Genetic structure and ecological niche segregation of Indian gray mongoose (Urva edwardsii) in Iran
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Abstract Combining genetic data with ecological niche models is an effective approach for exploring climatic and nonclimatic environmental variables affecting spatial patterns of intraspecific genetic variation. Here, we adopted this combined approach to evaluate genetic structure and ecological niche of the Indian gray mongoose ( Urva edwardsii ) in Iran, as the most western part of the species range. Using mtDNA, we confirmed the presence of two highly differentiated clades. Then, we incorporated ensemble of small models (ESMs) using climatic and nonclimatic variables with genetic data to assess whether genetic differentiation among clades was coupled with their ecological niche. Climate niche divergence was also examined based on a principal component analysis on climatic factors only. The relative habitat suitability values predicted by the ESMs for both clades revealed their niche separation. Between‐clade climate only niche comparison revealed that climate space occupied by clades is similar to some extent, but the niches that they utilize differ between the distribution ranges of clades. We found that in the absence of evidence for recent genetic exchanges, distribution models suggest the species occurs in different niches and that there are apparent areas of disconnection across the species range. The estimated divergence time between the two Iranian clades (4.9 Mya) coincides with the uplifting of the Zagros Mountains during the Early Pliocene. The Zagros mountain‐building event seems to have prevented the distribution of U. edwardsii populations between the western and eastern parts of the mountains as a result of vicariance events. Our findings indicated that the two U. edwardsii genetic clades in Iran can be considered as two conservation units and can be utilized to develop habitat‐specific and climate change‐integrated management strategies.Keywords:
Environmental niche modelling
Genetic divergence
Avian evolutionary studies have recently benefited from a plethora of new techniques as well as conceptual progresses on the evolution of ecological niches. The so-called species distribution models (SDMs) allow for niche quantifications in a way that permits comparisons among species and populations. This review will introduce the theoretical background of niche concepts and niche conservatism, followed by an outline of popular methods for modeling and analyzing environmental niches. A comparison of ecological niches among native and non-native populations of invasive species can reveal niche shifts. They can point to evolutionary changes that evolved over comparatively short time scales of decades to a few centuries. On the other hand, ecological niches can also remain conserved over the invasion process. In a similar way, comparisons of ecological niches are also applicable among closely related taxa. Thereby, it is possible to infer changes of ecological niches over longer time scales and reveal otherwise hidden patterns and processes in the evolutionary history of avian clades. Finally, SDMs offer the potential to contribute to integrative taxonomic studies.
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Climatic niche models for invasive plants are usually constructed with occurrence records taken from literature and collections. Because these data neither discriminate among life-cycle stages of plants (adult or juvenile) nor the origin of individuals (naturally established or man-planted), the resulting models may mispredict the distribution ranges of these species. We propose that more accurate predictions could be obtained by modelling climatic niches with data of naturally established individuals, particularly with occurrence records of juvenile plants because this would restrict the predictions of models to those sites where climatic conditions allow the recruitment of the species. To test this proposal, we focused on the Peruvian peppertree (Schinus molle), a South American species that has largely invaded Mexico. Three climatic niche models were constructed for this species using high-resolution dataset gathered in the field. The first model included all occurrence records, irrespective of the life-cycle stage or origin of peppertrees (generalized niche model). The second model only included occurrence records of naturally established mature individuals (adult niche model), while the third model was constructed with occurrence records of naturally established juvenile plants (regeneration niche model). When models were compared, the generalized climatic niche model predicted the presence of peppertrees in sites located farther beyond the climatic thresholds that naturally established individuals can tolerate, suggesting that human activities influence the distribution of this invasive species. The adult and regeneration climatic niche models concurred in their predictions about the distribution of peppertrees, suggesting that naturally established adult trees only occur in sites where climatic conditions allow the recruitment of juvenile stages. These results support the proposal that climatic niches of invasive plants should be modelled with data of naturally established individuals because this improves the accuracy of predictions about their distribution ranges.
