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19 results for “cophylogeny”
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)
<p>GENERAL INFORMATION</p> <p>1. Title of Dataset: Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)</p> <p>2. Author Information<br> A. Principal Investigator Contact Information<br> Name: Scott Burgess<br> Institution: Florida State University<br> Address: 319 Stadium Drive, Tallahassee, FL, USA 32306<br> Email: sburgess@bio.fsu.edu</p> <p><br> 3. Date of data collection (single date, range, approximate date): 2019-08</p> <p>4. Geographic location of data collection: Moorea, French Polynesia</p> <p>5. Information about funding sources that supported the collection of the data: National Science Foundation (NSF; OCE-1829867)</p> <p> </p> <p><br> DATA & FILE OVERVIEW</p> <p>1. File List:<br> Figure 2 Make.R<br> Figure 4 Make.R<br> Figure 5b Make.R<br> Figure 6 Make.R</p> <p>Figure 1 SNAPP species tree.xml<br> Figure 2.txt<br> Figure 2.vcf<br> Figure 3b - Pocillopora mt genomes.nex<br> Figure 4 and 6 data.csv<br> Figure 4 colors.csv<br> Figure 5a - Cladocopium_psbA.nex<br> Figure 5b - Clad clades.csv<br> Figure 5b_Cladocopium.nex<br> Figure 5b_Pocillopora.nex<br> Figure 5b.csv</p> <p><br> 2. Relationship between files:<br> Figure 2 Make.R uses Figure 2.txt and Figure 2.vcf<br> Figure 4 Make.R uses Figure 4 and 6 data.csv and Figure 4 colors.csv<br> Figure 5b Make.R uses Figure 5b - Clad clades.csv, Figure 5b_Cladocopium.nex, Figure 5b_Pocillopora.nex, and Figure 5b.csv<br> Figure 6 Make.R Figure 4 and 6 data.csv</p> <p> </p> <p>3. Metadata</p> <p>Figure 2 Make.R:<br> R code to produce Figure 2, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 2.txt', 'Figure 2.vcf'</p> <p><br> Figure 4 Make.R:<br> R code to produce Figure 4, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 4 data.csv', 'Figure 4 colors'</p> <p><br> Figure 5b Make.R:<br> R code to produce Figure 5b, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 5b - Clad clades.csv', 'Figure 5b_Cladocopium.nex', 'Figure 5b_Pocillopora.nex', 'Figure 5b.csv'</p> <p><br> Figure 6 Make.R:<br> R code to produce Figure 6, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 6 data.csv'</p> <p><br> Figure 1 SNAPP species tree.xml:<br> Data for species tree used in Figure 1</p> <p>Figure 2.txt:<br> Metadata<br> Sample_ID: Sample ID<br> Hap_Spp: Pocillopora species or haplotype</p> <p>Figure 2.vcf:<br> Linked dataset of 7,887 SNPs</p> <p>Figure 3b - Pocillopora mt genomes.nex:<br> Nexus tree of Pocillopora mitochondrial genomes used in Figure 3b</p> <p><br> Figure 4 and 6 data.csv:<br> Metadata<br> Species.haplotype: Pocillopora species or haplotype<br> Depth.m: Sampling depth in meters<br> Site: Sampling site, label corresponds to the site used in the Moorea Coral Reef Long-Term Ecological Research (MCR-LTER) program.<br> Coral.ID: Coral colony identifier<br> Type_profile: ITS2 type profile generated by SymPortal<br> Type_profile_Prop: Proportion of that given ITS2 type profile in colony sampled<br> Remaining columns: Proportion of ITS2 sequences in colony sampled</p> <p>Figure 4 colors.csv:<br> Metadata<br> my_colors: Custom colors for each ITS2 sequence<br> Symbio.clade: ITS2 sequences</p> <p>Figure 5a - Cladocopium_psbA.nex:<br> Nexus tree of Cladocopium taxa in figure 5a</p> <p>Figure 5b - Clad clades.csv:<br> Metadata<br> UCI_links: Sample ID that contains Pocillopora species or haplotype, sample ID, and ITS2 type profile<br> Clad_clades: Clade assignment from figure 5a</p> <p>Figure 5b_Cladocopium.nex:<br> Nexus tree of Cladocopium taxa in Figure 5b</p> <p>Figure 5b_Pocillopora.nex:<br> Nexus tree of Pocillopora taxa used in PACo analysis, Figure 5b</p> <p>Figure 5b.csv:<br> Matrix of Pocillopora host and Cladocopium symbiont links</p>
Cophylogeny reconstruction allowing for multiple associations through approximate Bayesian computation
