Prediction of bird community composition based on point-occurrence data and inferential algorithms: a valuable tool in biodiversity assessments

Local biological communities are made up of species, each of which has its own particular relationship with the environment. To the extent that these autecological niches limit species’ distributions, and by extension community composition, models of species’ ecological niches can predict species composition at particular sites, or at least provide a null hypothesis of potential species composition in the absence of effects of species interactions. We developed distributional predictions (ecological niche models) for 89 species occurring in dry tropical forest in the Balsas Basin of south‐western Mexico using an interpolation technique, and predicted the species likely to occur at 8 sites across the region. Onsite field inventory data were then used to test the community predictions, all of which were statistically significant. These results suggest that inventory efforts can be made more efficient by development beforehand of hypotheses that focus onsite collecting and inventory.     

Effect of habitat degradation on competition,carrying capacity,and species assemblage stability

Changes in species’ trophic niches due to habitat degradation can affect intra‐ and interspecific competition, with implications for biodiversity persistence. Difficulties of measuring species’ interactions in the field limit our comprehension of competition outcomes along disturbance gradients. Thus, information on how habitat degradation can destabilize food webs is scarce, hindering predictions regarding responses of multispecies systems to environmental changes. Seagrass ecosystems are undergoing degradation. We address effects of Posidonia oceanica coverage reduction on the trophic organization of a macroinvertebrate community in the Tyrrhenian Sea (Italy), hypothesizing increased trophic generalism, niche overlap among species and thus competition and decreased community stability due to degraded conditions. Census data, isotopic analysis, and Bayesian mixing models were used to quantify the trophic niches of three abundant invertebrate species, and intra‐ and interspecific isotopic and resource‐use similarity across locations differing in seagrass coverage. This allowed the computation of (1) competition strength, with respect to each other and remaining less abundant species and (2) habitat carrying capacity. To explore effects of the spatial scale on the interactions, we considered both individual locations and the entire study area (“‘meadow scale”). We observed that community stability and habitat carrying capacity decreased as P. oceanica coverage declined, whereas niche width, similarity of resource use and interspecific competition strength between species increased. Competition was stronger, and stability lower, at the meadow scale than at the location scale. Indirect effects of competition and the spatial compartmentalization of species interactions increased stability. Results emphasized the importance of trophic niche modifications for understanding effects of habitat loss on biodiversity persistence. Calculation of competition coefficients based on isotopic distances is a promising tool for describing competitive interactions in real communities, potentially extendible to any subset of ecological niche axes for which specimens’ positions and pairwise distances can be obtained.     

The role of phenotypic plasticity in shaping ecological networks

Plasticity-mediated changes in interaction dynamics and structure may scale up and affect the ecological network in which the plastic species are embedded. Despite their potential relevance for understanding the effects of plasticity on ecological communities, these effects have seldom been analysed. We argue here that, by boosting the magnitude of intra-individual phenotypic variation, plasticity may have three possible direct effects on the interactions that the plastic species maintains with other species in the community: may expand the interaction niche, may cause a shift from one interaction niche to another or may even cause the colonization of a new niche. The combined action of these three factors can scale to the community level and eventually expresses itself as a modification in the topology and functionality of the entire ecological network. We propose that this causal pathway can be more widespread than previously thought and may explain how interaction niches evolve quickly in response to rapid changes in environmental conditions. The implication of this idea is not solely eco-evolutionary but may also help to understand how ecological interactions rewire and evolve in response to global change.     

Trait‐based life strategies,ecological niches,and niche overlap in the nekton of the data‐poor Mediterranean Sea

Biological traits can determine species ecological niches and define species responses to environmental variation. Species have a specific functional position in the biological community, resulting in interactions like interspecific competition. In this study, we used biological traits in order to define the life strategies of 205 nektonic species of the Mediterranean Sea. Furthermore, traits related to resource use were analyzed to determine the level of trait and niche overlap and their relationship to life strategies. Focusing on habitats of importance (Posidonia beds, coralligène formations, and lagoons), we investigated strategies and niches of the species present there. Finally, we examined the life strategy of Lessepsian species and investigated the niche overlap between them and indigenous species. Archetypal analysis indicated the existence of three life histories corresponding to strategies already documented for fish (equilibrium, periodic, and opportunistic), with some species also placed in intermediate positions. Niche overlap was evaluated by multiple correspondence analysis and the generation of a single distance metric between all species pairs. This identified species occupying relatively empty (underexploited) ecological niches, like the Lessepsian species Siganus luridus and S. rivulatus, a finding that can also be associated with their establishment in the Mediterranean. Most Lessepsian species were associated with the opportunistic life history strategy, again an important aspect related to their establishment. Also, we documented that most species occurring in important habitats have a relatively high overlap of niches. No significant differences were found in the life strategies across Mediterranean habitats; however, variation in niche overlap and traits related to habitat use was detected. The findings can be useful to determine theoretical competition between species and to identify empty ecological niches. Fisheries science can also benefit from comprehending the dynamics of competing stocks or predict the responses of data‐poor stocks to anthropogenic stressors from known examples of species with shared life strategies.     

Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution

Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of "niche conservatism" within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.     

Niche partitioning in orbweaving spiders Meta menardi and Metellina merianae (Tetragnathidae)

Hypogean habitats are relatively simple exhibiting low diversity, low production and relative constancy of environmental factors, and are therefore appropriate for studying species coexistence in situ. We investigated the coexistence of two closely related, similarly sized orb-weaving spider species, Meta menardi and Metellina merianae, living syntopically in a Slovenian cave. We studied the annual dynamics of both species within a mixed population, and the impact of the ambient temperature, relative humidity, airflow and illumination, and compared their trophic niches to legacy data on prey of both species from 55 caves in Slovenia. We predicted a large overlap in their spatial niches and substantial differences in their temporal and trophic niches. We found that their spatial niches overlap greatly with few exceptions, mostly on the dates of notable meteorological changes in the cave but that their temporal niches differ significantly with r-strategy resembling epigean annual dynamic in M. merianae and a steady low abundance course in M. menardi within the cave. We also found that different predatory strategies significantly segregate their trophic niches: M. merianae uses a typical orb-weaving hunting strategy, while M. menardi combines web hunting with off-web hunting. Our findings suggest that both the diverse dynamics and trophic niches enable the coexistence of M. menardi and M. merianae despite their similar spatial niches, and that M. menardi, in particular, is optimally adapted to the epigean/hypogean ecotone.     

Complex relationships between species niches and environmental heterogeneity affect species co-occurrence patterns in modelled and real communities

Species co-occurrence analysis is commonly used to assess how interspecific interactions dictate community assembly. Non-random co-occurrences, however, may also emerge from niche differences as well as environmental heterogeneity. The relationships between species co-occurrence patterns, environmental heterogeneity and species niches are not fully understood, due to complex interactions among them. To analyse the relationships among these patterns and processes, I developed synthetic community models and analysed a large dataset of tree species across the conterminous United States. Niche overlap and environmental heterogeneity had significant and contrasting effects on species co-occurrence patterns, in both modelled and real communities. Niche breadth, in turn, affected the effect sizes of both variables on species co-occurrence patterns. The effect of niche breadth on the relationship between co-occurrence and niche overlap was markedly consistent between modelled and real communities, while its effect on the relationship between co-occurrence and environmental heterogeneity was mostly consistent between real and modelled data. The results of this analysis highlight the complex and interactive effects of species niche overlap, niche breadth and environmental heterogeneity on species co-occurrence patterns. Therefore, inferring ecological processes from co-occurrence patterns without accounting for these fundamental characteristics of species and environments may lead to biased conclusions.     

Resource partitioning and interspecific interactions among sympatric rain forest arboreal mammals of the Western Ghats, India

Resource partitioning in a community of diurnal arboreal mammalsconsisting of the lion-tailed macaque Macaca silenus, bonnetmacaque (BM) Macaca radiata, Nilgiri langur Semnopithecus johnii,and the Indian giant squirrel Ratufa indica of the Western Ghats,southern India, was studied. Differences in their diet, verticalstratification, food resource niche breadth, niche overlap,and behavioral interactions were examined. Resource partitioningwas through differential habitat use, resource use, and verticalstratification. Of the four species, the BM was not a residentspecies and made frequent forays into evergreen forest fromthe adjacent deciduous forest during the flowering season ofCullenia exarillata and fruiting season of Ficus microcarpa.The macaques had narrower niches, and the langur and the squirrelhad wider niches. Niche overlap was highest between the twomacaques. Overlap among the study species was particularly pronouncedduring the flowering of C. exarillata. There was significantcorrelation between niche overlap and intolerance among thestudy species. Certain species pairs showed little or no mutualintolerance despite high overlap. Cooperative interactions suchas alarm calls occurred more frequently among the resident species.Interaction matrices revealed an underlying pattern of interspecificdominance hierarchy, with the BM dominating over the other threespecies. Our study suggests that the BM do not coexist withthe other three because of high overlap with its congener andlow occurrence of cooperative interactions.     

