Niche divergence accelerates evolution in Asian endemic Procapra gazelles

Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage

Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species' evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). The genus Progne includes migrant and resident species, as well as geographically restricted taxa and widespread, intercontinentally distributed taxa, thus providing an ideal group in which to study the nature of niche divergence within a broad geographic mosaic. I obtained distributional information for the genus from publicly available databases and created ecological niche models for each species to create pairwise comparisons of environmental space. I combined these data with the most up-to-date phylogeny of Progne currently available to examine the patterns of niche evolution within the genus. I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, like extant basal Progne lineages, and several geographically localized descendant species occupy only portions of this larger ancestral niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages, and sheds light on the ways in which apparently divergent niches may arise through allopatry while not involving any true niche shifts through evolutionary time. Even taxa that appear unique in terms of habitat or behavior may not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.

Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage

Ecological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species' evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (Progne). Despite containing species with distributions that go from continent-spanning to locally endemic, I found limited evidence for niche divergence across the breeding distributions of Progne, and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral Progne had a relatively broad ecological niche, similar to extant basal Progne lineages, and several geographically localized descendant species occupy only portions of the larger ancestral Progne niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread, continental species (Southern Martin P. elegans vs. Gray-breasted Martin P. chalybea). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin P. subis and P. chalybea. I analyzed populations of P. subis separately, as a microcosm of Progne evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages. Even taxa that appear unique in terms of habitat or behavior may still not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.

Projected Shifts in Bird Distribution in India under Climate Change

Global climate change is causing unprecedented impacts on biodiversity. In India, there is little information available regarding how climate change affects biodiversity at the taxon/group level, and large-scale ecological analyses have been lacking. In this study, we demonstrated the applicability of eBird and GBIF (Global Biodiversity Information Facility), and produced national-scale forecasts to examine the possible impacts of climate change on terrestrial avifauna in India. Using data collected by citizen scientists, we developed fine-tuned Species Distribution Models (SDMs) and predicted 1091 terrestrial bird species that would be distributed in India by 2070 on two climatic surfaces (RCP 4.5 and 8.5), using Maximum Entropy-based species distribution algorithms. Of the 1091 species modelled, our findings indicate that 66–73% of bird species in India will shift to higher elevations or shift northward, and 58–59% of bird species (RCP 4.5 and 8.5) would lose a portion of their distribution ranges. Furthermore, distribution ranges of 41–40% of bird species would increase. Under both RCP scenarios (RCP 4.5 and 8.5), bird species diversity will significantly increase in regions above 2500 m in elevation. Both RCP scenarios predict extensive changes in the species richness of the western Himalayas, Sikkim, northeast India, and the western Ghats regions by 2070. This study has resulted in novel, high-resolution maps of terrestrial bird species richness across India, and we predict predominantly northward shifts in species ranges, similar to predictions made for avifauna in other regions, such as Europe and the USA.

Niche Divergence at Intraspecific Level in the Hyrcanian Wood Frog, Rana pseudodalmatina: A Phylogenetic, Climatic, and Environmental Survey

The role of ecological niche divergence in lineage speciation has recently stimulated the interest of evolutionary biologists and ecologists. Phylogenetic analysis has revealed that the Hyrcanian wood frog, Rana pseudodalmatina, has diverged into two western and eastern regional clades (WRC and ERC) within the Hyrcanian forest. The goal of this study was to investigate whether the ecological niches of WRC and ERC are conserved or diverged, as well as to figure out what variables promote niche conservatism or divergence. For this purpose, the maximum entropy model was employed to assess environmental niche modeling in geographical (G) space utilizing climatic and macro-environmental data. The niche overlap, equivalency, and similarity tests based on PCAenv analyses were used to assess niche divergence or conservatism in environmental (E) space. The findings strongly support the hypothesis that WRC and ERC have undergone substantial niche divergence and are constrained by a unique set of climatic and macro-environmental conditions. This study by ecological niche comparisons based on phylogenetic data provides new insights into the exploration of species diversification processes in the Hyrcanian forests.

