The importance of defining the geographic distribution of species for conservation: The case of the Bearded Wood-Partridge

Delimitation of the distribution areas of species has fundamental implications for the understanding of biodiversity and for decision-making in conservation. This is illustrated by the case of the Bearded Wood-Partridge (Dendrortyx barbatus), which is endemic to Mexico and was classified as threatened by the IUCN. Recently the discovery of this species in new locations caused an increase in the known distribution area whereupon it was reclassified in a lower risk category. In our study, delimitation and comparison of the Bearded Wood-Partridge distribution area is carried out utilising five different methods: minimum convex polygon; areographic; cartographic; ecological niche modeling; and, “free hand”. A number of locality records are also used to demonstrate the chronological order of appearance. The results show that the size and shape of the distribution area of this species vary depending on the number of records and on their spatial and environmental location, as well as on the particular delimitation method used. However, ecological niche modeling provides the best results in terms of spatial and numerical sensitivity as well as lower values of omission and a moderate extent of predicted areas. We suggest that decisions related to species conservation (categories of risk, areas of endemism, etc.), particularly those species of high geographical restriction, should be contingent on the formalised delimitation of distribution areas based on ecological niche modeling methods.     

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

Despite a growing appreciation of the need to protect sensitive deep sea ecosystems such as cold-water corals, efforts to map the extent of their distribution are limited by their remoteness. Here we develop ecological niche models to predict the likely distributions of cold-water corals based on occurrence records and data describing environmental parameters (e.g. seafloor terrain attributes and oceanographic conditions). This study has used bathymetric data derived from ship-borne multibeam swath systems, species occurrence data from remotely operated vehicle video surveys and oceanographic parameters from hydrodynamic models to predict coral locations in regions where there is a paucity of direct observations. Predictions of the locations of the scleractinian coral, Lophelia pertusa are based primarily upon ecological niche modelling using a genetic algorithm. Its accuracy has been quantified at local (~ 25 km²) and regional scales (~ 4000 km²) along the Irish continental slope using a variety of error assessment techniques and a comparison with another ecological niche modelling technique. With appropriate choices of parameters and scales of analyses, ecological niche modelling has been effective in predicting the distributions of species at local and regional scales. Refinements of this approach have the potential to be particularly useful for ocean management given the need to manage areas of sensitive habitat where survey data are often limited.     

Ecological niche modelling and nDNA sequencing support a new, morphologically cryptic beetle species unveiled by DNA barcoding

Background

DNA sequencing techniques used to estimate biodiversity, such as DNA barcoding, may reveal cryptic species. However, disagreements between barcoding and morphological data have already led to controversy. Species delimitation should therefore not be based on mtDNA alone. Here, we explore the use of nDNA and bioclimatic modelling in a new species of aquatic beetle revealed by mtDNA sequence data.

Methodology/Principal Findings

The aquatic beetle fauna of Australia is characterised by high degrees of endemism, including local radiations such as the genus Antiporus. Antiporus femoralis was previously considered to exist in two disjunct, but morphologically indistinguishable populations in south-western and south-eastern Australia. We constructed a phylogeny of Antiporus and detected a deep split between these populations. Diagnostic characters from the highly variable nuclear protein encoding arginine kinase gene confirmed the presence of two isolated populations. We then used ecological niche modelling to examine the climatic niche characteristics of the two populations. All results support the status of the two populations as distinct species. We describe the south-western species as Antiporus occidentalis sp.n.

Conclusion/Significance

In addition to nDNA sequence data and extended use of mitochondrial sequences, ecological niche modelling has great potential for delineating morphologically cryptic species.     

Integrating expert knowledge and ecological niche models to estimate Mexican primates’ distribution

Ecological niche modeling is used to estimate species distributions based on occurrence records and environmental variables, but it seldom includes explicit biotic or historical factors that are important in determining the distribution of species. Expert knowledge can provide additional valuable information regarding ecological or historical attributes of species, but the influence of integrating this information in the modeling process has been poorly explored. Here, we integrated expert knowledge in different stages of the niche modeling process to improve the representation of the actual geographic distributions of Mexican primates (Ateles geoffroyi, Alouatta pigra, and A. palliata mexicana). We designed an elicitation process to acquire information from experts and such information was integrated by an iterative process that consisted of reviews of input data by experts, production of ecological niche models (ENMs), and evaluation of model outputs to provide feedback. We built ENMs using the maximum entropy algorithm along with a dataset of occurrence records gathered from a public source and records provided by the experts. Models without expert knowledge were also built for comparison, and both models, with and without expert knowledge, were evaluated using four validation metrics that provide a measure of accuracy for presence-absence predictions (specificity, sensitivity, kappa, true skill statistic). Integrating expert knowledge to build ENMs produced better results for potential distributions than models without expert knowledge, but a much greater improvement in the transition from potential to realized geographic distributions by reducing overprediction, resulting in better representations of the actual geographic distributions of species. Furthermore, with the combination of niche models and expert knowledge we were able to identify an area of sympatry between A. palliata mexicana and A. pigra. We argue that the inclusion of expert knowledge at different stages in the construction of niche models in an explicit and systematic fashion is a recommended practice as it produces overall positive results for representing realized species distributions.     

