Evolutionary applications of phylogenetically-informed ecological niche modelling (ENM) to explore cryptic diversification over cryptic refugia

Niche conservatism providing support for using ecological niche modeling in biological invasions has been widely noticed; nonetheless, the impacts of human disturbance on niche changes and model predictions are not fully recognized. In this study, climate niche changes during the invasion of Japanese beetle (Popillia japonica) were studied under the framework of niche unfilling, stability, and expansion situations. The beetle might undergo niche expansion because of the small native range (Japan) relative to the broad invade range (North America). Relative roles of climatic and anthropogenic factors and their interactions in determining the spread of P. japonica were investigated. Results suggest that the climate niche was conserved during P. japonica invasion, climate niche unfilling rather than niche expansion was observed, suggesting there are suitable climate space remain unoccupied. Inclusion of anthropogenic factors into climate niche model has improved niche model prediction values in areas of high human activity. During P. japonica invasion, anthropogenic factors influenced the climate niche expression and altered the effect of climate suitability. In areas of poor or unsuitable climate, the human activities facilitated the establishment of P. japonica and functioned synergistically, whereas in highly suitable areas, including anthropogenic variables decreased climate suitability. These findings are pivotal to our understanding of climate niche conservatism and niche model transferability when predicting areas of invasion of P. japonica and can be applied elsewhere for predicting other pest’s invasion potential.

Hyrcanian (Caspian) forest in northern Iran has a richness of biological diversity, with endemic and endangered species, and a diverse range of economic and social conditions. The aim of this study is a study of the plant diversity in Lajim forest, Mazandaran province, north of Iran (Hyrcanian forest). In this study 100 circle sample plots (400 m2) were collected by random method. In every sample plot the kind of species and number of trees, shrub and Herbaceous were recorded. Species diversity indexes including Shannon Wiener (H׳), Simpson (1-D) and Margaleff (R1). Data analyzing was done by Past and Ecological Methodological software’s. Results showed that a total of 58 plant species were found in the studied area, of which 14 woody species (10 trees, 4 shrubs) and 44 herbaceous species existed (Table 1). Rosaceae and Fagaceae families play an important role in among plant species. Overall showed that the herbaceous are highest richness, evenness and diversity and Margaleff index has highest average in this study area.

Preferred prey reduce species realized niche shift and improve range expansion prediction

BackgroundDue to climate change, the geographical distribution of sand flies during the last decades has shifted northward from latitudes below 45°N in southern Europe to latitudes just above 50○N. Recent studies show that some phlebotomine sand flies were recorded in several parts of Germany and Belgium. In central Europe, some autochthone leishmaniasis cases are being recorded in regions traditionally regarded as leishmaniasis-free. An important challenge is to predict the geographical distribution of leishmaniasis vectors under new climatic conditions. In this study, we attempted to predict the current distribution of six leishmaniasis vectors in the Mediterranean basin and forecast species’ geographical shift under future climate scenarios using an ensemble ecological niche modeling approach. Species records were obtained from scientific surveys published in the research literature between 2006 and 2016. A series of climate metrics describing temperature and precipitation in the study area under two climatic scenarios were obtained from WorldClim database. A consensus model was derived from six varieties of modeling approaches (regression, machine learning and classification techniques) in order to ensure valid prediction of distribution of vectors under different climate scenarios.ResultsModel performance was generally high for the included species with a specificity (true negative rate) ranging from 81.03 to 96.52% (mean = 86.94%) and a sensitivity (true positive rate) ranging from 87.93 to 100% (mean = 96.98%). Our work evidenced the hypothesis of the widespread of Leishmania vectors under climate change scenarios. All of the studied species are prospected to gain new areas that are actually not suitable for vectors’ survival. Phlebotomine sand flies are prospected to invade extra-Mediterranean regions, especially western and central Europe.ConclusionsOur study confirmed the importance of environmental and climate factors on the distribution of leishmaniasis vectors and demonstrated the performance of ecological niche modeling in the prediction of the geographical spread of vector-borne diseases. Ecological niche modeling should be considered in the future as a valuable tool in addition to experimental laboratory studies for a better understanding of the biology of vector species.

Endogenous selection is often implicated in the maintenance of stability of natural hybrid zones. Environmental conditions often vary across these zones, suggesting that local adaptation to ecological conditions could also play a role in this process. We used niche modeling to investigate these alternatives in a hybrid zone between two species of brown lemur (Eulemur rufifrons and E. cinereiceps) in southeastern Madagascar. We produced ecological niche models (ENMs) for parental and hybrid populations and compared values of niche overlap to null expectations using identity and background tests. All three taxonomic groups had nonequivalent ENMs with limited spatial overlap, supporting a role for niche divergence and local adaptation in the maintenance of this zone. However, values of niche overlap between ENMs were not greater than null expectations controlling for background environmental differences. These results could suggest that taxa in this hybrid zone inhabit portions of their environments that are more similar to their backgrounds, i.e., niche conservatism. Nevertheless, we did find evidence of niche divergence when using background tests that examined environmental variables separately. Although we could not rule out models indicating selection against hybrids, most lines of evidence were consistent with predictions for the bounded superiority model of hybrid zone stability. This study thus provides support that exogenous, environmental selection may be responsible for maintaining the hybrid zone, and may be implicated in the evolutionary divergence of these taxa.

