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12 results for “anomaly zone”
Gravity, Free-Air and Bouguer Anomaly Data in the Ivrea-Verbano Zone (Western Alps, Italy)
<p>Gravity dataset collected in the Ivrea-Verbano Zone (IVZ, Western Alps, Italy). </p><p>The data was collected in the frame of a gravity-based investigation and modelling of the Ivrea Geophysical Body. </p><p>For citation and further details on the work see Scarponi et al. (2020, GJI): <a href="https://doi.org/10.1093/gji/ggaa263">https://doi.org/10.1093/gji/ggaa263</a></p><p>The file contains the gravity data collected in the IVZ region, including free-air anomaly and Bouguer gravity anomaly (in mGal).</p><p>Longitude, Latitude coordinates are in degrees, elevation in meters.</p><p>Uncertainty on the final gravity data products and gravity data is 1 mGal.</p><p>---</p><p>Data collection, as well as the associated research, were supported by the Swiss National Science Foundation (SNF) (grant numbers PP00P2_157627 and PP00P2_187199).</p>
Daily Anomalies and High Productivity Zone Mask for Northern Peruvian Coastal Marine Ecosystem during the 2017 Coastal El Niño (December 2016 - May 2017)
<p>This dataset is part of the manuscript entitled "Chlorophyll Response and High Productivity Zone Contraction in Northern Perú During the 2017 Coastal El Niño."</p> <p>The dataset is designed to assess the atmospheric and oceanographic drivers of productivity changes during the 2017 Coastal El Niño. It allows detailed analysis of the interactions between physical processes (e.g., wind-driven upwelling rates, heat flux changes) and biological responses (e.g., chlorophyll concentration variations) in a region highly susceptible to ENSO-related variability. This comprehensive dataset provides valuable insight into the physical-biological coupling and the impacts of rapid climate events on marine ecosystems. The dataset, covering the period from December 1, 2016, to May 31, 2017, includes:</p> <p>1. Chlorophyll-a Anomalies (chla): Represents deviations in surface chlorophyll concentrations, a proxy for phytoplankton biomass, highlighting variations in primary productivity during the event.</p> <p>2. Sea Surface Temperature Anomalies (sst): Captures changes in sea surface temperatures relative to the climatological mean, providing insight into the warming pattern typical of marine heatwaves associated with the Coastal El Niño.</p> <p>3. Sea Level Anomaly (sla): Indicates changes in sea surface height, which reflects thermal expansion of water masses and potential contributions from coastal trapped waves propagating along the Peruvian coast.</p> <p>4. Wind Component Anomalies (u,v): Daily anomalies for both zonal (east-west) and meridional (north-south) wind components, which are critical for understanding changes in wind patterns including upwelling and Ekman transport processes.</p> <p>5. Ekman Pumping Anomalies (w): Represents variations in vertical water movement forced by wind stress curl, highlighting the suppression or enhancement of upwelling during the event.</p> <p>6. Latent Heat Flux Anomalies (lathf): Indicates deviations in heat loss from the ocean surface due to evaporation, affecting surface temperature regulation.</p> <p>7. Shortwave Radiation Anomalies (swrad): Shows changes in solar radiation (and also a proxy for PAR) reaching the ocean surface, influencing upper ocean heat content and the light availability for phytoplankton.</p> <p>8. High Productivity Zone (mask): A binary mask with daily values of 1 indicating areas meeting the HPZ criterion and 0 otherwise, allowing for spatial tracking of the HPZ's extent during the period of study.</p> <p> </p>
Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
<p>A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony (as well as an approach based on MDC) typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e., local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100,000 parsimony-informative RIs. We found that, when given just 1,000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e clades separated by branches >0.3 CUs) with high support and identified rapid radiations (i.e., shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.</p>
Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
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Data from: Why concatenation fails near the anomaly zone
Genome-scale sequencing has been of great benefit in recovering species trees, but has not provided final answers. Despite the rapid accumulation of molecular sequences, resolving short and deep branches of the tree of life has remained a challenge, and has prompted the development of new strategies that can make the best use of available data. One such strategy – the concatenation of gene alignments – can be successful when coupled with many tree estimation methods, but has also been shown to fail when there are high levels of incomplete lineage sorting. Here, we focus on the failure of likelihood-based methods in retrieving a rooted, asymmetric four-taxon species tree from concatenated data when the species tree is in or near the anomaly zone – a region of parameter space where the most common gene tree does not match the species tree because of incomplete lineage sorting. First, we use coalescent theory to prove that most informative sites will support the species tree in the anomaly zone, and that as a consequence maximum-parsimony succeeds in recovering the species tree from concatenated data. We further show that maximum-likelihood tree estimation from concatenated data fails both inside and outside the anomaly zone, and that this failure cannot be easily predicted from the topology of the most common gene tree. We show that likelihood-based methods often fail in a region partially overlapping the anomaly zone, likely because of the lower relative cost of substitutions on discordant gene tree branches that are absent from the species tree. Our results confirm and extend previous reports on the performance of these methods applied to concatenated data from a rooted, asymmetric four-taxon species tree, and highlight avenues for future work improving the performance of methods aimed at recovering species tree.
Data for: Electrical Conductivity of Superionic Hydrous SiO2 and the Origin of Lower-mantle High Conductivity Anomalies Beneath Subduction Zones
<p><strong>Dataset S1.</strong> Experimental conditions and the measured resistance and conductivity of hydrous Al-bearing SiO2. </p>
Data from: Why concatenation fails near the anomaly zone
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Data from: Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totalling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4,274 CR1 retroelements identified from multi-species whole genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other non-ostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.
FESOM model data used in the study on the buffer zone for great salinity anomaly
<p>Model data used in the study on the buffer zone for great salinity anomaly</p>
Dataset for "Electrical Conductivity of H2O-rich Silicate Melt: Implications for Subduction Zone Magnetotelluric Anomalies"
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Data from: Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
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Data from: Detecting the anomaly zone in species trees and evidence for a misleading signal in higher-level skink phylogeny (Squamata: Scincidae)
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