Distribution Pattern and Climate Preferences of the Representatives of the Cosmopolitan Genus Sirthenea Spinola, 1840 (Heteroptera: Reduviidae: Peiratinae)

The main goal of this study was to predict, through the use of GIS tool as ecological niche modelling, potentially suitable ecological niche and defining the conditions of such niche for the representatives of the cosmopolitan genus Sirthenea. Among all known genera of the subfamily Peiratinae, only Sirthenea occurs on almost all continents and zoogeographical regions. Our research was based on 521 unique occurrence localities and a set of environmental variables covering the whole world. Based on occurrence localities, as well as climatic variables, digital elevation model, terrestrial ecoregions and biomes, information about the ecological preferences is given. Potentially useful ecological niches were modelled using Maxent software, which allowed for the creation of a map of the potential distribution and for determining climatic preferences. An analysis of climatic preferences suggested that the representatives of the genus were linked mainly to the tropical and temperate climates. An analysis of ecoregions also showed that they preferred areas with tree vegetation like tropical and subtropical moist broadleaf forests biomes as well as temperate broadleaf and mixed forest biomes. Therefore, on the basis of the museum data on the species occurrence and ecological niche modelling method, we provided new and valuable information on the potentially suitable habitat and the possible range of distribution of the genus Sirthenea along with its climatic preferences.     

Ecology and Geography of Transmission of Two Bat-Borne Rabies Lineages in Chile

Rabies was known to humans as a disease thousands of years ago. In America, insectivorous bats are natural reservoirs of rabies virus. The bat species Tadarida brasiliensis and Lasiurus cinereus, with their respective, host-specific rabies virus variants AgV4 and AgV6, are the principal rabies reservoirs in Chile. However, little is known about the roles of bat species in the ecology and geographic distribution of the virus. This contribution aims to address a series of questions regarding the ecology of rabies transmission in Chile. Analyzing records from 1985–2011 at the Instituto de Salud Pública de Chile (ISP) and using ecological niche modeling, we address these questions to help in understanding rabies-bat ecological dynamics in South America. We found ecological niche identity between both hosts and both viral variants, indicating that niches of all actors in the system are undifferentiated, although the viruses do not necessarily occupy the full geographic distributions of their hosts. Bat species and rabies viruses share similar niches, and our models had significant predictive power even across unsampled regions; results thus suggest that outbreaks may occur under consistent, stable, and predictable circumstances.     

Patterns of Diversity,Areas of Endemism,and Multiple Glacial Refuges for Freshwater Crabs of the Genus Sinopotamon in China (Decapoda: Brachyura: Potamidae)

Previous research has shown that the geographical distribution patterns of freshwater fishes and amphibians have been influenced by past climatic oscillations in China resulting from Pleistocene glacial activity. However, it remains unknown how these past changes have impacted the present-day distribution of Chinese freshwater crabs. This work describes the diversity and endemism of freshwater crabs belonging to Sinopotamon, a highly speciose genus endemic to China, and evaluates its distribution in terms of topography and past climatic fluctuations. Species diversity within Sinopotamon was found to be concentrated in an area from the northeastern edge of the Yunnan-Guizhou Plateau to the Jiangnan Hills, and three areas of endemism were identified. Multiple regression analysis between current climatic variables and Sinopotamon diversity suggested that regional annual precipitation, minimum temperature in the coldest month, and annual temperature range significantly influenced species diversity and may explain the diversity patterns of Sinopotamon. A comparison of ecological niche models (ENMs) between current conditions and the last glacial maximum (LGM) showed that suitable habitat for Sinopotamon in China severely contracted during the LGM. The coincidence of ENMs and the areas of endemism indicated that southeast of the Daba Mountains, and central and southeastern China, are potential Pleistocene refuges for Sinopotamon. The presence of multiple Pleistocene refuges within the range of this genus could further promote inter- and intraspecific differentiations, and may have led to high Sinopotamon species diversity, a high endemism rate and widespread distribution.     

Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar

Although the systematic utility of ecological niche modeling is generally well known (e.g., concerning the recognition and discovery of areas of endemism for biogeographic analyses), there has been little discussion of applications concerning species delimitation, and to date, no empirical evaluation has been conducted. However, ecological niche modeling can provide compelling evidence for allopatry between populations, and can also detect divergent ecological niches between candidate species. Here we present results for two taxonomically problematic groups of Phelsuma day geckos from Madagascar, where we integrate ecological niche modeling with mitochondrial DNA and morphological data to evaluate species limits. Despite relatively modest levels of genetic and morphological divergence, for both species groups we find divergent ecological niches between closely related species and parapatric ecological niche models. Niche models based on the new species limits provide a better fit to the known distribution than models based upon the combined (lumped) species limits. Based on these results, we elevate three subspecies of Phelsuma madagascariensis to species rank and describe a new species of Phelsuma from the P. dubia species group. Our phylogeny continues to support a major endemic radiation of Phelsuma in Madagascar, with dispersals to Pemba Island and the Mascarene Islands. We conclude that ecological niche modeling offers great potential for species delimitation, especially for taxonomic groups exhibiting low vagility and localized endemism and for groups with more poorly known distributions. In particular, niche modeling should be especially sensitive for detecting recent parapatric speciation driven by ecological divergence, when the environmental gradients driving speciation are represented within the ecological niche models.     

Microhabitat of critically endangered Lupinus aridorum (Fabaceae) at wild and introduced locations in Florida scrub

Elucidating microhabitat preferences of a rare species are critical for its conservation. Lupinus aridorum McFarlin ex Beckner (Fabaceae) is a critically endangered plant known only from a few locations in imperiled Florida scrub habitat and nothing is known about its preferred microhabitat. Our goals were threefold. First, determine whether L. aridorum has multiple cytotypes because this can influence its spatial distribution. Second, measure how microhabitat characteristics at locations supporting wild L. aridorum vary from random locations, which will provide information about microhabitat characteristics that influence the spatial distribution of individuals. Third, measure whether microhabitat characteristics differ between locations supporting wild or introduced plants, which will provide information about the realized and fundamental niche. Our research determined that L. aridorum is diploid and grew, on average, in areas closer to trees and shrubs, with lower soil moisture, and with a greater mixture of detritus than random locations. Some microhabitat characteristics at locations where L. aridorum were introduced were similar to microhabitat supporting wild L. aridorum, but multiple soil characteristics differed as did the plant community, which contained more nonnative plant species near introduced plants. Therefore, the realized niche is narrower than the fundamental niche. Overall, information about the microhabitat of L. aridorum can be used to design appropriate management programs to conserve and restore populations of this plant species and species that occupy a similar niche in imperiled Florida scrub.     

Pleistocene survival on central Alpine nunataks: genetic evidence from the jumping bristletail Machilis pallida

Mechanisms of survival during the Pleistocene glaciation periods have been studied for more than a century. Until now, molecular studies that confirmed animal survival on Alpine nunataks, that is, ice‐free summits surrounded by glaciers, were restricted to peripheral areas. Here, we search for molecular signatures of inner‐Alpine survival of the narrow endemic and putatively parthenogenetic Alpine jumping bristletail Machilis pallida combining mitochondrial and AFLP data from its three known populations. The mitochondrial data indicate survival on both peripheral and central nunataks, the latter suggesting that refugia in the centre of the Alpine main ridge were more widespread than previously recognized. Incongruences between mitochondrial and AFLP patterns suggest a complex evolutionary history of the species and may be explained via parallel fixation of parthenogenesis of different origins during the last glacial maximum. We suggest that the inferred parthenogenesis may have been essential for central nunatak survival, but may pose a serious threat for M. pallida in consideration of the present climatic changes.     

