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.     

Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula

The major intention of the present study was to investigate whether an approach combining the use of niche-based palaeodistribution modeling and phylo-geography would support or modify hypotheses about the Quaternary distributional history derived from phylogeographic methods alone. Our study system comprised two closely related species of Alpine Primula. We used species distribution models based on the extant distribution of the species and last glacial maximum (LGM) climate models to predict the distribution of the two species during the LGM. Phylogeographic data were generated using amplified fragment length polymorphisms (AFLPs). In Primula hirsuta, models of past distribution and phylogeographic data are partly congruent and support the hypothesis of widespread nunatak survival in the Central Alps. Species distribution models (SDMs) allowed us to differentiate between alpine regions that harbor potential nunatak areas and regions that have been colonized from other areas. SDMs revealed that diversity is a good indicator for nunataks, while rarity is a good indicator for peripheral relict populations that were not source for the recolonization of the inner Alps. In P. daonensis, palaeo-distribution models and phylogeographic data are incongruent. Besides the uncertainty inherent to this type of modeling approach (e.g., relatively coarse 1-km grain size), disagreement of models and data may partly be caused by shifts of ecological niche in both species. Nevertheless, we demonstrate that the combination of palaeo-distribution modeling with phylogeographical approaches provides a more differentiated picture of the distributional history of species and partly supports (P. hirsuta) and partly modifies (P. daonensis and P. hirsuta) hypotheses of Quaternary distributional history. Some of the refugial area indicated by palaeodistribution models could not have been identified with phylogeographic data.     

Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful?

Modelling strategies for predicting the potential impacts of climate change on the natural distribution of species have often focused on the characterization of a species’ bioclimate envelope. A number of recent critiques have questioned the validity of this approach by pointing to the many factors other than climate that play an important part in determining species distributions and the dynamics of distribution changes. Such factors include biotic interactions, evolutionary change and dispersal ability. This paper reviews and evaluates criticisms of bioclimate envelope models and discusses the implications of these criticisms for the different modelling strategies employed. It is proposed that, although the complexity of the natural system presents fundamental limits to predictive modelling, the bioclimate envelope approach can provide a useful first approximation as to the potentially dramatic impact of climate change on biodiversity. However, it is stressed that the spatial scale at which these models are applied is of fundamental importance, and that model results should not be interpreted without due consideration of the limitations involved. A hierarchical modelling framework is proposed through which some of these limitations can be addressed within a broader, scale‐dependent context.     

Modelled spatial distribution of marine fish and projected modifications in the North Atlantic Ocean

The objectives of this work were to examine the past, current and potential influence of global climate change on the spatial distribution of some commercially exploited fish and to evaluate a recently proposed new ecological niche model (ENM) called nonparametric probabilistic ecological niche model (NPPEN). This new technique is based on a modified version of the test called Multiple Response Permutation Procedure (MRPP) using the generalized Mahalanobis distance. The technique was applied in the extratropical regions of the North Atlantic Ocean on eight commercially exploited fish species using three environmental parameters (sea surface temperature, bathymetry and sea surface salinity). The numerical procedure and the model allowed a better characterization of the niche (sensu Hutchinson) and an improved modelling of the spatial distribution of the species. Furthermore, the technique appeared to be robust to incomplete or bimodal training sets. Despite some potential limitations related to the choice of the climatic scenarios (A2 and B2), the type of physical model (ECHAM 4) and the absence of consideration of biotic interactions, modelled changes in species distribution explained some current observed shifts in dominance that occurred in the North Atlantic sector, and particularly in the North Sea. Although projected changes suggest a poleward movement of species, our results indicate that some species may not be able to track their climatic envelope and that climate change may have a prominent influence on fish distribution during this century. The phenomenon is likely to trigger locally major changes in the dominance of species with likely implications for socio‐economical systems. In this way, ENMs might provide a new management tool against which changes in the resource might be better anticipated.     

The evolution and extinction of the ichthyosaurs from the perspective of quantitative ecospace modelling

The role of niche specialization and narrowing in the evolution and extinction of the ichthyosaurs has been widely discussed in the literature. However, previous studies have concentrated on a qualitative discussion of these variables only. Here, we use the recently developed approach of quantitative ecospace modelling to provide a high-resolution quantitative examination of the changes in dietary and ecological niche experienced by the ichthyosaurs throughout their evolution in the Mesozoic. In particular, we demonstrate that despite recent discoveries increasing our understanding of taxonomic diversity among the ichthyosaurs in the Cretaceous, when viewed from the perspective of ecospace modelling, a clear trend of ecological contraction is visible as early as the Middle Jurassic. We suggest that this ecospace redundancy, if carried through to the Late Cretaceous, could have contributed to the extinction of the ichthyosaurs. Additionally, our results suggest a novel model to explain ecospace change, termed the ‘migration model’.     

