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51 results for “niche conservatism”
Data set: Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes
<h1>Repository for "Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes"</h1> <p>---</p> <p>These data scripts were used to perform analyses included in the research paper "Morphological evolution and niche conservatism across a continental radiation of Australian blindsnakes" </p> <p>Main questions for the study:</p> <p>1. What are the main axes of morphological variation?<br>2. Does variation in morphology among species correlate with their current environments? <br>3. Are lineages that occupy ecologically similar habitats morphologically convergent? <br>4. Is speciation predominantly allopatric or sympatric? <br>5. Do sister species have greater morphological and ecological niche overlap than expected relative to non-sister species pairs?</p> <h2>## Data structure</h2> <p>Contents in the data folder is archived as a zip and can be downloaded from Zenodo (for all versions see https://zenodo.org/doi/10.5281/zenodo.10397830). Once you unzip the zipped files, you will see three folders and some files that are no in any folders. </p> <p>/data/ - files that were manually created and the phylogeny</p> <p>/data/script_generated_data/ - A combination of processed data needed to run the analyses </p> <p>/data/dorsal/ - photographs of the head from the dorsal view. These photos were used for digitising landmarks and semilandmarks. </p> <p>/data/worldclim2_30s/ - cropped and merged annual temperature from WorldClim2 (Fick and Hijmans 2017), soil bulk density from <a href="https://esoil.io/TERNLandscapes/Public/Pages/SLGA/GetData.html">Soil and Landscape Grid of Australia</a>, and Global Aridity Index from Zomer et al. (2022). <br><br>/DREaD/ - contains some files required to replicate DREaD analysis</p> <h2>## Code/Software</h2> <p>All scripts can be run using open source software. Scripts should be run in order to create necessary files that will be saved in /data/script_generated_data/ for further scripts. R is required to run R scripts (.R).</p> <h3>### /Code</h3> <p> - utility/*.R - scripts for custom functions. These are sourced in other scripts.<br> - DREaD/*.R - scripts associated with DREaD analyses<br> - 00_linear_measurement_shaperatio.R - script used to account for sexual dimorphism and calculate conventional PCA. Addresses Q1.<br> - 01_model_fitting.R - script used to address Q2 and plot visualisations.<br> - 02_convergence.R - this script calculates Ct1-4 and C5 scores. Addresses Q3.<br> - 02_convergence_model_fitting.R - this script evaluates fit of different evolutionary models to traits. Addresses Q3.<br> - 02_convergence_test_simulations.R - simulation studies to show that our phylogeny has sufficient power to detect convergence.<br> - 03_niche_enmtools_bias_account.R - calculates ecological niche models (ENMs) for each species using MAXENT. Runs Age-Overlap Correlation tests for geography and ENMs. Partially addresses Q4.<br> - 03_DREaD_Blindsnakes_AS.R - script to run DREaD analysis. <br> - 03_morpho_niche_overlap_plots.R - Runs Age-Overlap Correlation tests for body shape and snout shape. Plots AOCs. Partially addresses Q4. <br> - 04_pairwise_distance_test.R - Binomial tests between sister and non-sister pairs for ENMs and Geographic Range. Partially addresses Q5<br> - 04_morpho_pairwise.R - Binomial tests between sister and non-sister pairs for body shape and snout shape. Partially addresses Q5</p> <h2>## Contact</h2> <p>Should you have questions about these scripts or would like to request raw data, please do not hesitate to contact Sarin Tiatragul (contact information can be found in the paper) or on Github (https://github.com/stiatragul/blindsnakemorphoevo)</p> <h2>## References</h2> <p><a name="ref-fickWorldClim2017"></a>Fick, S. E., and R. J. Hijmans. 2017. <a href="https://doi.org/10.1002/joc.5086">WorldClim 2: New 1-km spatial resolution climate surfaces for global land areas</a>. International Journal of Climatology 37:4302–4315.</p> <p><a name="ref-zomerVersion2022"></a>Zomer, R. J., J. Xu, and A. Trabucco. 2022. <a href="https://doi.org/10.1038/s41597-022-01493-1">Version 3 of the global aridity index and potential evapotranspiration database</a>. Scientific Data 9:409.</p>
Climatic niche conservatism in a clade of disease vectors (Diptera: Phlebotominae)