Disentangling the drivers of continental mammalian endemism

Endemic species and species with small ranges are ecologically and evolutionarily distinct and are vulnerable to extinction. Determining which abiotic and biotic factors structure patterns of endemism on continents can advance our understanding of global biogeographic processes, but spatial patterns of mammalian endemism have not yet been effectively predicted and reconstructed. Using novel null model techniques, we reconstruct trends in mammalian endemism and describe the isolated and combined effects of physiographic, ecological, and evolutionary factors on endemism. We calculated weighted endemism for global continental ecoregions and compared the spatial distribution of endemism to niche-based, geographic null models of endemism. These null models distribute species randomly across continents, simulating their range sizes from their degree of climatic specialization. They isolate the effects of physiography (topography and climate) and species richness on endemism. We then ran linear and structural models to determine how topography and historical climate stability influence endemism. The highest rates of mammalian endemism were found in topographically rough, climatically stable ecoregions with many species. The null model that isolated physiography did not closely approximate the observed distribution of endemism (r² = .09), whereas the null model that incorporated both physiography and species richness did (r² = .59). The linear models demonstrate that topography and climatic stability both influenced endemism values, but that average climatic niche breadth was not highly correlated with endemism. Climate stability and topography both influence weighted endemism in mammals, but the spatial distribution of mammalian endemism is driven by a combination of physiography and species richness. Despite its relationship to individual range size, average climate niche breadth has only a weak influence on endemism. The results highlight the importance of historical biogeographic processes (e.g. centers of speciation) and geography in driving endemism patterns, and disentangle the mechanisms structuring species ranges worldwide.     

Interpreting the Process behind Endemism in China by Integrating the Phylogeography and Ecological Niche Models of the Stachyridopsis ruficeps

An area of endemism (AOE) is a complex expression of the ecological and evolutionary history of a species. Here we aim to address the principal drivers of avian diversification in shaping patterns of endemism in China by integrating genetic, ecological, and distributional data on the Red-headed Tree Babbler (Stachyridopsis ruficeps), which is distributed across the eastern Himalayas and south China. We sequenced two mtDNA markers from 182 individuals representing all three of the primary AOEs in China. Phylogenetic inferences were used to reconstruct intraspecific phylogenetic relationships. Divergence time and population demography were estimated to gain insight into the evolutionary history of the species. We used Ecological niche modeling to predict species’ distributions during the Last Glacial Maximum (LGM) and in the present. Finally, we also used two quantitative tests, an identity test and background test to assess the similarity of ecological niche preferences between adjacent lineages. We found five primary reciprocally monophyletic clades, typically separated approximately 0.2–2.27 MYA, of which three were deeply isolated endemic lineages located in the three AOEs. All phylogroups were detected to have undergone population expansion during the past 0.3 MY. Niche models showed discontinuous habitats, and there were three barriers of less suitable habitat during the LGM and in modern times. Ecoclimatic niches may diverge significantly even over recent timescales, as each phylogroup had a unique distribution, and unique niche characteristics. Vicariant events associated with geographical and ecological barriers, glacial refuges and ecological differentiation may be the main drivers forming the pattern of endemism in China.     

Potential distributions of phlebotomine sandfly vectors of human visceral leishmaniasis caused by Leishmania infantum in Morocco

Zoonotic visceral leishmaniasis is a common vector-borne systemic disease caused by Leishmania infantum (Kinetoplastida: Trypanosomatidae). In Morocco the situation is complex: many sandfly species have been collected in areas in which the disease is endemic, but only Phlebotomus ariasi, Phlebotomus perniciosus and Phlebotomus longicuspis (Diptera: Psychodidae) have been confirmed to have vectorial roles. The objective of the present study was to ascertain the potential distribution of L. infantum and its vectors in Morocco, using ecological niche modelling. Vector records were obtained from field collections of the Laboratory team and from previously published entomological observations. Epidemiological data for L. infantum modelling were obtained from Moroccan Ministry of Health reports. The jackknife test indicated that the bioclimatic variables with the greatest influence on model development for all species were annual precipitation and precipitation in the driest quarter of the year. MaxEnt model representations for sandfly species that act as vectors of L. infantum showed the widespread geographic distribution of these species in Morocco, specifically in northern and central Morocco, where foci of visceral leishmaniasis are found. The ecological niche modelling points out areas in which the probability of occurrence of these species is higher. This information should be considered as a starting point for further research to fully elucidate the ecology and epidemiology of these species, as well as of the pathogens they transmit.     

Predicting fundamental and realized distributions based on thermal niche: A case study of a freshwater turtle

Species distribution models (SDM) have been broadly used in ecology to address theoretical and practical problems. Currently, there are two main approaches to generate SDMs: (i) correlative, which is based on species occurrences and environmental predictor layers and (ii) process-based models, which are constructed based on species' functional traits and physiological tolerances. The distributions estimated by each approach are based on different components of species niche. Predictions of correlative models approach species realized niches, while predictions of process-based are more akin to species fundamental niche. Here, we integrated the predictions of fundamental and realized distributions of the freshwater turtle Trachemys dorbigni. Fundamental distribution was estimated using data of T. dorbigni's egg incubation temperature, and realized distribution was estimated using species occurrence records. Both types of distributions were estimated using the same regression approaches (logistic regression and support vector machines), both considering macroclimatic and microclimatic temperatures. The realized distribution of T. dorbigni was generally nested in its fundamental distribution reinforcing theoretical assumptions that the species' realized niche is a subset of its fundamental niche. Both modelling algorithms produced similar results but microtemperature generated better results than macrotemperature for the incubation model. Finally, our results reinforce the conclusion that species realized distributions are constrained by other factors other than just thermal tolerances.     

