A stable niche assumption-free test of ecological divergence

AimAssessing the relevance of niche evolution in the diversification patterns and geographical distribution of species driven by climate remains a challenge. We apply an integrative approach to evaluate the role of the environment on the phylogeography of bear species, incorporating fossil data to characterize the changes in the ecological niche through time. We evaluate our approach with the four extant species of bears within Ursus, the best represented taxon in the fossil record of the family Ursidae.LocationEurasia and North America.TaxaAsian black bear, Ursus thibetanus; American black bear, U. americanus; Brown bear, U. arctos; and Polar bear, U. maritimus.MethodsWe built a genetic and a geographical database from all published mitochondrial DNA sequences and of species occurrence records. We defined the most significant climatic variables based on each species ecological realm using correlation matrices, and characterized the ecological niches and existing environmental conditions with ellipsoid models. We inferred their current and Last Glacial Maximum (LGM) ecological niche modellings (ENMs) and compared the results with the fossil record. We estimated the times of divergence (d‐loop sequences) of lineages and applied a phyloclimatespace approach to discern the phylogeographical patterns along each species’ ecological space.ResultsEcological niche modelling showed wider niches for U. thibetanus and U. americanus encompassing higher temperature and precipitation, while U. arctos and U. maritimus showed an opposite pattern. LGM models were consistent with the fossil record, predicting 55%–89% of the fossil occurrences (within their suitability areas). The phyloclimatespace revealed different degrees of environmental signal in the lineages’ phylogeographical patterns and ecological trajectories associated with LGM climatic conditions. Results indicated habitat tracking and ecological expansion since the LGM towards more extreme precipitation and temperature conditions for three species, except U. maritimus that showed ecological niche reduction.Main ConclusionsIncorporating fossil information from the LGM improved our characterization and interpretation of ecological models, by enabling definition of the limits of the climatic conditions explored by the species in the past. Our approach also provided insights about the existing set of environmental conditions shaping the ecological niche divergence of Ursus bears. We were able to depict key features of the lineages’ evolutionary history, ecology and distribution, revealing the dynamics of niche occupation and the environmental signal on the phylogeographical patterns of Ursus.

We attempted to clarify how coastal lands temporarily exposed during the last glacial maximum (LGM) contributed to the northward colonisation of Kalopanax septemlobus (Thunb. ex Murray) Koidzumi during the postglacial period in the Japanese Archipelago. Distribution records in 30‐arc‐s pixels were related to bioclimate variables using the maximum entropy technique to model the ecological niche of this species. Bioclimatic conditions in the exposed coastal lands during the LGM were reconstructed based on simulated palaeoclimate and fine‐resolution marine topography. Potential distribution ranges were then estimated under the climatic conditions during the LGM, mid‐Holocene and the present. The ecological niche of this species was influenced mainly by the temperature component of the bioclimates, leading to northward range shift after the LGM as the climate warmed. On average, 26% of the potential range of K. septemlobus during the LGM was located on the exposed seafloor. The northern edges of the species range on both sides of Honshu Island were estimated by up to several hundred kilometres farther north, when compared to the prediction assuming no sea level change. Application of ecological niche modelling provided new insight into the role of exposed seafloor as cryptic glacial refugia for this species, which has never been evidenced by fossil records. In a temperate island system characterised by long coastlines, the northern exposed seafloor would have been more important in terms of harbouring the putative source populations for northward directional colonisation during the postglacial period.

Aim Increasing our understanding of the effects of the Last Glacial Maximum (LGM) and determining the location of refugia requires studies on widely distributed species with dense sampling of populations. We have reconstructed the biogeographic history of Clitarchus hookeri (White), a widespread species of New Zealand stick insect that exhibits geographic parthenogenesis, using phylogeographic analysis and ecological niche modelling.Location New Zealand.Methods We used DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene to reconstruct phylogenetic relationships among haplotypes from C. hookeri and two undescribed Clitarchus species. We also used distribution data from our own field surveys and museum records to reconstruct the geographic distribution of C. hookeri during the present and the LGM, using ecological niche modelling.Results The ecological niche models showed that the geographic distribution of C. hookeri has expanded dramatically since the LGM. Our model predicted large areas of suitable LGM habitat in upper North Island, and small patches along the east coast of South Island. The phylogeographic analysis shows that populations in the northern half of North Island contain much higher levels of genetic variation than those from southern North Island and South Island, and is congruent with the ecological niche model. The distribution of bisexual populations is also non‐random, with males completely absent from South Island and very rare in southern North Island.Main conclusions During the LGM C. hookeri was most likely restricted to several refugia in upper North Island and one or more smaller refugia along the east coast of South Island. The unisexual populations predominate in post‐glacial landscapes and are clearly favoured in the recolonization of such areas. Our study exemplifies the utility of integrating ecological niche modelling and phylogeographic analysis.

Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada

Reconstructing ecological niches and geographic distributions of caribou ( Rangifer tarandus) and red deer ( Cervus elaphus) during the Last Glacial Maximum

Ecological niche modeling shed light on new insights of the speciation processes and historical distribution of Japanese fire-bellied newt Cynops pyrrhogaster (Amphibia: Urodela)

The giant panda (Ailuropoda melanoleuca) is the most basal living species in the phylogeny of the family Ursidae, with a specialized diet composed of a variety of bamboo species. The evolutionary history and past distribution patterns of the giant panda remain poorly understood. Our aim was to integratively apply distinct methods to evaluate the evolutionary history and distributional patterns of the giant panda; these included phylogeography, ecological niche modeling (ENM), and fossil data. To this end, we characterized the panda’s past and present ecological niches and the environmental conditions that define them. To estimate the panda’s phylogeographic patterns and the environmental conditions (precipitation and temperature) available across its historical geographic range, we evaluated its past distribution during the Last Glacial Maximum (LGM). Considering that modeling biotic interactions (e.g., foraging, predation) is still an enormous challenge, we propose a novel modeling strategy based on the panda’s specialized diet, using an ensemble of three bamboo genera with distribution across the panda’s historical geographic range. Finally, we tested the accuracy of our approach by evaluating its ability to predict the LGM fossils. Our results support that the panda’s diversification across its distribution happened ca. 2.7 million years (Mya), coinciding with the likely period when the panda changed from a carnivorous to a vegetarian diet (from the Pleistocene to the Pliocene), acquiring its exclusively bamboo-feeding habits until the mid-Holocene. Our findings provide evidence of a historical directional niche change along which the panda has currently reached the lower limits of temperature and precipitation conditions existing on the geography where its food is available. Our proposed ENM based on the panda’s food habits accurately predicted 85.7% of the LGM fossils, in stark contrast with the traditional approach of modeling the distribution of species by using exclusively its own occurrences. These results provide insights on how to include Eltonian components to undertake more robust ENM when only abiotic variables are available. We emphasize the importance of integrating fossil information, whenever available, into the niche modeling process to include the historical component when estimating species ecological niches.

In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool-temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial-interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high-latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.

ABSTRACTBased on organelle DNA phylogeographic analyses and ecological niche modeling (ENM), we investigated the range-shift history of the Japanese wingnut (Pterocarya rhoifolia) during the Quaternary climatic oscillations with particular emphasis on the Last Glacial Maximum (LGM). Phylogeographic patterns of this species were determined using 376 individuals from 53 populations for chloroplast DNA sequencing of three spacers. Spatial analysis of molecular variance revealed that the current phylogeographic structure would be sculptured by multiple range shifts from each glacial refugium, which would have been repeated several times during the Quaternary climatic oscillations. High haplotype diversity and private haplotypes were detected in southwestern Japan, where wingnut is currently infrequent and found mainly in high mountains, whereas in northernmost Japan, haplotype diversity was low though this plant is quite common at present. According to ENM approach, during the LGM, the climatically suitable distribution areas were not recovered in northeastern Japan but in lowlands of southwestern Japan. Our combined results suggest that Japanese wingnut primarily persisted in the lowlands of southwestern Japan and coastlines below 36.5°N latitude during the LGM, having led to the postglacial range expansion from the refugia in each area of southwestern and lower latitudinal northeastern Japan, and to the wide-range recolonization from the southerly refugium/refugia to the north in northernmost Japan. The southwestern and coastal refugia have played a role in shaping the current haplotype diversity and phylogeographic structure, whereas some rear edge populations, harboring unique haplotypes, have been also maintained.

Aim To provide a test of the conservatism of a species’ niche over the last 20,000 years by tracking the distribution of eight pollen taxa relative to climate type as they migrated across eastern North America following the Last Glacial Maximum (LGM).Location North America.Methods We drew taxon occurrence data from the North American pollen records in the Global Pollen Database, representing eight pollen types – all taxa for which ≥5 distinct geographic occurrences were available in both the present day and at the LGM (21,000 years ago ± 3000 years). These data were incorporated into ecological niche models based on present‐day and LGM climatological summaries available from the Palaeoclimate Modelling Intercomparison Project to produce predicted potential geographic distributions for each species at present and at the LGM. The output for each time period was projected onto the ‘other’ time period, and tested using independent known occurrence information from that period.Results The result of our analyses was that all species tested showed general conservatism in ecological characteristics over the climate changes associated with the Pleistocene‐to‐Recent transition.Main conclusions This analysis constitutes a further demonstration of general and pervasive conservatism in ecological niche characteristics over moderate periods of time despite profound changes in climate and environmental conditions. As such, our results reinforce the application of ecological niche modelling techniques to the reconstruction of Pleistocene biodiversity distribution patterns, and to project the future potential distribution range of species in the face of global‐scale climatic changes.

