A simple method to estimate the probable distribution of species

Species distribution models (SDMs) are broadly used to predict species distributions from available presence data. However, SDMs results have been criticized for several reasons mainly related to two basic characteristics of most SDMs: 1) general lack of reliable species absence information, 2) the frequent use of an arbitrary geographical extent (GE) or accessible area of the species. These impediments have motivated us to generate a procedure called niche of occurrence (NOO). NOO provides the probable distribution of species (realized niche) relying solely on partial information about presence of species. It operates within a natural geographical extent delimited by available observations and avoids using misleading thresholds to obtain binary presence–absence estimations when the species prevalence is unknown. In this study the main characteristics of NOO are presented, comparing its performance with other recognized and more complex SDMs by using virtual species to avoid the omnipresent error sources of real data sets.     

Ecological divergence and speciation between lemur (Eulemur) sister species in Madagascar

Understanding ecological niche evolution over evolutionary timescales is crucial to elucidating the biogeographic history of organisms. Here, we used, for the first time, climate‐based ecological niche models (ENMs) to test hypotheses about ecological divergence and speciation processes between sister species pairs of lemurs (genus Eulemur) in Madagascar. We produced ENMs for eight species, all of which had significant validation support. Among the four sister species pairs, we found nonequivalent niches between sisters, varying degrees of niche overlap in ecological and geographic space, and support for multiple divergence processes. Specifically, three sister‐pair comparisons supported the null model that niches are no more divergent than the available background region. These findings are consistent with an allopatric speciation model, and for two sister pairs (E. collaris–E. cinereiceps and E. rufus–E. rufifrons), a riverine barrier has been previously proposed for driving allopatric speciation. However, for the fourth sister pair E. flavifrons–E. macaco, we found support for significant niche divergence, and consistent with their parapatric distribution on an ecotone and the lack of obvious geographic barriers, these findings most strongly support a parapatric model of speciation. These analyses thus suggest that various speciation processes have led to diversification among closely related Eulemur species.     

The geography and ecology of plant speciation: range overlap and niche divergence in sister species

A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under ‘budding’ speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister–non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities.     

Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula

Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake ( Lampropeltis getula ), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b . We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.     

Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda

Aim Because of their broad distribution in geographical and ecological dimensions, seaweeds (marine macroalgae) offer great potential as models for marine biogeographical inquiry and exploration of the interface between macroecology and macroevolution. This study aims to characterize evolutionary niche dynamics in the common green seaweed genus Halimeda, use the observed insights to gain understanding of the biogeographical history of the genus and predict habitats that can be targeted for the discovery of species of special biogeographical interest. Location Tropical and subtropical coastal waters. Methods The evolutionary history of the genus is characterized using molecular phylogenetics and relaxed molecular clock analysis. Niche modelling is carried out with maximum entropy techniques and uses macroecological data derived from global satellite imagery. Evolutionary niche dynamics are inferred through application of ancestral character state estimation. Results A nearly comprehensive molecular phylogeny of the genus was inferred from a six‐locus dataset. Macroecological niche models showed that species distribution ranges are considerably smaller than their potential ranges. We show strong phylogenetic signal in various macroecological niche features. Main conclusions The evolution of Halimeda is characterized by conservatism for tropical, nutrient‐depleted habitats, yet one section of the genus managed to invade colder habitats multiple times independently. Niche models indicate that the restricted geographical ranges of Halimeda species are not due to habitat unsuitability, strengthening the case for dispersal limitation. Niche models identified hotspots of habitat suitability of Caribbean species in the eastern Pacific Ocean. We propose that these hotspots be targeted for discovery of new species separated from their Caribbean siblings since the Pliocene rise of the Central American Isthmus.     

