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48 results for “phylogeny reconstruction”
Data from: Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.
The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multi-locus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multi-locus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as OTUs, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.
FIGURE 7. Phylogeny reconstructed from D2D3 in Heterorhabditis beicherriana n. sp. (Nematoda: Heterorhabditidae), a new entomopathogenic nematode from the Shunyi district of Beijing, China
FIGURE 7. Phylogeny reconstructed from D2D3 rDNA sequences of Heterorhabditis species (only bacteriophora-group shown). Heterorhabditis beicherriana n. sp. showing one autapomorphy (transition in the position 127). NC = number of change.
Training data for 'Maximum Likelihood Phylogeny Reconstruction'' (Galaxy Training Material)
<p>This data is used for Galaxy Training Network (GTN) training 'Maximum Likelihood Phylogeny Reconstruction'. It consists of 173 amino acid alignments of orthologs found in chromosome 5 of four strains of S. cerevisiae. Original sequence data (https://zenodo.org/record/6610704) was processed in Galaxy following GTN 'Preparing genomic data for phylogeny reconstruction' training (10.48546/workflowhub.workflow.359.1) to generate alignments of orthologs.</p>
Exon-based phylogenomics and the relationships of African cichlids: Tackling the challenges of reconstructing phylogenies with repeated rapid radiations
<p>African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/<em>de novo</em> assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.</p>
FIGURE 3. Phylogenetic reconstruction for 30 in Revision of the Genus Leptogomphus Selys in Borneo, including gene trees and a two marker molecular phylogeny (Odonata: Anisoptera: Gomphidae)
FIGURE 3. Phylogenetic reconstruction for 30 specimens of Leptogomphus and three outgroup taxa using the combined COI+ITS dataset. The best Maximum Likelihood tree is shown, with posterior probabilities from the Bayesian Inference analysis also depicted on the branches. Bootstrap values and posterior probabilities are shown if less than 100 or 1.0 respectively. RMNH collection codes are shown for each specimen, as well as the sex of the specimen and an indication of where it was collected.
Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 in A multigene phylogeny demonstrates that Tuber aestivum and Tuber uncinatum are conspecific
Fig. 2 Coalescent tree reconstruction for all concatenated genes. Only posterior probabilities higher than 0.95 are indicated. The tree is rooted with MAC (T. macrosporum) and MAG (T. magnatum)
Fig. 3 A in Recent progress in reconstructing lophotrochozoan (spiralian) phylogeny
Fig. 3 A hypothesis of lophotrochozoan phylogeny as discussed in this review. This topology shows a summary of different phylogenomic studies (Weigert et al. 2014; Wey-Fabrizius et al. 2014; Schiffer et al. 2018; Marlétaz et al. 2019). *Please note that several taxa formerly regarded to be placed outside Annelida (Echiura, Myzostomida, Orthonectida, Pogonophora, Sipuncula and Vestimentifera) are now firmly placed as annelid ingroups. Annelida relationships are (mostly) well resolved, see discussion in the text and Struck (2019) for review
Fig. 2 in Recent progress in reconstructing lophotrochozoan (spiralian) phylogeny
Fig. 2 Hypotheses of lophotrochozoan relationships. a State-of-the-art review from Telford et al. (2015) summarizing the knowledge at that point. b Phylogenomic analysis of Lophotrochozoa based on 638 orthologs by Kocot et al. (2017). c Phylogenomic analysis of Lophotrochozoa based on 1/6 of 638 orthologs selected to mini- mize the patristic distance across taxa by Kocot et al. (2017). d Phylogenomic analysis of 267 orthologs with amino acids recoded according 6 Dayhoff groups to reduce saturation by Marlétaz et al. (2019)
