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Background Climate is often considered as a key ecological factor limiting the capability of expansion of most species and the extent of suitable habitats. In this contribution, we implement Species Distribution Models (SDMs) to study two parapatric amphibians, Lissotriton vulgaris meridionalis and L. italicus, investigating if and how climate has influenced their present and past (Last Glacial Maximum and Holocene) distributions. A database of 901 GPS presence records was generated for the two newts. SDMs were built through Boosted Regression Trees and Maxent, using the Worldclim bioclimatic variables as predictors. Results Precipitation-linked variables and the temperature annual range strongly influence the current occurrence patterns of the two Lissotriton species analyzed. The two newts show opposite responses to the most contributing variables, such as BIO7 (temperature annual range), BIO12 (annual precipitation), BIO17 (precipitation of the driest quarter) and BIO19 (precipitation of the coldest quarter). The hypothesis of climate influencing the distributions of these species is also supported by the fact that the co-occurrences within the sympatric area fall in localities characterized by intermediate values of these predictors. Projections to the Last Glacial Maximum and Holocene scenarios provided a coherent representation of climate influences on the past distributions of the target species. Computation of pairwise variables interactions and the discriminant analysis allowed a deeper interpretation of SDMs’ outputs. Further, we propose a multivariate environmental dissimilarity index (MEDI), derived through a transformation of the multivariate environmental similarity surface (MESS), to deal with extrapolation-linked uncertainties in model projections to past climate. Finally, the niche equivalency and niche similarity tests confirmed the link between SDMs outputs and actual differences in the ecological niches of the two species. Conclusions The different responses of the two species to climatic factors have significantly contributed to shape their current distribution, through contractions, expansions and shifts over time, allowing to maintain two wide allopatric areas with an area of sympatry in Central Italy. Moreover, our SDMs hindcasting shows many concordances with previous phylogeographic studies carried out on the same species, thus corroborating the scenarios of potential distribution during the Last Glacial Maximum and the Holocene emerging from the models obtained. Electronic supplementary material The online version of this article (10.1186/s12983-017-0239-4) contains supplementary material, which is available to authorized users.

This research was supported by the Natural Science Foundation of China (No. 31471898) and the Key Technology Research of Oil Peony Industry in Shaanxi Province (2014HXFWYL016) and Special project to Build World‐class Disciplines Of Beijing Forestry University (2019XKJS0324). Determining the factors promoting speciation is a major task in ecological and evolutionary research and can be aided by phylogeographic analysis. The Qinling–Daba Mountains (QDM) located in central China form an important geographic barrier between southern subtropical and northern temperate regions, and exhibit complex topography, climatic, and ecological diversity. Surprisingly, few phylogeographic analyses and studies of plant speciation in this region have been conducted. To address this issue, we investigated the genetic divergence and evolutionary histories of three closely related tree peony species (Paeonia qiui, P. jishanensis, and P. rockii) endemic to the QDM. Forty populations of the three tree peony species were genotyped using 22 nuclear simple sequence repeat markers (nSSRs) and three chloroplast DNA sequences to assess genetic structure and phylogenetic relationships, supplemented by morphological characterization and ecological niche modeling (ENM). Morphological and molecular genetic analyses showed the three species to be clearly differentiated from each other. In addition, coalescent analyses using DIYABC conducted on nSSR variation indicated that the species diverged from each other in the late Pleistocene, while ecological niche modeling (ENM) suggested they occupied a larger area during the Last Glacial Maximum (LGM) than at present. The combined genetic evidence from nuclear and chloroplast DNA and the results of ENM indicate that each species persisted through the late Pleistocene in multiple refugia in the Qinling, Daba, and Taihang Mountains with divergence favored by restricted gene flow caused by geographic isolation, ecological divergence, and limited pollen and seed dispersal. Our study contributes to a growing understanding of the origin and population structure of tree peonies and provides insights into the high level of plant endemism present in the Qinling–Daba Mountains of Central China. Publisher PDF

The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.

