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2,603 results for “Ecological data”
Data from: Experimental assemblage of novel plant-herbivore interactions: ecological host shifts after 40 million years of isolation
Geographic isolation is the first step in insect herbivore diet specialization. Such specialization is postulated to increase insect fitness, but may simultaneously reduce insect ability to colonize novel hosts. During the Paleocene-Eocene, plants from the order Zingiberales became isolated either in the Paleotropics or in the Neotropics. During the Cretaceous, rolled-leaf beetles diversified in the Neotropics concurrently with neotropical Zingiberales. Using a community of Costa Rican rolled-leaf beetles and their Zingiberales host plants as study system, we explored if previous geographic isolation precludes insects to expand their diets to exotic hosts. We recorded interactions between rolled-leaf beetles and native Zingiberales by combining DNA barcodes and field records for 7450 beetles feeding on 3202 host plants. To determine phylogenetic patterns of diet expansions, we set 20 field plots including five exotic Zingiberales, recording beetles feeding on these exotic hosts. In the laboratory, using both native and exotic host plants, we reared a subset of insect species that had expanded their diets to the exotic plants. The original plant-herbivore community comprised 24 beetle species feeding on 35 native hosts, representing 103 plant-herbivore interactions. After exotic host plant introduction, 20% of the beetle species expanded their diets to exotic Zingiberales. Insects only established on exotic hosts that belong to the same plant family as their native hosts. Laboratory experiments show that beetles are able to complete development on these novel hosts. In conclusion, rolled-leaf beetles are pre-adapted to expand their diets to novel host plants even after millions of years of geographic isolation.
Data from: Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua
The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)—from two Great Lakes and two crater lakes in Nicaragua—to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ13C and δ15N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution.
Data from: Ecological correlates of ghost lineages in ruminants
Integration between phylogenetic systematics and paleontological data has proved to be an effective method for identifying periods that lack fossil evidence in the evolutionary history of clades. In this study we aim to analyze whether there is any correlation between various ecomorphological variables and the duration of these underrepresented portions of lineages, which we call ghost lineages for simplicity, in ruminants. Analyses within phylogenetic (Generalized Estimating Equations) and non-phylogenetic (ANOVAs and Pearson correlations) frameworks were performed on the whole phylogeny of this suborder of Cetartiodactyla (Mammalia). This is the first time ghost lineages are focused in this way. To test the robustness of our data, we compared the magnitude of ghost lineages among different continents and among phylogenies pruned at different ages (4, 8, 12, 16, and 20 Ma). Differences in mean ghost lineage were not significantly related to either geographic or temporal factors. Our results indicate that the proportion of the known fossil record in ruminants appears to be influenced by the preservation potential of the bone remains in different environments. Furthermore, large geographical ranges of species increase the likelihood of preservation.
Data from: Keystone individuals alter ecological and evolutionary consumer-resource dynamics
Intraspecific variation is central to our understanding of evolution and ecology, but these fields generally consider either the mean trait value or its variance. Alternatively, the keystone individual concept from behavioral ecology posits that a single individual with an extreme phenotype can have disproportionate and irreplaceable effects on group dynamics. Here, I generalize this concept to include non-behavioral traits and broader ecological and evolutionary dynamics. I test for the effects of individuals with extreme phenotypes on the ecology and evolution or a gall-forming fly and its natural enemies that select for opposite gall sizes. Specifically I introduce a putatively keystone predator-attracting individual gall-maker, hypothesizing that the presence of such an individual should (i) increase gall-maker population-level mortality, (ii) cause consumer communities to be dominated by species that are most attracted to the keystone individual, (iii) increase selection for traits conferring defense against the most common consumer, and (iv) weaken patterns of stabilizing selection. I find support for both the ecological and evolutionary consequences of single individuals with extreme phenotypes, suggesting that they can be considered keystone individuals. I discuss the generality of the keystone individual concept, suggesting likely consequences for ecology and evolution.