<p>Phylogenetic tree reconciliation is extensively employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation. Although certain approaches deduce event probabilities unique to each pair of host and symbiont trees, which can subsequently be converted into cost values, a significant limitation lies in their inability to model the <em>invasion</em> of diverse host species by the same symbiont species (termed as a spread event), which is believed to occur in symbiotic relationships. Invasions lead to the observation of multiple associations between symbionts and their hosts (indicating that a symbiont is no longer exclusive to a single host), which are incompatible with the existing methods of coevolution. </p> <p>Here, we present a method called AmoCoala (an enhanced version of the tool Coala) that provides a more realistic estimation of cophylogeny event probabilities for a given pair of host and symbiont trees, even in the presence of spread events. We expand the classical 4-event coevolutionary model to include 2 additional spread events (vertical and horizontal spreads) that lead to multiple associations. In the initial step, we estimate the probabilities of spread events using heuristic frequencies. Subsequently, in the second step, we employ an approximate Bayesian computation (ABC) approach to infer the probabilities of the remaining 4 classical events (cospeciation, duplication, host switch, and loss) based on these values.</p> <p>By incorporating spread events, our reconciliation model enables a more accurate consideration of multiple associations. This improvement enhances the precision of estimated cost sets, paving the way to a more reliable reconciliation of host and symbiont trees. To validate our method, we conducted experiments on synthetic datasets and demonstrated its efficacy using real-world examples. Our results showcase that AmoCoala produces biologically plausible reconciliation scenarios, further emphasizing its effectiveness.The software is accessible at <a href="https://github.com/sinaimeri/AmoCoala" rel="noopener">https://github.com/sinaimeri/AmoCoala</a>.</p>
Linked collectors and determiners for: Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny.
Natural history specimen data linked to collectors and determiners held within, "Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/b41d1ad7-2165-409f-ac9e-08f60a27b820">https://bionomia.net/dataset/b41d1ad7-2165-409f-ac9e-08f60a27b820</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/b41d1ad7-2165-409f-ac9e-08f60a27b820">https://gbif.org/dataset/b41d1ad7-2165-409f-ac9e-08f60a27b820</a>. Formatted as a Frictionless Data package.
Cophylogeny reconstruction allowing for multiple associations through approximate Bayesian computation
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FIGURE 12 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 12. Hypothetical coevolutionary scenarios linking species of Thyroptera pix, 1823 with Hershkovitzia coeca Theodor, 1967. A. Tanglegram with T. wynneae Velazco, Gregorin, Voss & Simmons, 2014. B. Trillogram with T. wynneae. C. Tanglegram with T. discifera (Lichtenstein & Peters, 1855). D. Trillogram with T. discifera. E. Tanglegram with T. tricolor Spix, 1823. F. Trillogram with T. tricolor. G. Tanglegram with T. devivoi Gregorin, Gonçalves & Engstrom, 2006. H. Trillogram with T. devivoi. I. Tanglegram with T. lavali Pine, 1993. J. Trillogram with T. lavali. Symbols: hollow circle = cospeciation; Full circle = duplication; Arrow = duplication and host switch; Dotted line = Loss.
FIGURE 10 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 10. Most parsimonious cladogram obtained for Hershkovitzia Guimar"es & D'Andretta, 1956. A. Cladogram with DELTRAN optimization of the characters (L=51, CI=72, RI=81). B. Same, with numbers above the branches indicating Bootstrap support and numbers below the branches indicating decay index (Bremer support).
FIGURE 8 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 8. Hershkovitzia autinoae sp. nov. (ZUFMS 2379/2380) A. Abdomen, female, dorsal view. B. Abdomen, female, ventral view. C. Abdomen, male, dorsal view. D. Abdomen, male, ventral view. E. Head, lateral view. F. Head, dorsal view. Scale bars: 0.5 mm (A, B); 0.2 mm (C, D); 0.01 mm (E, F).
