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414 results for “Ecology: evolutionary”
Ecology and Evolutionary Biology Field Trip at the Coweeta Hydrologic Laboratory (Watershed 18) in 2004: Aquatic Invertebrates (Adult) data
As part of an educational project, we intend to conduct a short "bioblitz" that will focus on 4 major groups of organisms: (1) vertebrates, especially birds and salamanders; (2) the local flora, especially fungi, trees, and any herbaceous species present this early; (3) aquatic invertebrates; (4) terrestrial invertebrates. Data will be compared to available lists of taxa from Coweeta and Great Smoky Mountains National Park.
Basic list of international academic societies related to ecology and evolutionary biology.
<p>List of international societies related to ecology, evolutionary biology or whole-organism biology. The list is based on the table from Lagisz et al. (2023) (top 16 societies), appended with additional societies from internet searches, personal communication and societies associated with journals listed in SCImago under Ecology, Evolution, Behaviour and Systematics category. Alternative society names (usually in a non-English language) are not shown. Abbreviated society names (non-unique) usually match the official abbreviated society names (English or nn-English), but if abbreviation was not found on the website it was made up from the English society name. In the "Extract" column, "Yes" indicates active societies with individual membership.</p>
Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist
<p>With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form, but also in their functional specialization and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some one of the most dramatic examples of trophic specialization. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (<em>Cetoscarus ocellatus</em>). We find significant expansion, selection, and duplication within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialized teleostean radiation.</p>
Fig. 1 in (macro-) Evolutionary ecology of parasite diversity: From determinants of parasite species richness to host diversification
Fig. 1. Expression of the basic transmission rate (R0) for the case of microparasites (i.e. viruses) and macroparasites (i.e. helminths with direct transmission) (for derivations of these expressions see Morand and Deter, 2008), emphasizing the importance of two host traits, longevity and density, as likely determinants of parasite invasion and then parasite species richness. In the right panel, relationships showing that both density and longevity are in allometry with host body mass (after Brown, 1995).
Fig. 2 in (macro-) Evolutionary ecology of parasite diversity: From determinants of parasite species richness to host diversification
Fig. 2. (A) Variability of ectoparasite species richness among 113 families of mammals (20 orders) (data from Kim, 1985;see Poulin and Morand, 2004). (B) Ectoparasite species richness is related to mammal diversification. The statistical analysis follows Nunn et al. (2004), where the change in the number of descendent clades is related to the change in the number of ectoparasite species, estimated using a modified version of the independent contrast method (Agapow and Isaac, 2002), for each node of the mammal phylogeny (from Binida-Emonds et al., 2007).
Evolutionary effects of nitrogen are not easily predicted from ecological responses
<p>Anthropogenic nitrogen (N) addition might alter the evolutionary trajectories of plant populations, in part because it alters the abiotic and biotic environment by increasing aboveground primary productivity, light asymmetry, and herbivory intensity, and reducing plant species diversity. Such evolutionary impacts could be caused by N altering patterns of natural selection (i.e., trait-fitness relationships) and the opportunity for selection (i.e., variance in relative fitness). Because at the community level N addition favors species with light acquisition strategies (e.g., tall species), we predict that N would also increase selection favoring those same traits. We also hypothesize that N could alter the opportunity for selection via its effects on mean fitness and/or competitive asymmetries.To investigate these evolutionary consequences of N, we quantified the strength of selection and the opportunity for selection in replicated populations of the annual grass Setaria faberi Herrm. (giant foxtail) growing in a long-term N addition experiment. We also correlated our measures of selection and opportunity for selection with light asymmetry, diversity, and herbivory intensity to identify the proximate causes of any N effects on evolutionary processes. N addition increased aboveground productivity, light asymmetry, and reduced species diversity. Contrary to expectations, N addition did not strengthen selection for trait values associated with higher light acquisition such as greater height and specific leaf area (SLA); rather, it strengthened selection favoring lower SLA. Increased light asymmetry was associated with stronger selection for lower SLA and lower species diversity was associated with stronger selection for greater height and lower SLA, suggesting a role for these factors in driving N-mediated selection. The opportunity for selection was not influenced by N addition (despite increased mean fitness) but was negatively associated with species diversity. Our results indicate that anthropogenic N enrichment can affect evolutionary processes, but that evolutionary changes in plant traits within populations are unlikely to parallel the shifts in plant traits observed at the community level.</p>
Intracellular infection of ecologically important diatom species by an evolutionary distinct relative of the Fungi
