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2,315 results for “Comparative analysis”
Data from: Angiosperm fleshy fruits and seed dispersers: a comparative analysis of adaptation and constraints in plant-animal interactions
Variation in phenotypic traits of angiosperm fleshy fruits has been explained as the result of adaptations to their mutualistic seed dispersers. By analyzing the information available on fleshy fruit characteristics of 910 angiosperm species, I assess the hypothesis of evolutionary association between fruit phenotypic traits and type of seed disperser (birds, mammals, and mixed dispersers) and address explicitly and quantitatively alternative null hypotheses about phylogenetic effects. Phylogenetic affinity among plant taxa is accounted for by comparative methods including nested ANOVA, phylogenetic autocorrelation, and independent contrasts. Averaging over the 16 fruit traits examined, phylogenetic effects down to genus level explain 61% of total variance. Phylogenetic autocorrelations are strong among close relatives, reaching significance for 11 of the 16 fruit traits examined. When assessed by independent contrast methods, correlated evolution between type of disperser and fruit traits is confined to fruit diameter. Differences among dispersal syndromes in other traits vanish after accounting for phylogenetic effects. These analyses reveal that seed dispersal syndromes are not entirely interpretable as current adaptations to seed dispersers. Their status as exaptations can be assessed by combining experimental studies of natural selection on fruit size and rigorous comparative and cladistic tests of adaptational hypotheses.
Data from: Comparative analysis indicates historical persistence and contrasting contemporary structure in sympatric woody perennials of semi-arid south-west Western Australia
We used a comparative approach to assess congruence of phylogeographic and genetic structure and diversity, demographic signals, and ratios of pollen to seed dispersal, in the context of species-specific life-history traits, for two widespread sympatric perennial plant species. We sampled Grevillea paradoxa and Melaleuca nematophylla across the species' ranges throughout the Transitional Rainfall Zone and extending slightly into the Arid Zone of south-west Western Australia. Both species exhibited range-wide phylogeographic and contemporary genetic structure. Moderate haplotype diversity centred in populations on Banded Ironstone Formation (BIF) outcrops and within the Murchison River gorge supports a hypothesis of historical persistence and evolution in these mesic refugia. These features are likely to play important roles in evolutionary persistence with ongoing climate change. There was little evidence of particularly complex demographic histories for the region. More limited haplotype diversity, as well as more limited nuclear genetic diversity and connectivity, in G. paradoxa was consistent with predictions from life-history traits of shorter lifespan, lower fecundity, more limited seed dispersal, and shorter plants, but inconsistent with a prediction of greater pollen dispersal by bird pollinators. Low pollen to seed dispersal ratios suggest seed dispersal plays a greater than expected role in maintaining connectivity in this semi-arid landscape. The study highlights a need for research that integrates aspects of seed ecology and seed and pollen dispersal as well as phylogeographic and genetic patterns in Gondwanan shrublands and other semi-arid landscapes globally.
Data from: Comparative analysis of adaptive and neutral markers of Drosophila mediopunctata populations dispersed among forest fragments
Comparison of adaptive and neutral genetic markers is a valuable approach to characterize the evolutionary consequences of populations living in environments threatened by anthropogenic disturbances, such as forest fragmentation. Shifts in allele frequencies, low genetic variability, and a small effective population size can be considered clear signs of forest fragmentation effects (due to genetic drift) over natural populations, while adaptive responses correlate with environmental variables. Brazilian Atlantic Forest had its landscape drastically reduced and fragmented. Now, several forest remnants are isolated from each other by urban and crop areas. We sampled Drosophila mediopunctata populations from eight forest remnants dispersed on two adjacent geomorphological regions, which are physiognomic and climatically quite distinct. Microsatellite data of inversion‐free chromosomes (neutral genetic marker) indicate low structuration among populations suggesting that they were panmictic and greatly influenced by gene flow. Moreover, significant differences in chromosomal inversion frequencies (adaptive genetic marker) among populations and their correlations with climatic and geographical variables indicate that genetic divergence among populations could be an adaptive response to their environment. Nonetheless, we observed a significant difference in inversion frequencies of a population in two consecutive years that may be associated with edge and demographic effects. Also, it may be reflecting seasonal changes of inversion frequencies influenced by great temperature variation due to edge effects. Moreover, the forest fragment size does not affect genetic variation of neutral markers. Our data indicate that despite oscillations in chromosomal inversion frequencies, D. mediopunctata populations from Brazilian Atlantic Forest and their divergence may be driven by adaptive factors to local differences, perhaps because it is a small flying insect easily carried by the wind increasing its migration rates.
