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1,344 results for “phylogenomics”
Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination
<p>Extended Data S1-S2 and Tables S6-S9 corresponding to the publication entitled Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination. Data S1 contains the phylogeny analyzed in the aforementioned study, and Data S2 contains a table of all samples considered to be descendant of a recombinant node in the study, as well as the relevant recombinant node ID. Tables S6-S9 are acknowledgments tables corresponding to GISAID (Table S6), China National Center for Bioinformation (Table S7), COVID-19 Genomics UK (COG-UK) (Table S8), and National Center for Biotechnology Information database (Table S9) on which the study was based.</p>
Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts and All Other Lineages
<p><strong>Abstract</strong></p> <p>Advances in phylogenetic methods and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolutionary history of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most ‘popular’ (i.e. in textbooks and reviews) hypothesis for the root is between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion and a limited sampling of eukaryotic lineages. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within the Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses), nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree – species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. Our results estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative popular roots from the literature. Based on further analysis of genome size we propose Opisthokonta + others as the most likely root. Finding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes.</p> <p>Methods<br> Here we provide the alignments, gene trees, inputs, and outputs from our project entitled "Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts and All Other Lineages". Sequences and alignments were produced using the phylogenomic pipeline PhyloToL, which contains a taxon- and gene-rich database (including eukaryotes, archaea, and bacteria). These data were then used for 1) assessing the root of the eukaryotes and 2) for comparison with other previously published hypotheses. In both cases, we used the species tree - gene tree reconciliation tool iGTP. We also did a comparison of hypotheses using the likelihood-based tool SpeciesRax</p> <p><strong>iGTP</strong></p> <p>Input data</p> <p>These data are divided into four datasets based on taxa selection. For dataset SEL+, taxa were selected based on their taxonomy; for RAN+, taxa were selected randomly among the major eukaryotic clades Opisthokonta, Amoebozoa, Archaeplastida, Excavata, SAR, and some orphan lineages. Datasets SEL- and RAN- are the same as SEL+ and RAN+, but exclude microsporidians in order to account for and avoid long branch attraction due to microsporidians fast-evolutionary rates. We chose the gene families that contain at least 25 taxa representing at least four of the five major eukaryotic clades. Additionally, at least 2 of the major clades had to contain at least 2 minor clades (e.g. Glaucophytes and Rhodophyta are minor clades in the major clade Archaeplastida). In a pilot analysis, we produced an alignment and a phylogenetic tree for each gene family using the default settings of a previous version of PhyloToL (GUIDANCE V1.3.1 sequence cutoff = 0.3 and column cutoff = 0.4; RAxML quick tree with model PROTGAMMALG and no bootstraps). Then, we kept the gene families that are exclusive of eukaryotes or the ones in which eukaryotes were monophyletic. From a total of 3,002 gene families that met our criteria, 2786 passed the initial steps of PhyloToL when including only the data from the dataset SEL+. These 2,786 gene families were used for further analyses with all datasets.</p> <p>MSAs were produced with PhyloToL (GUIDANCE V2.02 sequence cutoff = 0.3, column cutoff = 0.4, number of iterations = 5; Sela, et al. 2015). The default parameters of PhyloToL include up to five iterations of GUIDANCE V2.02 with 10 bootstraps and MAFFT V7 with algorithm E-INS-i for less than 200 sequences or “auto” option if more than 200 sequences, and maxiterate = 1000. Instead, here we run up to five iterations of GUIDANCE with 20 bootstraps and the simple MAFFT algorithm FFT-NS-2. Then, we perform an additional GUIDANCE run with 100 bootstraps and the default MAFFT parameters for PhyloToL.