Data from: Causes of ecological gradients in leaf margin entirety: Evaluating the roles of biomechanics, hydraulics, vein geometry, and bud packing
PREMISE OF THE STUDY: A recent commentary by Edwards et al. (Am. J. Bot. 103: 975–978) proposed that constraints imposed by the packing of young leaves in buds could explain the positive association between non-entire leaf margins and latitude but did not thoroughly consider alternative explanations. METHODS: We review the logic and evidence underlying six major hypotheses for the functional significance of marginal teeth, involving putative effects on (1) leaf cooling, (2) optimal support and supply of the areas served by major veins, (3) enhanced leaf-margin photosynthesis, (4) hydathodal function, (5) defense against herbivores, and (6) bud packing. KEY RESULTS: Theoretical and empirical problems undermine all hypotheses except the support–supply hypothesis, which implies that thinner leaves should have non-entire margins. Phylogenetically structured analyses across angiosperms, the El Yunque flora, and the genus Viburnum all demonstrate that non-entire margins are indeed more common in thinner leaves. Across angiosperms, the association of leaf thickness with non-entire leaf margins is stronger than that of latitude. CONCLUSION: We outline a synthetic model showing how biomechanics, hydraulics, vein geometry, rates of leaf expansion, and length of development within resting buds, all tied to leaf thickness, drive patterns in the distribution of entire vs. non-entire leaf margins. Our model accounts for dominance of entire margins in the tropics, Mediterranean scrub, and tundra, non-entire margins in cold temperate deciduous forests and tropical vines and early-successional trees, and entire leaf margins in monocots. Spinose-toothed leaves should be favored in short-statured evergreen trees and shrubs, primarily in Mediterranean scrub and related semiarid habitats.
Data from: Movement ecology of Afrotropical birds: Functional traits provide complementary insights to species identity
Effects of anthropogenic activities on habitats and species communities and populations are complex and vary across species depending on their ecological traits. Movement ecology may provide important insights into species´ responses to habitat structures and quality. We investigated how movement behavior across a human-modified landscape depends on species identity and species traits, with particular focus on habitat specialization, feeding guilds and dispersal behavior. We tracked 34 individuals of nine Afrotropical bird species during three years in an anthropogenic riparian landscape of East Africa. We investigated whether species' functional traits predicted their habitat use and movement behavior better than species´ identities. Our results indicate that habitat specialists mainly occur in dense riparian thickets, while habitat generalists do occur in agricultural land. Home-ranges of omnivorous habitat generalists are larger than of frugivorous and insectivorous generalists and omnivorous and insectivorous specialists. Movement speed was highest in settlement areas for all species, with activity peaks during morning and afternoon for habitat specialists. Our results reveal that functional traits and species identity provide complementary insights into responses of organisms to habitat structures and habitat quality.
Data from: Divergent estimates of herd-wide caribou calf survival: ecological factors and methodological biases
Population monitoring is a critical part of effective wildlife management, but methods are prone to biases that can hinder our ability to accurately track changes in populations through time. Calf survival plays an important role in ungulate population dynamics and can be monitored using telemetry and herd composition surveys. These methods, however, are susceptible to unrepresentative sampling and violations of the assumption of equal detectability, respectively. Here we capitalized on 55 herd-wide estimates of woodland caribou (Rangifer tarandus caribou) calf survival in Newfoundland, Canada using telemetry (n = 1,175 calves) and 252 herd-wide estimates of calf:cow ratios (C:C) using herd composition surveys to investigate these potential biases. These data included 17 herd-wide estimates replicated from both methods concurrently (n = 448 calves and n =17 surveys) which we used to understand which processes and sampling biases contributed to disagreement between estimates of herd-wide calf survival. We used Cox proportional hazards models to determine if estimates of calf mortality risk were biased by the date a calf was collared. We also used linear mixed effects models to determine if estimates of C:C ratios were biased by survey date and herd size. We found that calves collared later in the calving season had a higher mortality risk and that C:C tended to be higher for surveys conducted later in the autumn. When we used these relationships to modify estimates of herd-wide calf survival derived from telemetry and herd composition surveys concurrently, we found that formerly disparate estimates of woodland caribou calf survival now overlapped (within a 95% confidence interval) in a majority of cases. Our case study highlights the potential of under-appreciated biases to impact our understanding of population dynamics and suggests ways that managers can limit the influence of these biases in the two widely applied methods for estimating herd-wide survival.
