The role of seasonal timing and phenological shifts for species coexistence

Shifts in the phenologies of coexistence species are altering the temporal structure of natural communities worldwide. However, predicting how these changes affect the structure and long‐term dynamics of natural communities is challenging because phenology and coexistence theory have largely proceeded independently. Here, I propose a conceptual framework that incorporates seasonal timing of species interactions into a well‐studied competition model to examine how changes in phenologies influence long‐term dynamics of natural communities. Using this framework I demonstrate that persistence and coexistence conditions strongly depend on the difference in species’ mean phenologies and how this difference varies across years. Consequently, shifts in mean and interannual variation in relative phenologies of species can fundamentally alter the outcome of interactions and the potential for persistence and coexistence of competing species. These effects can be predicted by how per‐capita effects scale with differences in species’ phenologies. I outline how this approach can be parameterized with empirical systems and discuss how it fits within the context of current coexistence theory. Overall, this synthesis reveals that phenology of species interactions can play a crucial yet currently understudied role in driving coexistence and biodiversity patterns in natural systems and determine how species will respond to future climate change.     

Population and geographic range dynamics: implications for conservation planning

Continuing downward trends in the population sizes of many species, in the conservation status of threatened species, and in the quality, extent and connectedness of habitats are of increasing concern. Identifying the attributes of declining populations will help predict how biodiversity will be impacted and guide conservation actions. However, the drivers of biodiversity declines have changed over time and average trends in abundance or distributional change hide significant variation among species. While some populations are declining rapidly, the majority remain relatively stable and others are increasing. Here we dissect out some of the changing drivers of population and geographic range change, and identify biological and geographical correlates of winners and losers in two large datasets covering local population sizes of vertebrates since 1970 and the distributions of Galliform birds over the last two centuries. We find weak evidence for ecological and biological traits being predictors of local decline in range or abundance, but stronger evidence for the role of local anthropogenic threats and environmental change. An improved understanding of the dynamics of threat processes and how they may affect different species will help to guide better conservation planning in a continuously changing world.     

Phenotypic variation in Galerida larks in Morocco: the role of history and natural selection

The relative influences of history, natural selection and hybridization in shaping phenotypic variation in closely related taxa is a crucial issue in current evolutionary biology. In this study, we used as a model two sibling but paradoxically highly variable species of larks (Galerida theklae and Galerida cristata) of Morocco to separate the impacts of these evolutionary forces. In the former species, variation is manifested mainly in colouration, while in the latter, variation also encompasses bill size and shape. Mitochondrial and nuclear DNA sequencing were used to identify the historical relationships among the subspecies and species. According to our analyses, G. cristata and G. theklae diverged about 3.7 million years ago (Ma), and we found no evidence for a role of hybridization in maintaining their similarity. In G. theklae, there was no further subdivision, while in G. cristata two major mtDNA groups were identified (divergence approximately 1.1 Ma). These two lineages are parapatric and regroup, respectively, the three short-billed subspecies [G. (cristata) cristata] and the two long-billed subspecies [G. (cristata) randonii]. Patterns of morphological variation were then contrasted to this pattern of neutral relationships: we found that G. (c.) cristata was morphologically more similar to G. theklae than to G. (c.) randonii. Overall, these results point towards the prominent role of (i) natural selection and/or phenotypic plasticity in adapting the plumage to local conditions and (ii) natural selection in combination with historical isolation in driving the divergence in size and bill morphology in the crested larks.     

Winter bird communities in the northern Negev: species dispersal patterns, habitat use and implications for habitat conservation

Bird habitat conservation may require different management strategies for different seasonal bird assemblages. We studied habitat use by winter birds in forest and scrubland habitat patches in the northern Negev, Israel. Our goal was to assess whether differences in responses to landscape and habitat structure between breeding and non-breeding seasons require changes in future conservation plans that have been suggested for the Negev breeding bird community. We evaluated habitat and area effects on bird abundance and distribution and tested whether species habitat use during winter involves niche shifts. Compared with breeding birds, a larger proportion of winter bird species occupied both scrubland and forest. As in summer, forest bird species responded to habitat structure, whereas scrubland species were associated with both habitat structure and area. Resident birds disperse into habitats in which they were not present during summer. Consequently, for several species, the correlation between bird densities and environmental factors showed a better fit at the landscape rather than at the habitat scale. In addition, rather than niche shift, birds actually extended their niche breadth. Nest site selection may constrain bird distribution into a realized niche, smaller than their fundamental niche. Despite the scale differences in habitat use, the similar species diversity patterns between seasons suggest that both winter and summer birds would benefit from conservation of scrub patches larger than 50 ha, and enrichment of foliage layers within the planted forests.     