Data from: Comparing the performance of microsatellites and RADseq in population genetic studies: analysis of data for pike (Esox lucius) and a synthesis of previous studies
<p>Population genetic studies reveal biodiversity patterns and inform about drivers of evolutionary differentiation and adaptation, including gene flow, drift and selection. This can advance our understanding and aid decision making regarding management and conservation efforts. Microsatellites have long been used in population genetic studies.Thanks to the development of newer techniques, sequencing approaches such as restriction site associated DNA sequencing (RADseq) are on their way to replace microsatellites for some applications. However, the performance of these two marker types in population genetics have rarely been systematically compared. We utilized three neutrally and adaptively differentiated populations of anadromous pike (<i>Esox lucius</i>) to assess the relative performance of microsatellites and RADseq with respect to resolution and conclusiveness of estimates of population differentiation and genetic structure. To this end, the same set of individuals (<i>N</i> = 64) were genotyped with both RADseq and microsatellite markers. To assess effects of sample size, the same subset of 10 randomly chosen individuals from each population (<i>N</i> = 30 in total) were also genotyped with both methods. Comparisons of estimated genetic diversity and structure showed that both markers were able to uncover genetic structuring. The full RADseq dataset provided the clearest detection of the finer scaled genetic structuring, and the other three datasets (full and subset microsatellite, and subset RADseq) provided comparable results. A search for outlier loci performed on the full SNP dataset poninted to signs of selection potentially associated with salinity and temperature, exemplifying the utility of RADseq to inform about the importance of different environmental factors. To evaluate whether performance differences between the markers are general or context specific, the results of previous studies that have investigated population structure using both marker types were synthesized. The synthesis revealed that RADseq performed as well as, or better than microsatellites in detecting genetic structuring in the included studies. The differences in the ability to detect population structure, both in the present and the previous studies, are likely explained by the higher number of loci typically utilized in RADseq compared to microsatellite analysis, as increasing the number of markers will (regardless of the marker type) increase power and allow for clearer detection and higher resolution of genetic structure.</p>
Data from: How do baleen whales stow their filter? A comparative biomechanical analysis of baleen bending
Bowhead and right whale (balaenid) baleen filtering plates, longer in vertical dimension (3-4+ m) than the closed mouth, presumably bend during gape closure. This has not been observed in live whales, even with scrutiny of videorecorded feeding sequences. To determine what happens to baleen as gape closes, we conducted an integrative, multifactorial study including materials testing, functional (flow tank and kinematic) testing, and histological examination. We measured baleen bending properties along the dorsoventral length of plates and anteroposterior location within a rack of plates via mechanical (axial bending, composite flexure, compression, and tension) tests of hydrated and air-dried tissue samples from balaenid and other whale baleen. Balaenid baleen is remarkably strong yet pliable, with ductile fringes and low stiffness and high elasticity when wet; it likely bends in the closed mouth when not used for filtration. Calculation of flexural modulus from stress/strain experiments shows baleen is slightly more flexible where it emerges from the gums and at its ventral terminus, but kinematic analysis indicates plates bend evenly along their whole length. Fin and humpback whale baleen has similar material properties but less flexibility, with no dorsoventral variation. Internal horn tubes have greater external and hollow luminal diameter but lower density in lateral relative to medial baleen of bowhead and fin whales, suggesting greater capacity for lateral bending. Baleen bending has major consequences not only for feeding morphology and energetics but also conservation given that entanglement in fishing gear is a leading cause of whale mortality.
Data from: The evolution of reproductive diversity in Afrobatrachia: a phylogenetic comparative analysis of an extensive radiation of African frogs
The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift towards using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans.
Data from: MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild growing species
Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cytosine methylation in genomic DNA obtained by HPLC analysis. A screening of literature revealed that methylation of cytosines at cleavage sites assayed by MSAP was greater than genome-wide estimates obtained by HPLC, and percentages of methylation at different nucleotide contexts varied within and across species. Concurrent HPLC and MSAP analyses of DNA from 200 individuals of the perennial herb Helleborus foetidus confirmed that methyl-cytosine was more frequent in CCGG contexts than in the genome as a whole. In this species, global methylation was unrelated to methylation at the inner CG site. We suggest that global HPLC and context-specific MSAP methylation estimates provide complementary information whose combination can improve our current understanding of methylation-based epigenetic processes in nonmodel plants.