</p> <p>Gene trees were inferred with RAxML v.8.2.4 with 10 ML searches for best-ML tree (option "-# 10"), using the rapid hill-climbing algorithm (option "-f d") and no bootstrap replicates. The protein evolution model used was evaluated during the gene tree inference (option "-m PROTCATAUTO") by testing all models available in RAxML (e.g. JTT, LG, WAG, etc) with optimization of substitution rates and of site-specific evolutionary rates which were categorized into four distinct rate categories for greater computational efficiency.</p> <p>We ran 100 repetitions of iGTP analyses per dataset. But, given the complexity of the datasets and the heuristic nature of some key steps of the iGTP algorithm (e.g. gene tree rooting and initial starting species tree generation), in a preliminary analysis, we faced two systematic challenges with iGTP as the inferred species tree was affected by: 1) the order of the leaves in the input unrooted gene tree Newick strings (i.e. the input trees were treated as rooted even though we specified that they were not); and 2) the input gene order in the 100 replicates. Therefore, we randomly shuffled the order of the leaves in the unrooted gene trees (keeping the same topology), and randomly shuffled the order of the input gene trees in each of the 100 replicates per dataset. Here we provide the 100 input files generated for those iGTP analyses. </p> <p>Output data</p> <p>Here we also share the data generated after two analyses: 1) root assessment and 2) hypothesis testing. For the former, we allowed iGTP to calculate the more parsimonious root given our input files. For the latter, we allowed iGTP to calculate the reconciliation cost of the gene trees given the input files and constraints in the species trees to reflect previously published root hypotheses. The constraints are explained in the README file.</p> <p>SpeciesRax</p> <p>Since we removed LGT and contamination from our dataset using a series of filters, we applied the model UndatedDL instead of UndatedDTL, which implies that we only took into consideration duplications and losses and ignored the transferences. Then, the command used for SpeciesRax was...</p> <p>./generax --families forGeneRax/famFile --species-tree forGeneRax/spsTreeAn.newick --strategy SKIP --rec-model UndatedDL --per-family-rates --prefix An_DS1 --si-strategy EVAL </p> <p>input </p> <p>Here, we are sharing all the necessary files to run SpeciesRax, including the mapping file (famFile), the species trees (spsTrees; the best iGTP constrained species trees per hypothesis), and their underlying gene trees (trees_r)</p> <p>output</p> <p>Output folder from SpeciesRax, which includes log files, events (duplications, losses) counts, and statistics (i.e., reconciliation likelihood values)</p> <p>Note: <br> * As in the iGTP analyses, for the SpeciesRax files, the words Op, Fu, Di, Un, An, refer to the five root hypotheses compared: Opisthokonta-others, Fungi-others, Discoba-others, Unikonta-Bikonta, and (Ancyromonadida + Metamonada)-others, respectively. <br> * For the SpeciesRax analyses, the Un word refers to Ut (Cavalier-Smith 2003) <br> </p>
Figs 80–81 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 80–81. Geographic distribution of the four taxa treated in this study. Note that the shallow water area (light grey) between Sicily and the Maltese Islands roughly corresponded to a land bridge during glaciations.
Figs 64–74 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 64–74. Specimens of Temnothorax vivianoi Schifani, Alicata & Prebus sp. nov. in lateral (left), dorsal (center) and head view (right). Photos by Enrico Schifani, available onwww.antweb.org, specimen identifiers in parentheses. 64–66. Holotype worker from Monte Pellegrino (Palermo Mountains, Sicily) (ANTWEB1041551). 67–69. Paratype worker from Monte Pellegrino (Palermo Mountains, Sicily) (ANTWEB1041552). 70–72. Paratype queen from Monte Pellegrino (Palermo Mountains, Sicily) (ANTWEB1041553). 73–74. Damaged male from Palermo Mountains (Sicily) (ANTWEB1041554). Scale bars = 0.5 mm.
Figs 75–78 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 75–78. Morphometric differentiation of the four taxa treated in this study based on the worker caste. 75. Principal component analysis of all nine morphometric characters (excluding indices). 76. Scatter plot of eye size index (EYE/CS) against cephalic length index (CL/CW). 77. Scatter plot of absolute spines length (SPST) against cephalic size (CS). 78. Scatter plot of spine length index (SPST/ CL) against scape length index (SL/CS).