FIGURE 1 in An updated generic circumscription for Cryptangieae (Cyperaceae, Poales) based on a molecular phylogeny and a morphological character reconstruction
FIGURE 1. Phylogenetic hypothesis on Cryptangieae genera based on a combined matrix with two chloroplast (rbcL and trnL-F) and three nuclear ribosomal (ITS, ETS and 5S-NTS) regions using Bayesian Inference [full circle—PP=1], and summary of: combined (a'), rbcL (b), trnLF (c), ITS (d), ETS (e) and 5S-NTS (f) reconstructions [Group/genus color: black—outgroup; purple—Krenakia; pink—Didymiandrum; brownish-green—Exochogyne; orange—Cryptangium; blue and green—Cephalocarpus(including Everardia); red—Lagenocarpus]
FIGURE 3 in An updated generic circumscription for Cryptangieae (Cyperaceae, Poales) based on a molecular phylogeny and a morphological character reconstruction
FIGURE 3. Mapping of 13 diagnostic characters applied the Ancestral Character State analyses and Ancestral Character States Recovered (ACSR) to Cryptangieae (see selected diagnostic characters at Table 4) [Group/genus color: black—outgroup; pink—Didymiandrum; purple—Krenakia; brownish-green—Exochogyne; orange—Cryptangium; blue and green—Cephalocarpus (including Everardia); red— Lagenocarpus; state of character: (0) white; (1) black; (2) grey; (3) yellow; Characters: (a) Sexual system, (b) caudex development, (c) Inflorescence position, (d) Inflorescence general morphology, (e) Paracladia sexual morphology, (f) Stigma color, (g) Hypogynous scales, (h) hypogynous scales development, (i) hypogynous scales ornamentation, (j) nutlet shape in cross section, (k) nutlet beak presence, (l)nutlet ornamentation, (m)nutlet constriction area].
FIGURE 2. Cryptangieae general morphology. A in An updated generic circumscription for Cryptangieae (Cyperaceae, Poales) based on a molecular phylogeny and a morphological character reconstruction
FIGURE 2. Cryptangieae general morphology. A. Cephalocarpus confertus (habit), B-C. Cephalocarpus montanus habit (B) and caudex in cross section (C); D-E. Krenakia minarum habit (D) and detail of leaves reduced to sheaths (E); F-G. Exochogyne amazonica with mature male (F) and female (G) spikelets; H. Cryptangium verticillatum male spikelets; I. Krenakia sp. spikelets. J. Lagenocarpus rigidus inflorescence (female spikelets apical and in rigid peduncles and male spikelets basal and in flexible peduncles); K. Cephalocarpus confertus inflorescence detail (male and female spikelets at the same cluster); L. Cephalocarpus montanus uniflowered spikelets with immature nutlets.
Fig. 3. Phylogenetic reconstruction for 356 in Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata)
Fig. 3. Phylogenetic reconstruction for 356 specimens from the combined maximum likelihood analysis of 28S and 16S. Bootstrap values are shown only if below 100. Species names and classification as proposed are shown. (a) Lestoidea and Platystictoidea; (b, c) various groups; (d) Platycnemididae; (e) Coenagrionidae.
Fig. 2. Phylogenetic reconstruction for 295 in Redefining the damselfly families: a comprehensive molecular phylogeny of Zygoptera (Odonata)
Fig. 2. Phylogenetic reconstruction for 295 specimens from the combined Bayesian analysis of 28S, 16S and COI. Posterior probabilities are shown (as percentages) only if below 100%. Species names and classification as proposed are shown. (a) Lestoidea and Platystictoidea; (b, c) various groups; (d) Platycnemididae; (e) Coenagrionidae.