Climatic-niche evolution with key morphological innovations across clades within Scutiger boulengeri (Anura: Megophryidae)

The studies of climatic-niche shifts over evolutionary time accompanied by key morphological innovations have attracted the interest of many researchers recently. We applied ecological niche models (ENMs), ordination method (environment principal component analyses; PCA-env), combined phylogenetic comparative methods (PCMs), and phylogenetic generalized least squares (PGLS) regression methods to analyze the realized niche dynamics and correspondingly key morphological innovations across clades within Scutiger boulengeri throughout their distributions in Qinghai-Tibet Plateau (QTP) margins of China. Our results show there are six clades in S. boulengeri and obvious niche divergences caused by niche expansion in three clades. Moreover, in our system, niche expansion is more popular than niche unfilling into novel environmental conditions. Annual mean temperature, annual precipitation, and precipitation of driest month may contribute to such a shift. In addition, we identified several key climatic factors and morphological traits that tend to be associated with niche expansion in S. boulengeri clades correspondingly. We found phenotypic plasticity [i.e., length of lower arm and hand (LAHL), hind-limb length (HLL), and foot length (FL)] and evolutionary changes [i.e., snout-vent length (SVL)] may together contribute to niche expansion toward adapting novel niche, which provides us a potential pattern of how a colonizing toad might seed a novel habitat to begin the process of speciation and finally adaptive radiation. For these reasons, persistent phylogeographic divisions and accompanying divergences in niche occupancy and morphological adaption suggest that for future studies, distinct genetic structure and morphological changes corresponding to each genetic clade should be included in modeling niche evolution dynamics, but not just constructed at the species level.

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts

Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here, we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.

Niche-Driven Socio-Environmental Linkages and Regional Sustainable Development

The changes in niche roles and functions caused by competition for survival resources have implications in various domains, with natural science and social science standing out. Currently, expanding the ecological niche concept and its practical interpretation in the fields of social ecology, geography and sustainable science is becoming a crucial challenge. This paper is based on niche theory to observe niche evolution and resulting socio-ecological effects of 1186 towns in 19 prefecture cities in Yangtze River delta. The results indicate that: Towns around the Taihu Lake displayed obvious spatial agglomeration, which was leading the development of the entire region. The town niche shows obvious characteristics of north-south differences and hierarchy distribution. The niche coordination degree of Jiangsu Province was higher than that of Zhejiang Province. The higher the subsystem coordination degree, the better the town development. Towns with poor ecological conditions are often subject to competition, while towns with better ecological conditions often benefit from cooperative development. The niche separation and collaboration could enhance niche competition of towns and cities in the region. The proposed framework can facilitate interdisciplinary exchanges among geography, sociology, landscape ecology and regional planning and provide insights for understanding regional co-opetition relationship and regional sustainable development.

Change of niche in guanaco (Lama guanicoe): the effects of climate change on habitat suitability and lineage conservatism in Chile

Background

The main goal of this contribution was to define the ecological niche of the guanaco (Lama guanicoe), to describe potential distributional changes, and to assess the relative importance of niche conservatism and divergence processes between the two lineages described for the species (L.g. cacsilensis and L.g. guanicoe).

Methods

We used maximum entropy to model lineage’s climate niche from 3,321 locations throughout continental Chile, and developed future niche models under climate change for two extreme greenhouse gas emission scenarios (RCP2.6 and RCP8.5). We evaluated changes of the environmental niche and future distribution of the largest mammal in the Southern Cone of South America. Evaluation of niche conservatism and divergence were based on identity and background similarity tests.

Results

We show that: (a) the current geographic distribution of lineages is associated with different climatic requirements that are related to the geographic areas where these lineages are located; (b) future distribution models predict a decrease in the distribution surface under both scenarios; (c) a 3% decrease of areal protection is expected if the current distribution of protected areas is maintained, and this is expected to occur at the expense of a large reduction of high quality habitats under the best scenario; (d) current and future distribution ranges of guanaco mostly adhere to phylogenetic niche divergence hypotheses between lineages.

Discussion

Associating environmental variables with species ecological niche seems to be an important aspect of unveiling the particularities of, both evolutionary patterns and ecological features that species face in a changing environment. We report specific descriptions of how these patterns may play out under the most extreme climate change predictions and provide a grim outlook of the future potential distribution of guanaco in Chile. From an ecological perspective, while a slightly smaller distribution area is expected, this may come with an important reduction of available quality habitats. From the evolutionary perspective, we describe the limitations of this taxon as it experiences forces imposed by climate change dynamics.