Alpine glacial relict species losing out to climate change: The case of the fragmented mountain hare population (Lepus timidus) in the Alps

Alpine and Arctic species are considered to be particularly vulnerable to climate change, which is expected to cause habitat loss, fragmentation and—ultimately—extinction of cold‐adapted species. However, the impact of climate change on glacial relict populations is not well understood, and specific recommendations for adaptive conservation management are lacking. We focused on the mountain hare (Lepus timidus) as a model species and modelled species distribution in combination with patch and landscape‐based connectivity metrics. They were derived from graph‐theory models to quantify changes in species distribution and to estimate the current and future importance of habitat patches for overall population connectivity. Models were calibrated based on 1,046 locations of species presence distributed across three biogeographic regions in the Swiss Alps and extrapolated according to two IPCC scenarios of climate change (RCP 4.5 & 8.5), each represented by three downscaled global climate models. The models predicted an average habitat loss of 35% (22%–55%) by 2100, mainly due to an increase in temperature during the reproductive season. An increase in habitat fragmentation was reflected in a 43% decrease in patch size, a 17% increase in the number of habitat patches and a 34% increase in inter‐patch distance. However, the predicted changes in habitat availability and connectivity varied considerably between biogeographic regions: Whereas the greatest habitat losses with an increase in inter‐patch distance were predicted at the southern and northern edges of the species’ Alpine distribution, the greatest increase in patch number and decrease in patch size is expected in the central Swiss Alps. Finally, both the number of isolated habitat patches and the number of patches crucial for maintaining the habitat network increased under the different variants of climate change. Focusing conservation action on the central Swiss Alps may help mitigate the predicted effects of climate change on population connectivity.     

Assessing the impact of deforestation and climate change on the range size and environmental niche of bird species in the Atlantic forests,Brazil

Aim Habitat loss and climate change are two major drivers of biological diversity. Here we quantify how deforestation has already changed, and how future climate scenarios may change, environmental conditions within the highly disturbed Atlantic forests of Brazil. We also examine how environmental conditions have been altered within the range of selected bird species. Location Atlantic forests of south‐eastern Brazil. Methods The historical distribution of 21 bird species was estimated using Maxent . After superimposing the present‐day forest cover, we examined the environmental niches hypothesized to be occupied by these birds pre‐ and post‐deforestation using environmental niche factor analysis (ENFA). ENFA was also used to compare conditions in the entire Atlantic forest ecosystem pre‐ and post‐deforestation. The relative influence of land use and climate change on environmental conditions was examined using analysis of similarity and principal components analysis. Results Deforestation in the region has resulted in a decrease in suitable habitat of between 78% and 93% for the Atlantic forest birds included here. Further, Atlantic forest birds today experience generally wetter and less seasonal forest environments than they did historically. Models of future environmental conditions within forest remnants suggest generally warmer conditions and lower annual variation in rainfall due to greater precipitation in the driest quarter of the year. We found that deforestation resulted in a greater divergence of environmental conditions within Atlantic forests than that predicted by climate change. Main conclusions The changes in environmental conditions that have occurred with large‐scale deforestation suggest that selective regimes may have shifted and, as a consequence, spatial patterns of intra‐specific variation in morphology, behaviour and genes have probably been altered. Although the observed shifts in available environmental conditions resulting from deforestation are greater than those predicted by climate change, the latter will result in novel environments that exceed temperatures in any present‐day climates and may lead to biotic attrition unless organisms can adapt to these warmer conditions. Conserving intra‐specific diversity over the long term will require considering both how changes in the recent past have influenced contemporary populations and the impact of future environmental change.     

Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges

Aim The goal of this study was to determine the extent of suitable habitats across the basins and ranges of the Great Basin for 13 montane mammals in the present and during the Last Glacial Maximum (LGM). For all these mammal species, we test whether: (1) more suitable habitat was available in basin areas during the LGM; (2) suitable habitat shifted upwards in elevation between the LGM and the present; (3) more ranges have suitable habitat than are currently occupied; and (4) these species are currently restricted to suitable habitats at higher‐elevation range areas. We also examine whether and how much distributional response varies among these montane mammal species. Location The Great Basin of western North America. Methods We re‐examine the past and present distributions of 13 Great Basin montane mammals using ecological niche modelling techniques that utilize now widely available species occurrence data and new, fine‐scale past climatological GIS layers in the present and at the LGM. These methods provide an objective, repeatable means for visual comparison of past and present modelled distributions for species examined in previous biogeographical studies. Results Our results indicate greater areal and lower elevational suitable habitat in the LGM than at present for nearly all montane mammals, and that there is more suitable habitat at present than is currently occupied. Our results also show that lowland areas provide suitable dispersal routes between ranges for most of the montane mammals both at the LGM and at present. However, three of the 13 species have little to no predicted suitable habitat in the LGM near currently occupied ranges, in contrast to the pattern for the other 10. For these species, the model results support more recent long‐distance colonization. Main conclusions Our finding of suitable lowland dispersal routes in the present for most species supports and greatly extends similar findings from single‐species studies. Our results also provide a visually striking confirmation that changes in species distribution and colonization histories of Great Basin montane mammals vary in a fashion related to the tolerances and requirements of each of these species; this has previously been hypothesized but not rigorously tested for multiple montane mammals in the region.     

Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species

Evolutionary biologists have often suggested that ecology is important in speciation, in that natural selection may drive adaptive divergence between lineages that inhabit different environments. I suggest that it is the tendency of lineages to maintain their ancestral ecological niche (phylogenetic niche conservatism) and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation. Niche conservatism may be an important and widespread component of allopatric speciation but is largely unstudied. The perspective outlined here suggests roles for key microevolutionary processes (i.e., natural selection, adaptation) that are strikingly different from those proposed in previous literature on ecology and speciation. Yet, this perspective is complementary to the traditional view because it focuses on a different temporal stage of the speciation process.     

Combined modelling of distribution and niche in invasion biology: a case study of two invasive Tetramorium ant species

Spatial modelling of species distributions has become an important tool in the study of biological invasions. Here, we examine the utility of combining distribution and ecological niche modelling for retrieving information on invasion processes, based on species occurrence data from native and introduced ranges. Specifically, we discuss questions, concerning (1) the global potential to spread to other ranges, (2) the potential to spread within established invasions, (3) the detectability of niche differences across ranges, and (4) the ability to infer invasion history through data from the introduced range. We apply this approach to two congeneric pavement ants, Tetramorium sp.E (formerly T. caespitum (Linnaeus 1758)) and T. tsushimae Emery 1925, both introduced to North America. We identify (1) the potential of both species to inhabit ranges worldwide, and (2) the potential of T. sp.E and T. tsushimae, to spread to 23 additional US states and to five provinces of Canada, and to 24 additional US states and to one province of Canada, respectively. We confirm that (3) niche modelling can be an effective tool to detect niche shifts, identifying an increased width of T. sp.E and a decreased width of T. tsushimae following introduction, with potential changes in niche position for both species. We make feasible that (4) combined modelling could become an auxiliary tool to reconstruct invasion history, hypothesizing admixture following multiple introductions in North America for T. sp.E, and a single introduction to North America from central Japan, for T. tsushimae. Combined modelling represents a rapid means to formulate testable explanatory hypotheses on invasion patterns and helps approach a standard in predictive invasion research.     

Evidence of environmental niche differentiation in the striped mouse (Rhabdomys sp.): inference from its current distribution in southern Africa

