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52 results for “niche shift”
Stomach contents (1977-1981) and stable isotopes (1994) from the Everglades, Florida, USA from the publication "Fishes in a seasonally pulsed wetland show spatiotemporal shifts in diet and trophic niche but not shifts in trophic position"
Stomach contents of fishes (1977-1981) and stable isotopes of fishes, invertebrates, and basal resources (1994) were collected from spikerush marsh, sawgrass ridge, and alligator pond habitats in Shark River Slough, Everglades National Park, Florida, USA. These data were used to quantify diet, trophic niche area, trophic position, basal resource use and how these metrics vary among size classes, seasons, and habitats. Data collection is complete. These data support Flood et al. (2023). Associated R code will be made available through Peter Flood's GitHub: https://github.com/pjflood/historic_everglades_aquatic_food_web. References: Flood, Peter J., William F. Loftus, and Joel C. Trexler. "Fishes in a seasonally pulsed wetland show spatiotemporal shifts in diet and trophic niche but not shifts in trophic position." Food Webs 34 (2023): e00265. https://doi.org/10.1016/j.fooweb.2022.e00265
Data from: Species distribution models of the Spotted Wing Drosophila (Drosophila suzukii, Diptera: Drosophilidae) in its native and invasive range reveal an ecological niche shift
<p>The Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>) is native to Southeast Asia. Since its first detection in 2008 in Europe and North America, it has been a pest to the fruit production industry as it feeds and oviposits on ripening fruit. Here we aim to model the potential geographical distribution of <em>D. suzukii</em>. We performed an extensive literature review to map the current records. In total, 517 documented occurrences (96 native and 421 invasive) were identified spanning 52 countries. Next, we constructed three species distribution models (SDMs) based on occurrence records in: 1) the native range (SDMnative), 2) the invasive range in Europe (SDMEurope) and 3) a global model of all records (SDMglobal). The models aimed to investigate, whether this species will be able to occupy additional ecological niches beyond its native range and expand its current geographic distribution both globally and in Europe. The SDMs were generated using Maximum Entropy algorithms (Maxent) based on present occurrence records and bioclimatic variables (WorldClim). Predictions of habitat suitability vary greatly depending on the origins of occurrence records. According to all models, precipitation and low temperatures were key limiting factors for the distribution of <em>D. suzukii</em>, which suggests that this species requires a humid environment with mild winters in order to establish a permanent population in its invasive range. Several regions in the invasive range, not presently occupied by this species, were predicted highly suitable, especially in northern Europe, suggesting that <em>D. suzukii</em> is not occupying its full fundamental niche yet. Synthesis and applications. Based on these models of potential geographic distribution of the Spotted Wing Drosophila (<em>Drosophila</em> <em>suzukii</em>), we show a shift in the ecological niche in <em>D. suzukii</em> populations, emphasizing the importance of using presence and local environmental data. Further investigation regarding new occurrences is recommended to secure optimal pest management. Despite a continuing expansion, many countries still lack proper surveillance schemes, and we urge policymakers to initiate appropriate management programs.</p>
Data from: Fluctuation of ecological niches and geographic range shifts along chile pepper's domestication gradient
<p>Domestication is an ongoing well-described process. However, while many have stud- ied the changes domestication causes in plant genetics, few have explored its impact on the portion of the geographic landscape in which the plants exist. Therefore, the goal of this study was to understand how the process of domestication changed the geographic space suitable for chile pepper (<em>Capsicum annuum</em>) in its center of origin (domestication). <em>C. annuum</em> is a major crop species globally whose center of domes- tication, Mexico, has been well-studied. It provides a unique opportunity to explore the degree to which ranges of different domestication classes diverged and how these ranges might be altered by climate change. To this end, we created ecological niche models for four domestication classes (wild, semiwild, landrace, modern cultivar) based on present climate and future climate scenarios for 2050, 2070, and 2090. Considering present environment, we found substantial overlap in the geographic niches of all the domestication classes. Yet, environmental and geographic aspects of the current ranges did vary among classes. Wild and commercial varieties could grow in desert conditions, while landraces could not. With projections into the future, habitat was lost asymmetrically, with wild, semiwild, and landraces at greater risk of territorial declines than modern cultivars. Further, we identified areas where future suitability overlap between landraces and wilds is expected to be lost. While range expansion is widely associated with domestication, we found little support of a con- stant niche expansion (either in environmental or geographical space) throughout the domestication gradient in chile peppers in Mexico. Instead, particular domestication transitions resulted in loss, followed by capturing or recapturing environmental or geographic space. The differences in environmental characterization among domes- tication gradient classes and their future potential range shifts increase the need for conservation efforts to preserve landraces and semiwild genotypes</p>