Limulus polyphemus is the sole extant representative of horseshoe crabs distributed along the Atlantic coast, and is threatened by human activities. Conservation priority to safeguard its habitat usually treats L. polyphemus as a whole, without consideration of different intraspecific ecological requirements. We seek to identify intraspecific ecological niche divergence or conservatism in L. polyphemus. In this study, ocean and coastal environmental conditions occupied by the six distinct metapopulations of L. polyphemus were collected, and compared using correlative approaches, niche overlaps among these six metapopulations were compared with geographical and genetic distances, the realized niche divergence/conservatism among these six metapopulations were tested, and ecological niche models were fitted for the six metapopulations separately and for L. polyphemus as a whole using state-of-the-art techniques. We found that mean sea surface temperature, tidal regime, chlorophyll a concentration, distance to shore and depth of seafloor were limiting factors in the geographic distribution of L. polyphemus. In addition to the former hypothesis that tidal amplitude and type account for the absence of L. polyphemus in the western Gulf of Mexico, our niche model predictions suggest that the narrow and high-depth seafloor in the western Gulf of Mexico also explain the absence. We found that realized niche overlaps among six metapopulations were not correlated with their geographic and genetic distances; rather the six metapopulations each occupied a unique combination of habitat conditions, showing different responses to environmental factors, although these divergences might be due a background effect. Results here showed that the distribution of one metapopulation of L. polyphemus cannot be inferred from changes in distribution of another, highlighting the inadequacy of one-size-fits-all conservation actions. We recommend that conservation priority assignment by IUCN and Natureserve for L. polyphemus would better consider the six metapopulations separately rather than L. polyphemus as a whole, which will deliver more useful information on guiding regional conservation efforts.

Aim To infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico. Location Central Mexico. Methods We collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA. Results Both cpDNA and nSSRs data indicated the presence of three highly differentiated genetic groups, mostly geographically congruent with the three main hydrological basins. According to nSSRs, the three genetic groups can be further subdivided into eight subgroups corresponding to different rivers within the main basins. The niche equivalency test showed that the niches of the species in the Balsas and Lerma basins are significantly nonequivalent. The RDA indicated a significant association of genetic variation among populations with climate variables (particularly those related to the precipitation regime), while controlling for geographic distribution. Main conclusions The genetic structure of S. humboldtiana is strongly associated with the historical and current geological configuration of the basins and the rivers within basins. The observed hierarchical genetic differentiation can be due to gene flow limitation resulting from physical barriers to the dispersal of S. humboldtiana, but also to some degree of isolation by environment, as suggested by the significant association between genetic variation among populations and precipitation regime.

Invasive species can cause substantial ecological impacts on native biodiversity. While ecological theory attempts to explain the processes involved in the trophic integration of invaders into native food webs and their competitive impacts on resident species, results are equivocal. In addition, quantifying the relative strength of impacts from non‐native species (interspecific competition) versus the release of native conspecifics (intraspecific competition) is important but rarely completed.Two model non‐native fishes, the globally invasive Cyprinus carpio and Carassius auratus, and the model native fish Tinca tinca, were used in a pond experiment to test how increased intra‐ and interspecific competition influenced trophic niches and somatic growth rates. This was complemented by samples collected from three natural fish communities where the model fishes were present. The isotopic niche, calculated using stable isotope data, represented the trophic niche.The pond experiment used additive and substitutive treatments to quantify the trophic niche variation that resulted from intra‐ and interspecific competitive interactions. Although the trophic niche sizes of the model species were not significantly altered by any competitive treatment, they all resulted in patterns of interspecific niche divergence. Increased interspecific competition caused the trophic niche of T. tinca to shift to a significantly higher trophic position, whereas intraspecific competition caused its position to shift towards elevated δ13C. These patterns were independent of impacts on fish growth rates, which were only significantly altered when interspecific competition was elevated.In the natural fish communities, patterns of trophic niche partitioning between the model fishes was evident, with no niche sharing. Comparison of these results with those of the experiment revealed the most similar results between the two approaches were for the niche partitioning between sympatric T. tinca and C. carpio.These results indicate that trophic niche divergence facilitates the integration of introduced species into food webs, but there are differences in how this manifests between introductions that increase inter‐ and intraspecific competition. In entirety, these results suggest that the initial ecological response to an introduction appears to be a trophic re‐organisation of the food web that minimises the trophic interactions between competing species. A plain language summary is available for this article.