The aim of this study was to characterize environmental differentiation of lineages within Rhabdomys and provide hypotheses regarding potential areas of contact between them in the Southern African subregion, including the Republic of South Africa, Lesotho, and Namibia. Records of Rhabdomys taxa across the study region were compiled and georeferenced from the literature, museum records, and field expeditions. Presence records were summarized within a 10 × 10 km grid covering the study area. Environmental information regarding climate, topography, land use, and vegetation productivity was gathered at the same resolution. Multivariate statistics were used to characterize the current environmental niche and distribution of the whole genus as well as of three mitochondrial lineages known to occur in southern Africa. Distribution modeling was carried out using MAXENT in order to generate hypotheses regarding current distribution of each taxa and their potential contact zones. Results indicate that the two species within Rhabdomys appear to have differentiated across the precipitation/temperature gradient present in the region from east to west. R. dilectus occupies the wettest areas in eastern southern Africa, while R. pumilio occupies the warmer and drier regions in the west, but also penetrates in the more mesic central part of the region. We provide further evidence of environmental differentiation within two lineages of R. dilectus. Contact zones between lineages appear to occur in areas of strong environmental gradients and topographic complexity, such as the transition zones between major biomes and the escarpment area where a sharp altitudinal gradient separates coastal and plateau areas, but also within more homogeneous areas such as within grassland and savannah biomes. Our results indicate that Rhabdomys may be more specialized than previously thought when considering current knowledge regarding mitochondrial lineages. The genus appears to have differentiated along two major environmental axes in the study region, but results also suggest dispersal limitations and biological interactions having a role in limiting current distribution boundaries. Furthermore, the projection of the potential geographic distribution of the different lineages suggests several contact zones that may be interesting study fields for understanding the interplay between ecological and evolutionary processes during speciation.     

Bio‐ORACLE: a global environmental dataset for marine species distribution modelling

Aim The oceans harbour a great diversity of organisms whose distribution and ecological preferences are often poorly understood. Species distribution modelling (SDM) could improve our knowledge and inform marine ecosystem management and conservation. Although marine environmental data are available from various sources, there are currently no user‐friendly, high‐resolution global datasets designed for SDM applications. This study aims to fill this gap by assembling a comprehensive, uniform, high‐resolution and readily usable package of global environmental rasters. Location Global, marine. Methods We compiled global coverage data, e.g. satellite‐based and in situ measured data, representing various aspects of the marine environment relevant for species distributions. Rasters were assembled at a resolution of 5 arcmin (c. 9.2 km) and a uniform landmask was applied. The utility of the dataset was evaluated by maximum entropy SDM of the invasive seaweed Codium fragile ssp. fragile. Results We present Bio‐ORACLE (ocean rasters for analysis of climate and environment), a global dataset consisting of 23 geophysical, biotic and climate rasters. This user‐friendly data package for marine species distribution modelling is available for download at http://www.bio‐oracle.ugent.be . The high predictive power of the distribution model of C. fragile ssp. fragile clearly illustrates the potential of the data package for SDM of shallow‐water marine organisms. Main conclusions The availability of this global environmental data package has the potential to stimulate marine SDM. The high predictive success of the presence‐only model of a notorious invasive seaweed shows that the information contained in Bio‐ORACLE can be informative about marine distributions and permits building highly accurate species distribution models.     

Pliocene–Pleistocene ecological niche evolution shapes the phylogeography of a Mediterranean plant group

Estimating species ability to adapt to environmental changes is crucial to understand their past and future response to climate change. The Mediterranean Basin has experienced remarkable climatic changes since the Miocene, which have greatly influenced the evolution of the Mediterranean flora. Here, we examine the evolutionary history and biogeographic patterns of two sedge sister species (Carex, Cyperaceae) restricted to the western Mediterranean Basin, but with Pliocene fossil record in central Europe. In particular, we estimated the evolution of climatic niches through time and its influence in lineage differentiation. We carried out a dated phylogenetic–phylogeographic study based on seven DNA regions (nDNA and ptDNA) and fingerprinting data (AFLPs), and modelled ecological niches and species distributions for the Pliocene, Pleistocene and present. Phylogenetic and divergence time analyses revealed that both species form a monophyletic lineage originated in the late Pliocene–early Pleistocene. We detected clear genetic differentiation between both species with distinct genetic clusters in disjunct areas, indicating the predominant role of geographic barriers limiting gene flow. We found a remarkable shift in the climatic requirements between Pliocene and extant populations, although the niche seems to have been relatively conserved since the Pleistocene split of both species. This study highlights how an integrative approach combining different data sources and analyses, including fossils, allows solid and robust inferences about the evolutionary history of a plant group since the Pliocene.