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The ecological niche sensu Hutchinson is defined as the set of environmental conditions allowing a species to grow, maintain, and reproduce. This conception of the niche, which is assimilated to a p-dimensional hypervolume, with p representing all environmental variables, has been widely applied in ecology. However, displaying the niche hypervolume has proved challenging when more than three environmental dimensions are considered simultaneously. We propose a simple method (implemented in the specieschrom R package) that displays the full multidimensionality of the ecological niche of a species into a two-dimensional space by means of a graphic we call species chromatogram. This method gives a graphical summary of the niche by representing together abundance gradients with respect to all environmental variables. A chromatogram enables niche optimums and breaths to be rapidly quantified, and when several chromatograms are examined (one per species), rapid comparisons can be made. From our chromatograms, we proposed a procedure that quantifies niche optimum and breadth as well as niche overlapping (index D) and the identification of the most discriminant combination of environmental variables. We apply these analyses on eight planktonic species collected by the Continuous Plankton Recorder (CPR) survey in the North Atlantic Ocean using 10 environmental variables. We display their full multidimensional niches and quantify their niche optimums and breadths along each dimension. We also compare our index D with other indices by means of hypervolume and dynRB R packages. By catching the full complexity of the niche, species chromatograms allow many different niche properties to be rapidly assessed and compared among species from niche optimums and breadths to the identification of the most relevant environmental parameters and the degree of niche overlapping among species. Species chromatograms may be seen as species' fingerprint and may also allow a better identification of the mechanisms involved in species assembly.
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It has frequently been reported that species with strong niche conservatism will not be able to adapt to new climatic conditions, so they must migrate or go extinct. We have evaluated the shifts in climatic niche occupation of the species Astrophytum coahuilense and its potential distribution in Mexico. We understand niche occupation as the geographic zones with available habitats and with the presence of the species. To assess shifts in climatic niche occupation, we used niche overlap analysis, while potential distribution modeling was performed based on the principle of maximum entropy. The results indicate that this species presents a limited amplitude in its climate niche. This restriction of the climatic niche of A. coahuilense limits its ability to colonize new geographical areas with different climatic environments. On the other hand, the potential distribution models obtained from the present study allow us to identify potential zones based on the climatic requirements of the species. This information is important to identify high priority areas for the conservation of A. coahuilense.
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The aim of the present study was to evaluate the current distribution of suitable niches for the invasive orchid species, Epipactis helleborine, and to estimate the possibility of its further expansion. Moreover, niche modeling tools were used to explain its rapid expansion in North America and to test the niche conservatism of the species. The maximum entropy method was used to create models of the suitable niche distribution. A database of E. helleborine localities was prepared based on the examination of herbarium specimens, information from electronic databases as well as data gathered during field works. The differences between the niches occupied by native and invasive populations were evaluated using the niche overlap and niche identity test indexes. Moreover, the coverage of the most suitable habitats for the species was measured for three future scenarios as well as for the present time model. Populations of E. helleborine occupy North American west coast habitats very similar to those preferred by native, Eurasian populations, while the expansion in the east coast is related to the niche shift. The created models of suitable niche distribution indicate that the species does not realize its potential niche in the native range. The total surface of the habitats potentially available for E. helleborine will decrease in all climate change scenarios created for 2080.
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Abstract Aim Identifying niche shifts is key for forecasting future species distributions. Non‐indigenous species (NIS) are one of the greatest threats to biodiversity, and understanding how niche shifts affect the spread of NIS is fundamental. Here, we modelled the native and introduced niches, as well as the potential geographical extent of a widely distributed NIS, the Pacific oyster Magallana gigas . We then tested for niche shifts in environmental space and predicted spread under contemporary climate change (CCC) conditions. Location Global. Methods We used: (1) the two‐dimensional Centroid shift, Overlap, Unfilling and Expansion (COUE) framework and (2) the n ‐dimensional hypervolume framework (NDH) to quantify the niches in both analogue and total environmental spaces. Niches were tested for equivalency by comparing the observed and randomized overlaps. Ensemble ecological niche models (ENMs) were then used to predict habitat suitability for the present‐day and two future CCC scenarios. Results The NDH framework indicated that the introduced niche of M . gigas has shifted into new environmental conditions compared to the native niche. In contrast, COUE framework implied no niche shift, but the first two dimensions only accounted for a small proportion of the overall environmental variability. Ensemble ENMs revealed suitable areas where M . gigas has yet to be recorded and predicted both a poleward expansion and a tropical contraction of suitable habitat for M . gigas by 2100. Main conclusions We found that M . gigas has rapidly shifted its niche in both analogue and non‐analogue environmental spaces since it was first recorded as introduced species over 50 years ago. Our results suggested that niche shifts facilitate both present‐day and future spread of NIS. Additionally, our study demonstrated the importance of modelling niche dynamics in multidimensional space for predicting range shifts of NIS under CCC.