Geographic distribution and phenetic skull variation in two close species of Graomys (Rodentia, Cricetidae, Sigmodontinae)

The interspecific differentiation of South American rodents of the genus Graomys was assayed at ecological and morphometric levels in two species. At the ecological level, niche modelling was used. At the morphometric level, the hypothesis that the size and shape of the skull vary with the geographic location was tested using geometric morphometrics by assessing the extent and spatial distribution of phenotypic skull variation within and among two species, Graomys griseoflavus and Graomys chacoensis. Our results of niche modelling indicate the spatial differentiation between the two species, with G. chacoensis inhabiting preferably the Chaco ecoregion and G. griseoflavus inhabiting mainly the Monte ecoregion. In multiple linear regressions, approximately 20% of the skull size variation is explained by latitude, altitude, and temperature seasonality. The partial least square analysis reveals strong correlation between shape and environmental variables, mainly with latitude, annual mean temperature, and annual precipitation. Discrimination between G. griseoflavus and G. chacoensis was highly reliable when using geometric morphometric tools. These results permit us to elucidate some evolutionary processes that have occurred in these species.     

Modeling the distribution of a wide‐ranging invasive species using the sampling efforts of expert and citizen scientists

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Conservation study of an endangered stingless bee (Melipona capixaba—Hymenoptera: Apidae) with restricted distribution in Brazil

Melipona capixaba, popularly known as “uruçu preta”, is a stingless bee restricted to the mountainous Atlantic Rainforest areas of Espírito Santo State, Brazil. Due to the endemism and small population size, this species discovered in 1994 is now considered “vulnerable to extinction”. Using ISSR, PCR–RFLP and microsatellites markers, we studied the genetic variability and structure of M. capixaba from 88 colonies collected throughout the distribution area of the species within Espírito Santo State. The microsatellite, ISSR and mitochondrial haplotype analyses showed that M. capixaba has low genetic variability compared to other insect species. The molecular analyses also indicated a high genetic similarity among the M. capixaba samples, with no clear pattern of structuring. The analyses of molecular variance results indicated that most of the total genetic variation in M. capixaba was explained by the genetic diversity within local populations. Results suggest that the analyzed samples could be treated as a single population for preservation purposes. Thus, given its endemism, local adaptation and low number of natural colonies, efforts for the conservation of M. capixaba should focus on preservation and increasing the number of colonies in the wild, so that M. capixaba can support constant captures and the effects of habitat deforestation in Espírito Santo State.     

Worldwide Niche and Future Potential Distribution of Culicoides imicola,a Major Vector of Bluetongue and African Horse Sickness Viruses

We modelled the ecoclimatic niche of Culicoides imicola, a major arthropod vector of midge-borne viral pathogens affecting ruminants and equids, at fine scale and on a global extent, so as to provide insight into current and future risks of disease epizootics, and increase current knowledge of the species'' ecology. Based on the known distribution and ecology of C. imicola, the species'' response to monthly climatic conditions was characterised using CLIMEX with 10′ spatial resolution climatic datasets. The species'' climatic niche was projected worldwide and under future climatic scenarios. The validated model highlights the role of irrigation in supporting the occurrence of C. imicola in arid regions. In Europe, the modelled potential distribution of C. imicola extended further West than its reported distribution, raising questions regarding ongoing process of colonization and non-climatic habitat factors. The CLIMEX model highlighted similar ecological niches for C. imicola and the Australasian C. brevitarsis raising questions on biogeography and biosecurity. Under the climate change scenarios considered, its'' modelled potential distribution could expand northward in the Northern hemisphere, whereas in Africa its range may contract in the future. The biosecurity risks from bluetongue and African horse sickness viruses need to be re-evaluated in regions where the vector''s niche is suitable. Under a warmer climate, the risk of vector-borne epizootic pathogens such as bluetongue and African horse sickness viruses are likely to increase as the climate suitability for C. imicola shifts poleward, especially in Western Europe.