Testing Bergmann's rule in the presence of potentially confounding factors: a case study with three species of Galerida larks in Morocco

Aim  To test Bergmann's rule (which predicts a larger body size in colder areas within warm-blooded vertebrate species) in three partially sympatric species of larks ( Galerida theklae , Galerida cristata and Galerida randonii ) that occur in Morocco.
Location  Morocco.
Methods  Restriction fragment length polymorphism techniques applied on cytochrome b haplotypes were used to discriminate G. cristata and G. randonii , and to investigate the effects of interspecific hybridization in their contact zone. A comprehensive statistical framework was then designed to test Bergmann's rule in our three Galerida species (using altitude as a proxy for cold temperatures), while controlling for the possible influence of interspecific hybridization and competition and accounting for spatial autocorrelation. The method we propose is conservative in the sense that potentially confounding factors are adjusted so as to maximize their influence on the variable of interest.
Results  Bergmann's rule was strongly supported in G. theklae and G. randonii . However, body size did not respond to altitude in G. cristata , a result that was not simply explained by species-specific differences in geographical ranges and altitudinal span. In G. cristata , we detected a tendency for body size to increase with aridity, in agreement with an alternative definition of Bergmann's rule. However, since G. cristata also hybridizes with G. randonii in a contact zone located in the most arid part of the range of G. cristata , we could not tease apart the relative contribution of selection and hybridization in driving this pattern.
Main conclusions  This study highlights the need for careful statistical designs that allow meaningful variables to be picked out from large sets of potential factors. When taking these factors into account, we found that Bergmann's rule was still strongly supported in two out of the three species examined.     

Temporally explicit habitat ecology and the coexistence of species

Habitats may have dynamics that exist independently of the population densities of species occupying the habitat. For example, ephemeral habitat patches may disappear regardless of whether a particular species is present or not. Such habitat dynamics are frequently modelled by ignoring age-related variation in patch turnover rates. This can be thought of as a temporally implicit approach. An alternative, temporally explicit approach involves using age-structured models in order to describe variations in habitat dynamics. Simple models of coexistence between competing species show that temporally implicit models may be misleading where there is age-related variation in patch dynamics. Changing the shape of the patch survivorship function but not the average patch survivorship can result in mutual extinction, monocultures or coexistence of an inferior and a superior competitor. An explicit treatment of habitat demography may therefore offer improved predictive models and alternative landscape management strategies.     

物种分布区范围地理格局的Rapoport法则

Rapoport法则最初是关于物种分布的纬度位置与纬度分布宽度的关系的假说, 被认为是宏观生态学的重要假说之一。Rapoport法则提出以后引发了广泛的实证检验和理论探讨, 并扩展到海拔和海洋深度梯度的分析。对Rapoport法则的检验发展了多种算法, 包括基于中域效应模型的比较分析法, 提出了气候变异性等多种机理解释, 并建立了物种分布区范围格局与物种丰富度格局、分布边界限制等重要宏观生态学现象之间的联系。关于该法则的普适性仍存在明显的意见分歧, 但分析和检验方法被认为是影响结果的重要因素, 方法的改进将是这一领域今后研究的关键。本文主要从Rapoport法则的概念、检验方法、机理性解释, 关于其普适性的争论及其与物种丰富度格局的关系等方面, 综述这一领域的研究进展。     

Factors affecting seasonal habitat use,and predicted range of two tropical deer in Indonesian rainforest

There is an urgent recognized need for conservation of tropical forest deer. In order to identify some environmental factors affecting conservation, we analyzed the seasonal habitat use of two Indonesian deer species, Axis kuhlii in Bawean Island and Muntiacus muntjak in south-western Java Island, in response to several physical, climatic, biological, and anthropogenic variables. Camera trapping was performed in different habitat types during both wet and dry season to record these elusive species. The highest number of photographs was recorded in secondary forest and during the dry season for both Bawean deer and red muntjac. In models, anthropogenic and climatic variables were the main predictors of habitat use. Distances to cultivated area and to settlement were the most important for A. kuhlii in the dry season. Distances to cultivated area and annual rainfall were significant for M. muntjak in both seasons. Then we modelled their predictive range using Maximum entropy modelling (Maxent). We concluded that forest landscape is the fundamental scale for deer management, and that secondary forests are potentially important landscape elements for deer conservation. Important areas for conservation were identified accounting of habitat transformation in both study areas.     

