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16 results for “incomplete sampling”
Text-fig. 7. Vertical polished sections of samples from selected layers. a: Layer No. 2, completely bioturbated, collection of the Czech Geological Survey (abbr. BK), BK 7; b: Layer No. 3, low: nearly completely bioturbated, upper: cross- to ripple bedding, weakly bioturbated, BK 6; c: Layer No. 7, incompletely bioturbated siltstone/mudstone, BK 5; d: Layer No. 8, low: totally bioturbated background with Zoophycos ichnofabric, upper: spotted, completely bioturbated siltstone, BK 4; e: Layer No. 8, low: in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic
Text-fig. 7. Vertical polished sections of samples from selected layers. a: Layer No. 2, completely bioturbated, collection of the Czech Geological Survey (abbr. BK), BK 7; b: Layer No. 3, low: nearly completely bioturbated, upper: cross- to ripple bedding, weakly bioturbated, BK 6; c: Layer No. 7, incompletely bioturbated siltstone/mudstone, BK 5; d: Layer No. 8, low: totally bioturbated background with Zoophycos ichnofabric, upper: spotted, completely bioturbated siltstone, BK 4; e: Layer No. 8, low:
Data from: Quantifying and estimating ecological network diversity based on incomplete sampling data
<p>An ecological network refers to the ecological interactions among sets of species. Quantification of ecological network diversity and related sampling/estimation challenges have explicit analogues in species diversity research. A unified framework based on Hill numbers and their generalizations was developed to quantify taxonomic, phylogenetic, and functional diversity. Drawing on this unified framework, we propose three dimensions of network diversity that incorporate the frequency (or strength) of interactions, species' phylogenies and traits. As with surveys in species inventories, nearly all network studies are based on sampling data and thus also suffer from under-sampling effects. Adapting the sampling/estimation theory and the iNEXT (interpolation/extrapolation) standardization developed for species diversity research, we propose the iNEXT.link method to analyze network sampling data. The proposed method integrates the following four inference procedures: (i) Assessment of sample completeness of networks, (ii) asymptotic analysis via estimating the true network diversity, (iii) non-asymptotic analysis based on standardizing sample completeness via rarefaction and extrapolation with network diversity, and (iv) estimation of the degree of unevenness or specialization in networks based on standardized diversity. Interaction data between European trees and saproxylic beetles are used for illustrating the proposed procedures. The software iNEXT.link is developed to facilitate all computations and graphics.</p>
Data from: Quantifying and estimating ecological network diversity based on incomplete sampling data
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Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions
<p>Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (TACT: Taxonomic Addition for Complete Trees) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling.</p>
Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions
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Data from: Methods to account for incomplete viewsheds in distance sampling
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Data from: Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling
Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth–death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18–0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48–1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89–3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36–1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World.
Missing data in sea turtle population monitoring: a Bayesian statistical framework accounting for incomplete sampling
<p>Monitoring how populations respond to sustained conservation measures is essential to detect changes in their population status and determine the effectiveness of any interventions. In the case of sea turtles, their populations are difficult to assess because of their complicated life histories. Ground-derived clutch counts are most often used as an index of population size for sea turtles; however, data are often incomplete with varying sampling intensity within and among sites and seasons. To address these issues, we: (1) develop a Bayesian statistical modelling framework that can be used to account for sampling uncertainties in a robust probabilistic manner within a given site and season; and (2) apply this to a previously unpublished long-term sea turtle dataset (n = 17 years) collated for the Republic of the Congo, which hosts two sympatrically nesting species of sea turtle (leatherback turtle [<em>Dermochelys coriacea</em>] and olive ridley turtle [<em>Lepidochelys olivacea</em>]). The results of this analysis suggest that leatherback turtle nesting levels dropped initially and then settled into quasi-cyclical levels of interannual variability, with an average of 573 (mean, 95% prediction interval: 554–626) clutches laid annually between 2012 and 2017. In contrast, nesting abundance for olive ridley turtles has increased more recently, with an average of 1,087 (mean, 95% prediction interval: 1,057–1,153) clutches laid annually between 2012 and 2017. These findings highlight the regional and global importance of this rookery with the Republic of the Congo, hosting the second largest documented populations of olive ridley and the third largest for leatherback turtles in Central Africa; and the fourth largest non-arribada olive ridley rookery globally. Furthermore, whilst the results show that Congo's single marine and coastal national park provides protection for over half of sea turtle clutches laid in the country, there is scope for further protection along the coast. Although large parts of the African coastline remain to be adequately monitored, the modelling approach used here will be invaluable to inform future status assessments for sea turtles given that most datasets are temporally and spatially fragmented. </p>
Replication data for: Sensitivity of bipartite network analyses to incomplete sampling and taxonomic uncertainty
<p>Simulated host-parasite communities in Llopis‐Belenguer, C., J. A. Balbuena, I. Blasco‐Costa, A. Karvonen, V. Sarabeev, and J. Jokela. 2022. Sensitivity of bipartite network analyses to incomplete sampling and taxonomic uncertainty. Ecology</p> <ul> <li>Full communities</li> </ul> <p>01_full_communities.RDS</p> <ul> <li>Resampled communities affected by host sampling completeness. From 90% to 10% of host sampling completeness every 10% steps</li> </ul> <p>02_resampled_sampling_completeness_90.RDS, </p> <p>03_resampled_sampling_completeness_80.RDS, </p> <p>04_resampled_sampling_completeness_70.RDS, </p> <p>05_resampled_sampling_completeness_60.RDS, </p> <p>06_resampled_sampling_completeness_50.RDS, </p> <p>07_resampled_sampling_completeness_40.RDS, </p> <p>08_resampled_sampling_completeness_30.RDS, </p> <p>09_resampled_sampling_completeness_20.RDS, </p> <p>10_resampled_sampling_completeness_10.RDS</p> <ul> <li>Resampled communities affected by parasite taxonomic resolution at all levels of host sampling completeness. From 90% to 10% of parasite taxonomic resolution and from 100% to 10% of host sampling completeness every 10% steps</li> </ul> <p>11_resampled_taxonomic_resolution_90_sampling_completeness_100-10.RDS, </p> <p>12_resampled_taxonomic_resolution_80_sampling_completeness_100-10.RDS, </p> <p>13_resampled_taxonomic_resolution_70_sampling_completeness_100-10.RDS, </p> <p>14_resampled_taxonomic_resolution_60_sampling_completeness_100-10.RDS, </p> <p>15_resampled_taxonomic_resolution_50_sampling_completeness_100-10.RDS, </p> <p>16_resampled_taxonomic_resolution_40_sampling_completeness_100-10.RDS, </p> <p>17_resampled_taxonomic_resolution_30_sampling_completeness_100-10.RDS, </p> <p>18_resampled_taxonomic_resolution_20_sampling_completeness_100-10.RDS, </p> <p>19_resampled_taxonomic_resolution_10_sampling_completeness_100-10.RDS</p> <p> </p>
Data from: Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling
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Data from: Rarity and incomplete sampling in DNA-based species delimitation
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Missing data in sea turtle population monitoring: a Bayesian statistical framework accounting for incomplete sampling
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Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates
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Data from: Likelihood inference of non-constant diversification rates with incomplete taxon sampling
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Sample Collection for Systems Evaluation of Patients With Unknown or Incompletely Characterized Immune Defects
ClinicalTrials.gov study NCT04408950. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: How to estimate complementarity and selection effects from an incomplete sample of species
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