Data from: Kin discrimination and outer membrane exchange in Myxococcus xanthus: a comparative analysis among natural isolates
Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer-membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer-membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear. Using natural isolates from a centimetre-scale patch of soil, we analyse patterns of TraA diversity and ask whether relatedness at TraA is causally related to patterns of kin discrimination in the form of both colony-merger incompatibilities (CMIs) and inter-strain antagonisms. A large proportion of predicted TraA functional diversity documented among global isolates is contained within the cm-scale population. We find evidence of balancing selection on the PA14-portion of TraA and extensive transfer of traA alleles across genomic backgrounds. CMIs are shown to be common among strains identical at TraA, suggesting that CMI kin discrimination is not generally caused by TraA dissimilarity. Finally, it has been proposed that inter-strain antagonisms might be caused by OME-mediated toxin transfer. However, we find that most strain pairs exhibiting strong antagonisms are predicted to be incapable of OME due to TraA dissimilarity. Overall, our results suggest that documented patterns of kin discrimination in a defined natural population of M. xanthus are not causally related to the degree of TraA relatedness among interactants.
Data from: Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying
Camellia seed oil has been used as high quality and healthy food for over two thousand years. Seed drying management effects oil quality and quantity. however, the molecular mechanisms of fatty acid biosynthesis and accumulation during the drying process remain unknown. In this study, the transcriptomes of Camellia meiocarpa and C. oleifera seed were characterized at five moisture content levels (10 - 50%) to identify the major processes and reveal genes affecting lipid metabolism in response to nature drying. We found a total of 111,156 unigenes by de novo assembled from RNA-Seq libraries of five moisture content levels during after-ripening of C. meiocarpa (74,016) and C. oleifera (76,374). Ten pathways were closely linked to changes in oil content and composition with 244 genes involved in fatty acid synthesis and accumulation. Gene Ontology enrichment of differentially expressed genes (DEGs) indicated that fatty acid synthesis and accumulation are essential in C. meiocarpa while fatty acid accumulation in C. oleifera during nature drying process. Comparative analyses of DEGs between any two consecutive moisture contents, identified six and three key unigenes in C. Meiocarpa and C. oleifera seeds, respectively, and one additional unigene responsible for the difference between the two species' fatty acid synthesis and accumulation. Natural drying has improved the quality and quantity of the camellia seed oil. The study provided: a) global transcriptional profiles at five moisture content levels during seed nature drying, b) insights into highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for lipid metabolism, and c) an opportunity to discovering genes associated with oil seed quantity and quality improvement for the studied two camellia species.
Data from: A comparative analysis of the behavioral response to fishing boats in two albatross species
Anthropogenic food resources have significantly modified the foraging behavior of many animal species. They enhance large multi-specific aggregations of individuals, with strong ecological consequences. It is challenging to predict how individuals or species can differ in their reaction to these resources. For instance, there are wide variations in seabird species abundance behind fishing boats, and individual variations in interaction rates. Whether this is reflecting variations in fine-scale encounter rates or rather variations in attraction strength is poorly quantified. Here we compare the response of Wandering (WA) and Black-browed (BBA) albatrosses to fishing boats operating in sub-Antarctic waters. We use GPS tracking data from both birds and boats (Vessel Monitoring System). Attraction distances were similar between the 2 species (up to 30 km). BBA foraged further from fishing grounds and encountered boats less frequently than WA, but once they encountered a boat BBA were more strongly attracted (80% vs. 60% chance) and had a higher level of active interaction, compared to WA. Furthermore, in the absence of boats, BBA were rarely observed foraging over the habitat where the fisheries mainly operate, in contrast with WA. We thus report qualitative and quantitative differences in the response of these 2 species to the same fishing fleet. WA, the larger, more dominant and more generalist species was unexpectedly less attracted to fishing vessels. Comparing our results with previously published studies, we suggest that energetic requirements of individuals may be a crucial predictor for assessing risks of interactions with anthropogenic food resources.