Geographic distribution of phlebotomine sandfly species (Diptera: Psychodidae) in Central-West Brazil

This study updates the geographic distributions of phlebotomine species in Central-West Brazil and analyses the climatic factors associated with their occurrence. The data were obtained from the entomology services of the state departments of health in Central-West Brazil, scientific collections and a literature review of articles from 1962-2014. Ecological niche models were produced for sandfly species with more than 20 occurrences using the Maxent algorithm and eight climate variables. In all, 2,803 phlebotomine records for 127 species were analysed. Nyssomyia whitmani, Evandromyia lenti and Lutzomyia longipalpis were the species with the greatest number of records and were present in all the biomes in Central-West Brazil. The models, which were produced for 34 species, indicated that the Cerrado areas in the central and western regions of Central-West Brazil were climatically more suitable to sandflies. The variables with the greatest influence on the models were the temperature in the coldest months and the temperature seasonality. The results show that phlebotomine species in Central-West Brazil have different geographical distribution patterns and that climate conditions in essentially the entire region favour the occurrence of at least one Leishmania vector species, highlighting the need to maintain or intensify vector control and surveillance strategies.     

Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak

Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether genetic diversity is associated with climatic niche suitability and stability since the Last Glacial Maximum (LGM). Second, we use causal modelling to analyse the potential influence of climatic factors (current and LGM niche suitability) and altitude in the observed patterns of genetic structure. We found that genetic diversity is negatively associated with local climatic stability since the LGM, which may be due to higher immigration rates in unstable patches during favourable climatic periods and/or temporally varying selection. Analyses of spatial genetic structure revealed the presence of three main genetic clusters, a pattern that is mainly driven by two highly differentiated populations located in the northern edge of the species distribution range. After controlling for geographic distance, causal modelling analyses showed that genetic relatedness decreases with the environmental divergence among sampling sites estimated as altitude and current and LGM niche suitability. Natural selection against nonlocal genotypes and/or asynchrony in reproductive phenology may explain this pattern. Overall, this study suggests that local environmental conditions can shape patterns of genetic structure and variability even in species with high potential for gene flow and relatively small distribution ranges.     

Size-structure-based models of forest dynamics to interpret population- and community-level mechanisms

Functional size-structure-based models of forest tree population dynamics present a unifying explanation for population-level patterns and tree community organization. Density-dependent regulation can be explicitly replaced by the effect of size-structure-dependent suppression on demographic processes in functional size-structure models. This suppression effect sufficiently explains various patterns reported for crowded evenaged populations. Further, it stabilizes natural forest populations of overlapping generations at a stationary state with balanced recruitment and mortality. The spatial heterogeneity of light resources created by tree size structure offers an opportunity for multiple species to coexist by means of trade-offs between demographic parameters. The energy correlation of tree species diversity at a geographic scale is also attributable to the architectural feature of forests. Recipient of the Botanical Society Award of Young Scientists, 1992.     

Detecting cryptic speciation in the widespread and morphologically conservative carpet chameleon (Furcifer lateralis) of Madagascar

Species delimitation within recently evolved groups can be challenging because species may be difficult to distinguish morphologically. Following the General Lineage Concept, we apply a multiple evidence approach to assess species limits within the carpet chameleon Furcifer lateralis, which is endemic to Madagascar and exported in large numbers for the pet trade. Cryptic speciation within F. lateralis was considered likely because this species (1) has a vast distribution, (2) occupies exceptionally diverse habitats and (3) exhibits subtle regional differences in morphology. Phylogenetic trees reconstructed using nuclear and mitochondrial genes recovered three well-supported clades corresponding with geography. Morphological results based on canonical variates analysis show that these clades exhibit subtle differences in head casque morphology. Ecological niche modelling results found that these phylogenetic groups also occupy unique environmental space and exhibit patterns of regional endemism typical of other endemic reptiles. Combined, our findings provide diverse yet consistent evidence for the existence of three species. Consequently, we elevate the subspecies F. lateralis major to species rank and name a new species distributed in northern and western Madagascar. Initial ecological divergence, associated with speciation of F. lateralis in humid eastern habitat, fits the Ecographic Constraint model for species diversification in Madagascar. By contrast, the second speciation event provides some support for the Riverine Barrier model, with the Mangoky River possibly causing initial isolation between species. These findings thus support two contrasting models of speciation within closely related species and demonstrate the utility of applying a combined-evidence approach for detecting cryptic speciation.     

