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139 results for “reconcilation”
Data from: Efficient exploration of the space of reconciled gene trees
Gene trees record the combination of gene-level events, such as duplication, transfer and loss, and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree-species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al., 2013), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with resp. 24%,59% and 46% percent reductions in the mean numbers of duplications, transfers and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git.
Data from: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. Results: We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Conclusions: Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
Data from: Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei:Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion
Squirrelfishes and soldierfishes (Holocentridae) are among the most conspicuous species in the nocturnal reef fish community. However, there is no clear consensus regarding their evolutionary relationships, which is reflected in a complicated taxonomic history. We collected DNA sequence data from multiple single copy nuclear genes and one mitochondrial gene sampled from over fifty percent of the recognized holocentrid species and infer the first species-level phylogeny of the Holocentridae. Our results strongly support the monophyly of the clades Myripristinae (soldierfishes) and Holocentrinae (squirrelfishes). The molecular phylogenies differ with regard to previous hypotheses of relationships within the Myriprisitinae, resolving a clade of cryptic reef associated and deep water non-reef dwelling lineages (Corniger+Plectrypops+Ostichthys) that is the sister lineage to a monophyletic Myripristis. Within Holocentrinae, Neoniphon and Sargocentron are strongly supported as paraphyletic, while Holocentrus is nested within Sargocentron. Using Bayesian ancestral state reconstruction methods, we demonstrate the taxonomically diagnostic characters for Neoniphon and Sargocentron likely represent character states with a complex evolutionary history that is not reflective of shared common ancestry. We propose a new classification for Holocentrinae, recognizing four lineages that are treated as genera: Sargocentron Fowler, 1904, Holocentrus Scopoli, 1777, Flameo Jordan and Evermann, 1898, and Neoniphon Castelnau, 1875.
Supplementary Materials for article entitled 'On Italian Spatial Prepositions and Measure Phrases: Reconciling Data with Theoretical Accounts', published in Linguistics
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Distribution records: Reconciling biodiversity conservation and flood risk reduction: the new strategy for freshwater protected areas
<p><span><strong>Aim:</strong> </span><span>Natural disaster risk reduction (DRR) is becoming a more important function of protected area (PAs) for current and future global warming. However, biodiversity conservation and DRR have been handled separately and their interrelationship has not been explicitly addressed. This is mainly because, due of prevailing strategies and criteria for PA placement, a large proportion of PAs are currently located far from human-occupied areas, and habitats in human-occupied areas have been largely ignored as potential sites for conservation despite their high biodiversity. If intensely developed lowland areas with high flooding risk overlap with important sites for biodiversity conservation, it would be reasonable to try to harmonize biodiversity conservation and human development in human-inhabited lowland areas. Here, we examined whether extant PAs can conserve macroinvertebrate and freshwater fish biodiversity and whether human-inhabited lowland flood risk management sites might be suitable to designate as freshwater protected areas (FPAs).</span></p> <p><span><strong>Location:</strong> </span><span>Across Japan</span></p> <p><span><strong>Methods:</strong> </span><span>We examined whether extant PAs can conserve macroinvertebrate and freshwater fish biodiversity and analyzed the relationship between candidate sites for new FPAs and flood disaster risk and land use intensity at a national scale across Japan based on</span><span> distribution data for 131 freshwater fish species and 1395 macroinvertebrate species.</span></p> <p><span><strong>Results:</strong> </span><span>We found that extant PAs overlapped with approximately 30% of conservation-priority grid cells (1 km<sup>2</sup>) for both taxa. Particularly for red-listed species, only one species of freshwater fish and three species of macroinvertebrate achieved the representation target within extant PAs.</span><span> Moreover, more than 40% of candidate conservation-priority grid cells were located in </span><span>flood risk and human-occupied areas for both taxa.</span></p> <p><span><strong>Main conclusions:</strong> </span><span>Floodplain conservation provides suitable habitat for many freshwater organisms and helps control floodwaters, so establishing new FPAs in areas with high flood risk could be a win-win strategy for conserving freshwater biodiversity and enhancing ecosystem-based DRR (eco-DRR).</span></p>
FIGURE 1 in The generic classification of the Trochilini (Aves: Trochilidae): Reconciling taxonomy with phylogeny
FIGURE 1. The currently accepted classification of the Trochilini, with groups A, B, C and D and their subgroups, as derived from the phylogeny; at the extreme right of each group are the new generic circumscriptions recommended and explained in the text. See Appendix 2 for the complete generic reclassification of the Trochilini.