Data from: Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica
The role of natural selection in speciation has received increasing attention and support in recent years. Different types of approaches have been developed that can detect genomic regions influenced by selection. Here we address the question whether two highly different methods - Fst outlier analysis and admixture analysis - detect largely the same set of non-neutral genomic elements or, instead, complementary sets. We study genetic architecture in a natural secondary contact zone where extensive admixture occurs. The marine bivalves Macoma balthica rubra and M. b. balthica descend from two independent trans-Arctic invasions of the north Atlantic and hybridize extensively where they meet, for example in the Kattegat - Danish Straits - Baltic Sea region. The Kattegat - Danish Straits region forms a steep salinity cline and is the only entrance to the recently (ca 8000 years ago) established brackish water basin the Baltic Sea. Salinity along the contact zone drops from 30‰ (Skagerrak, M.b.rubra) to 3‰ (Baltic, M.b.balthica). Both outlier analysis and genomic clines analysis suggest that large parts of the genome are influenced by non-neutral effects. Contrasting samples from well outside the hybrid zone, outlier analysis detects 16 of 84 amplified fragment length polymorphism (AFLP) markers as significant Fst outliers. Genomic clines analysis detects 31 out of 84 markers as non-neutral inside the hybrid zone. Remarkably, only three markers are detected by both methods. We conclude that the two methods together identify a suite of markers that are under the influence of non-neutral effects.
Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci
Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates, but did not affect the observed pattern of population structure.
Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics - Data Supplement
<p>This the is Data Supplement for the article "Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics" submitted to the Journal of Proteomics 2015.</p>
FIGURE 4. Principal component analysis comparing Ancistrus falconensis n in Ancistrus falconensis n. sp. and A. gymnorhynchus Kner (Siluriformes: Loricariidae) from central Venezuelan Caribbean coastal streams
FIGURE 4. Principal component analysis comparing Ancistrus falconensis n. sp. and A. gymnorhynchus. PC2 and PC3 are Principal Component axes two and three.
FIGURE 7. NHM 1936.5. 13 in A comparative analysis of the spatangoid echinoid genera Brissopsis and Metalia: a new genus and species of spatangoid (Echinodermata: Echinoidea: Brissop- sidae) from the Philippines and the reassignment of Brissopsis persica to Metalia
FIGURE 7. NHM 1936.5. 13, denuded specimen (1 of 16) of Metalia sternalis from the Red Sea: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
FIGURE 3. NHM 81.11. 22.37 in A comparative analysis of the spatangoid echinoid genera Brissopsis and Metalia: a new genus and species of spatangoid (Echinodermata: Echinoidea: Brissop- sidae) from the Philippines and the reassignment of Brissopsis persica to Metalia
FIGURE 3. NHM 81.11. 22.37, denuded test of Brissopsis luzonica from between northern Australia and Papua New Guinea: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
FIGURE 6. NHM 1962.8. 16.17 in A comparative analysis of the spatangoid echinoid genera Brissopsis and Metalia: a new genus and species of spatangoid (Echinodermata: Echinoidea: Brissop- sidae) from the Philippines and the reassignment of Brissopsis persica to Metalia
FIGURE 6. NHM 1962.8. 16.17, Brissopsis persica from the Persian Gulf: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
FIGURE 5. ECH – 261 in A comparative analysis of the spatangoid echinoid genera Brissopsis and Metalia: a new genus and species of spatangoid (Echinodermata: Echinoidea: Brissop- sidae) from the Philippines and the reassignment of Brissopsis persica to Metalia
FIGURE 5. ECH – 261, paratype of Brissopsis persica from the Persian Gulf: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view; ECH – 275, holotype of Brissopsis persica var. elevata: H, aboral view; I, sternal view; J, (right side) lateral view.
FIGURE 1. NHM 2008.619 in A comparative analysis of the spatangoid echinoid genera Brissopsis and Metalia: a new genus and species of spatangoid (Echinodermata: Echinoidea: Brissop- sidae) from the Philippines and the reassignment of Brissopsis persica to Metalia
FIGURE 1. NHM 2008.619, paratype of Brissalius vannoordenburgi gen. nov., sp. nov.: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
FIGURE 4. NHM 1968.6. 14.16 in A comparative analysis of the spatangoid echinoid genera Brissopsis and Metalia: a new genus and species of spatangoid (Echinodermata: Echinoidea: Brissop- sidae) from the Philippines and the reassignment of Brissopsis persica to Metalia
FIGURE 4. NHM 1968.6. 14.16, Brissopsis luzonica from the Solomon Islands: A, aboral view; B, oral view; C (left side) & D (right side), lateral views; E, anterior; F, posterior; G, sternal view.
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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.