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WEBINAR: Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation

Schmidt-Lebuhn, Alexander

This record includes training materials associated with the Australian BioCommons webinar ‘Conflict in multi-gene datasets: why it happens and what to do about it - deep coalescence, paralogy and reticulation’. This webinar took place on 20 May 2021.

Multi-gene datasets used in phylogenetic analyses, such as those produced by the sequence capture or target enrichment used in the Genomics for Australian Plants: Australian Angiosperm Tree of Life project, often show discordance between individual gene trees and between gene and species trees. This webinar explores three different forms of discordance: deep coalescence, paralogy, and reticulation. In each case, it considers underlying biological processes, how discordance presents in the data, and what bioinformatic or phylogenetic approaches and tools are available to address these challenges. It covers Yang and Smith paralogy resolution and general information on options for phylogenetic analysis.

This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focused on the analysis of target capture sequence data. In addition to two public webinars, the GAP bioinformatics working group is offering training workshops in the use of newly developed and existing scripts in an integrated workflow to participants in the 2021 virtual Australasian Systematic Botany Society Conference.

The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.

Files and materials included in this record:

  • Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.

  • Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.

  • Schmidt-Lebuhn - paralogy lineage sorting reticulation - slides (PDF): Slides presented during the webinar

 

Materials shared elsewhere:

A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/1bw81q898z8

Files (9.2 MB)
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Event metadata.pdf
md5:66e544c047a0b8f5a3729391a2696c36 		105.4 kB Download
Index of training materials.pdf
md5:51464e239240f08ca02b801db830a440 		90.9 kB Download
Schmidt-Lebuhn - paralogy lineage sorting reticulation-slides.pdf
md5:0e7402bab16a57da635da51f39393323 		9.0 MB Download

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  • Stegemann S, Keuthe M, Greiner S, Bock R, 2012. Horizontal transfer of chloroplast genomes between plant species. Proc. Natl. Acad. Sci. 109: 2434–2438. https://doi.org/10.1073/pnas.1114076109

  • Flouri T, Jiao X, Rannala B, Yang Z, 2020. A Bayesian implementation of the multispecies coalescent model with introgression for phylogenomic analysis. Mol. Biol. Evol. 37: 1211-1223. https://doi.org/10.1093/molbev/msz296

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  • Joly S, McLenachan PA, Lockhart PJ, 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Amer. Nat. 174: E54-E70. https://doi.org/10.1086/600082

  • Morel B, Schade P, Lutteropp S, Williams TA, Sz llősi GJ, Stamatakis A, 2021. SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss. https://doi.org/10.1101/2021.03.29.437460

  • Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K, 2020. HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets. BioRxiv. https://doi.org/10.1101/2020.10.27.354589

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Publication date:
July 15, 2021
DOI:
10.5281/zenodo.5104998

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Keyword(s):
Phylogenetics Bioinformatics Phylogeny Genomics Target capture sequencing
Subject(s):
Phylogenetics
Bioinformatics
Phylogeny
Genomics
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License (for files):
Creative Commons Attribution 4.0 International

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