Data from: Metabarcoding under Brine: Microbial ecology of five hyper-saline lakes at Rottnest Island (WA, Australia)
<p>Hypersaline<b> </b>ecosystems - aquatic environments where concentration of salt exceeds 35 g/L - host microbial communities which are highly specialized to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this lack of knowledge may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (Total Dissolved Solids) and alkalinity amongst the most influential parameters driving the community assemblages. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.</p>
Data from: Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies
Rapid diversification is often associated with morphological or ecological adaptations that allow organisms to radiate into novel niches. Neotropical Adelpha butterflies, which comprise over 200 species and subspecies, are characterized by extraordinary breadth in host plant use and wing colour patterns compared to their closest relatives. To examine the relationship between phenotypic and species diversification, we reconstructed the phylogenetic history of Adelpha and its temperate sister genus Limenitis using genomewide restriction-site-associated DNA (RAD) sequencing. Despite a declining fraction of shared markers with increasing evolutionary distance, the RAD-Seq data consistently generated well-supported trees using a variety of phylogenetic methods. These well-resolved phylogenies allow the identification of an ecologically important relationship with a toxic host plant family, as well as the confirmation of widespread, convergent wing pattern mimicry throughout the genus. Taken together, our results support the hypothesis that evolutionary innovations in both larvae and adults have permitted the colonization of novel host plants and fuelled adaptive diversification within this large butterfly radiation.
Data from: Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows
Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection on twelve candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection on loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.
Local ecological knowledge of fisheries charts decline of sharks in data-poor regions
<p>Scientific knowledge is lacking on marine species of economic and conservation importance, hindering their sustainable management. Local Ecological Knowledge (LEK) has the potential to provide valuable insights on large (spatial and temporal) scales, by drawing on the collective experiences of those who work closely with the taxa of interest. This study explored the status of shark population over time in four countries across eastern and southern Arabia (i.e. Kuwait, Bahrain, Oman and Yemen). Results indicate strong declines, with highly experienced fishermen reporting greater perceived declines (80%) in the abundance of sharks (in general), with mean year of perceived decline starting in the late 1990s to early 2000s. For three specific taxa investigated, hammerhead sharks (e.g. Sphyrna mokarran) had the greatest mean perceived decline (80%), while even the group with the least decline (small carcharhinids) had mean perceived declines of 50%. Management measures are urgently required in the region to ensure sustainability of historic shark fisheries that provide food security and coastal livelihoods (e.g. Yemen and Oman), and to prevent regional extinctions (e.g. hammerhead sharks). Older and more experienced fishermen who are both; witness to the greatest declines and may have local standing and influence could be valuable resources in developing more community-based sustainable fisheries, especially given the apparent lack of success of formal management measures.</p>
Data from: Molecular detection of invertebrate prey in vertebrate diets: trophic ecology of Caribbean island lizards
Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for a common Caribbean lizard that has been intensively studied in the context of small island food webs: Anolis sagrei (a semi-arboreal 'trunk-ground' anole ecomorph). Novel PCR primers were identified in silico and tested in vitro. Illumina sequencing successfully characterized the arthropod component of 168 faecal DNA samples collected during three field trips spanning 12 months, revealing 217 molecular operational taxonomic units (mOTUs) from at least nine arthropod orders (including Araneae, Blattodea, Coleoptera, Hemiptera, Hymenoptera, Isoptera, Lepidoptera and Orthoptera). Three mOTUs (one beetle, one cockroach and one ant) were particularly frequent, occurring in ≥50% of samples, but the majority of mOTUs were infrequent (180, or 83%, occurred in ≤5% of samples). Species accumulation curves showed that dietary richness and composition were similar between size-dimorphic sexes; however, female lizards had greater per-sample dietary richness than males. Overall diet composition (but not richness) was significantly different across seasons, and we found more pronounced interindividual variation in December than in May. These methods will be generally useful in characterizing the diets of diverse insectivorous vertebrates.
Figure 4 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data
Figure 4. Time-calibrated phylogram from the partitioned BEAST analyses of the combined dataset (COI and 16s). Bayesian inference (BI) and maximum likelihood (ML) reconstructions provided very similar and largely overlapping topologies. Numbers below nodes are BI posterior probabilities (only values> 0.95 are shown) and ML bootstrap values (only values> 70% are shown). Numbers above nodes are estimated dates of diversification. Terminal taxa labels refer to individual sequence numbers used in Table 2.