Measuring ecological niche overlap from occurrence and spatial environmental data

Aim Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data. Location Europe, North America and South America. Methods The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with pre‐defined distributions and amounts of niche overlap to evaluate several ordination and species distribution modelling techniques for quantifying niche overlap. We illustrate the approach with data on two well‐studied invasive species. Results We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographical space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results. Main conclusions The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate for studying niche differences between species, subspecies or intra‐specific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intra‐specific lineage has changed over time.     

里海西北部Caspian地区草原扩大与啮齿类群落结构的变化

于1997-1999年检测了俄联邦卡尔梅克(Kalmyki)共和国ChernieZemly半干旱草原由10个物种组成的啮齿类群落。该区域的植被特点是家畜大量减少后形成的恢复植被。我们的任务之一就是了解不同啮齿动物的生境需求,以预测不同物种对环境变化的特异性反应。我们也检测了群落空间结构、生态位参数和物种多样性。逐步回归分析表明,各种啮齿动物的空间分布仅部分地决定于已知环境因子(2-6个变量)。虽然方程式具有强显著性,但决定系数R2很低,不超过18%。对于大多数种类,这种结果可由最近草原扩大而来的生境异质性降低解释。物种生境选择条件和资源的明显低水平可能是由物种对环境变化的惯性反应造成的。判别函数分析和主分量分析结果表明,群落结构以及单个物种的生态位参数在不同年间并不稳定。空间分层结构在种间中等和低重叠的高物种多样性年度表现明显。多样性、生态位组成和生态位宽度分析结果表明,不同物种对环境条件和资源变化的反应具有不同的个性化方式。同时,物种对环境动态的明显个性化反应成为物种多样性定向变化的原因。限定空间和相对单一条件下的结果表明,啮齿类α多样性与生境结构复杂性呈正相关,而与生境生产力特征呈负相关。观察表明,卡尔梅克国草原扩大伴随着初级生产力的升高和生境异质性的降低。随着时间的推移会导致大多数草原和半干旱区域啮齿类多样性的降低,并形成动物区系核心.     

Contrasting climate niches among co‐occurring subdominant forbs of the sagebrush steppe

Aim

Abiotic conditions are key components that determine the distribution of species. However, co‐occurring species can respond differently to the same factors, and determining which climate components are most predictive of geographic distributions is important for understanding community response to climate change. Here, we estimate and compare climate niches of ten subdominant, herbaceous forb species common in sagebrush steppe systems, asking how niches differ among co‐occurring species and whether more closely related species exhibit higher niche overlap.

Location

Western United States.

Methods

We used herbarium records and ecological niche modelling to estimate area of occupancy, niche breadth and overlap, and describe characteristics of suitable climate. We compared mean values and variability in summer precipitation and minimum temperatures at occurrence locations among species, plant families, and growth forms, and related estimated phylogenetic distances to niche overlap.

Results

Species varied in the size and spatial distribution of suitable climate and in niche breadth. Species also differed in the variables contributing to their suitable climate and in mean values, spatial variation and interannual variation in highly predictive climate variables. Only two of ten species shared comparable climate niches. We found family‐level differences associated with variation in summer precipitation and minimum temperatures, as well as in mean minimum temperatures. Growth forms differed in their association with variability in summer precipitation and minimum temperatures. We found no relationship between phylogenetic distance and niche overlap among our species.

Main conclusions

We identified contrasting climate niches for ten Great Basin understorey forbs, including differences in both mean values and climate variability. These estimates can guide species selection for restoration by identifying species with a high tolerance for climate variability and large climatic niches. They can also help conservationists to understand which species may be least tolerant of climate variability, and potentially most vulnerable to climate change.