陕北黄土高原辽东栎(Quercus liaotungensis)群落类型划分及其生态位特征

根据陕北黄龙林区辽东栎群落30个样地资料,通过聚类对该群落进行了类型划分,共划分为6个群丛,分别为A．辽东栎（Quercus liaotungensis）-土庄绣线菊（Spiraea pubescens）、B．辽东栎-虎榛子（Ostryopsis davidiana）、c．辽东栎-胡枝子（Lespedeza bicolor）、D．辽东栎．水枸子（Cotoneasten multtflorus）、E．辽东栎-白刺花（Sophora viciifolia）、F．辽东栎-黄蔷薇（Rosa hugonis）。另外,对各类型辽东栎林和不同坡向辽东栎群落的生物多样性进行了计算,结果表明各群落Whittaker多样性指数存在明显的差异,并与其所处的生境条件密切相关,其中与坡向关系较大,即北坡〉西北坡〉东南坡〉西南坡〉南坡。最后,对辽东栎林乔木层和灌木层组成种类生态位和生态位重叠进行了计算分析,结果表明,乔木层,辽东栎、油松、白桦不仅生态位宽度较大（LB值1．2—1．5）,而且三者之间的生态位重叠值也较大（0ik值0．7—0．9）;在现演替阶段它们之间存在着较为激烈的资源利用性竞争;灌木层,土庄绣线菊、榛子、铁杆蒿、黄蔷薇生态位宽度较大（LB〉1）,而葱皮忍冬、南蛇藤、鼠李、鞘柄菝葜较小（LB为0．4—0．45）;生态位重叠值〉0．8的种对仅占灌木计算种对的2．8％,而〈0．6的种对占87．4％。     

Patterns of differential introgression in a salamander hybrid zone: inferences from genetic data and ecological niche modelling

Hybrid zones have yielded considerable insight into many evolutionary processes, including speciation and the maintenance of species boundaries. Presented here are analyses from a hybrid zone that occurs among three salamanders –Plethodon jordani, Plethodon metcalfi and Plethodon teyahalee– from the southern Appalachian Mountains. Using a novel statistical approach for analysis of non‐clinal, multispecies hybrid zones, we examined spatial patterns of variation at four markers: single‐nucleotide polymorphisms (SNPs) located in the mtDNA ND2 gene and the nuclear DNA ILF3 gene, and the morphological markers of red cheek pigmentation and white flecks. Concordance of the ILF3 marker and both morphological markers across four transects is observed. In three of the four transects, however, the pattern of mtDNA is discordant from all other markers, with a higher representation of P. metcalfi mtDNA in the northern and lower elevation localities than is expected given the ILF3 marker and morphology. To explore whether climate plays a role in the position of the hybrid zone, we created ecological niche models for P. jordani and P. metcalfi. Modelling results suggest that hybrid zone position is not determined by steep gradients in climatic suitability for either species. Instead, the hybrid zone lies in a climatically homogenous region that is broadly suitable for both P. jordani and P. metcalfi. We discuss various selective (natural selection associated with climate) and behavioural processes (sex‐biased dispersal, asymmetric reproductive isolation) that might explain the discordance in the extent to which mtDNA and nuclear DNA and colour‐pattern traits have moved across this hybrid zone.     

Litter-associated bacteria and fungi – a comparison of biomass and communities across lakes and plant species

1. We investigated the importance of lake water chemistry and substrate properties in regulating microbial decomposer communities on macrophyte litter. Ten lakes of differing water chemistry, including such variables as nutrient concentration, pH and dissolved organic carbon, were sampled in October 2003. Water chemistry was analysed, and litter from the macrophytes Phragmites australis, Schoenoplectus lacustris and Nuphar lutea was collected from both above and below the water surface. 2. The three plant species differed widely in carbon and nitrogen content. The aerial parts of P. australis had highest C : N ratio (mean value 125), while the lowest values were found in leaves of N. lutea (19.8). 3. Fungal carbon ranged from 0.15 to 6.4 mg g^?1 dry weight (DW), and was higher on aerial than on submerged plant parts. Fungal biomass was highest on S. lacustris and lowest on N. lutea. Denaturing gradient gel electrophoresis revealed no differences in the number of fungal taxa between plant species or plant parts, with the limitation that no molecular analysis was possible for N. lutea. 4. In contrast, bacteria were most abundant on N. lutea, but showed no significant difference between leaf and stem parts. The number of bacterial taxa was highest on the submerged parts of P. australis. 5. The correlations between microbial variables and the properties of lakes and litter were analysed using multivariate statistics. In a principal component analysis, litter properties explained 78% of the variation in microbial variables. In contrast, redundancy analysis revealed that the explanatory power of lake water chemistry was only 20%, indicating that the properties of the growth substratum were more important than those of the lake water for the attached microbial communities.