<p>Data and R script from the publication "Intracellular infection of ecologically important diatom species by an evolutionary distinct relative of the Fungi":</p> <p>-plotting_and_testing_association.r: R script for the s.tatistical testing of NCLC1-diatom associations.</p> <p>-OSD_protist_ASV_table.csv: Amplicon Sequence Variant (ASV) table, comma separated. Lists the distribution of 7766 ASVs across 145 samples collected during the Ocean Sampling Day (OSD) 2014.</p> <p>-OSD_protist_ASV_sequences.fasta: fasta nucleotide file of the 7766 V4-18S ASVs sequenced as part of OSD and classified as unicellular eukaryotes ('protists'; re-processed in the present publication via DADA2).</p> <p>-sparCC_analysis.tar.gz: gzip'd archive with results from co-occurrence analyses ran on the protist OSD V4-18S dataset using sparCC (OSD_protist_ASV_sparCC_cor.csv: correlation output; OSD_protist_ASV_sparCC_100perm_pvals_twosided.csv: results of two-sided t-tests based on 100 sparCC permutations).</p> <p>-holomycota_alignment.fasta: multiple sequence alignment of reference holomycota 18S.</p> <p>-holomycota_MLtree_100nonparamboot.nwk: 18S maximum likelihood tree inferred using IQ-Tree; branch supports assessed with 100 non-parametric bootstrap replicates.</p> <p> </p>
Results and code associated with «Predictability of ecological and evolutionary dynamics in a changing world»
<p>Below you'll find results and code associated with the following article (*):</p> <p>Bozzuto, C, Ives, AR (2024): Predictability of ecological and evolutionary dynamics in a changing world. <em>Proceedings of the Royal Society B</em>, <strong>291</strong>: 20240980. https://doi.org/10.1098/rspb.2024.0980</p> <p>ABSTRACT: Ecological and evolutionary predictions are being increasingly employed to inform decision-makers confronted with intensifying pressures on biodiversity. For these efforts to effectively guide conservation actions, knowing the limit of predictability is pivotal. In this study, we provide realistic expectations for the enterprise of predicting changes in ecological and evolutionary observations through time. We begin with an intuitive explanation of predictability (the extent to which predictions are possible) employing an easy-to-use metric, predictive power <em>PP</em>(<em>t</em>). To illustrate the challenge of forecasting, we then show that among insects, birds, fishes and mammals, (i) 50% of the populations are predictable at most 1 year in advance and (ii) the median 1-year-ahead predictive power corresponds to a prediction <em>R</em><sup>2</sup> of only 20%. Predictability is not an immutable property of ecological systems. For example, different harvesting strategies can impact the predictability of exploited populations to varying degrees. Moreover, incorporating explanatory variables, accounting for time trends and considering multivariate time series can enhance predictability. To effectively address the challenge of biodiversity loss, researchers and practitioners must be aware of the information within the available data that can be used for prediction and explore efficient ways to leverage this knowledge for environmental stewardship.</p> <p>(*) previously a preprint on <em>bioRxiv</em>: https://doi.org/10.1101/2023.11.01.565089</p>
Secondary metabolites from nectar and pollen: a resource for ecological and evolutionary studies
<p>Floral chemistry mediates plant interactions with herbivores, pathogens, and pollinators. The chemistry of floral nectar and pollen—the primary food rewards for pollinators—can affect both plant reproduction and pollinator health. Although the existence and functional significance of nectar and pollen secondary metabolites has long been known, comprehensive quantitative characterizations of secondary chemistry exist for only a few species. Moreover, little is known about intraspecific variation in nectar and pollen chemical profiles. Because the ecological effects of secondary chemicals are dose-dependent, heterogeneity across genotypes and populations could influence floral trait evolution and pollinator foraging ecology. To better understand within- and across-species heterogeneity in nectar and pollen secondary chemistry, we undertook exhaustive LC-MS and LC-UV-based chemical characterizations of nectar and pollen methanol extracts from 31 cultivated and wild plant species. </p> <p>Nectar and pollen were collected from farms and natural areas in Massachusetts, Vermont, and California, USA, in 2013 and 2014. For wild species, we aimed to collect 10 samples from each of 3 sites. For agricultural and horticultural species, we aimed for 10 samples from each of 3 cultivars. Our dataset (1535 samples, 102 identified compounds) identifies and quantifies each compound recorded in methanolic extracts, and includes chemical metadata that describe the molecular mass, retention time, and chemical classification of each compound. A reference phylogeny is included for comparative analyses.</p> <p>We found that each species possessed a distinct chemical profile; moreover, within species, few compounds were found in both nectar and pollen. The most common secondary chemical classes were flavonoids, terpenoids, alkaloids and amines, and chlorogenic acids. The most common compounds were quercetin and kaempferol glycosides. Pollens contained high concentrations of hydroxycinnamoyl-spermidine conjugates, mainly triscoumaroyl and trisferuloyl spermidine, found in 71% of species. When present, pollen alkaloids and spermidines had median nonzero concentrations of 23,000 µM (median 52% of recorded micromolar composition). Although secondary chemistry was qualitatively consistent within each species and sample type, we found significant quantitative heterogeneity across cultivars and sites. These data provide a standard reference for future ecological and evolutionary research on nectar and pollen secondary chemistry, including its role in pollinator health and plant reproduction.</p>
Figure 1 in Climatic preferences and distribution of 6 evolutionary lineages of Typhlops vermicularis Merrem, 1820 in Turkey using ecological niche modeling
Figure 1. Important mountain chains of Anatolia and ecological niche modeling of T. vermicularis in Turkey under current climatic conditions.