FIGURE 7. Phylogenetic maximum likelihood reconstruction using partial 28S in A new species of Cycloporus from the Adriatic Sea, with an updated phylogeny of the families Euryleptidae and Stylostomidae (Polycladida, Platyhelminthes)
FIGURE 7. Phylogenetic maximum likelihood reconstruction using partial 28S sequences (accession numbers in brackets) of polyclads, rooted with Macrostomum lignano; branches other than Euryleptidae and Stylostomidae collapsed. Bootstrap nodal support of 200 non-parametric bootstrap replicates. Full tree in Suppl. Mat. 2. Cycloporus pinkipus sp. n. marked in pink. Additional representatives of Cycloporus written in red. Representatives of Eurylepta written in light green. Branches of Euryleptidae in light green. Branches of Stylostomidae in light blue. Branches of Pseudocerotidae in purple. Scale bar indicates the number of substitutions per site.
Data from: Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.
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Exon-based phylogenomics and the relationships of African cichlids: Tackling the challenges of reconstructing phylogenies with repeated rapid radiations
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Data from: The evolution of skull and body shape in Triturus newts reconstructed from 3D morphometric data and phylogeny
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Data from: Reconstructing phylogeny from reduced-representation genome sequencing data without assembly or alignment
Reduced-representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data. Alignment-free methods are both efficient and accurate for phylogenetic reconstructions with whole genomes and are especially practical for non-model organisms; nonetheless, alignment-free methods have not been applied with reduced genome sequencing data. Here, we test a full-genome assembly and alignment-free method, AAF, in application to RADseq data and propose two procedures for reads selection to remove reads from restriction sites that were not found in taxa being compared. We validate these methods using both simulations and real datasets. Reads selection improved the accuracy of phylogenetic construction in every simulated scenario and the two real datasets, making AAF as good or better than a comparable alignment-based method, even though AAF had much lower computational burdens. We also investigated the sources of missing data in RADseq and their effects on phylogeny reconstruction using AAF. The AAF pipeline modified for RADseq or other reduced-representation sequencing data, phyloRAD, is available on github (https://github.com/fanhuan/phyloRAD).
Table 4. Molecular dating and ancestral area reconstruction results for Liphistius using S in Molecular phylogeny, biogeography, and species delimitation of segmented spider genus Liphistius (Araneae: Liphistiidae) in Thailand
<p><b>Table 4.</b> Molecular dating and ancestral area reconstruction results for <i>Liphistius</i> using S-DIVALIKE+J. The letters A–I correspond to geographical locations shown in Figure 4. The notation shows the biogeographic event in the phylogenetic tree (Fig. 4A) includes →: from the parent node to descendent nodes; ^: Sympatric speciation; |: Vicariance.</p><table><tbody><tr><th><b>Diversification events</b></th><th><b>Dates</b></th><th><b>DIVALIKE+J</b></th><th></th><th></th></tr><tr><th></th><th><b>(Mya)</b></th><th><b>Ancestral areas</b></th><th><b>Process</b></th><th><b>Route and probability</b></th></tr></tbody><tbody><tr><th>The most recent common ancestor of Liphistiidae</th><td>100</td><td>BCI 13.60</td><td>Dispersal:0</td><td>BCI→I|BC</td></tr><tr><th>(Fig. 4, number 1)</th><td></td><td>CEI 13.33</td><td>Vicariance:1</td><td>prob:.02</td></tr><tr><th></th><td></td><td>BEI 10.96</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Heptathelinae</th><td>58.43</td><td>I 100</td><td>Dispersal:0</td><td>I→I^I→I| I</td></tr><tr><th></th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>Liphistius</i></th><td>53.61</td><td>BC 14.34</td><td>Dispersal:0</td><td>BC→C|B</td></tr><tr><th>(Fig. 4, number 2)</th><td></td><td>CE 14.05</td><td>Vicariance:1</td><td>prob:.03</td></tr><tr><th></th><td></td><td>C 12.37</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>L. indra</i> + <i>L.