Figure 2 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data
Figure 2. Paramera of male at left (lateral and dorsal views) and parts of left valves of female Propomacrus at right. The dashed line separates different scales and sexes. (a–d): 'P. cypriacus'; (e–h) P. bimucronatus from the Lebanon; (i–l): P. bimucronatus from Turkey; a, g and k: basal parts of valves; d, h and l: distal parts of valves.
Figure 1 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data
Figure 1. Map of Cyprus with new and previous records of P. cypriacus. Localities where unsuccessful searches were performed are also shown.
Figure 3 in Revisiting the saproxylic beetle 'Propomacrus cypriacus Alexis & Makris, 2002' (Coleoptera: Euchiridae) using molecular, morphological and ecological data
Figure 3. Protibiae of P. bimucronatus (left) from Turkey (upper), the Lebanon (middle), and Greece (lower), and 'P. cypriacus' (upper right: holotype; middle and lower: paratypes; Vretsia, Cyprus, leg. Makris). All photos are at the same scale.
Figure 3 in The reproductive ecology of Leptodactylus fuscus (Anura, Leptodactylidae): new data from natural temporary ponds in the Brazilian Cerrado and a review throughout its distribution
Figure 3. Intra-specific distance of Leptodactylus fuscus males in the Ponte Pond in the Estação Ecológica de Itirapina, São Paulo, from December 2002 and January 2003. In December: NC, non-calling males (N528) and C, calling males (N59); in January: NC, noncalling males (N536) and C, calling males (N519). Points indicate medians; boxes represent first and third quartiles (between 25% and 75% of the variation); bars indicate minimum and maximum values.
Figure 2 in The reproductive ecology of Leptodactylus fuscus (Anura, Leptodactylidae): new data from natural temporary ponds in the Brazilian Cerrado and a review throughout its distribution
Figure 2. Corrected number Leptodactylus fuscus males observed in calling activity every hour in the three temporary ponds at the Estação Ecológica de Itirapina, São Paulo, from November 2002 to March 2003. Dotted line represents number expected; continuous line represents number observed.
Figure 1 in The reproductive ecology of Leptodactylus fuscus (Anura, Leptodactylidae): new data from natural temporary ponds in the Brazilian Cerrado and a review throughout its distribution
Figure 1. Maximum number of individuals of Leptodactylus fuscus (bars), accumulated rainfall (dotted lines; mm) and height of the water column (continuous line; mm) reported in each sampling period, in the three temporary ponds at the Estação Ecológica de Itirapina, São Paulo, from November 2002 to March 2003.
Ecological resilience and resistance to extreme weather events - review data
<p>Extreme weather events (EWEs) are expected to increase in stochasticity, frequency, and intensity due to climate change. Documented effects of EWEs, such as droughts, hurricanes, and temperature extremes, range from shifting community stable states to species extirpations. To date, little attention has been paid to how populations resist and/or recover from EWEs through compensatory (behavioural, demographic or physiological) mechanisms; limiting the capacity to predict species responses to future changes in EWEs. Here, we systematically reviewed the global variation in species' demographic responses, resistance to, and recovery from EWEs across weather types, species, and biogeographic regions. Through a literature review and meta-analysis, we <span>tested the prediction that population abundance and probability of persistence will decrease in populations after an EWE and how compensation affects that probability. Across 524 species population responses to EWEs reviewed (27 articles), we noted large variation in responses, such that, on average, the effect of EWEs on population demographics was not negative as predicted. The majority of species populations (80.4%) demonstrated compensatory mechanisms during events to reduce their deleterious effects. However, for populations that were negatively impacted, the demographic consequences were severe. Nearly 20% of the populations monitored experienced declines of over 50% after an EWE</span>, and 6.8% of populations were extirpated. Population declines were reflected in a <span>reduction in survival. Further, resilience was not common, as 80.0% of populations that declined did not recover to before EWE levels while monitored. </span>However, average monitoring time was only two years with over a quarter of studies tracking recovery for less than the study species generation time. We conclude that EWEs have positive and negative impacts on species demography, and this varies by taxa. Species population recovery over short time intervals is rare, but long-term studies are required to accurately assess species resilience to current and future events.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.