Figure 3 in Climatic preferences and distribution of 6 evolutionary lineages of Typhlops vermicularis Merrem, 1820 in Turkey using ecological niche modeling
Figure 3. Predicted models of lineages G, H, and I according to Last Interglacial (LIG) and Last Glacial Maximum (LGM; CCSM and MIROC) (4, 4A, 4B, 4C for lineage G; 5, 5A, 5B, 5C for lineage H; 6, 6A, 6B, 6C for lineage I).
Figure 2 in Climatic preferences and distribution of 6 evolutionary lineages of Typhlops vermicularis Merrem, 1820 in Turkey using ecological niche modeling
Figure 2. Predicted models of lineages B, C, and E according to Last Interglacial (LIG) and Last Glacial Maximum (LGM; CCSM and MIROC) (1, 1A, 1B, 1C for lineage B; 2, 2A, 2B, 2C for lineage C; 3, 3A, 3B, 3C for lineage E).
Virophage replication mode drives ecological and evolutionary shifts in a host-virus-virophage system
<p>We studied how virophage replication modes affect the ecological dynamics of a host-virus-virophage system and the virophage’s evolutionary responses. By manipulating the level of virophage (Mavirus) integration into the host (Cafeteria burkhardae) alongside the Cafeteria roenbergensis virus (CroV), we found that higher integration improved host survival but decreased virophage reactivation. These communities had lower population densities and fewer fluctuations in host and virus populations, while virophage fluctuations increased. The virophage’s dual replication mode plays a key role in maintaining microbial community stability.</p>
Fig. 169 in Mammals Of The Rio Juruá And The Evolutionary And Ecological Diversification Of Amazonia
Fig. 169. Geological crosssection through the central portion of the Rio Juruá illustrating the position of the underlying structural Iquitos Arch relative to Upper Central and Lower Central sample sites, the positional shift of major soils from the downriver Alter do Chãu to upriver Solimes formations and position and depths of the upper Acre Subbasin and lower Central Amazon Subbasin. The geographic position of drill core sites from the Brazilian oil consortium, Petrabras, are indicated. Redrawn from Fig. 10 in volume 15 of the Projeto RadamBrasil (1977).
Fig. 170 in Mammals Of The Rio Juruá And The Evolutionary And Ecological Diversification Of Amazonia
Fig. 170. Hypothesis of area relationships for lowland tropical forests of South America based on analyses of avian phyletic and distributional data (from Cracraft and Prum, 1988).
Fig. 166 in Mammals Of The Rio Juruá And The Evolutionary And Ecological Diversification Of Amazonia
Fig. 166. Sample localities and distribution of haplotypes of the cytochromeb gene for the spiny tree rat Mesomys hispidus (above) and two species of terrestrial spiny rats Proechimys simonsi (middle) and P. steerei (below) along the Rio Jurua´. Single haplotypes shared among localities are indicated by ellipses connecting them. The number of haplotypes unique to each locality is also indicated.
Fig. 161 in Mammals Of The Rio Juruá And The Evolutionary And Ecological Diversification Of Amazonia
Fig. 161. Phenogram of Jaccard's similarity coefficients in comparisons of species composition between all documented species of marsupials, murid rodents, and echimyid rodents from each of 21 lowland Neotropical forest sample sites (see text). Terminal branches are identified by locality, as in the map (fig. 162). Mantel's matrix correlation coefficient for the association between the similarity matrix and the cophenetic correlation matrix is 0.946, p <0.001.
Fig. 162 in Mammals Of The Rio Juruá And The Evolutionary And Ecological Diversification Of Amazonia
Fig. 162. Sample sites in lowland neotropical forests for which reasonably complete species inventories are available for marsupials, murid rodents, and echimyid rodents (data largely from Voss and Emmons, 1996; see text). Regional groupings of localities, based on the phenogram of Jaccard's similarity coefficients in fig. 161, are drawn to indicate geographic relationships in community composition Localities outside of the Rio Juruá are identified by letters corresponding to the names given in the phenogram, fig. 161.
Fig. 158 in Mammals Of The Rio Juruá And The Evolutionary And Ecological Diversification Of Amazonia
Fig. 158. Karyotypes of four specimens of Proechimys steerei: A, Female; 2n = 24, FN = 40 MNFS 2096; Macaco, left bank Rio Jau´, Amazonas, Brazil. B, Female; 2n = 24, FN = 40; JUR 307 VaiQuemQuer (locality 15), right bank Rio Jurua´, Amazonas, Brazil. C, Female; 2n = 24, FN = 41 Sacado (locality 5), right bank Rio Jurua´, Amazonas, Brazil. And, D, Male; 2n = 24, FN = 42; MNFS 1545; Nova Vida (locality 3), right bank Rio Jurua´, Acre, Brazil.
Fig. 156 in Mammals Of The Rio Juruá And The Evolutionary And Ecological Diversification Of Amazonia
Fig. 156. Geographic trend in overall size, as indexed by mean scores on the first principal components axis for samples of Proechimys steerei along the Rio Jurua´. Samples are positioned from left to right from the headwaters downriver to mouth localities. Solid circles represent population means; bars on either side represent 95% confidence limits.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.