     

Seasonal climatic niches diverge in migratory birds

Migratory birds occupy different geographical areas during breeding and non-breeding periods, and thus different factors may determine their range limits depending on each season. One such factor is the spatial climatic component of the niche, which is widely used to model species distributions, yet the temporal component is often neglected and is generally assumed to be constant. We tested the hypothesis that the climatic niche is conserved between breeding and non-breeding areas in 355 bird species migrating through Eurasian–African flyways. For this, we performed niche overlap analyses and compared niche differences between sister or phylogenetically closely related species, as well as linking the differences to migratory distances. For more than 80% of the species, there was no or very little overlap between their breeding and non-breeding climatic niches. For most closely related species, the degree of overlap of their breeding climatic niches was larger than the overlap observed within each species, but not for their wintering climatic niches, suggesting a phylogenetic conservation of breeding climatic niches. Finally, there was a clear negative relationship between migratory distances and climatic niche overlap within each species. Our results confirmed that the climatic niche of most Eurasian–African migratory species differs between both breeding and non-breeding ranges, suggesting distinctive seasonal climatic requirements. Given these results and the geographically uneven effects of climate change, the impact of global change is likely to have different effects in each seasonal range. Hence, both breeding and non-breeding climatic data need to be considered when using species distribution models.     

Ecological distribution and niche segregation of sibling species: the case of bean beetles, Acanthoscelides obtectus Say and A. obvelatus Bridwell

Abstract.  1. Molecular techniques have greatly added to the number of known sympatric cryptic species in insects. Ecological differences between these newly distinguished species are little explored, but niches often appear to overlap strongly. These cases are good models for exploring new ideas about species coexistence and community structure.
2.  Acanthoscelides obtectus and A. obvelatus are two sister species of bean bruchids, which have been confused until the last decade. One important ecological difference between them has emerged, however: A. obtectus is multivoltine and now distributed worldwide, whereas A. obvelatus is univoltine and restricted to Mesoamerica. Where their ranges overlap, the two species share the same host plants and larvae can sometimes complete development in the same seed.
3. The analysis of 27 622 Mexican individuals of the two species in 2001-2002 and 2002-2003 indicates that their niches overlap, but are differentiated with respect to altitude and the kind of beans (wild vs. domesticated). The principal patterns in their relative abundance in different habitats, and at different seasons, were constant from one year to the next.
4. As sympatry of these species seems to be of recent origin, the observed niche differentiation may not have evolved in response to competition, but could instead be the consequence of physiological differences, evolved independently in each species in allopatry, that pre-adapted them for different altitudes and kinds of resources.
5. The combination of biological and historical factors thus appears to allow these two sibling species to coexist in sympatry, despite their broadly overlapping ecological niches.     

A framework for priority effects

History of species arrival can influence plant community assembly. In this issue of the Journal of Vegetation Science, Sarneel et al. show that the strength of such historical contingency, or priority effects, varies with soil moisture in riparian plants. We discuss this study within a theoretical framework describing how and when priority effects occur via destabilizing and equalizing mechanisms.     

Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae)

Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour.     

Phylogenetic relatedness predicts priority effects in nectar yeast communities

Priority effects, in which the outcome of species interactions depends on the order of their arrival, are a key component of many models of community assembly. Yet, much remains unknown about how priority effects vary in strength among species in a community and what factors explain this variation. We experimented with a model natural community in laboratory microcosms that allowed us to quantify the strength of priority effects for most of the yeast species found in the floral nectar of a hummingbird-pollinated shrub at a biological preserve in northern California. We found that priority effects were widespread, with late-arriving species experiencing strong negative effects from early-arriving species. However, the magnitude of priority effects varied across species pairs. This variation was phylogenetically non-random, with priority effects stronger between closer relatives. Analysis of carbon and amino acid consumption profiles indicated that competition between closer relatives was more intense owing to higher ecological similarity, consistent with Darwin's naturalization hypothesis. These results suggest that phylogenetic relatedness between potential colonists may explain the strength of priority effects and, as a consequence, the degree to which community assembly is historically contingent.     

Timing is everything: does early and late germination favor invasions by herbaceous alien plants?

Aims Plant invasions represent a unique opportunity to study the mechanisms underlying community assembly rules and species distribution patterns. While a superior competitive ability has often been proposed as a major driver of successful plant invasions, its significance depends crucially on the timing of any competitive interaction. We assess whether a mismatch in germination phenology can favor the establishment of alien species, allowing them to exploit vacant niches where competition is low. As well as having important effects on the survival, growth and fitness of a species, asymmetric competition and potential soil legacies resulting from early or late germination can also impact on species recruitment. However, early or late germination comes at a cost, increases the risks of exposure to unfavorable conditions and requires an enhanced abiotic resistance if it is to lead to successful establishment.Important findings While there are several anecdotal accounts of early and late germination for invasive species, there are limited comparative data with resident species growing under natural conditions. Available evidence from grassland communities indicates that a short-term germination advantage or priority (few days/weeks) provides invasive species with a strong competitive advantage over native species and is a critical factor in many invasions. While the exploitation of periods of low competition is a plausible mechanism for the successful establishment of many invasive plants, direct evidence for this strategy is still scarce. This is particularly true with regard to the exploitation of late germination niches. Consequently, long-term comparative monitoring of the germination phenology of invasive and native plants in situ is needed to assess its significance in a range of ecosystems and its impact on community dynamics.     