Genomic changes underlying repeated niche shifts in an adaptive radiation
<p>In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, i.e. the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by re-sequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.</p>
Supplementary Data for: Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous
<p>This compendium of files includes a list of statistical routines (Data S1) and cleaned fossil datasets from the Paleobiology Database (Data S2 to S3) for the <em>Science Avances</em> paper "<em>Shifts in food webs and niche stability shaped survivorship and extinction at the end-Cretaceous</em>". Data S1 and Data S2 can be opened in Microsoft Office and Data S3 can be imported in R using the <em>load()</em> command. Data S2 and S3 contain the same information (i.e., cleaned fossil datasets) but in different formats (<em>xlsx</em> vs. <em>RData</em>).</p> <p>Please, feel free to send an email to the maintainer Dr. Jorge García Girón (jogarg@unileon.es) if you face any trouble downloading, opening or using these files.</p>
Data for: Does the evolution of ontogenetic niche shifts favor species coexistence? An empirical test in Trinidadian streams
<p>A major question in ecology is how often competing species evolve to reduce competitive interactions and facilitate coexistence. One untested route for a reduction in competitive interactions is through ontogenetic changes in the trophic niche of one or more of the interacting species. In such cases, theory predicts that two species can coexist if the weaker competitor changes its resource niche to a greater degree with increased body size than the superior competitor. We tested this prediction using stable isotopes that yield information about the trophic position (δ15N) and carbon source (δ13C) of two coexisting fish species: Trinidadian guppies (Poecilia reticulata) and killifish (Rivulus hartii). We examined fish from locations representing three natural community types: 1) where killifish and guppies live with predators; 2) where killifish and guppies live without predators; and 3) where killifish are the only fish species. We also examined killifish from communities in which we had introduced guppies, providing a temporal sequence of the community changes following the transition from a killifish only to a killifish-guppy community. We found that killifish, which are the weaker competitor, had a much larger ontogenetic niche shift in trophic position than guppies in the community where competition is most intense (killifish-guppy only). This result is consistent with theory for size-structured populations, which predicts that these results should lead to stable coexistence of the two species. Comparisons with other communities containing guppies, killifish and predators and ones where killifish live by themselves revealed that these results are caused primarily by a loss of ontogenetic niche changes in guppies, even though they are the stronger competitor. Comparisons of these natural communities with communities in which guppies were translocated into sites containing only killifish showed that the experimental communities were intermediate between the natural killifish-guppy community and the killifish-guppy-predator community, suggesting contemporary evolution in these ontogenetic trophic differences. These results provide comparative evidence for ontogenetic niche shifts in contributing to species coexistence and comparative and experimental evidence for evolutionary or plastic changes in ontogenetic niche shifts following the formation of new communities. </p>
Genomic changes underlying repeated niche shifts in an adaptive radiation
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Data from: Fluctuation of ecological niches and geographic range shifts along chile pepper's domestication gradient
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Data for: Does the evolution of ontogenetic niche shifts favor species coexistence? An empirical test in Trinidadian streams
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Ecomorphological convergence following niche shifts in montane ground beetles (Carabidae: Nebria)
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Data from: Species distribution models of the Spotted Wing Drosophila (Drosophila suzukii, Diptera: Drosophilidae) in its native and invasive range reveal an ecological niche shift
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Supplementary data to Clade-specific biogeographic history and climatic niche shifts of the southern Andean-southern Brazilian disjunction in plants