Agricultural adaptation to reconcile food security and water sustainability under climate change: the case of cereals in Iran
<p>In this study, we simulate the crop yield and water footprint (WF) of major food crops of Iran on irrigated and rainfed croplands for the historical and the future climate. We assesse the effects of three agricultural adaptation strategies to climate change in terms of potential blue water savings. We then evaluate to what extent these savings can reduce unsustainable blue WF. We find that cereal production increases under climate change in both irrigated and rainfed croplands (by 2.6-3.1 and 1.4-2.3 million t y<sup>-1</sup>, respectively) due to increased yields (6.6%-78.7%). Simultaneously, the unit WF (m<sup>3</sup> t<sup>-1</sup>) tends to decrease in most scenarios. However, the annual consumptive water use increases in both irrigated and rainfed croplands (by 0.3-1.8 and 0.5-1.7 billion m<sup>3</sup> y<sup>-1</sup>, respectively). This is most noticeable in the arid regions, where consumptive water use increases by roughly 70% under climate change. Off-season cultivation is the most effective adaptation strategy to alleviate additional pressure on blue water resources, with blue water savings of 14-15 billion m<sup>3</sup> y<sup>-1</sup>. The second most effective is WF benchmarking, which results in blue water savings of 1.1-3.5 billion m<sup>3</sup> y<sup>-1</sup>. The early planting strategy is less effective, but still leads to blue water savings of 1.7-1.9 billion m<sup>3</sup> y<sup>-1</sup>. In the same order of effectiveness, these three strategies can reduce blue water scarcity and unsustainable blue water use in Iran under current conditions. However, we find that these strategies do not mitigate water scarcity in all provinces per se, nor all months of the year.</p>
Data from: Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record
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Data from: Phylogenetic informativeness reconciles ray-finned fish molecular divergence times
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Data from: Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei:Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion
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Distribution records: Reconciling biodiversity conservation and flood risk reduction: the new strategy for freshwater protected areas
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Data from: Efficient exploration of the space of reconciled gene trees
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Data from: Reconciling hierarchical taxonomy with molecular phylogenies
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Data from: Reconciling multiple impacts of nitrogen enrichment on soil carbon: plant, microbial, and geochemical controls
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Fig. 6 A in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 6 A Lateral view of the Deccan Mahseer, T. khudree (GQ469788). Ai Ventral and lateral view of head and anterior part of body of T. khudree (GQ469788). B Lateral view of the Hump Mahseer, T. mussullah (GQ469798), Bi Lateral view of head and anterior part of body of T. mussullah (GQ469798)
Fig. 7 A in Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India
Fig. 7 A Lateral view of the chocolate mahseer, N. hexagonolepis (EU714096). Ai Ventral and lateral view of head and anterior part of body of N. hexagonolepis (EU714096). B Lateral view of the black Mahseer, N. chelynoides (EU714101). Bi Lateral view of head and anterior part of body of N. chelynoides (EU714101)
Fig. 1 in Reconciling ecological and phytogeographical spatial boundaries to clarify the limits of the montane and alpine regions of sub-Sahelian Africa
Fig. 1. The most prominent high elevation areas of the Afromontane region in sub-Sahelian Africa (A–X) as well as the location of the Cape Floristic Region (Y). Adapted from Hedberg (1994), Carbutt and Edwards (2001) and Wesche et al. (2008). The Great Rift is represented by B–N, Q–U; the Albertine Rift is represented by O and P; and the Great Escarpment is represented by V–X. Key to abbreviations: A, Mount Cameroon, Cameroon (4040 m); B–K, Ethiopian Highlands (north-east Africa, Ethiopia); B, Simen Mountains (4543 m); C, Mount Guna (4225 m); D, Mount Abuna Yosef (4260 m); E, Mount Choqa (4113 m); F, Mount Abuye Meda (4012 m); G, Mangestu Mountains (4072 m); H, Mount Bada (4036 m); I, Mount Kaka (4200 m); J, Bale Mountains (4377 m); K, Mount Guge (4203 m); L, Mount Elgon, Kenya/Uganda (4315 m); M, Mount Kenya, Kenya (5199 m); N, Aberdare Mountains, Kenya (3994 m); O, Rwenzori Mountains, Democratic Republic of Congo/Uganda (5109 m); P, Virunga Mountains, Democratic Republic of Congo/Rwanda/Uganda (4507 m); Q, Mount Kilimanjaro, Tanzania (5895 m); R, Mount Hanang, Tanzania (3417 m); S, Mount Meru, Tanzania (4565 m); T, Nyika Plateau, Malawi (2605 m); U, Mount Mulanje, Malawi (3002 m); V, Mount Nyangani, Zimbabwe (2592 m); W, Chimanimani Mountains, Mozambique/Zimbabwe (2440 m); X, Drakensberg Alpine Centre, Lesotho/South Africa (3482 m) bisecting the northeastern escarpment (X1) and the south-eastern escarpment (X2); Y, Cape Floristic Region.
FIGURE 3 in Reconciling diagnostic traits in living and fossil taxa: The taxonomy and evolution of the genus Microceratina (Crustacea, Ostracoda, Cytheruridae)
FIGURE 3. Microceratina martensi Namiotko et al., 2004, valve and carapace morphology, external views (A–D: 'LV-1'; E, F: 'C-4'; G–J: 'RV-6'): A–D—LV; A—general view; B–D—details of primary reticula cells and secondary fossae, and shape of ribs, ridges, pore conuli (A"-type) and LStPC located within shallow alveolar excavations; E, F—carapace in latero-ventral and dorsal view; G–J—RV; G—general view; H—normal pore with sensillum, located on conulus (A"-type); I–J—various combinations of LStPC located within shallow alveolar excavations.
microRNA396 is a coordinative regulator that can be modulated to reconcile the reverse relationship between fruit size and quality in tomato
GEO Series GSE265866. Solanum lycopersicum. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.