Insights from ecological niche modeling on the taxonomic distinction and niche differentiation between the black‐spotted and red‐spotted tokay geckoes (Gekko gecko)

The black‐spotted tokay and the red‐spotted tokay are morphologically distinct and have largely allopatric distributions. The black‐spotted tokay is characterized by a small body size and dark skin with sundry spots, while the red‐spotted tokay has a relatively large body size and red spots. Based on morphological, karyotypic, genetic, and distribution differences, recent studies suggested their species status; however, their classifications remain controversial, and additional data such as ecological niches are necessary to establish firm hypotheses regarding their taxonomic status. We reconstructed their ecological niches models using climatic and geographic data. We then performed niche similarity tests (niche identity and background tests) and point‐based analyses to explore whether ecological differentiation has occurred, and whether such differences are sufficient to explain the maintenance of their separate segments of environmental ranges. We found that both niche models of the black‐ and the red‐spotted tokay had a good fit and a robust performance, as indicated by the high area under the curve (AUC) values (“black” = 0.982, SD = ± 0.002, “red” = 0.966 ± 0.02). Significant ecological differentiation across the entire geographic range was found, indicating that the involvement of ecological differentiation is important for species differentiation. Divergence along the environmental axes is highly associated with climatic conditions, with isothermality being important for the “black” form, while temperature seasonality, precipitation of warmest quarter, and annual temperature range together being important for the “red” form. These factors are likely important factors in niche differentiation between the two forms, which result in morphological replacement. Overall, beside morphological and genetic differentiation information, our results contribute to additional insights into taxonomic distinction and niche differentiation between the black‐ and the red‐spotted tokay.     

Climate‐driven geographic distribution of the desert locust during recession periods: Subspecies’ niche differentiation and relative risks under scenarios of climate change

The desert locust is an agricultural pest that is able to switch from a harmless solitarious stage, during recession periods, to swarms of gregarious individuals that disperse long distances and affect areas from western Africa to India during outbreak periods. Large outbreaks have been recorded through centuries, and the Food and Agriculture Organization keeps a long‐term, large‐scale monitoring survey database in the area. However, there is also a much less known subspecies that occupies a limited area in Southern Africa. We used large‐scale climatic and occurrence data of the solitarious phase of each subspecies during recession periods to understand whether both subspecies climatic niches differ from each other, what is the current potential geographical distribution of each subspecies, and how climate change is likely to shift their potential distribution with respect to current conditions. We evaluated whether subspecies are significantly specialized along available climate gradients by using null models of background climatic differences within and between southern and northern ranges and applying niche similarity and niche equivalency tests. The results point to climatic niche conservatism between the two clades. We complemented this analysis with species distribution modeling to characterize current solitarious distributions and forecast potential recession range shifts under two extreme climate change scenarios at the 2050 and 2090 time horizon. Projections suggest that, at a global scale, the northern clade could contract its solitarious recession range, while the southern clade is likely to expand its recession range. However, local expansions were also predicted in the northern clade, in particular in southern and northern margins of the current geographical distribution. In conclusion, monitoring and management practices should remain in place in northern Africa, while in Southern Africa the potential for the subspecies to pose a threat in the future should be investigated more closely.     

High invasion potential of Hydrilla verticillata in the Americas predicted using ecological niche modeling combined with genetic data

Ecological niche modeling is an effective tool to characterize the spatial distribution of suitable areas for species, and it is especially useful for predicting the potential distribution of invasive species. The widespread submerged plant Hydrilla verticillata (hydrilla) has an obvious phylogeographical pattern: Four genetic lineages occupy distinct regions in native range, and only one lineage invades the Americas. Here, we aimed to evaluate climatic niche conservatism of hydrilla in North America at the intraspecific level and explore its invasion potential in the Americas by comparing climatic niches in a phylogenetic context. Niche shift was found in the invasion process of hydrilla in North America, which is probably mainly attributed to high levels of somatic mutation. Dramatic changes in range expansion in the Americas were predicted in the situation of all four genetic lineages invading the Americas or future climatic changes, especially in South America; this suggests that there is a high invasion potential of hydrilla in the Americas. Our findings provide useful information for the management of hydrilla in the Americas and give an example of exploring intraspecific climatic niche to better understand species invasion.     

Toward ecologically realistic predictions of species distributions: A cross‐time example from tropical montane cloud forests

There is an urgent need for more ecologically realistic models for better predicting the effects of climate change on species’ potential geographic distributions. Here we build ecological niche models using MAXENT and test whether selecting predictor variables based on biological knowledge and selecting ecologically realistic response curves can improve cross‐time distributional predictions. We also evaluate how the method chosen for extrapolation into nonanalog conditions affects the prediction. We do so by estimating the potential distribution of a montane shrew (Mammalia, Soricidae, Cryptotis mexicanus) at present and the Last Glacial Maximum (LGM). Because it is tightly associated with cloud forests (with climatically determined upper and lower limits) whose distributional shifts are well characterized, this species provides clear expectations of plausible vs. implausible results. Response curves for the MAXENT model made using variables selected via biological justification were ecologically more realistic compared with those of the model made using many potential predictors. This strategy also led to much more plausible geographic predictions for upper and lower elevational limits of the species both for the present and during the LGM. By inspecting the modeled response curves, we also determined the most appropriate way to extrapolate into nonanalog environments, a previously overlooked factor in studies involving model transfer. This study provides intuitive context for recommendations that should promote more realistic ecological niche models for transfer across space and time.     