The black-spotted tokay and the red-spotted tokay are morphologically distinct and have largely allopatric distributions. The black-spotted tokay is characterized by a small body size and dark skin with sundry spots, while the red-spotted tokay has a relatively large body size and red spots. Based on morphological, karyotypic, genetic, and distribution differences, recent studies suggested their species status; however, their classifications remain controversial, and additional data such as ecological niches are necessary to establish firm hypotheses regarding their taxonomic status. We reconstructed their ecological niches models using climatic and geographic data. We then performed niche similarity tests (niche identity and background tests) and point-based analyses to explore whether ecological differentiation has occurred, and whether such differences are sufficient to explain the maintenance of their separate segments of environmental ranges. We found that both niche models of the black- and the red-spotted tokay had a good fit and a robust performance, as indicated by the high area under the curve (AUC) values (“black” = 0.982, SD = ± 0.002, “red” = 0.966 ± 0.02). Significant ecological differentiation across the entire geographic range was found, indicating that the involvement of ecological differentiation is important for species differentiation. Divergence along the environmental axes is highly associated with climatic conditions, with isothermality being important for the “black” form, while temperature seasonality, precipitation of warmest quarter, and annual temperature range together being important for the “red” form. These factors are likely important factors in niche differentiation between the two forms, which result in morphological replacement. Overall, beside morphological and genetic differentiation information, our results contribute to additional insights into taxonomic distinction and niche differentiation between the black- and the red-spotted tokay.

The interplay between evolution and its role in diversification of Nepenthes binds the studies of this thesis. How evolutionary mechanisms and timing relate to molecular divergence and phylogenetic signal in the genus Nepenthes were investigated. This in conjunction with distribution modeling and mapping anatomical characters – an approach that led to a broad understanding of why and how best to protect specific geographical areas for conservation of Nepenthes. All work was framed with an interdisciplinary approach, each chapter furthering exploration of the connective ties in how past evolutionary history and its impact on diversity helps us to predict future diversity.

The opposing effects of environmental filtering and competitive interactions may influence community assembly and coexistence of related species. Competition, both in the domain of ecological resources, and in the sensory domain (for example, acoustic interference) may also result in sympatric species evolving divergent traits and niches. Delineating these scenarios within communities requires understanding trait distributions and phylogenetic structure within the community, as well as patterns of trait evolution. We report that sympatric assemblages of Asian barbets (frugivorous canopy birds) consist of a random phylogenetic sample of species, but are divergent in both morphological and acoustic traits. Additionally, we find that morphology is more divergent than expected under Brownian evolution, whereas vocal frequency evolution is close to the pattern expected under Brownian motion (i.e. a random walk). Together, these patterns are consistent with a role for competition or competitive exclusion in driving community assembly. Phylogenetic patterns of morphological divergence between related species suggest that these traits are key in species coexistence. Because vocal frequency and size are correlated in barbets, we therefore hypothesize that frequency differences between sympatric barbets are a by-product of their divergent morphologies.

How micro-topography affecting plant communities classification and species composition at one stand-level was investigated through the plant communities and species composition varied across fine-scale environmental heterogeneity at the 25-ha Lienhuachih broad-leaved forest dynamics plot (FDP). All free-standing woody plants with diameter at breast height ≧1 cm were identified, measured, tagged and mapped. Four plant communities were identified and represented with dominant and indicating species based on two-way indicator species analysis (TWINSPAN). Type I, Pasania nantoensis - Randia cochinchinensis, locating on the ridge and the highest elevation was with the highest stem density; Type II, Mallotus paniculatus - Engelhardtia roxburghiana, locating on the upper slope was an ecotone between type I and type III, with the middle stem density and basal area among four plant community types; Type III, Diospyros morrisiana - Cryptocarya chinensis, locating on the lower slope and stream side was with lower stem density but the highest species heterogeneity; and Type IV, Machilus japonica var. kusanoi - Helicia formosana locating on west stream side was with the lowest stem density and basal area. Detrended Correspondence Analysis (DCA) results showed nearly 27.11% of the plant species composition was attributable to micro-topographic variables. Ridge distance, stream distance and convexity were the most important factors effected the changes of plant community and species composition. Classification and regression tree (CART) method was also used to examine the relationship between each single specie and micro-topographic variables. Over 70% species had more than 27.11 % variations which explained by DCA results. To conclude, our results support the existence of habitat association and niche divergence related to micro-topography in a subtropical evergreen broad-leaved forest.

Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter- and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process., JO was supported by a Ramón y Cajal Fellowship (RYC-2013-12501) and a research contract funded by Severo Ochoa Program (SEV-2012-0262). VN was supported by a FPI predoctoral fellowship from Ministerio de Economía y Competitividad. This work was supported by an internal EBD ‘Microproyectos’ grant to JO, financed by the Spanish Ministry of Economy and Competitiveness through the Severo Ochoa Program for Centres of Excellence in R + D + I (SEV-2012-0262).