate treatments for survey bias, unprojected data, locally restricted species, and predicting to environments outside the range of the training data are demonstrated, and new capabilities discussed. Online appendices include additional details of the model and the mathematical links between previous explanations and this one, example code and data, and further information on the case studies.     

Effects of Tree Guards and Weed Mats on the Establishment of Native Tree Seedlings: Implications for Forest Restoration in Hong Kong, China

The effects of tree guards and weed mats on establishment and growth of native tree seedlings, Thick‐leaved oak (Cyclobalanopsis edithiae (Skan) Schott., Fagaceae), planted in an exposed hillside grassland in Hong Kong, were investigated. The natural regeneration of C. edithiae is poor due to a lack of seed dispersal agents and high seed predation, and therefore, this species is often targeted for forest restoration. The experiment lasted for 3.5 years during which the height, basal diameter, and crown diameter of individual seedlings were measured and survivorship recorded. The use of weed mats alone did not have a significant effect, but a combination of tree guards and weed mats led to a significant improvement in establishment, survivorship, and growth of the seedlings during the experimental period. Initially, the guards promoted rapid height growth of the seedlings, although lateral growth and secondary stem thickening were compromised. After the seedlings grew over the tree guards, the basal diameter and crown diameter increased at a notably faster rate. The combined effect of the tree guard and weed mat on the seedling growth pattern was found to be beneficial and contributed to the high survivorship of the seedlings. Comparing the survivorship data and the costs of various treatments, the use of tree guards in combination with the weed mats was demonstrated to be more cost‐effective than planting the seedlings without tree guards or weed mats. The potential for applying the technique in afforestation programs with native tree species for forest restoration in Hong Kong and other tropical regions is discussed.     

西双版纳热带季节雨林的树种组成和群落结构动态

研究了西双版纳热带季节雨林1 hm2(hectare)动态监测样地1993年与2007年之间树种组成和群落结构的变化。对样地中胸径≥5 cm的乔木进行了每木调查。目前其树种组成的热带分布科、属所占比例分别为91%和94%,具有较高比例的热带植物区系性质。在1993年与2007年两次调查之间,树种数量由145种增至179种,仅有1到2个个体的稀有树种所占比例从54%降为51.1%。从森林的垂直结构来看,A、B、C三层的个体死亡率分别为12.8%、12.9%和19.0%,各层树木的增长率分别为-8.5%、-1.4%和44.8%。与此相对应,C层小径级的树木所占比例有较大提高。虽然小径级的树木在种类和数量上比例增大,但个体数量和种类组成相对稳定的A、B层优势树种变化不大,维持了群落结构的稳定性。14 a间,群落中新增加的具有先锋性质的树种不超过5个。1993年时,A、B两层尚有先锋树种存在,2007年已经从A、B两层中退出。因此,从14 a间树种组成和群落结构的变化来看,虽然具有树木的死亡和增补,但其物种成分和群落结构的总体格局没有明显的变化,处于动态平衡过程中。     

Automatic extraction and measurement of individual trees from mobile laser scanning point clouds of forests

Background and AimsIn addition to terrestrial laser scanning (TLS), mobile laser scanning (MLS) is increasingly arousing interest as a technique which provides valuable 3-D data for various applications in forest research. Using mobile platforms, the 3-D recording of large forest areas is carried out within a short space of time. Vegetation structure is described by millions of 3-D points which show an accuracy in the millimetre range and offer a powerful basis for automated vegetation modelling. The successful extraction of single trees from the point cloud is essential for further evaluations and modelling at the individual-tree level, such as volume determination, quantitative structure modelling or local neighbourhood analyses. However, high-precision automated tree segmentation is challenging, and has so far mostly been performed using elaborate interactive segmentation methods.MethodsHere, we present a novel segmentation algorithm to automatically segment trees in MLS point clouds, applying distance adaptivity as a function of trajectory. In addition, tree parameters are determined simultaneously. In our validation study, we used a total of 825 trees from ten sample plots to compare the data of trees segmented from MLS data with manual inventory parameters and parameters derived from semi-automatic TLS segmentation.Key ResultsThe tree detection rate reached 96 % on average for trees with distances up to 45 m from the trajectory. Trees were almost completely segmented up to a distance of about 30 m from the MLS trajectory. The accuracy of tree parameters was similar for MLS-segmented and TLS-segmented trees.ConclusionsBesides plot characteristics, the detection rate of trees in MLS data strongly depends on the distance to the travelled track. The algorithm presented here facilitates the acquisition of important tree parameters from MLS data, as an area-wide automated derivation can be accomplished in a very short time.     

Quick start guide to soil methods for ecologists

Increasingly biologists and ecologists are becoming aware of the vital importance of soil to processes observed aboveground and are incorporating soil analyses into their research. Because of the dynamic and heterogeneous nature of soil, proper incorporation of soil analysis into ecological studies requires knowledge and planning. Unfortunately, many ecologists may not be current (or trained at all) in soil science. We provide this review, based on our cumulative >60 years of work in soil science, to help familiarize researchers with essential information to appropriately incorporate soil analyses into ecological studies. Specifically, we provide a brief introduction into soils and then discuss issues related to soil sterilization, choosing a soil for a greenhouse project, sampling soils, and soil analyses.     

Tropical rain forest conservation and the twin challenges of diversity and rarity

Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world.     

不同林分类型林缘华北落叶松细胞特征

以塞罕坝机械林场华北落叶松纯林及华北落叶松-白桦混交林为对象,研究林地边缘华北落叶松边界木与林内木径向生长、年轮细胞大小及数量的差异,分析林缘对不同林分类型华北落叶松径向生长及细胞特征的影响。结果表明: 纯林中边界木的径向生长显著快于林内木,年轮总宽、早材和晚材总生长量在边界木较林内木分别增加48.9%、58.9%和29.6%,而混交林边界木与林内木的径向生长差距并不明显。纯林边界木早材细胞总数、早材大细胞和小细胞数量较林内木分别增加63.3%、55.6%和70.0%,晚材细胞总数、晚材大细胞和小细胞数量边界木较林内木分别增加35.4%、37.5%和28.5%,而早晚材细胞大小在边界木与林内木间无显著差异。混交林边界木早晚材细胞数量与林内木无显著差异,但边界木早材细胞大小较林内木增大50.0%,边界木早材最大细胞、最小细胞、大细胞及小细胞的大小较林内木分别增大28.6%、33.3%、16.6%和25.0%。通过混交的方式营造混交林可以有效地缓解林缘导致的纯林中边界木生长过快而林内木生长较慢的现象。