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389 results for “ancestral”
Figure 3 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Figure 3. Mean genome size (in picograms and megabase pairs) estimated for Formicidae subfamilies. The phylogenetic tree generated in the present study was redrawn, with collapsed branches corresponding to species of the same subfamily.
Figure 2 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Figure 2. Bayesian consensus tree resulting from the LW-Rh and Wg gene alignments (871 bp). Coloured dots on the branches indicate the values of posterior probability (PP): green dots represent values between 1.00 and 0.95, yellow dots between 0.94 and 0.90, and red dots ≤ 0.89. The nodes are indicated with numbers. Values above and below the branches represent the ancestral genome size (GS; 1C-values, in picograms) at particular nodes: in blue is the value generated by the maximum likelihood (ML) [asterisks are related to confidence interval (CI) values shown in Supporting Information, Table S4]; orange is the value generated by maximum parsimony (MP); and black, given below the branches, is the value generated by Bayesian inference (BI). Genome size data (1C-values) were obtained in the present work (pink dots) or taken from the literature (grey dots).
Modeling pulsed evolution and time-independent variation improves the confidence level of ancestral and hidden state predictions
<p><span><span><span><span><span><span><span><span><span><span>Ancestral state reconstruction is not only a fundamental tool for studying trait evolution, but also very useful for predicting the unknown trait values (hidden states) of extant species. A well-known problem in ancestral and hidden state predictions is that the uncertainty associated with predictions can be so large that predictions themselves are of little use. Therefore, for meaningful interpretation of predicted traits and hypothesis testing, it is prudent to accurately assess the uncertainty of the predictions. Commonly used constant-rate Brownian motion (BM) model fails to capture the complexity of tempo and mode of trait evolution in nature, making predictions under the BM model vulnerable to lack-of-fit errors from model misspecification. Using empirical data (mammalian body size and bacterial genome size), we show that the distribution of residual Z-scores under the BM model is neither homoscedastic nor normal as expected. Consequently, the 95% confidence intervals (CIs) of predicted traits are so unreliable that the actual coverage probability ranges from 33% (strongly permissive) to 100% (strongly conservative). Alternative methods such as BayesTraits and StableTraits that allow variable rates in evolution improve the predictions but are computationally expensive. Here we develop RasperGade, a method of ancestral and hidden state prediction that uses the Levy process to explicitly model gradual evolution, pulsed evolution and time-independent variation. Using the same empirical data, we show that RasperGade outperforms both BayesTraits and StableTraits and is orders-of-magnitude faster. Our results suggest that, when predicting the ancestral and hidden states of continuous traits, the tempo and mode of evolution should always be assessed and the quality of confidence estimates should always be examined.</span></span></span></span></span></span></span></span></span></span></p>
Supplementary material 5 from: Royzenblat S, Kulacic J, Friedrich M (2023) Evidence of ancestral nocturnality, locomotor clock regression, and cave zone-adjusted sleep duration modes in a cave beetle. Subterranean Biology 45: 79-94. https://doi.org/10.3897/subtbiol.45.100717
Activity stats comparisons of monitor-adjusted LD animals in D phase with monitor-adjusted DD animals
Phylogenetic reconstruction and functional characterization of the ancestral Nef protein of primate lentiviruses
<p>Supplementary data accompanying the manuscript "Phylogenetic reconstruction and functional characterization of the ancestral<br> Nef protein of primate lentiviruses".</p> <ul> <li><a href="https://zenodo.org/api/files/f0659c40-8118-4e4d-969b-6b8fa6ed6243/group_m_ancestry_consensus_gaps_removed.afa?versionId=9eaf7592-5bb6-4d38-bb9d-6b79e5fe1306">group_m_ancestry_consensus_gaps_removed.afa</a> - consensus amino acid sequences for ancestral reconstructions at the six internal nodes in FASTA format</li> <li><a href="https://zenodo.org/api/files/f0659c40-8118-4e4d-969b-6b8fa6ed6243/node35.fa.mafft?versionId=24cfcdbd-9943-4a7d-b034-23b9300d5832">node35.fa.mafft</a> - multiple sequence alignment of ancestral amino acid sequence reconstructions at the root of the primate lentivirus phylogeny (node 35) for 1,000 trees sampled from the posterior distribution</li> <li><a href="https://zenodo.org/api/files/f0659c40-8118-4e4d-969b-6b8fa6ed6243/node35.fa.mafft?versionId=24cfcdbd-9943-4a7d-b034-23b9300d5832">node51.fa.mafft</a> - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVsun (node 51) for 1,000 trees sampled from the posterior distribution</li> <li><a href="https://zenodo.org/api/files/f0659c40-8118-4e4d-969b-6b8fa6ed6243/node35.fa.mafft?versionId=24cfcdbd-9943-4a7d-b034-23b9300d5832">node52.fa.mafft</a> - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVcpz (node 52) for 1,000 trees sampled from the posterior distribution</li> <li><a href="https://zenodo.org/api/files/f0659c40-8118-4e4d-969b-6b8fa6ed6243/node35.fa.mafft?versionId=24cfcdbd-9943-4a7d-b034-23b9300d5832">node55.fa.mafft</a> - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 and SIVcpzptt (node 55) for 1,000 trees sampled from the posterior distribution</li> <li><a href="https://zenodo.org/api/files/f0659c40-8118-4e4d-969b-6b8fa6ed6243/node35.fa.mafft?versionId=24cfcdbd-9943-4a7d-b034-23b9300d5832">node56.fa.mafft</a> - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 groups M and N and SIVcpzptt (node 56) for 1,000 trees sampled from the posterior distribution</li> <li><a href="https://zenodo.org/api/files/f0659c40-8118-4e4d-969b-6b8fa6ed6243/node35.fa.mafft?versionId=24cfcdbd-9943-4a7d-b034-23b9300d5832">node59.fa.mafft</a> - multiple sequence alignment of ancestral amino acid sequence reconstructions for the common ancestor of HIV-1 group M (node 59) for 1,000 trees sampled from the posterior distribution</li> </ul>
Data from: Genetic diversity, population structure and ancestral origin of Australian wheat
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Data from: Female song is widespread and ancestral in songbirds
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Data from: A test of the "flexible stem" model of evolution: ancestral plasticity, genetic accommodation, and morphological divergence in the threespine stickleback radiation
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Data from: Metamorphosis is ancestral for crown euarthropods, and evolved in the Cambrian or earlier
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Data from: Ancestral remnants or peripheral segregates? Phylogenetic relationships of two narrowly endemic Euphrasia species (Orobanchaceae) from the eastern European Alps
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Post-embryonic development of Fritzolenellus suggests the ancestral morphology of the early developmental stages in Trilobita
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Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny
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Preference, performance, and chemical defense in an endangered butterfly using novel and ancestral host plants
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Snout shape and masticatory apparatus of the rodent-like mesotheriid ungulates (Typotheria, Notoungulata): Exploring evolutionary trends in dietary strategies through ancestral reconstructions
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Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates
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Data from: Ancestral chytrid pathogen remains hypervirulent following its long co-evolution with amphibian hosts
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Data from: Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae)
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Experimental evolution of ancestrally reconstructed BCL2 family proteins
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Data from: Ancestral reconstruction of reproductive traits shows no tendency toward terrestriality in Leptodactyline frogs
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Data from: A consensus method for ancestral recombination graphs
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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.