<p>Sandflies of the family Psychodidae show notable diversity in both disease vector status and climatic niche. Psychodid species' ranges can be solely tropical, confined to the temperate zones, or span both. We obtained observation site data, and associated climate data, for 223 psychodid species to understand which aspects of climate most closely predict distribution. Temperature and seasonality are strong determinants of species occurrence within the clade. We built a mitochondrial DNA phylogeny of Psychodidae, and found a positive relationship between pairwise genetic distance and climate niche differentiation, which indicates strong niche conservatism. This result is also supported by strong phylogenetic signals of metrics of climate differentiation. Finally, we used ancestral trait reconstruction to infer the tropicality (i.e., proportion of latitudinal range in the tropics minus the proportion of the latitudinal range in temperate areas) of ancestral species, and counted transitions to and from tropicality states, finding that tropical and temperate species respectively produced almost entirely tropical and temperate descendant species, a result consistent for vector and non-vector species. Taken together, these results imply that while vectors of Leishmania can survive in a variety of climates, their climate niches are strongly predicted by phylogeny.</p>
Data used in: Phenological sensitivities to climate are similar in two Clarkia congeners: Indirect evidence for facilitation, convergence, niche conservatism, or genetic constraints
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Climatic niche conservatism in a clade of disease vectors (Diptera: Phlebotominae)
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Data from: Marine latitudinal diversity gradients, niche conservatism, and out of the tropics and Arctic: climatic sensitivity of small organisms
<ul> <li>Aim</li> </ul> <p>The latitudinal diversity gradient (LDG) is a consequence of evolutionary and ecological mechanisms acting over long history, and thus is best investigated with organisms that have rich fossil records. However, combined neontological-paleontological investigations are mostly limited to large, shelled invertebrates, which keeps our mechanistic understanding of LDGs in its infancy. This paper aims to describe the modern meiobenthic ostracod LDG and to explore the possible controlling factors and the evolutionary mechanisms of this large-scale biodiversity pattern.</p> <ul> <li>Location</li> </ul> <p>Present-day Western North Atlantic</p> <ul> <li>Taxon</li> </ul> <p>Ostracoda</p> <ul> <li>Methods</li> </ul> <p>We compiled census data from ostracods living in shallow marine environments of the western North Atlantic Ocean. Using these data, we documented the marine LDG with multiple metrics of alpha, beta (nestedness and turnover), and gamma diversity, and we tested whether macroecological patterns could be governed by different environmental factors, including temperature, salinity, dissolved oxygen, pH and primary productivity. We also explored the geologic age distribution of ostracod genera to investigate the evolutionary mechanisms underpinning the LDG.</p> <ul> <li>Results</li> </ul> <p>Our results show that temperature and climatic niche conservatism are important in setting LDGs of these small, poorly-dispersing organisms. We also found evidence for some dispersal-driven spatial dynamics in the ostracod LDG. Compared to patterns observed in marine bivalves, however, dispersal dynamics were weaker and they were bi-directional, rather than following the "out-of-the-tropics" model.</p> <ul> <li>Main Conclusions</li> </ul> <p>Our detailed analyses revealed that meiobenthic organisms, which comprise two-thirds of marine diversity, do not always follow the same rules as larger, better-studied organisms. Our findings suggest that the under-studied majority of biodiversity may be more sensitive to climate than are well-studied, large organisms. This implies that the impacts of ongoing Anthropocene climatic change on marine ecosystems may be much more serious than presently thought.</p>
Tropical niche conservatism explains the Eocene migration from India to Southeast Asia in Ochyroceratid spiders
<p><span>Biological migrations between India and Southeast (SE) Asia provide an ideal system for exploring the effects of geology and climate on species ranges. Geologists have confirmed that the direct collision between India and Eurasia occurred in the Early Eocene, but most migrations occurred between the Indian subcontinent and SE Asia rather than the former and the southern margin of Eurasia. To explain this seemingly paradoxical disconnect between the routes of plate movement and biological migration, we studied the evolutionary history of the tropical spider family Ochyroceratidae based on 101 globally distributed species. We infer a robust dated phylogeny using both transcriptomic data and a dataset of classical markers and relate these to biogeographic and climatic analyses. Our results indicate that the monophyly of Ochyroceratidae is strongly supported, and the divergence times suggest a Cretaceous Gondwanan origin of the family. Reconstructed biogeographic histories support a dispersal event from the Indian subcontinent to islands of SE Asia 55–38 million years ago. Climatic analyses and the fossil record reveal that ochyroceratids are characterized by a high degree of tropical niche conservatism, and that the ancestor of the Indian and SE Asian clades originated in very warm, wet environments. Early Eocene tropical, perhumid climates in India and SE Asia may have facilitated ochyroceratid migration, whereas the dry or seasonal climate extending from the eastern coast of China to Central Asia may have acted as a barrier, preventing dispersal. Our analyses suggest that climate plays a more important role than geology in biological migration from the Indian subcontinent to SE Asia, providing new insights into the Indian–Asian biogeographic link.</span></p>