Inferring ecological explanations for biogeographic boundaries of parapatric Asian mountain frogs

Background

Identifying and understanding the mechanisms that shape barriers to dispersal and resulting biogeographic boundaries has been a longstanding, yet challenging, goal in ecology, evolution and biogeography. Characterized by stable, adjacent ranges, without any intervening physical barriers, and limited, if any, range overlap in a narrow contact zone, parapatric species are an interesting system for studying biogeographic boundaries. The geographic ranges of two parapatric frog species, Feirana quadranus and F. taihangnica, meet in a contact zone within the Qinling Mountains, an important watershed for East Asia. To identify possible ecological determinants of the parapatric range boundaries for two closely related frog species, we quantified the extent of their niche differentiation in both geographical and environmental space combining ecological niche models with an ordination technique. We tested two alternative null hypotheses (sharp environmental gradients versus a ribbon of unsuitable habitat dividing two highly suitable regions) for biogeographic boundaries, against the null expectation that environmental variation across a given boundary is no greater than expected by chance.

Results

We found that the niches of these two parapatric species are more similar than expected by chance, but not equivalent. No sharp environmental gradient was found, while a ribbon of unsuitable habitat did act as a barrier for F. quadranus, but not for F. taihangnica.

Conclusions

Integrating our findings with historical biogeographic information, our results suggest that at a contact zone, environmental tolerance restricted F. quadranus from dispersing further north, while interspecific competition most likely prevented the southward expansion of F. taihangnica. This study highlights the importance of both climate and competition in exploring ecological explanations for parapatric range boundaries between ecologically similar frog species, in particular under the effects of changing climate.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0160-5) contains supplementary material, which is available to authorized users.

Niche conservatism in Gynandropaa frogs on the southeastern Qinghai-Tibetan Plateau

The role of ecological niche in lineage diversification has been the subject of long-standing interest of ecologists and evolutionary biologists. Gynandropaa frogs diversified into three independent clades endemic to the southeastern Qinghai-Tibetan Plateau. Here, we address the question whether these clades kept the same niche after separation, and what it tells us about possible diversification processes. We applied predictions in geographical (G)-space and tests of niche conservatism in environmental (E)-space. Niche models in G-space indicate separate regions with high suitability for the different clades, with some potential areas of sympatry. While the pair of central and eastern clades displayed the largest niche overlap for most variables, and strict niche equivalency was rejected for all clade-pairs, we found no strong evidence for niche divergence, but rather the signature of niche conservatism compared to null models in E-space. These results suggest a common ancestral ecological niche, and as such give good support to divergence through allopatric speciation, but alternative explanations are also possible. Our findings illustrate how testing for niche conservatism in lineage diversification can provide insights into underlying speciation processes, and how this information may guide further research and conservation practices, as illustrated here for amphibians on the Qinghai-Tibetan Plateau.

Marble Algorithm: a solution to estimating ecological niches from presence-only records

We describe an algorithm that helps to predict potential distributional areas for species using presence-only records. The Marble Algorithm is a density-based clustering program based on Hutchinson's concept of ecological niches as multidimensional hypervolumes in environmental space. The algorithm characterizes this niche space using the density-based spatial clustering of applications with noise (DBSCAN) algorithm. When MA is provided with a set of occurrence points in environmental space, the algorithm determines two parameters that allow the points to be grouped into several clusters. These clusters are used as reference sets describing the ecological niche, which can then be mapped onto geographic space and used as the potential distribution of the species. We used both virtual species and ten empirical datasets to compare MA with other distribution-modeling tools, including Bioclimate Analysis and Prediction System, Environmental Niche Factor Analysis, the Genetic Algorithm for Rule-set Production, Maximum Entropy Modeling, Artificial Neural Networks, Climate Space Models, Classification Tree Analysis, Generalised Additive Models, Generalised Boosted Models, Generalised Linear Models, Multivariate Adaptive Regression Splines and Random Forests. Results indicate that MA predicts potential distributional areas with high accuracy, moderate robustness, and above-average transferability on all datasets, particularly when dealing with small numbers of occurrences.