Niche divergence or conservatism and phenotypic adaptation are important in lineage diversification. We used mitochondrial DNA (mtDNA), morphology and ecological niche models to examine these processes in three subspecies of Sage Sparrow (Artemisiospiza belli belli, A. b. canescens and A. b. nevadensis) that breed in bioclimatically diverse ecoregions in western North America. Overall, mtDNA and morphology are congruent with subspecies, ecoregion and bioclimatic niche. Niche divergence, rather than niche conservatism, accompanied by phenotypic adaptation, is associated with lineage diversification between subspecies. This diversification has occurred with and without physical barriers or accompanying genetic divergence. Populations of A. b. canescens are divided by a montane barrier into two bioclimatic regions (San Joaquin Valley, Mojave Desert), where they are indistinguishable phenotypically, but show distinctive genetic patterns. Although there is no physical barrier between A. b. canescens in the San Joaquin Valley and A. b. belli in the Coast Ranges, these populations occupy different bioclimatic niches and are phenotypically, but not genetically, diagnosable. Niche overlap is greatest between A. b. canescens from the Mojave Desert and A. b. nevadensis from the Great Basin, yet these subspecies maintain distinctive phenotypes and mtDNA, even in local secondary contact and sympatry. Palaeoclimatic niche models for the Last Glacial Maximum (c. 21 000 bp) and the Last Interglacial (c. 120 000 bp) suggest that ecoregionally distinct populations of Artemisiospiza belli experienced different Pleistocene range fluctuations and glacial refugia, with temporal niche conservatism. Populations probably reached their current distributions as favourable climates and habitats expanded after the last glaciation. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.

This chapter discusses the conceptual basis of using ecological niche modeling for discovering new elements of biodiversity. More specifically, it examines the use of ecological niche models to guide searches for and discovery of unknown populations of species as well as species limits. It also explains how niche conservatism provides some degree of predictability across related taxa and makes the use of niche models for discovering biodiversity possible. For applications focused on discovery of unknown species, the chapter shows that niche conservatism is necessary if predictions of likely distributional areas are to prove realistic. Finally, it reviews practical considerations that must be taken into account in applications of ecological niche models oriented at discovering biodiversity, along with the caveats and limitations of such applications.

Sparse distributional data, taxonomic uncertainty, and cryptic diversity present significant barriers to building reliable species‐level ecological niche models (ENMs). Supraspecific ENMS hold potential to address these challenges by combining data across multiple species to capture shared habitat associations. This study investigated the application of supraspecific ENMs to predict the distribution of primary burrowing crayfish, a freshwater faunal group with taxonomic ambiguity and limited historical data. We developed four Maxent ENMs for three of the most widespread burrowing crayfish species in the United States— Creaserinus fodiens (Cottle 1863), Procambarus gracilis (Bundy 1876), and Lacunicambarus ludovicianus (Faxon 1884)—and a combined supraspecific dataset using spatially filtered historical records of all three species. We conducted field validation across 96 semi‐randomly selected sites in Missouri, United States, stratified by habitat suitability quartiles. Model performance was assessed using a suite of threshold dependent and independent metrics to evaluate discrimination and calibration. Modelling above the species level successfully identified suitable habitat for burrowing crayfish as a group. Field validation confirmed the model's predictive ability, with crayfish detected at 35 locations, including 11 sites where Lacunicambarus species not used in model training were found. Our Maxent models performed significantly better than expected by chance and showed that broadly suitable burrowing crayfish habitat consisted of shallow water tables, low elevation, low average maximum daily temperatures, and moderate annual precipitation. Our findings suggest that burrowing crayfish species may exhibit shared habitat associations, making them strong candidates for supraspecific modelling approaches, especially in regions with limited historical records or lineages with unresolved taxonomy and cryptic diversity. Further, by using species from three different genera, we demonstrated that supraspecific ENMs based on ecological traits, rather than phylogeny, offer a promising tool for extending distributional knowledge and informing conservation planning for data‐poor taxa.