Spatial patterns of coexistence of competing species in patchy habitat

The single-species spatially realistic patch occupancy metapopulation model is, in this study, extended to a metacommunity of many competing species. Competition is assumed to reduce the local carrying capacity (effective patch area), which in turn increases local extinction rates and reduces colonization rates because of smaller population sizes. Each species is described by three parameters: pre-competitive abundance (equilibrium incidence of patch occupancy, which reflects the rate of colonization in relation to extinction rate), the spatial range of migration, and competitive ability. The model ignores spatio–temporal correlations caused by interspecific interactions, because in metacommunities of unequal competitors inhabiting heterogeneous landscapes, correlations in the occurrence of species are driven more by patch heterogeneity than by competition. The model allows the calculation of multispecies equilibria in patchy habitats without simulations. In general, the number of coexisting species in the metacommunity increases with decreasing strength of competition, increasing rate of colonization, and decreasing range of migration. Habitat heterogeneity in the form of spatial variation in patch areas tends to facilitate coexistence. Poor competitors may coexist with superior competitors in the patch network if the former have higher colonization rates (competition–colonization trade-off). When migration distances are short, competition leads to spatial pattern formation: Species tend to have restricted spatial distributions in the network, but contrary to intuitive expectations, often the distributions of many species are nested. Having more dispersive species enhances both local and global diversity, whereas more local migration decreases local but increases global diversity.     

Predator-mediated habitat use: some consequences for species interactions

Synopsis Behavioral responses to predators can have a major impact on a fishes' diet and habitat choice. Studies with the bluegill sunfish, Lepomis macrochirus, demonstrate that bluegills undergo pronounced shifts in diet and habitat use as they grow in response to changes in their vulnerability to predators. Other species of fish exhibit similar habitat shifts with body size, presumably also in response to changing predation risks and/or foraging gains. An important but little appreciated consequence of this type of predator-mediated habitat use is that predation risk, by structuring size and/or age-specific resource use, may also indirectly affect species interactions. This paper discusses some of the ways in which behavioral responses to predators may affect intra- and interspecific competition in fish. Observational and experimental studies with sunfish (Centrarchidae) provide most of the examples. These studies suggest that the nonlethal effects of predators may be as important as the actual killing of prey.     

Unidirectional hybridization at a species' range boundary: implications for habitat tracking

Aim  Introgressive hybridization between a locally rare species and a more abundant congener can drive population extinction via genetic assimilation, or the replacement of the rare species gene pool with that of the common species. To date, however, few studies have assessed the effects of such processes at the limits of species' distribution ranges. In this study, we have examined the potential for hybridization between range-edge populations of the wintergreen Pyrola minor and sympatric populations of Pyrola grandiflora .
Location  Qeqertarsuaq, Greenland and Churchill, Manitoba, Canada.
Methods  Genetic analysis of samples from Greenland and Canada was carried out using a combination of nuclear and chloroplast single nucleotide polymorphisms (SNPs).
Results  Analysis of nuclear SNPs confirmed hybridization in populations of morphologically intermediate individuals, as well as revealing the existence of cryptic hybrids in ostensibly morphologically pure P. minor populations. Analysis of chloroplast SNPs revealed that this hybridization is unidirectional and suggests that hybrids originate via pollen swamping of P. minor by the more common P. grandiflora .
Main conclusions  Extensive unidirectional hybridization may lead to the extinction of peripheral populations of P. minor where the two species grow sympatrically. Extinction could occur as a result of genetic assimilation where F₁s are fertile, or via the removal of unidirectionally pollinated sterile F₁s, or by a combination of these processes. This could compromise the ability of species to respond to climate change via habitat tracking, although the final outcome of these processes may ultimately depend on the rate of global climate change and its effect on the species' distributions.     

Population genetics and the evolution of geographic range limits in an annual plant

Abstract Theoretical models of species' geographic range limits have identified both demographic and evolutionary mechanisms that prevent range expansion. Stable range limits have been paradoxical for evolutionary biologists because they represent locations where populations chronically fail to respond to selection. Distinguishing among the proposed causes of species' range limits requires insight into both current and historical population dynamics. The tools of molecular population genetics provide a window into the stability of range limits, historical demography, and rates of gene flow. Here we evaluate alternative range limit models using a multilocus data set based on DNA sequences and microsatellites along with field demographic data from the annual plant Clarkia xantiana ssp. xantiana. Our data suggest that central and peripheral populations have very large historical and current effective population sizes and that there is little evidence for population size changes or bottlenecks associated with colonization in peripheral populations. Whereas range limit populations appear to have been stable, central populations exhibit a signature of population expansion and have contributed asymmetrically to the genetic diversity of peripheral populations via migration. Overall, our results discount strictly demographic models of range limits and more strongly support evolutionary genetic models of range limits, where adaptation is prevented by a lack of genetic variation or maladaptive gene flow.     