Evidence for niche conservatism in alpine beetles under a climate-driven species pump model
<p>Aim</p> <p>Past glacial climate cycles have generated lineage diversity in alpine habitats, acting as a climate-driven species pump. It is not clear how much this process contributes to ecological diversification of alpine species. To examine this problem, we test patterns of genetic and phenotypic divergence in two co-distributed species complexes of flightless alpine ground beetles. Greater differentiation in ecologically-important functional traits would indicate that ecological selection is an outcome of oscillating climate change, whereas greater differentiation in non-ecological traits would indicate niche conservatism.</p> <p>Location</p> <p>The Cascades Range and Trinity Mountains of western North America.</p> <p>Taxon</p> <p>Members of the <i>Nebria paradisi</i> and <i>N. vandykei</i> species complexes (Insecta: Coleoptera: Carabidae: Nebriinae)</p> <p>Methods</p> <p>We generated genome-wide single nucleotide polymorphism data and mitochondrial sequence data, as well as morphological and physiological data, to compare populations spanning the range of both species. Phylogenetic and population genetic analyses were used to infer the relationships among taxa and populations within each species complex, as well as historical population demography. Support vector machines were used to test for classification of taxa and populations based on ecomorphological, ecophysiological, and male reproductive traits. Mantel tests were then used to assess statistical associations between phenotypic and genetic divergence among populations.</p> <p>Results</p> <p>The <i>N. vandykei</i> and <i>N. paradisi</i> species complexes are each comprised of genetically distinctive populations exhibiting long-term demographic declines. Each phylogeny supports multiple monophyletic groups with geographical cohesion. By examining phenotypic traits among populations in both species' complexes, we show that reproductive trait divergence can discriminate species and population status more effectively than ecomorphological or ecophysiological traits. Reproductive and genetic divergence are significantly correlated in the <i>N. vandykei</i> species complex.</p> <p>Main Conclusions</p> <p>We found limited evidence of ecological selection acting on functional traits. Instead, reproductive and genetic divergence evolved among isolated populations in both species complexes, suggesting niche conservatism may be a common outcome in alpine species diversification.</p>
Niche conservatism limits the distribution of Medicago in the tropics
<p>The increase in species number from poles to the equator is one of the most fundamental patterns in ecology. Although several hypotheses have been proposed, there is a lack of consensus on the mechanisms underlying this pattern. While most hypotheses provide plausible explanation for high tropical diversity of tropical clades, it is unclear if similar mechanisms drive the diversity of extra-tropical clades. Here, we investigated the environmental drivers influencing the diversity pattern of a Mediterranean plant genus <em>Medicago</em> and dissect their effects across continents and biomes. We compiled a comprehensive dataset on the distribution of all <em>Medicago</em> species and mapped their distribution at the spatial resolution of 100 × 100 km<sup>2</sup>. We used generalized linear models to quantify the relative effects of environmental factors on the richness patterns of <em>Medicago</em> and its two life forms. Next, using geographically weighted regression, we explored the variation in richness-environment relationship across latitude. We found that Quaternary climate change and environmental energy were important explanatory variables, and their effects were consistent at global, continental and biome scales. However, we found contrasting effect of environmental energy in temperate and tropical regions, with species richness increasing with energy in the temperate and decreasing in the tropics. We also found strong affinity of <em>Medicago</em> species to its ancestral Mediterranean climatic niche. Our results suggest that the spatial variation in <em>Medicago</em> richness patterns may be strongly influenced by heat tolerance as opposed to the tropical clades that depend upon cold tolerance. This dependency on heat tolerance can be attributed to strong niche conservatism exhibited by <em>Medicago</em> species. Our findings provide new insights into the richness-energy hypothesis and suggest that high environmental energy may not necessarily yield high species diversity but may also lower species diversity, especially of extra-tropical clades towards the tropics.</p>