Understanding species distributions and the variation of assemblage structure in time and space are fundamental goals of biogeography and ecology. Here, we use an ecological niche modeling and macroecological approach in order to assess whether constraints patterns in carnivoran richness and composition structures in replicated assemblages through time and space should reflect environmental filtering through ecological niche constraints from the Last Inter-glacial (LIG), Last Glacial Maximum (LGM) to the present (C) time. Our results suggest a diverse distribution of carnivoran co-occurrence patterns at the continental scale as a result of spatial climatic variation as an important driver constrained by the ecological niches of the species. This influence was an important factor restructuring assemblages (more directly on richness than composition patterns) not only at the continental level, but also from regional and local scales and this influence was geographically different throughout the space in the continent. These climatic restrictions and disruption of the niche during the environmental changes at the LIG-LGM-C transition show a considerable shift in assemblage richness and composition across the Americas, which suggests an environmental filtering mainly during the LGM, explaining between 30 and 75% of these variations through space and time, with more accentuated changes in North than South America. LGM was likely to be critical in species functional adaptation and distribution and therefore on assemblage structuring and rearranging from continental to local scales through time in the continent. Still, extinction processes are the result of many interacting factors, where climate is just one part of the picture.

The application of transfer functions on fossil assemblages to reconstruct past environments is fundamentally based on the assumption of stable environmental niches in both space and time. We quantitatively test this assumption for six dominant planktic foraminiferal species (Globigerinoides ruber (pink), G. ruber (white), Trilobatus sacculifer, Truncorotalia truncatulinoides, Globigerina bulloides, and Neogloboquadrina pachyderma) by contrasting reconstructions of species realized and optimum distributions in the modern and during the Last Glacial Maximum (LGM) using an ecological niche model (ENM; MaxEnt) and ordination framework. Global ecological niche models calibrated in the modern ocean have high predictive performance when projected to the LGM for subpolar and polar species, indicating that the environmental niches of these taxa are largely stable at the global scale across this interval. In contrast, ENMs had much poorer predictive performance for the optimal niche of tropical‐dwelling species, T. sacculifer and G. ruber (pink). This finding is supported by independent metrics of niche margin change, suggesting that niche stability in environmental space was greatest for (sub)polar species, with greatest expansion of the niche observed for tropical species. We find that globally calibrated ENMs showed good predictions of species occurrences globally, whereas models calibrated in either the Pacific or Atlantic Oceans only and then projected globally performed less well for T. sacculifer. Our results support the assumption of environmental niche stability over the last ~21,000 years for most of our focal planktic foraminiferal species and, thus, the application of transfer function techniques for palaeoenvironmental reconstruction during this interval. However, the lower observed niche stability for (sub)tropical taxa T. sacculifer and G. ruber (pink) suggests that (sub)tropical temperatures could be underestimated in the glacial ocean with the strongest effect in the equatorial Atlantic where both species are found today.

The role of niche divergence and geographic arrangement in the speciation of Eared Pheasants (Crossoptilon, Hodgson 1938)

Climate changes can have fundamental impacts on the distributional patterns of montane species, and range shifts frequently lead to allopatric divergence followed by the establishment of secondary contact zones. Many European and North American organisms have retreated to southern refugia during glacial periods and colonized northward during postglacial periods, but little is known about the evolutionary response of cold‐adapted insects to Pleistocene climate changes in eastern Asia. The scorpionfly Dicerapanorpa magna (Chou), with cold temperate habitat preference and weak dispersal ability, provides a good model system to explore how climate changes have influenced the distribution and divergence of cold‐adapted insects in eastern Asia. This study reconstructed the demographic dynamics and evolutionary history of D. magna with phylogeographic approaches, and predicted the species’ suitable areas under the Last Glacial Maximum (LGM) and current scenarios with the ecological niche modelling analysis. The mitochondrial cytochrome c oxidase subunit I resolved three phylogenetic lineages in D. magna dating back to Pleistocene, corresponding well with the geographically isolated Qinling, Bashan and Minshan Mountains. The ecological niche modelling recovered the suitable habitats for D. magna were the Qinling and Bashan Mountains under LGM and current conditions. The three lineages of D. magna might be in a process of incipient speciation, and likely derived their current distribution from separate glacial origins, followed by vicariance and divergence.

Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis–concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis–concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory.