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3,225 results for “Case of study”
Data from: Genetic structure of a naturally regenerating post-fire seedling population: Pinus halepensis as a case study
To study the effects of wildfire on population genetics of a wind pollinated and wind dispersed tree, we have analyzed the genetic structure of a post-fire, naturally regenerating seedling population of Pinus halepensis Miller, on Mt. Carmel, Israel. We tested the existence of spatial genetic structure, which is expected due to the special spatial demographic structure of the post-fire seedling and sapling populations of this species. Explicitly, we asked whether or not seedlings that germinated under large, burned, dead pine trees are also their offspring. The results revealed that the post-fire seedling population is polymorphic, diverse, and reflects the pre-fire random mating system. In contrast to our prediction, we found no division of the post-fire seedling population to distinct sub-populations. Furthermore, as a result of post-fire seed dispersal to longer range than the average pre-fire inter-tree distance, seedlings found under individual burned trees were not necessarily their sole offspring. Although the population as a whole showed a Hardy-Weinberg equilibrium, significant excess of heterozygotes was found within each tallest seedlings group growing under single, large, burned pine trees. Our finding indicates the possible existence of intense natural selection for the most vigorous heterozygous genotypes that are best adapted to the special post-fire regeneration niche, which is the thick ash bed under large, dead, pine trees.
Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as sub-fossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established Maximum Likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a 'crown-giant' ecomorph anole hypothesized to have once been found throughout the Spanish, U.S., and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method.
Data from: Does trait variation within broadly distributed species mirror patterns across species? A case study in Puerto Rico
Although populations are phenotypically diverse, the majority of trait-based studies have focused on examining differences among species. The justification for this broadly applied approach is based on the assumption that differences among species are always greater than within species. This is likely true for local communities, but species are often broadly distributed across a wide range of environments and patterns of intraspecific variation might surpass differences among species. Therefore, an appropriate interpretation of the functional diversity requires an assessment of patterns of trait variation across different ecological scales. In this study, we examine and characterize patterns of leaf trait variation for species that are broadly distributed along an elevational gradient. We focus on seven leaf traits that represent a main axis of functional differentiation in plants reflecting the balance between photosynthetic efficiency, display, and stomatal conductance. We evaluated patterns of trait variance across ecological scales (elevation, species, populations, and individuals) and examined trait covariance at both within species and across species levels, along the elevation gradient. Our results show three key patterns: (1) intraspecific leaf trait variation for broadly distributed species is comparable to the inter-specific trait variation, (2) the trait variance structure is highly variable across species and (3) trait coordination between pairs of leaf traits is evident across-species along the gradient, but not always within species. Combined, our results show that trait coordination and covariance are highly idiosyncratic across broadly distributed and co-occurring species, indicating that species may achieve similar functional roles even when exhibiting different phenotypes. This result challenges the traditional paradigm of functional ecology that assumes single trait values as optimal solutions for environments. In conclusion, patterns of trait variation both across and within species should be considered in future studies that assess trade-offs among traits over environmental gradients.
Data from: Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study
In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool-temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial–interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high-latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.
Data from: Niche theory and its relation to morphology and phenotype in geographic space: a case study in woodpeckers (Picidae)
Ecogeographic analyses have recovered common environmental trends with respect to morphology; however discrepancies among trends exist. Hypothesized reasons for these divergences vary, but most relate a taxon's morphology to its ecological niche. Morphology is known to diverge when species co-occur with competitors or predators and when species occur across different habitats and environments. A less understood divergence from ecogeographic trends is niche fixation, wherein species become locked into particular niches due to their community interactions or foraging ecology. A form of niche fixation has been hypothesized in the theory of Interspecies Social Dominance Mimicry (ISDM), in which mimics maintain relatively constant size ratios with models to perpetuate their mimicry. If true, mimics should display variation and trends in tandem with their models. Here, I use mass as a proxy for body size and examine ecogeographic trends in two sets of woodpeckers (Picidae): a Nearctic group which has been reported to interact via ISDM, and a Neotropical group which, based on similar appearances and overlapping distributions, is a potential ISDM system. I found ecogeographic trends suggestive of differential evolutionary responses, and I found evidence against niche fixation in the Nearctic clade. The Neotropic clade showed limited evidence for tandem size evolution between models and mimics, but inconsistencies in the size ratios between mimic and model populations. Here, I discuss the implications of observing divergent ecogeographic trends within mimicry systems, with specific emphasis on how environment, ecology, and community interactions guide evolution.
Data from: Metapopulation vicariance, age of island taxa and dispersal: a case study using the pacific plant genus Planchonella (Sapotaceae)
Oceanic islands originate from volcanism or tectonic activity without connections to continental landmasses, are colonized by organisms, and eventually vanish due to erosion and subsidence. Colonization of oceanic islands occurs through long-distance dispersals or metapopulation vicariance, the latter resulting in lineages being older than the islands they inhabit. If metapopulation vicariance is valid, island ages cannot be reliably used to provide maximum age constraints for molecular dating. We explore the relationships between the ages of members of a widespread plant genus (Planchonella, Sapotaceae) and their host islands across the Pacific to test various assumptions of dispersal and metapopulation vicariance. We sampled three nuclear DNA markers from 156 accessions representing some 100 Sapotaceae taxa, and analyzed these in BEAST with a relaxed clock to estimate divergence times and with a phylogeographic diffusion model to estimate range expansions over time. The phylogeny was calibrated with a secondary point (the root) and fossils from New Zealand. The dated phylogeny reveals that the ages of Planchonella species are, in most cases, consistent with the ages of the islands they inhabit. Planchonella is inferred to have originated in the Sahul Shelf region, to which it back-dispersed multiple times. Fiji has been an important source for range expansion in the Pacific for the past 23 myr. Our analyses reject metapopulation vicariance in all cases tested, including between oceanic islands, evolution of an endemic Fiji–Vanuatu flora, and westward rollback vicariance between Vanuatu and the Loyalty Islands. Repeated dispersal is the only mechanism able to explain the empirical data. The longest (8900 km) identified dispersal is between Palau in the Pacific and the Seychelles in the Indian Ocean, estimated at 2.2 Ma (0.4–4.8 Ma). The first split in a Hawaiian lineage (P. sandwicensis) matches the age of Necker Island (11.0 Ma), when its ancestor diverged into two species that are distinguished by purple and yellow fruits. Subsequent establishment across the Hawaiian archipelago supports, in part, progression rule colonization. In summary, we found no explanatory power in metapopulation vicariance and conclude that Planchonella has expanded its range across the Pacific by long-distance dispersal. We contend that this will be seen in many other groups when analyzed in detail.
Figure 3 in The role of artificial ponds in maintaining dragonfly populations in an intensified farmland landscape. A case of study in Zamora, Spain
Figure 3. MDS two-dimensional plot (stress = 0.17) representing the samples of the four systems (Bray-Curtis index, square-root transformed abundances).
Figure 2 in The role of artificial ponds in maintaining dragonfly populations in an intensified farmland landscape. A case of study in Zamora, Spain
Figure 2. Estimated mean ± SE of dragonfly (A) richness, (B) abundance, and (C) Shannon's index values for each system (pond, reservoir, stream, and river).
Data from: Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands
When species within guilds perform similar ecological roles, functional redundancy can buffer ecosystems against species loss. Using data on the frequency of interactions between fish and fruit, we assessed whether co-occurring frugivores provide redundant seed dispersal services in three species-rich Neotropical wetlands. Our study revealed that frugivorous fishes have generalized diets; however, large-bodied fishes had greater seed dispersal breadth than small species, in some cases, providing seed dispersal services not achieved by smaller fish species. As overfishing disproportionately affects big fishes, the extirpation of these species could cause larger secondary extinctions of plant species than the loss of small specialist frugivores. To evaluate the consequences of frugivore specialization for network stability, we extracted data from 39 published seed dispersal networks of frugivorous birds, mammals and fish (our networks) across ecosystems. Our analysis of interaction frequencies revealed low frugivore specialization and lower nestedness than analyses based on binary data (presence–absence of interactions). In that case, ecosystems may be resilient to loss of any given frugivore. However, robustness to frugivore extinction declines with specialization, such that networks composed primarily of specialist frugivores are highly susceptible to the loss of generalists. In contrast with analyses of binary data, recently developed algorithms capable of modelling interaction strengths provide opportunities to enhance our understanding of complex ecological networks by accounting for heterogeneity of frugivore–fruit interactions.
Data from: Developing state and transition models of floodplain vegetation dynamics as a tool for conservation decision-making: a case study of the Macquarie Marshes Ramsar wetland
1. Floodplain vegetation states (communities) exhibit spatiotemporal dynamics in vegetation structure and composition, which reflect unique hydrological and connectivity patterns. Shifts in inundation regimes can drive succession and establish new stable states, determined by the magnitude and duration of the hydrological perturbation. 2. We aimed to develop a modelling approach that is able to capture ecosystem dynamics, identify and quantify the main drivers of change, and provide a tool for conservation decision-making. We developed state and transition models for floodplain vegetation states based on surveys in 1991 and 2008 in the Macquarie Marshes (Australia), a Ramsar wetland of international importance. We used a Bayesian logistic regression approach to model state and transitions between vegetation states and investigated how flood frequency, distance to stream and fire frequency were associated with vegetation dynamics during this period. 3. During 1991–2008, significant transitions have occurred towards drier states. Semi-permanent wetland vegetation had the lowest persistence probability (ppsis = 0·456) and a significant threshold response of transitioning to terrestrial vegetation (ptran = 0·505). Transition to drier states was driven by lower inundation probabilities followed by increased fire probability, and distance to nearest stream. 4. Using developed models, we predicted persistence probabilities of vegetation states under an unregulated (i.e. no dams or diversions) and regulated water availability system. Under a regulated system, semi-permanent wetland vegetation had an average persistence of ppsis = 0. 67 and 0·08 in the northern and southern sections of the nature reserve, respectively. Under an unregulated system, the predicted persistence of semi-permanent wetland vegetation was considerably higher: ppsis = 0·87 and 0·38, respectively. 5. Synthesis and applications. Developing quantitative models of state transitions significantly improved our understanding of ecosystem dynamics, identifying sensitive indicators for monitoring and thus supporting conservation decision-making. This helps managers understand potential trajectories of change in ecosystems in response to management options. For example, increasing environmental flows in the Macquarie Marshes is predicted to shift the community towards more of a wetland than the terrestrial state, resulting from river regulation. State and transition models identified how key ecological assets respond to drivers of change, particularly where these can be managed. This is critical for ensuring that all ecosystem components are managed and that these do not shift into undesirable states.
FIGURES 14A–14B in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 14A–14B. Chamaesiphon stratosus. Cell arrangement and initial stage after exospore germination (arrow). FIGURES 14C–14D. Hyella cf. caespitosa var. arbuscula. General thallus aspect and detail of baeocytes in mothers' sheath (arrow).
FIGURES 15A–15D in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 15A–15D. Pleurocapsa sp. General colony habit and details of baeocytes (arrows). FIGURES 15E–15G. Chroococcidiopsis sp. General colony habit and details of baeocytes (arrows).
FIGURES 12A–12C. Entophysalis granulosa FIGURES 12D–12E in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 12A–12C. Entophysalis granulosa FIGURES 12D–12E. Entophysalis cf. samoensis FIGURES 12F–12G. Entophysalis sp. 1
FIGURES 11A–11C in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 11A–11C. Chlorogloea sp. 3 FIGURES 11D–11E. Cyanoarbor aff. himalayensis FIGURES 11F–11H. Entophysalis arboriformis
FIGURES 8A–8C in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 8A–8C. Nephrococcus shilinensis. General colony habit and detail of reniform cells (arrows). FIGURES 8D–8E. Pseudocapsa dubia. General colony habit with colonies showing brown sheaths (arrow). FIGURES 8F–8G. Pseudocapsa sp. General colony habit and cells in fan disposition, which is typical from Pseudocapsa (arrow). FIGURE 8H. Chondrocystis dermochroa.
FIGURES 6L–7B. Gloeocapsopsis dvorakii. 6L. Colony collected from a rock. 7A. Colony collected from a rope. 7B. Colony collected from a in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 6L–7B. Gloeocapsopsis dvorakii. 6L. Colony collected from a rock. 7A. Colony collected from a rope. 7B. Colony collected from a roof.
FIGURES 6A–6D. Cyanostylon gelatinosus. 6C. Cells detail. 6D. Mucilage stalk detail. FIGURE 6E in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 6A–6D. Cyanostylon gelatinosus. 6C. Cells detail. 6D. Mucilage stalk detail. FIGURE 6E. Cyanostylon cf. gelatinosus. General colony habit with detail of mucilage stalks (arrows). FIGURES 6F–6G. Cyanostylon sp. 6G. Mucilage stalk detail (arrow). FIGURES 6H–6I. Endospora rubra. General colony habit with cell packets showing individual envelopes (arrows).
FIGURES 2A in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 2A. Gloeothece fuscolutea. General colony habit, with yellowish sheaths and a colony showing cells with an individual envelope (arrow).
FIGURES 1A–1B in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 1A–1B. Aphanothece saxicola. General colony habit with cells in an individual envelope (arrow).
FIGURES 5A–5B. Chroococcus tenax. 5A. General colony habit highlighting the lamellated sheaths. 5B in How diverse are coccoid cyanobacteria? A case study of terrestrial habitats from the Atlantic Rainforest (São Paulo, Brazil)
FIGURES 5A–5B. Chroococcus tenax. 5A. General colony habit highlighting the lamellated sheaths. 5B. Desiccated cell showing concentrically lamellate sheaths and blue color.
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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.