<p>Georeferenced locality data points used in the climatic analyses. Column "clade" indicate whether the species corresponds to the southern Andean (SA) or to the southern Brazilian (SB) clade. See the book chapter for details.</p> <p>Part of this dataset was built with information downloaded from GBIF (www.GBIF.org) for the following taxa:</p> <p><em>Araucaria</em><br> GBIF.org (06 November 2014) GBIF Occurrence Download https://doi.org/10.15468/dl.2nc359<br> GBIF.org (06 November 2014) GBIF Occurrence Download https://doi.org/10.15468/dl.aym9bi</p> <p><em>Butia</em><br> GBIF.org (30th May 2018) GBIF Occurrence Download https://doi.org/10.15468/dl.k42ama</p> <p><em>Colliguaja</em><br> GBIF.org (28 November 2014) GBIF Occurrence Download https://doi.org/10.15468/dl.nvqo4p<br> GBIF.org (13th January 2016) GBIF Occurrence Download http://doi.org/10.15468/dl.aoovox<br> GBIF.org (15th May 2018) GBIF Occurrence Download https://doi.org/10.15468/dl.mownio</p> <p><em>Griselinia</em><br> GBIF.org (28 November 2014) GBIF Occurrence Download https://doi.org/10.15468/dl.eytdse</p>
Supplementary material for "Analyzing potential niche shifts in alien pairs of mantis species (Insecta, Mantodea), with comments on the current taxonomic and ecological knowledge"
<p>###Supplementary data for "Analyzing potential niche shifts in alien pairs of mantis species (Insecta, Mantodea), with comments on the current taxonomic and ecological knowledge"</p><p>angui_intra: intra-species analyses for <i>Tenodera angustipennis</i>, with both complete and trimmed dataset.</p><p>contrhierodula: intra-species analyses for the <i>Hierodula</i> species with controversial status (<i>H. transcaucasica</i>/<i>H. tenuidentata</i>). It includes analyses between <i>H. transcaucasica</i> and <i>H. tenuidentata sensu stricto</i> and the populations treated as separated species.</p><p>hierodula_europe: inter-species analysis with the two <i>Hierodula</i> present in Europe.</p><p>kendall: scripts and table used for calculating Kendall's rank correlation.</p><p>pate_intra: intra-species analyses for <i>Hierodula patellifera</i>, with both complete and trimmed (no India, Nepal and Philippines points) datasets. There is also the analyses between Asian distribution and India, Nepal and Philippines points</p><p>sinensis_intra: intra-species analyses for <i>Tenodera sinesis</i>, with both complete and trimmed datasets.</p><p>tenodera_europe: inter-species analysis with the two <i>Tenodera</i> present in North America, with both complete and trimmed datasets.</p><p>####NOTE</p><p>I did not include the raw presence points (the elaborated ones are together with the values in a csv file per each folder) and the wordlclim variables. For the latter, you can get them from the WorldClim website. If you want the raw presence points, I will give them on request</p><p>WARNING: AN ITALIAN LOCALE HAS BEEN USED FOR THIS ANALYSES; IF YOU HAVE ANY FORMAT ISSUE WITH THE CSV, CONSIDER USING THIS FOR IMPORTING INTO R:<br><br>read_csv("namefile.csv", locale = locale(decimal_mark = ",", grouping_mark = "."))</p><p> </p><p>IF THAT DOES NOT WORK, PLEASE CONTACT ME</p>
A multivariate approach reveals diversity of ontogenetic niche shifts across taxonomic and functional groups
<p class="MsoBodyText">Shifts in the fundamental and realize niche of individuals during their ontogeny are ubiquitous in nature, but we know little about what aspects of the niche change and how these changes vary across species within communities. Yet, this knowledge is essential to predict the dynamics of populations and communities and how they respond to environmental change. Here I introduce a range of metrics to describe different aspects of shifts in the realized trophic niche of individuals based on stable isotopes. Applying this multi-variate approach to 2,272 individuals from 13 taxonomic and functional distinct species (Amphibia, Hemiptera, Coleoptera, Odonata) sampled in natural pond communities allowed me to: (1) describe and quantify the diversity of trophic niche shift patterns over ontogeny in multi-dimensional space, and (2) identify what aspects of ontogenetic shifts vary across taxa, and functional groups. Results revealed that species can differ substantially in which aspects of the trophic niche change and how they change over ontogeny. Interestingly, patterns of ontogenetic niche shifts grouped in distinct taxonomic clusters in multi-variate space, including two distinct groups of predators (Hemiptera vs. Odonata). Given the differences in traits (especially feeding mode) across groups, this suggests that differences in ontogenetic niche shifts across species could at least partially be explained by variation in traits and functional roles of species. These results emphasize the importance of a multivariate approach to capture the large diversity of trophic niche shifts patterns possible in natural communities, and suggest that differences in ontogenetic niche shifts follow general patterns. Shifts in the fundamental and realize niche of individuals during their ontogeny are ubiquitous in nature, but we know little about what aspects of the niche change and how these changes vary across species within communities. Yet, this knowledge is essential to predict the dynamics of populations and communities and how they respond to environmental change.</p>
Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion
Rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction and magnitude of phenotypic evolution during invasion has been underestimated. We explored the utility of niche-shift analyses in the red seaweed Gracilaria vermiculophylla, which expanded from the northeastern coastline of Japan to North America, Europe and northwestern Africa within the last 100 years. A genetically-informed climatic niche shift analysis indicates that native source populations occur in colder and highly seasonal habitats, while most non-native populations typically occur in warmer, less seasonal habitats. This climatic niche expansion predicts that non-native populations evolved greater tolerance for elevated heat conditions relative to native source populations. We assayed 935 field-collected and 325 common-garden thalli from 40 locations and as predicted, non-native populations had greater tolerance for ecologically-relevant extreme heat (40ºC) than did Japanese source populations. Non-native populations also had greater tolerance for cold and low-salinity stresses relative to source populations. The importance of local adaptation to warm temperatures during invasion was reinforced by evolution of parallel clines: populations from warmer, lower-latitude estuaries had greater heat tolerance than did populations from colder, higher-latitude estuaries in both Japan and eastern North America. We conclude that rapid evolution plays an important role in facilitating the invasion success of this and perhaps other non-native marine species. Genetically-informed ecological niche analyses readily generate clear predictions of phenotypic shifts during invasions, and may help to resolve debate over the frequency of niche conservatism versus rapid adaptation during invasion.
Data for: Recent range shifts of moths, butterflies, and birds are driven by the breadth of their climatic niche
<p><span>Species are altering their ranges as a response to climate change, but the magnitude and direction of observed range shifts vary considerably among species. The ability to persist in current areas and colonize new areas plays a crucial role in determining which species will thrive and which decline as climate change progresses. Several studies have sought to identify characteristics, such as morphological and life-history traits, that could explain differences in the capability of species to shift their ranges together with a changing climate. These characteristics have explained variation in range shifts only sporadically, thus offering an uncertain tool for discerning responses among species. As long-term selection to past climates have shaped species' tolerances, metrics describing species' contemporary climatic niches may provide an alternative means for understanding responses to on-going climate change. Species that occur in a broader range of climatic conditions may hold greater tolerance to climatic variability and could therefore more readily maintain their historical ranges, while species with more narrow tolerances may only persist if they are able to shift in space to track their climatic niche. Here, we provide a first-filter test of the effect of climatic niche dimensions on shifts in the leading range edges in three relatively well-dispersing species groups. Based on the realized changes in the northern range edges of 383 moth, butterfly, and bird species across a boreal 1100 km latitudinal gradient over c. 20 years, we show that while most morphological or life-history traits were not strongly connected with range shifts, moths and birds occupying a narrower thermal niche and butterflies occupying a broader moisture niche across their European distribution show stronger shifts towards the north. Our results indicate that the climatic niche may be important for predicting responses under climate change and as such warrants further investigation of potential mechanistic underpinnings. </span></p>
Tracing the future of epidemics: Coincident niche distribution of host animals and disease incidence revealed climate-correlated risk shifts of main zoonotic diseases in China
<p>This dataset contains host occurrence data from NACRC database and disease incidence data for the paper "Tracing the future of epidemics: Coincident niche distribution of host animals and disease incidence revealed climate-correlated risk shifts of main zoonotic diseases in China".</p>
Dissimilar climatic niche is predictive of contrasting historical demographic changes and altitudinal shifts in related oak species (<em>Quercus</em>)
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Data from: Rapid niche shifts in exotic species can be a million times faster than changes among native species and ten times faster than climate change
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Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion
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Annotated Behaviour and Observability Dataset (ABODe)
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