Pollinator‐mediated assemblage processes in California wildflowers

Community assembly is the result of multiple ecological and evolutionary forces that influence species coexistence. For flowering plants, pollinators are often essential for plant reproduction and establishment, and pollinator‐mediated interactions may influence plant community composition. Here, we use null models and community phylogenetic analyses of co‐occurrence patterns to determine the role of pollinator‐mediated processes in structuring plant communities dominated by congeners. We surveyed three species‐rich genera (Limnanthes, Mimulus and Clarkia) with centres of diversity in the Sierra Nevada of California. Each genus contains species that co‐flower and share pollinators, and each has a robust phylogeny. Within each genus, we surveyed 44–48 communities at three spatial scales, measured floral and vegetative traits and tested for segregation or aggregation of: (i) species, (ii) floral traits (which are likely to be influenced by pollinators), and (iii) vegetative traits (which are likely affected by other environmental factors). We detected both aggregation and segregation of floral traits that were uncorrelated with vegetative trait patterns; we infer that pollinators have shaped the community assembly although the mechanisms may be varied (competition, facilitation, or filtering). We also found that mating system differences may play an important role in allowing species co‐occurrence. Together, it appears that pollinators influence community assemblage in these three clades.     

Towards the top: niche expansion of Taraxacum officinale and Ulex europaeus in mountain regions of South America

In the current context of ongoing global change, the understanding of how the niches of invasive species may change between different geographical areas or time periods is extremely important for the early detection and control of future invasions. We evaluated the effect of climate and non‐climate variables and the sensitivity to various spatial resolutions (i.e. 1 and 20 km) on niche changes during the invasion of Taraxacum officinale and Ulex europaeus in South America. We estimated niche changes using a combination of principal components analyses (PCA) and reciprocal Ecological Niche Modelling (rENM). We further investigated future invasion dynamics under a severe warming scenario for 2050 to unravel the role of niche shifts in the future potential distribution of the species. We observed a clear niche expansion for both species in South America towards higher temperature, precipitation and radiation relative to their native ranges. In contrast, the set of environmental conditions only occupied in the native ranges (i.e. niche unfilling) were less relevant. The magnitude of the niche shifts did not depend on the resolution of the variables. Models calibrated with occurrences from native range predicted large suitable areas in South America (outside of the Andes range) where T. officinale and U. europaeus are currently absent. Additionally, both species could increase their potential distributions by 2050, mostly in the southern part of the continent. In addition, the niche unfilling suggests high potential to invade additional regions in the future, which is extremely relevant considering the current impact of these species in the Southern Hemisphere. These findings confirm that invasive species can occupy new niches that are not predictable from knowledge based only on climate variables or information from the native range.     

Genetic diversity and haplotype distribution of Pachymeniopsis gargiuli sp. nov. and P. lanceolata (Halymeniales,Rhodophyta) in Korea,with notes on their non‐native distributions

The red alga Pachymeniopsis lanceolata, formerly known as Grateloupia lanceolata, is a component of the native algal flora of northeast Asia and has been introduced to European and North American waters. It has been confused with a cryptic species collected from Korea and Italy. Our analyses of rbcL, cox3 and ITS from P. lanceolata and this cryptic species has revealed two distinct entities, forming a clade, which were clearly separated from its congeners and positioned with other Asian species. Here, we describe the cryptic species as P. gargiuli sp. nov., a species that differs from others by molecular sequence and subtle anatomical characters. We hypothesize that P. gargiuli may have been recently dispersed by anthropogenic vectors, possibly at or near the same time as was P. lanceolata. Our cox3 data set revealed that one haplotype of P. gargiuli, shared between Korea and Italy, and two haplotypes of P. lanceolata, commonly occurring in Korea and USA, are invasive haplotypes. This is the first report of the utility of the mitochondrial coding cox3 sequences in red algae.     

Phylogeographic structure in long‐tailed voles (Rodentia: Arvicolinae) belies the complex Pleistocene history of isolation,divergence, and recolonization of Northwest North America's fauna

Quaternary climate fluctuations restructured biodiversity across North American high latitudes through repeated episodes of range contraction, population isolation and divergence, and subsequent expansion. Identifying how species responded to changing environmental conditions not only allows us to explore the mode and tempo of evolution in northern taxa, but also provides a basis for forecasting future biotic response across the highly variable topography of western North America. Using a multilocus approach under a Bayesian coalescent framework, we investigated the phylogeography of a wide‐ranging mammal, the long‐tailed vole, Microtus longicaudus. We focused on populations along the North Pacific Coast to refine our understanding of diversification by exploring the potentially compounding roles of multiple glacial refugia and more recent fragmentation of an extensive coastal archipelago. Through a combination of genetic data and species distribution models (SDMs), we found that historical climate variability influenced contemporary genetic structure, with multiple isolated locations of persistence (refugia) producing multiple divergent lineages (Beringian or northern, southeast Alaska or coastal, and southern or continental) during glacial advances. These vole lineages all occur along the North Pacific Coast where the confluence of numerous independent lineages in other species has produced overlapping zones of secondary contact, collectively a suture zone. Finally, we detected high levels of neoendemism due to complex island geography that developed in the last 10,000 years with the rising sea levels of the Holocene.     