Assembly rules for functional groups of North American shrews: effects of geographic range and habitat partitioning

Trophic cascades exist in numerous terrestrial systems, including many systems with ants as the top predator. Many studies show how behavioral modifications of herbivores are especially important in mediating species interactions and trophic cascades. Although most studies of trophic cascades focus on predator-herbivore-plant links, the trophic cascades concept could be applied to almost any level of trophic interactions. Especially considering the importance of parasites we consider here the interactions between the parasitic phorid fly, Pseudacteon sp. (Diptera: Phoridae), its ant host, Azteca instabilis (F. Smith) (Hymenoptera: Formicidae), and the herbivore, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) in the coffee agroecosystem. We investigated the effects of phorid flies on ant behavior by monitoring ant recruitment to tuna baits over a 30-min period in the presence or absence of phorid flies. To study the indirect effects of phorids on larvae, we placed baits on coffee plants to elevate ant foraging levels to levels near to ant nests, placed larvae near baits, and recorded the effects of ants on larvae either in the presence or absence of phorid flies. We found that phorid fly presence significantly reduced ant ability to recruit to baits through behavioral modifications and also significantly lessened ant ability to attack, carry away, or force herbivores off plants. We conclude there is a behaviorally-modified species-level trophic cascade in the coffee agroecosystem, with potentially important effects in ant and herbivore communities as well as for coffee production.     

Home range and habitat use of translocated endangered species,Cottus koreanus,in South Korea

The home range and characteristics of Cottus koreanus were investigated using passive integrated transponder (PIT) telemetry in the Gulji Stream, Korea, where the target species was artificially translocated. After release, tagged individuals moved up to 78?m away from the release site in search of proper habitats. The average distance moved until settlement was 17.1?m. The observed home range of settled individuals had longitudinal sections of 9.9?±?3.6?m and surface areas of 7.2?±?2.7?m². This is comparable to congeneric species that inhabit similar ecological habitats. Once individuals had settled, they rarely moved from that site except during the spring season. The typical microhabitat characteristics of the sites where the released individuals settled are: water depth of 5–10?cm, water velocity of 0.1–0.3?m?s^?1, and the size of boulders and cobbles of 10–20?cm in diameter. This study of translocated C. koreanus individuals provides detailed information about habitats that can be used for effective habitat restoration and successful translocations attempts of this species.     

The use of spatial ecological modelling as a tool for improving the assessment of geographic range size of threatened species

We analysed endemic threatened tree and reptile species of Socotra Island (Yemen), characterised by different ecological requirements and spatial distribution, in order to evaluate the usefulness of spatial ecological modelling in the estimation of species extent of occurrence (EOO) and area of occupancy (AOO). Point occurrences for the entire species range were used to model their spatial distribution by Random Forest (RF) and Generalised Linear Model (GLM). For each species the suitability area (SA) was obtained by applying the 0% omission error criterion on the probability map, and compared or integrated with EOO and AOO area obtained by topological methods such as the minimum convex polygon (MCP), α-hull and 2 km × 2 km grid.RF showed a lower prediction error than GLM. Higher accuracy was achieved for species with higher number of occurrences and narrower ecological niche. SA was always greater than AOO measured with the 2 km × 2 km grid method. SA was greater than EOO, measured by both MCP and α-hull methods, for species with localised distribution, while it was smaller for widely distributed species. EOO-α-hull area was equal or smaller than that calculated by MCP depending on the spatial distribution of species. AOO measured considering the SA within the EOO-MCP was greater than that measured using the standard 2 km × 2 km grid. Conversely, AOO calculated considering the suitable area within the EOO-α-hull showed variable results, being smaller or greater than the 2 km × 2 km grid AOO depending on the ecological niche and spatial distribution of species. According to our results, SEM does not provide an effective alternative to topological methods for the estimate of EOO and AOO. However, it may be considered a useful tool to estimate AOO within the boundaries of EOO measured by the α-hull method, because it reduces some potential sources of inconsistency and bias.     

Endophytic Phomopsis species: host range and implications for diversity estimates

Foliar endophyte assemblages of teak trees growing in dry deciduous and moist deciduous forests of Nilgiri Biosphere Reserve were compared. A species of Phomopsis dominated the endophyte assemblages of teak, irrespective of the location of the host trees. Internal transcribed spacer sequence analysis of 11 different Phomopsis isolates (ten from teak and one from Cassia fistula) showed that they fall into two groups, which are separated by a relatively long branch that is strongly supported. The results showed that this fungus is not host restricted and that it continues to survive as a saprotroph in teak leaf, possibly by exploiting senescent leaves as well as the litter. Although the endophyte assemblage of a teak tree growing about 500 km from the forests was also dominated by a Phomopsis sp., it separated into a different group based on internal transcribed spacer sequence analysis. Our results with an endophytic Phomopsis sp. reinforce the earlier conclusions reached by others for pathogenic Phomopsis sp., i.e., that this fungus is not host specific, and the species concept of Phomopsis needs to be redefined.