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55 results for “ancestral reconstruction”
Figure 1 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition
Figure 1. Fluorescence intensity histograms obtained from three different species, with Drosophila melanogaster as internal standard, stained with propidium iodide (PI; A–C) or 4,6-diamidino-2-phenylindole (DAPI; D–F). The x-axis corresponds to the scale of fluorescence intensity, and the y-axis represents the number of nuclei with that fluorescence intensity.
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.
Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S in Cryptic species complex or an incomplete speciation? Phylogeographic analysis reveals an intricate Pleistocene history of Priapulus caudatus Lamarck, 1816
Fig. 10. Ancestral area reconstruction for Priapulus caudatus estimated from S-DIVA algorithm using ultrametric COI tree calculated in BEAST 2.4 software. Numbers at the tips of the trees correspond to the sampling locations on the map (designated as in Fig. 1). Letters represent most likely ancestral range. Sectors in circles indicate the percent of total range probability. Biogeographical regions in the map as in Piepenburg et al. (2011), Ekimova et al. (2019), Laakkonen et al. (2021).
Fig. 1 in PARAMO: A Pipeline for Reconstructing Ancestral Anatomies Using Ontologies and Stochastic Mapping
Fig. 1. Amalgamation of stochastic maps. Vertical bars are tree branches, their segments are mapped character states. The amalgamation of the stochastic map S1{0,1} and S2{0,1} yields the map S1,2{00,01,11,10}.
Fig. 3 in PARAMO: A Pipeline for Reconstructing Ancestral Anatomies Using Ontologies and Stochastic Mapping
Fig. 3. Amalgamation of stochastic maps corresponding to the characters of legs from Hymenoptera phylogeny (S7, S8, S9) into one 'leg character' (SL); see also Fig. 2.
Supplementary material 1 from: Pereira T, Reis A, Cardoso D, Cristiano M (2018) Molecular phylogenetic reconstruction and localization of the (TTAGG)n telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863) suggests a lower ancestral karyotype for leafcutter ants. Comparative Cytogenetics 12(1): 13-21. https://doi.org/10.3897/CompCytogen.v12i1.21799
Figure S1. Phylogenomic tree used to estimate the ancestral chromosome number. : Explanation note: Numbers at nodes represent the first and second most likely haploid chromosome number followed by posterior support values under Bayesian optimization and the ancestral haploid chromosome number with best likelihood under maximum likelihood optimization, as follows: [first haploid state (P.P.%)// second haploid state (P.P.%)// ML haploid state].
Fig. 1 in Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty
Fig. 1 Reconstruction of ancestral genomes. Evolutionary relationships of the major groups included in his study2. Different categories of HG are indicated in each node, from top to bottom, Ancestral HG, Novel HG, Novel Core HG, and Lost HG. Values assume sponges as the sister group to other animals, and placozoans as sister group to Planulozoa (=Cnidaria + Bilateria); alternative phylogenetic hypotheses are explored in Supplementary Data 3-8. Organism outlines from phylopic.org and the authors
Data from: Ancestral reconstruction of reproductive traits shows no tendency toward terrestriality in Leptodactyline frogs
Background:Traditionally, the evolution of terrestrial reproduction in anurans from ancestors that bred in water has been accepted in the literature. Still, the existence of intermediate stages of water dependency, such as species that lay eggs close to water (e.g., in burrows) instead of in bodies of water, supports the hypothesis of an ordered and gradual evolution in the direction of a more terrestrial form of reproduction. However, this conventional view has recently been challenged for some anurans groups. Leptodactylinae frogs are a remarkable example of anurans with an outstanding diversity in terms of reproductive features, with distinct water dependency among lineages. Here, we tested the hypothesis of a gradual and ordered tendency towards terrestriality in Leptodactylinae, including the existence of obligatory intermediate stages, such as semi-terrestrial reproductive strategies. We also addressed the association between reproductive modes and the morphological and ecological features. Results: An ancestral reconstruction analysis indicated that even though shifts from aquatic to terrestrial breeding occurred throughout the history of Leptodactylus and Adenomera, shifts from terrestrial to aquatic reproduction happened at almost the same frequency. Our results also demonstrated that reproductive modes for semi-terrestrial tadpoles were not necessarily an intermediate form between aquatic and terrestrial breeds. Correlations among reproductive modes and other life-history traits suggested that tadpole environment, clutch size, nuptial spines, and egg pigmentation were co-evolving and driven by water dependency. Conclusions: Our results found no evidence of evolutionary tendencies toward terrestriality in Leptodactylinae. We found reversals from terrestrial to aquatic tadpole development and no evidence of obligatory intermediate stages, such as semi-terrestrial reproductive strategies. We also found correlations between reproductive modes and other life-history traits driven by water dependence. Aquatic reproductive modes are associated with higher clutch sizes, lentic waters, and the presence of nuptial spines and egg pigmentation.
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).
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>
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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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: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification
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Reconstructing Ecological Niche Evolution via Ancestral State Reconstruction with Uncertainty Incorporated
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Ancestral state reconstruction for regeneration and autotomy in arthopods and reptiles
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Data from: Ancestral state reconstruction sheds new light on the loss of divarication hypothesis on New Zealand’s outlying islands
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ProtASR2: Ancestral Reconstruction of Protein Sequences accounting for Folding Stability
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Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed‐bearing structures
<p>This dataset contains three-dimensional model files for <em>Genomosperma</em> specimens LM19 (K1; Long, 1960), LM22, LM1 (L1; Long, 1960), and LM23, supporting the paper ‘Reconstructing development of the earliest seed integuments raises a new hypothesis for the evolution of ancestral seed‐bearing structures' published in New Phytologist <a href="https://doi.org/10.1111/nph.16792">https://doi.org/10.1111/nph.16792</a>.</p> <p>These models are saved in a single ZIP compressed folder as four SPV files and also four VAXML datasets in separate folders. All files are labelled with the working/specimen number they represent. SPV files are able to be viewed in SPIERSview, part of the free SPIERS software package (http://spiers-software.org/). The VAXML datasets comprise a VAXML file that provides metadata specifying how to put together accompanying STL files which define the geometry of the objects in the dataset. [Unzipped total size 1.74GB].</p>
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Allen Brain Atlas
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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.
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