Integrating mechanistic and empirical model projections to assess climate impacts on tree species distributions in northwestern North America

Empirical and mechanistic models have both been used to assess the potential impacts of climate change on species distributions, and each modeling approach has its strengths and weaknesses. Here, we demonstrate an approach to projecting climate‐driven changes in species distributions that draws on both empirical and mechanistic models. We combined projections from a dynamic global vegetation model (DGVM) that simulates the distributions of biomes based on basic plant functional types with projections from empirical climatic niche models for six tree species in northwestern North America. These integrated model outputs incorporate important biological processes, such as competition, physiological responses of plants to changes in atmospheric CO₂ concentrations, and fire, as well as what are likely to be species‐specific climatic constraints. We compared the integrated projections to projections from the empirical climatic niche models alone. Overall, our integrated model outputs projected a greater climate‐driven loss of potentially suitable environmental space than did the empirical climatic niche model outputs alone for the majority of modeled species. Our results also show that refining species distributions with DGVM outputs had large effects on the geographic locations of suitable habitat. We demonstrate one approach to integrating the outputs of mechanistic and empirical niche models to produce bioclimatic projections. But perhaps more importantly, our study reveals the potential for empirical climatic niche models to over‐predict suitable environmental space under future climatic conditions.     

Species‐Specific PCR‐Based Assay for Identification and Detection of Phomopsis (Diaporthe) azadirachtae Causing Die‐Back Disease in Azadirachta indica

Die‐back disease caused by Phomopsis (Diaporthe) azadirachtae is the devastating disease of Azadirachta indica. Accurate identification of P. azadirachtae is always problematic due to morphological plasticity and delayed appearance of conidia. A species‐specific PCR‐based assay was developed for rapid and reliable identification of P. azadirachtae by designing a species‐specific primer‐targeting ITS region of P. azadirachtae isolates. The assay was validated with DNA isolated from different Phomopsis species and other fungal isolates. The PCR assay amplified 313‐bp product from all the isolates of P. azadirachtae and not from any other Phomopsis species or any genera indicating its specificity. The assay successfully detected the pathogen DNA in naturally and artificially infected neem seeds and twigs indicating its applicability in seed quarantine and seed health testing. The sensitivity of the assay was 100 fg when genomic DNA of all isolates was analysed. The PCR‐based assay was 92% effective in comparison with seed plating technique in detecting the pathogen. This is the first report on the development of species‐specific PCR assay for identification and detection of P. azadirachtae. Thus, PCR‐based assay developed is very specific, rapid, confirmatory and sensitive tool for detection of pathogen P. azadirachtae at early stages.     

Predicting the future of forests in the Mediterranean under climate change,with niche‐ and process‐based models: CO2 matters!

Assessing the potential future of current forest stands is a key to design conservation strategies and understanding potential future impacts to ecosystem service supplies. This is particularly true in the Mediterranean basin, where important future climatic changes are expected. Here, we assess and compare two commonly used modeling approaches (niche‐ and process‐based models) to project the future of current stands of three forest species with contrasting distributions, using regionalized climate for continental Spain. Results highlight variability in model ability to estimate current distributions, and the inherent large uncertainty involved in making projections into the future. CO₂ fertilization through projected increased atmospheric CO₂ concentrations is shown to increase forest productivity in the mechanistic process‐based model (despite increased drought stress) by up to three times that of the non‐CO₂ fertilization scenario by the period 2050–2080, which is in stark contrast to projections of reduced habitat suitability from the niche‐based models by the same period. This highlights the importance of introducing aspects of plant biogeochemistry into current niche‐based models for a realistic projection of future species distributions. We conclude that the future of current Mediterranean forest stands is highly uncertain and suggest that a new synergy between niche‐ and process‐based models is urgently needed in order to improve our predictive ability.     

Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances

Although abiotic factors, together with dispersal and biotic interactions, are often suggested to explain the distribution of species and their abundances, species distribution models usually focus on abiotic factors only. We propose an integrative framework linking ecological theory, empirical data and statistical models to understand the distribution of species and their abundances together with the underlying community assembly dynamics. We illustrate our approach with 21 plant species in the French Alps. We show that a spatially nested modelling framework significantly improves the model's performance and that the spatial variations of species presence-absence and abundances are predominantly explained by different factors. We also show that incorporating abiotic, dispersal and biotic factors into the same model bring new insights to our understanding of community assembly. This approach, at the crossroads between community ecology and biogeography, is a promising avenue for a better understanding of species co-existence and biodiversity distribution.