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Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a likely genetically-based climatic niche expansion of an annual plant invader, the common ragweed (Ambrosia artemisiifolia L.), a highly allergenic invasive species causing substantial public health issues. To do so, we looked for recent evolutionary change at the upward migration front of its adventive range in the French Alps. Based on species climatic niche models estimated at both global and regional scales we stratified our sampling design to adequately capture the species niche, and localized populations suspected of niche expansion. Using a combination of species niche modeling, landscape genetics models and common garden measurements, we then related the species genetic structure and its phenotypic architecture across the climatic niche. Our results strongly suggest that the common ragweed is rapidly adapting to local climatic conditions at its invasion front and that it currently expands its niche toward colder and formerly unsuitable climates in the French Alps (i.e. in sites where niche models would not predict its occurrence). Such results, showing that species climatic niches can evolve on very short time scales, have important implications for predictive models of biological invasions that do not account for evolutionary processes.
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Ambrosia artemisiifolia
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Determining the degree to which climate niches are conserved across plant species' native and introduced ranges is valuable to developing successful strategies to limit the introduction and spread of invasive plants, and also has important ecological and evolutionary implications. Here, we test whether climate niches differ between native and introduced populations of Impatiens walleriana, globally one of the most popular horticultural species. We use approaches based on both raw climate data associated with occurrence points and ecological niche models (ENMs) developed with Maxent. We include comparisons of climate niche breadth in both geographic and environmental spaces, taking into account differences in available habitats between the distributional areas. We find significant differences in climate envelopes between native and introduced populations when comparing raw climate variables, with introduced populations appearing to expand into wetter and cooler climates. However, analyses controlling for differences in available habitat in each region do not indicate expansion of climate niches. We therefore cannot reject the hypothesis that observed differences in climate envelopes reflect only the limited environments available within the species' native range in East Africa. Our results suggest that models built from only native range occurrence data will not provide an accurate prediction of the potential for invasiveness if applied to areas containing a greater range of environmental combinations, and that tests of niche expansion may overestimate shifts in climate niches if they do not control carefully for environmental differences between distributional areas.
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Abstract Niche shifts and environmental non-equilibrium in invading alien species undermine niche-based predictions of alien species’ potential distributions and, consequently, their usefulness for invasion risk assessments. Here, we compared the realized climatic niches of four alien amphibian species ( Hylarana erythraea, Rhinella marina, Hoplobatrachus rugulosus , and Kaloula pulchra ) in their native and Philippine-invaded ranges to investigate niche changes that have unfolded during their invasion and, with this, assessed the extent of niche conservatism and environmental equilibrium. We investigated how niche changes affected reciprocal transferability of ecological niche models (ENMs) calibrated using data from the species’ native and Philippine-invaded ranges, and both ranges combined. We found varying levels of niche change across the species’ realized climatic niches in the Philippines: climatic niche shift for H. rugulosus ; niche conservatism for R. marina and K. pulchra ; environmental non-equilibrium in the Philippine-invaded range for all species; and environmental non-equilibrium in the native range or adaptive changes post-introduction for all species except H. erythraea . Niche changes undermined the reciprocal transferability of ENMs calibrated using native and Philippine-invaded range data. Our paper highlights the difficulty of predicting potential distributions given niche shifts and environmental non-equilibrium; we suggest calibrating ENMs with data from species’ combined native and invaded ranges, and to regularly reassess niche changes and recalibrate ENMs as species’ invasions progress.
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