Fig. 79. Maximum likelihood phylogeny inferred with IQTREE ver. 2.1.2 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Fig. 79. Maximum likelihood phylogeny inferred with IQTREE ver. 2.1.2. The major clades found in Prebus (2017) are highlighted, and the focal species of the current study (all within the 'Palearctic clade IV') are evidenced as in Figs 75–78. Maximum likelihood bootstrap support for all nodes are 100, except where indicated.
Figs 46–63 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 46–63. Specimens of Temnothorax poldii Alicata, Schifani & Prebus sp. nov. in lateral (left), dorsal (center) and head view (right). Photos by Enrico Schifani, available on www.antweb.org, specimen identifiers in parentheses. 46–48. Holotype worker from Monte Arso (Etna, Sicily) (ANTWEB1041545). 49–51. Worker from Vallone Madonne degli Angeli (Madonie, Sicily) (ANTWEB1041546). 52– 54. Paratype worker from Monte Ruvolo (Etna, Sicily) (ANTWEB1041547). 55–57. Worker from Monte Manfrè (Etna, Sicily) (ANTWEB1041548), with ergatogynes characters in the mesosoma. 58– 60. Paratype queen from Monte Arso (Etna, Sicily) (ANTWEB1041549). 61–63. Paratype male from Monte Ruvolo (Etna, Sicily) (ANTWEB1041550). Scale bars = 0.5 mm.
Figs 34–45 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 34–45. Specimens of Temnothorax marae Alicata, Schifani & Prebus sp. nov. in lateral (left), dorsal (center) and head view (right). Photos by Enrico Schifani, available on www.antweb.org, specimen identifiers in parentheses. 34–36. Holotype worker from Vendicari (Hyblaean Sicily) (ANTWEB1041541). 37–39. Paratype worker from Vendicari (Hyblaean Sicily) (ANTWEB1041542). 40–42. Queen from Bosco di Santo Pietro (Hyblaean Sicily) (ANTWEB1041543), note that the lateral image was edited to compensate for the fact that the petiole and gaster plus postpetiole were accidentally disarticulated. 43–45. Male from Bosco di Santo Pietro (Hyblaean Sicily) (ANTWEB1041544). Scale bars = 0.5 mm.
Figs 19–33 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 19–33. Specimens of Temnothorax lagrecai (Baroni Urbani, 1964) in lateral (left), dorsal (center) and head view (right). Photos available on www.antweb.org, specimen identifiers in parentheses. 19– 21. Worker from Monte Pellegrino (Palermo mountains, Sicily) (ANTWEB1041536), photo by Enrico Schifani. 22–24. Paratype worker from Bosco di Santo Pietro (Hyblaean Sicily) (ANTWEB1041537), photo by Elia Nalini. 25–27. Worker from Bosco di Linera (Etna, Sicily) (ANTWEB1041538), photo by Enrico Schifani. 28–30. Queen from Bosco di Santo Pietro (type locality, Hyblaean Sicily) (ANTWEB1041539), photo by Enrico Schifani. 31–33. Male from Bosco di Santo Pietro (type locality, Hyblaean Sicily) (ANTWEB1041540), photo by Enrico Schifani. Scale bars = 0.5 mm.
Figs 13–15 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 13–15.Head sculpture variation in workers of Temnothorax Mayr, 1861, photos fromwww.antweb.org, specimen identifiers in parentheses. 13. T. alienus Schulz, Heinze & Pusch, 2007, type specimen from Italy (ANTWEB1041297), photo by Roland Schultz, weak longitudinal striae on a background of dense alveolate sculpture. 14. T. flavicornis (Emery, 1870), type specimen from Italy (CASENT0904761), photo by Will Ericson, strong longitudinal striae with a shiny background. 15. T. tebessae (Forel, 1890), type specimen from Algeria (CASENT0909034), photo by Will Ericson, extremely weak and few longitudinal striae on a shiny background.