Data for: Beyond latitude: Temperature, productivity, and thermal niche conservatism drive global body size variation in Odonata
<p><strong><span>Aim</span></strong><span>: </span><span>So far, </span><span>latitudinal body size-clines have been primarily discussed in the context of thermoregulation, sensu Bergmann. However, body size patterns are ambiguous in ectotherms and this heterogeneity remains poorly understood. We tested whether Bergmann's rule and the resource availability rule which states that energetic requirements determine species' body size, apply to damselflies and dragonflies (Odonata). Furthermore, we hypothesised that the contrasting effects of thermoregulation and resource availability (e.g. productivity) can obscure the overall gradient in body size variation.</span></p> <p><span><strong>Location</strong>: </span><span>Global</span></p> <p><span><strong>Time</strong> <strong>period</strong>: </span><span>Contemporary</span></p> <p><span><strong>Major</strong> <strong>taxa</strong> <strong>studied</strong>: </span><span>Odonata</span></p> <p><span><strong>Methods</strong>:</span><span> Using data for 43% of all odonate species described so far, we tested our hypotheses in phylogenetically and spatially comparative analyses at assemblage and species level. </span><span>For the distribution data, we integrated expert range maps and ecoregional ranges based on all available occurrence records. To distinguish between long-term versus evolutionarily recent responses of environmental drivers in body size, we constructed a phylogenetically informed classification of all odonate species and decomposed the body size into its phylogenetic and specific component for our subset of species.</span></p> <p><span><strong>Results</strong>: </span><span>We documented a weak positive relationship between body length and latitude but found strong and contrasting effects for temperature between dragonflies and damselflies and consistent positive effects for productivity that explained 35%–57% of body size variation. Moreover, we showed a strong phylogenetic signal in sized-based thermoregulation that shaped the distribution of dragonflies, but not of damselflies.</span></p> <p><span><strong>Main</strong> <strong>conclusion</strong>: </span><span>We concluded that temperature, productivity, and conservatism in size-based thermoregulation synergistically determine the distribution of ectotherms, while the taxon-specific importance of these factors can lead to contrasting results and weak latitude–size relationships. Our results reinforce the importance of body size as a determinant of species distributions and responses to climate change.</span></p>
Niche conservatism limits the distribution of Medicago in the tropics
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Data from: Marine latitudinal diversity gradients, niche conservatism, and out of the tropics and Arctic: climatic sensitivity of small organisms
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Allopatric speciation and interspecific gene flow driven by niche conservatism of Diploderma tree lizards in Taiwan
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Radiation of tropical island bees and the role of phylogenetic niche conservatism as an important driver of biodiversity
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Data for: Beyond latitude: Temperature, productivity, and thermal niche conservatism drive global body size variation in Odonata
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Data from: Assessing niche conservatism using a multiproxy approach: dietary ecology of extinct and extant spotted hyenas
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Tropical niche conservatism explains the Eocene migration from India to Southeast Asia in Ochyroceratid spiders
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Geographic patterns of insect diversity across China's nature reserves: The roles of niche conservatism and range overlapping
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Differential speciation rates, colonization time, and niche conservatism affect community assembly across adjacent biogeographical regions
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Evidence for niche conservatism in alpine beetles under a climate-driven species pump model
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Niche conservatism and sympatric parallel evolution may help to maintain eight nascent tree taxa along a sharp elevation gradient
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