Maia, V. H., M. A. Gitzendanner, P. S. Soltis, Gane Ka-Shu Wong, and D. E. Soltis. 2014. Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data. International Journal of Plant Sciences 175:613–650. [Link to article]

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Vergara, R., M. A. Gitzendanner, D. E. Soltis, and P. S. Soltis. 2014. Population genetic structure, genetic diversity, and natural history of the South American species of Nothofagus subgenus Lophozonia (Nothofagaceae) inferred from nuclear microsatellite data. Ecol Evol 4:2450–2471. [Link to article]

Read More “Population genetic structure, genetic diversity, and natural history of the South American species of Nothofagus”

NGS data processing for phylogenetics

Our paper outlining how next-generation sequencing can be used in phylogenetics research has just beenpublished in Plant Ecology and Diversity. Grant Godden, Ingrid Jordn-Thaden et al review approaches and considerations that take into consideration the limited budgets of most evolutionary biology labs.

Grant T. Godden , Ingrid E. Jordon-Thaden , Srikar Chamala , Andrew A. Crowl , Nicolás García , Charlotte C. Germain-Aubrey , J. Michael Heaney , Maribeth Latvis , Xinshuai Qi & Matthew A. Gitzendanner (2012): Making next-generation sequencing work for you: approaches and practical considerations for marker development and phylogenetics, Plant Ecology & Diversity, 5:4, 427-450

See the article on the publisher’s site. If you do not subscribe to this journal, please email me and request one of the limited number of free reprints I can distribute.

Abstract

Recent reviews are setting the stage for the use of next-generation sequencing technologies in phylogenetic applications. However, the processes for developing new markers for phylogenetic analyses remain difficult to navigate for many researchers in plant systematics. We review several experimental approaches and practical considerations for developing new phylogenetic markers with next-generation sequencing technologies. We also outline a flexible framework for data acquisition that is readily adaptable to the needs of individual researchers and carefully consider cost-related issues that may be of concern to many laboratories in evolutionary biology. The next-generation and targeted sequencing approaches presented here offer considerable savings of time and money over the traditional PCR and Sanger sequencing approaches currently used in plant systematic research, particularly in cases involving large numbers of taxa and phylogenetic markers. Even with a limited research budget, next-generation sequence data can accommodate exploration of biological questions in ways that were not previously possible.

One of the side projects I’ve revisited from time to time is the application of plant DNA analyses in forensics. I’ve done some work on a couple of cases and tried to keep up with the literature. I recently wrote a chapter for David Hall and Jason Byrd’s new book Forensic Botany: A Practical Guide.

Gitzendanner, M. A. 2012. Use and guidelines for plant DNA analyses in forensics. In D. Hall and J. Byrd [eds.] Forensic Botany: A practical guide. Wiley-Blackwell. pp. 93-106.

Link to publisher’s site.