</i></th><td>45.51</td><td>C 45.23</td><td>Dispersal:1</td><td>C→CE→C|E</td></tr><tr><th><i>lahu</i> (Fig. 4, number 3)</th><td></td><td>E 38.20</td><td>Vicariance:1</td><td>prob:.45</td></tr><tr><th></th><td></td><td>CE 16.50</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>trang</i> species</th><td>49.61</td><td>B 39.38</td><td>Dispersal:1</td><td>B→DB→D|B</td></tr><tr><th>group + <i>bristowei</i> species group (Fig. 3, number 4)</th><td></td><td>D 30.43</td><td>Vicariance:1</td><td>prob:.30</td></tr><tr><th></th><td></td><td>BD 14.72</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>bristowei</i> spe-</th><td>32.86</td><td>D 75.76</td><td>Dispersal:0</td><td>D→D^D→D|D</td></tr><tr><th>cies group (Fig. 4, number 5)</th><td></td><td>C 21.28</td><td>Vicariance:0</td><td>prob:.55</td></tr><tr><th></th><td></td><td>A 2.02</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of <i>trang</i> species</th><td>46.54</td><td>B 99.88</td><td>Dispersal:0</td><td>B→B^B→B| B</td></tr><tr><th>group (Fig. 4, number 6)</th><td></td><td>A 0.08</td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td>H 0.01</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Sibumasu I</th><td>41.39</td><td>B 100</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>clade (Fig. 4, number 7)</th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Sinbumasu II–</th><td>42.48</td><td>B 99.76</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>IV and Indochina clades (Fig. 4, number 8)</th><td></td><td>A 0.18</td><td>Vicariance:0</td><td>prob:.96</td></tr><tr><th></th><td></td><td>G 0.03</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu II</th><td>30.56</td><td>B 99.91</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>(Fig. 4, number 9)</th><td></td><td>A 0.09</td><td>Vicariance:0</td><td>prob:.97</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu</th><td>38.89</td><td>B 96.03</td><td>Dispersal:1</td><td>B→AB→A|B</td></tr><tr><th>III–IV and Indochina clade (Fig. 4, number 10)</th><td></td><td>A 2.65</td><td>Vicariance:1</td><td>prob:.48</td></tr><tr><th></th><td></td><td>G 0.67</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu III</th><td>31.69</td><td>A 51.95</td><td>Dispersal:0</td><td>A→A^A→A| A</td></tr><tr><th>(Fig. 4, number 11)</th><td></td><td>B 48.05</td><td>Vicariance:0</td><td>prob:.26</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu</th><td>34.81</td><td>B 96.15</td><td>Dispersal:1</td><td>B→BG→B| G</td></tr><tr><th>IV + Indochina clade (Fig. 4, number 12)</th><td></td><td>G 1.94</td><td>Vicariance:1</td><td>prob:.48</td></tr><tr><th></th><td></td><td>H 1.90</td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Shibumasu IV</th><td>17.02</td><td>B 100</td><td>Dispersal:0</td><td>B→B^B→B|B</td></tr><tr><th>(Fig. 4, number 13)</th><td></td><td></td><td>Vicariance:0</td><td>prob: 1.00</td></tr><tr><th></th><td></td><td></td><td>Extinction:0</td><td></td></tr><tr><th>The most recent common ancestor of Indochina</th><td>31.15</td><td>G 50.43</td><td>Dispersal:1</td><td>G→GH→G|H</td></tr><tr><th>clade (Fig. 4, number 14)</th><td></td><td>H 49.38</td><td>Vicariance:1</td><td>prob:.50</td></tr><tr><th></th><td></td><td>D 0.20</td><td>Extinction:0</td><td></td></tr></tbody></table>
Figure 2 from: Yang M, Zhang Y (2015) Phylogenetic utility of ribosomal genes for reconstructing the phylogeny of five Chinese satyrine tribes (Lepidoptera, Nymphalidae). ZooKeys 488: 105-120. https://doi.org/10.3897/zookeys.488.9171
Figure 2 - 50% majority-rule trees obtained from Bayesian inference (BI) analyses based on the non-COI + Cytb +COII-3rds-dataset. Numbers on nodes are the posterior probabilities (PP).
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Allen Brain Atlas
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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.