FIGURE 7 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 7. Hershkovitzia mariae Hrycyna, Santos, Rebêlo & Graciolli, 2022 (ZUFMS 707615). A. Abdomen, female, dorsal view. B. Abdomen, female, ventral view. C. Abdomen, male, dorsal view. D. Abdomen, male, ventral view. E. Head, lateral view. F. Head, dorsal view. Scale bars: 0.5 mm (A, B); 0.2 mm (C, D); 0.01 mm (E, F).
FIGURE 5 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 5. Hershkovitzia cabala Peterson & Lacey, 1985 (INPA 004163). A. Abdomen, female, dorsal view. B. Abdomen, female, ventral view. C. Abdomen, male, dorsal view. D. Abdomen, male, ventral view. E. Head, lateral view. F. Head, dorsal view. Scale bars: 0.2 mm (A–D); 0.01 mm (E, F).
FIGURE 4. Hershkovitzia coeca Theodor, 1967 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 4. Hershkovitzia coeca Theodor, 1967 (NHMUK 010369545). A. Abdomen, female, dorsal view. B. Abdomen, female, ventral view. C. Tibia II, lateral view, highlighting rows of transverse and ventral setae (default for Primitiva group). D. Tibia II, lateral view, highlighting rows of transverse and ventral setae (default for Inaequalis group). E. Head, lateral view F. Head, dorsal view. Scale bars: 0.5 mm (A, B); 1 mm (C, D); 0.01 mm (E, F).
FIGURE 3 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 3. Hershkovitzia primitiva Guimar"es & D'Andretta, 1956 (MZUSP 46.107). A. Abdomen, female, dorsal view. B. Abdomen, female, ventral view. C. Abdomen, male, dorsal view. D. Abdomen, male, ventral view. E. Head, lateral view. F. Head, dorsal view. Scale bars: 0.2 mm (A–D); 0.01 mm (E, F).
FIGURE 2 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 2. Female of Hershkovitzia primitiva Guimar"es & D'Andretta, 1956 (MZUSP 46.107), ventral view. Morphological terminology indicated. Scale bar: 0.2 mm.
FIGURE 11. Most parsimonious cladogram obtained for Thyroptera Spix, 1823. A in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 11. Most parsimonious cladogram obtained for Thyroptera Spix, 1823. A. Cladogram with DELTRAN optimization of the characters (L=64, CI=62, RI=61). B. Same, with numbers above the branches indicating Bootstrap support and numbers below the branches indicating decay index (Bremer support).
FIGURE 1 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 1. Female of Hershkovitzia primitiva Guimar"es & D'Andretta, 1956 (MZUSP 46.107), dorsal view. Morphological terminology indicated. Scale bar: 0.5 mm.
FIGURE 9 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 9. Geographic distribution of species of Hershkovitzia Guimar"es & D'Andretta, 1956. Symbols: circle = H. primitiva Guimar"es & D'Andretta, 1956; star = H. cabala = Peterson & Lacey, 1985; triangle = H. inaequalis Theodor, 1967; rhombus = H. mariae Hrycyna, Santos, Rebêlo & Graciolli, 2022; plus = Hershkovitzia autinoae sp. nov.
FIGURE 6. Hershkovitzia inaequalis Theodor, 1967 in Hershkovitzia (Diptera: Nycteribiidae): revision, phylogeny, and cophylogeny
FIGURE 6. Hershkovitzia inaequalis Theodor, 1967 (FMNH 89121). A. Abdomen, female, dorsal view. B. Abdomen, female, ventral view. C. Abdomen, male, dorsal view. D. Abdomen, male, ventral view. E. Head, lateral view. F. Head, dorsal view. Scale bars: 0.2 mm (A–D); 0.01 mm (E, F).
Data from: paco: implementing Procrustean Approach to Cophylogeny in R
1. The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro-evolutionary processes. 2. We introduce paco (v.0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. 3. We demonstrate the functionality of paco through its application to empirical host-parasite and plant-pollinator communities 4. Although the package is intended to assess phylogenetic congruence between groups of interacting species, the method is also directly applicable to other scenarios that may show phylogenetic congruence including historical biogeography, molecular systematics, and cultural evolution.
Data from: Cophylogeny Reconstruction via an Approximate Bayesian Computation
Open the record for dataset details and reuse information.
Data from: paco: implementing Procrustean Approach to Cophylogeny in R
Open the record for dataset details and reuse information.
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