WEBINAR: Detection of and phasing of hybrid accessions in a target capture dataset
Creators: name: Nauheimer, Lars
Publisher: name: Zenodo
Year: 2021
Subjects: subject: Phylogenetics
subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Phylogeny
subject: Genomics
subject: Target capture sequencing
subject: http://edamontology.org/topic_3293
subject: http://edamontology.org/topic_0091
subject: http://edamontology.org/topic_0084
subject: http://edamontology.org/topic_0622

description: This record includes training materials associated with the Australian BioCommons webinar ‘Detection of and phasing of hybrid accessions in a target capture dataset’. This webinar took place on 10 June 2021. Hybridisation plays an important role in evolution, leading to the exchange of genes between species and, in some cases, generate new lineages. The use of molecular methods has revealed the frequency and importance of reticulation events is higher than previously thought and this insight continues with the ongoing development of phylogenomic methods that allow novel insights into the role and extent of hybridisation. Hybrids notoriously provide challenges for the reconstruction of evolutionary relationships, as they contain conflicting genetic information from their divergent parental lineages. However, this also provides the opportunity to gain insights into the origin of hybrids (including autopolyploids). This webinar explores some of the challenges and opportunities that occur when hybrids are included in a target capture sequence dataset. In particular, it describes the impact of hybrid accessions on sequence assembly and phylogenetic analysis and further explores how the information of the conflicting phylogenetic signal can be used to detect and resolve hybrid accessions. The webinar showcases a novel bioinformatic workflow, HybPhaser, that can be used to detect and phase hybrids in target capture datasets and will provide the theoretical background and concepts behind the workflow. This webinar is part of a series of webinars and workshops developed by the Genomics for Australian Plants (GAP) Initiative that focuses 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. <strong>Files and materials included in this record:</strong> 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. Nauheimer_hybphaser_slides (PDF): Slides presented during the webinar <strong>Materials shared elsewhere:</strong><br> A recording of the webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/japXwTAhA5U
description: {"references": ["Abbott, R., D. Albach, S. Ansell, J. W. Arntzen, S. J. E. Baird, N. Bierne, J. Boughman, et al. 2013. Hybridization and speciation. Journal of Evolutionary Biology26: 229\u2013246.", "Andermann, T., A. M. Fernandes, U. Olsson, M. T\u00f6pel, B. Pfeil, B. Oxelman, A. Aleixo, et al. 2019. Allele phasing greatly improves the phylogenetic utility of ultraconservedelements. Systematic Biology68: 32\u201346.", "Barker, M. S., N. Arrigo, A. E. Baniaga, Z. Li, and D. A. Levin. 2016. On the relative abundance of autopolyploidsand allopolyploids. New Phytologist210: 391\u2013398.", "Jiao, Y., N. J. Wickett, S. Ayyampalayam, A. S. Chanderbali, L. Landherr, P. E. Ralph, L. P. Tomsho, et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature473: 97\u2013100.", "Johnson, M. G., E. M. Gardner, Y. Liu, R. Medina, B. Goffinet, A. J. Shaw, N. J. C. Zerega, and N. J. Wickett. 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences4: 1600016.", "Kates, H. R., M. G. Johnson, E. M. Gardner, N. J. C. Zerega, and N. J. Wickett. 2018. Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus. American Journal of Botany105: 404\u2013416.", "Mallet, J. 2005. Hybridization as an invasion of the genome. Trends in Ecology &amp; Evolution20: 229\u2013237.", "Paun, O., F. Forest, M. F. Fay, and M. W. Chase. 2009. Hybrid speciation in angiosperms: parental divergence drives ploidy. New Phytologist182: 507\u2013518.", "Peer, Y. V. de, E. Mizrachi, and K. Marchal. 2017. The evolutionary significance of polyploidy. Nature Reviews Genetics18: 411\u2013424.", "Sang, T., and D. Zhang. 1999. Reconstructing hybrid speciation using sequences of low copy nuclear genes: hybrid origins of fivePaeoniaspecies based on adhgene phylogenies. Systematic Botany24: 148\u2013163.", "Soltis, D. E., C. J. Visger, D. B. Marchant, and P. S. Soltis. 2016. Polyploidy: Pitfalls and paths to a paradigm. American Journal of Botany103: 1146\u20131166.", "Tiley, G. P., A. A. Crowl, P. S. Manos, E. B. Sessa, C. Sol\u00eds-Lemus, A. D. Yoder, and J. G. Burleigh. 2021. Phasing Alleles Improves Network Inference with Allopolyploids. Evolutionary Biology."]}