Fig. 82 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Fig. 82. Spatial characterization of the sites where the four species treated in this study were found.
Figs 16–18 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 16–18. Morphometric characters recorded from workers of Temnothorax Mayr, 1861 in this study. The background image is a paratype worker of T. lagrecai (Baroni Urbani, 1964) from the Natural History Museum of Vienna, photos by Anna Pal available from www.antweb.org, specimen identifier CASENT0919741. 16. Head view. 17. Lateral profile view. 18. Dorsal view of the mesosoma.
Figs 8–10 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 8–10. Lateral view of male specimens of Temnothorax Mayr, 1861 from Algeria with a focus on the propodeum, drawings from Cagniant (1970). 8. T. curtulus (Santschi, 1929), dentiform propodeal spines. 9. T. gentilis (Santschi, 1923), well-developed propodeal spines. 10. T. tebessae (Forel, 1890), no propodeal spines.
Figs 11–12 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 11–12.Petiole shape variation in workers of Temnothorax Mayr, 1861, photos fromwww.antweb.org, specimen identifiers in parentheses. 11. T. atomous (Cagniant & Espadaler, 1997), type specimen from Morocco (CASENT0915391), photo by Will Ericson, petiole dorsal profile with a single edge and no horizontal component, subpetiolar process carina-like. 12. T. alienus Schulz, Heinze & Pusch, 2007, type specimen from Italy (ANTWEB1041297), photo by Roland Schultz, petiole dorsal profile with two edges and a horizontal component, subpetiolar process with a tooth-like protuberance.
Figs 6–7 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 6–7. Lateral view of the mesosoma of workers of Temnothorax Mayr, 1861 exhibiting different characters, photos by Will Ericson, available on www.antweb.org, specimen identifiers in parentheses. 6. T. curtulus (Santschi, 1929), type specimen from Morocco (CASENT0912922), metanotal groove present (indicated by an arrow) and short propodeal spines. 7. T. luteus (Forel, 1874), type specimen from France (CASENT0907603), no metanotal groove and long propodeal spines.
Figs 4–5 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 4–5. Eye size variation in workers of Temnothorax Mayr, 1861, photos from www.antweb.org, specimen identifiers in parentheses. 4. T. lichtensteini (Bondroit, 1918), type specimen from France (ANTWEB1008441), photo by Roland Schultz, normal eye size. 5. T. arenarius (Santschi, 1908), type specimen from Tunisia (CASENT0912903), photo by Will Ericson, large eye size.
Fig. 1 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Fig. 1. Sampling efforts across Sicily and neighboring regions according to the geographic origin of the samples in the authors' collections.
Figs 2–3 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Figs 2–3. Variation in antennae of workers of Temnothorax Mayr, 1861, photos from www.antweb.org, specimen identifiers in parentheses. 2. T. minozzii (Santschi, 1922), type worker from Italy (CASENT0912964), photo by Will Ericson, antenna of 12 segments and darkened club. 3. T. flavicornis (Emery, 1870), type worker from Italy (CASENT0904761), photo by Will Ericson, antenna of 11 segments and concolorous club.
SPAAM Summer School 2022: Introduction to Ancient Metagenomics - 5b Introduction to Phylogenomics
<p>Teaching data for practical session: "5b Introduction to Phylogenomics" of the 2022 SPAAM Summer School: Introduction to Ancient Metagenomics (Aug. 1-5 2022).</p> <p>See: <a href="https://spaam-community.github.io/wss-summer-school/#/2022/">https://spaam-community.github.io/wss-summer-school/#/2022/</a> or <a href="https://doi.org/10.5281/zenodo.6976711">https://doi.org/10.5281/zenodo.6976711</a> for slides.</p> <p>Once downloaded, run:</p> <pre><code>tar xvfz <session>.tar.gz</code></pre> <p> to decompress the data directory for the session.</p>
Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
<p>As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (<em>Colinus virginianus</em>), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.</p>
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