Aim To investigate relative niche stability in species responses to various types of environmental pressure (biotic and abiotic) on geological time‐scales using the fossil record.Location The case study focuses on Late Ordovician articulate brachiopods of the Cincinnati Arch in eastern North America.Methods Species niches were modelled for a suite of fossil brachiopod species based on five environmental variables inferred from sedimentary parameters using GARP and Maxent. Niche stability was assessed by comparison of (1) the degree of overlap of species distribution models developed for a time‐slice and those generated by projecting niche models of the previous time‐slice onto environmental layers of a second time‐slice using GARP and Maxent, (2) Schoener’s D statistic, and (3) the similarity of the contribution of each environmental parameter within Maxent niche models between adjacent time‐slices.Results Late Ordovician brachiopod species conserved their niches with high fidelity during intervals of gradual environmental change but responded to inter‐basinal species invasions through niche evolution. Both native and invasive species exhibited similar levels of niche evolution in the invasion and post‐invasion intervals. Niche evolution was related mostly to decreased variance within the former ecological niche parameters rather than to shifts to new ecospace.Main conclusions Although the species examined exhibited morphological stasis during the study interval, high levels of niche conservatism were observed only during intervals of gradual environmental change. Rapid environmental change, notably inter‐basinal species invasions, resulted in high levels of niche evolution among the focal taxa. Both native and invasive species responded with similar levels of niche evolution during the invasion interval and subsequent environmental reorganization. The assumption of complete niche conservatism frequently employed in ecological niche modelling (ENM) analyses to forecast or hindcast species geographical distributions is more likely to be accurate for climate change studies than for invasive species analyses over geological time‐scales.

The management of invasive plant species (IPS) requires knowledge of areas susceptible to invasion and the origin of the invasive biotypes. Ecological niche models (ENMs) are useful for these purposes, but modeling results depend on the data sources. We propose a synthetic approach to determine the selection of data source areas considering the invasion status of an IPS and management objectives to deal with the IPS. We assessed the importance of data source for ENMs and their projections to invasive areas using Chromolaena odorata, a Neotropical weed, in South Africa where this IPS is invading. We used MaxEnt to perform ENMs using different datasets from C. odorata's native range and from South Africa. We employed reciprocal ENM projections to find the probable native region of the plants invading South Africa. ENMs varied depending on the native area selected as the hypothetical invasion source. The modeling approach using worldwide data was most appropriate for prevention purposes, whereas the modelling approach using data from the Americas was most suitable for estimating invasion-susceptible areas in South Africa. The South African ENM was useful for reciprocal modelling but not for prediction of areas susceptible to invasion. ENM projections from the Americas to South Africa and vice-versa identified two native areas as possible invasion sources (northern Mexico and southern tropical South America). Their concordance with the South African ENM can be useful to search for natural enemies of C. odorata's and to reinforce the identification of invasion-susceptible areas in South Africa. We suggest that the various ENM obtained with the synthetic approach in modeling with different data sources for C. odorata cover the scenarios that depend on management purpose and invasion status for this weed.

Ecological niche modelling of the distribution of cold-water coral habitat using underwater remote sensing data

Most species data display spatial autocorrelation that can affect ecological niche models (ENMs) accuracy‐statistics, affecting its ability to infer geographic distributions. Here we evaluate whether the spatial autocorrelation underlying species data affects accuracy‐statistics and map the uncertainties due to spatial autocorrelation effects on species range predictions under past and future climate models. As an example, ENMs were fitted to Qualea grandiflora (Vochysiaceae), a widely distributed plant from Brazilian Cerrado. We corrected for spatial autocorrelation in ENMs by selecting sampling sites equidistant in geographical (GEO) and environmental (ENV) spaces. Distributions were modelled using 13 ENMs evaluated by two accuracy‐statistics (TSS and AUC), which were compared with uncorrected ENMs. Null models and the similarity statistics I were used to evaluate the effects of spatial autocorrelation. Moreover, we applied a hierarchical ANOVA to partition and map the uncertainties from the time (across last glacial maximum, pre‐insustrial, and 2080 time periods) and methodological components (ENMs and autocorrelation corrections). The GEO and ENV models had the highest accuracy‐statistics values, although only the ENV model had values higher than expected by chance alone for most of the 13 ENMs. Uncertainties from time component were higher in the core region of the Brazilian Cerrado where Q. grandiflora occurs, whereas methodological components presented higher uncertainties in the extreme northern and southern regions of South America (i.e. outside of Brazilian Cerrado). Our findings show that accounting for autocorrelation in environmental space is more efficient than doing so in geographical space. Methodological uncertainties were concentrated in outside the core region of Q. grandiflora 's habitat. Conversely, uncertainty due to time component in the Brazilian Cerrado reveals that ENMs were able to capture climate change effects on Q. grandiflora distributions.

Rethinking receiver operating characteristic analysis applications in ecological niche modeling

Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization of environmental tolerances. We present a new method for phylogenetic niche modeling, implemented in R. Given past and present climate data, taxon occurrence data, and a time-calibrated phylogeny, our method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. Models either at nodes or along branches of the phylogeny can be estimated. We demonstrate our method on a small group of dendrobatid frogs and show that it can make inferences given species with restricted ranges and little occurrence data. We also use simulations to show that our method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space. Our method brings together fields as disparate as ecological niche modeling, phylogenetics, and ancestral range estimation in a user-friendly package. [Ancestral range estimation; ancestral state reconstruction; biogeography; Dendrobatidae; ecological niche modeling; paleoclimate; phylogeography; species distribution modeling.].

Improving the validation of ecological niche models with remote sensing analysis