Trait‐based tests of coexistence mechanisms

Recent functional trait studies have shown that trait differences may favour certain species (environmental filtering) while simultaneously preventing competitive exclusion (niche partitioning). However, phenomenological trait‐dispersion analyses do not identify the mechanisms that generate niche partitioning, preventing trait‐based prediction of future changes in biodiversity. We argue that such predictions require linking functional traits with recognised coexistence mechanisms involving spatial or temporal environmental heterogeneity, resource partitioning and natural enemies. We first demonstrate the limitations of phenomenological approaches using simulations, and then (1) propose trait‐based tests of coexistence, (2) generate hypotheses about which plant functional traits are likely to interact with particular mechanisms and (3) review the literature for evidence for these hypotheses. Theory and data suggest that all four classes of coexistence mechanisms could act on functional trait variation, but some mechanisms will be stronger and more widespread than others. The highest priority for future research is studies of interactions between environmental heterogeneity and trait variation that measure environmental variables at within‐community scales and quantify species' responses to the environment in the absence of competition. Evidence that similar trait‐based coexistence mechanisms operate in many ecosystems would simplify biodiversity forecasting and represent a rare victory for generality over contingency in community ecology.     

五鹿山国家级自然保护区油松群落优势种生态位研究

根据五鹿山国家级自然保护区油松群落57个样地调查资料,通过TWINSPIN聚类分析对该群落类型进行了划分,将划分群丛类型作为资源轴,计算了乔木和灌木树种Shannon-Wiener和Hurbert生态位宽度及Morisita重叠指数。结果表明：油松群落共划分为7个群丛。乔木层油松、辽东栎、茶条槭的生态位宽度（Shannon-Wiener和Hurbert生态位宽度）较大,LB和HB分别是1.656、1.404、1.047和0.948、0.735、0.386。灌木层水栒子、土庄绣线菊、陕西荚蒾的生态位宽度较大,LB和HB分别是1.562、1.401、1.300和0.512、0.447、0.389。乔木层生态位高度重叠的占6%(>0.8),中度重叠的占10%(0.6~0.8),小于0.6的低度重叠的占84%,灌木层高度重叠者占7%(>0.8),中度重叠者占10.39%(0.6~0.8),小于0.6的低度重叠者占82.25%。说明油松群落组成植物对当地环境具有较高的适应性和资源环境利用能力,种间竞争较小,有些物种的生态位明显趋于特化,群落处于共摊阶段。     

猕猴桃园节肢动物群落重建及主要类群的生态位

为研究猕猴桃节肢动物群落重建过程和主要类群生态位移,本试验系统调查野生猕猴桃和人工栽植不同树龄(3年、9年、14年)猕猴桃园节肢动物群落,测定群落特征指标和主要类群的时空生态位。结果表明,群落包含3纲15目74科,约90种。不同桃园节肢动物群落的主要类群不同,各类群占群落总数的比例差异显著,野生猕猴桃园群落中各类群分布较均匀,栽植桃园群落中害虫比例较大。野生猕猴桃园和栽植猕猴桃园之间,群落的多样性指数、均匀度和优势度差异均极显著,群落稳定性表现为野生>9年>14年>3年。各类群的时空二维生态位也会随着栽植时间增长发生变化：蜘蛛和蝇类的生态位在不同树龄的猕猴桃园中都保持在较高水平;人工栽植初期,山楂叶螨和叶蝉占据的时空生态位较宽,成为优势类群,小薪甲与山楂叶螨生态位重叠较大,竞争激烈;随后,小薪甲和瘿蚊的时空二维生态位逐渐增大,到14年桃园中已经取代了山楂叶螨和叶蝉,成为主要害虫。总之,人工干扰的节肢动物群落重建是一个次级演替过程,与自然生态系统群落明显不同。