1st Sept (Sat) 10:50 - 12:20; 13:30 - 15:00

Root to Tip Legume Phylogenomics: Building the Phylogenetic Foundations for Next Generation Legume Systematics

Phylogenetics is rapidly being transformed into phylogenomics by the quickly growing availability of much larger, genome-scale DNA sequence data sets that can be generated via next generation sequencing (NGS). These new data sets have potential for building much enhanced phylogenies at all phylogenetic levels from the root to the tips of the tree, to resolve both deep higher-level relationships as well as the complex and often reticulate patterns at and around the species level. These data also provide the foundations needed for elucidating gene and genome evolution, including the history of whole genome and gene duplications, as well as levels of congruence / discordance among genes and genomes and signatures of selection, insights which are critical for accurate phylogeny reconstruction. These developments are also revolutionizing how we build phylogenies with promising new approaches and methods emerging. These more robust phylogenetic foundations are critical for marshalling massive amounts of comparative data to address a wide range of systematics questions. Despite major advances, including the recent LPWG phylogeny which encompasses almost all legume genera, reconstructing a robust legume phylogeny remains challenging given the large size of the family and the apparent rapid radiation of legumes as a whole as well as key other clades, that result in short branch lengths. Over the last five years since ILC6 a raft of new legume projects generating NGS data have started. These include new whole genome sequences for key taxa, large scale sequencing of plastomes, transcriptome sequencing of representative taxa across the family, large nuclear gene sequence datasets generated via targeted enrichment (hybrid sequence capture) for a number of legume clades, and RADseq data. This symposium aims to: (i) present results from a range of legume phylogenomics initiatives spanning different hierarchical levels; (ii) provide an overview of data types and approaches for different questions; (iii) review the state of play with respect to available genome-scale data for legumes; and (iv) prompt discussion about strategies for new sequencing efforts and for building the next generation legume phylogeny.

ORGANIZERS: Colin Hughes (University of Zurich, Switzerland); Toby Pennington (University of Exeter, U.K.); Jeff Doyle (Cornell University, U.S.A.)

1. Genomics, transcriptomics, and more: The making of a model non-model legume system, perennial Glycine (Phaseoleae)
Jeff J. Doyle* (Cornell University, Plant Breeding & Genetics Section)

2. Integrating phylogenomics and population genetics using target enrichment in Detarioideae, a group of ecologically dominant tropical African trees
Manuel de la Estrella*1, Sandra Cervantes3, Dario I Ojeda3, Erik Koenen4, Jeremy Migliore5, Boris Demenou5, Steven Janssen6, Anne Bruneau7, Olivier Hardy5, Felix Forest2 (1Universidad de Córdoba, Spain;2Royal Botanic Gardens, Kew;3Department of Ecology and genetics, Oulu University, Finland;4Department of Systematic & Evolutionary Botany, University of Zurich, Switzerland;5Université Libré de Bruxelles, Brussels, Belgium;6Botanic Garden Meise, Meise, Belgium;7Institut de Recherche en Biologie Végétale, Université de Montreal, Canada )

3. Plastid phylogenomic insights into the evolution of legumes
Ting-Shuang Yi * (Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China)

4. Phylogeny and plastome evolution of the legume family (Leguminosae).
Jian-Jun Jin* (Kunming Institute of Botany, Chinese Academy of Sciences)

5. Phylogeny and polyploidy in Leucaena resolved using genome-scale data from plastid, mitochondrial, and nuclear genomes
C. Donovan Bailey*1, Alex Abair1, Lynsey Kovar2, Nageswara-Rao Madhugiri3, Diana V. Dugas4, Erik Koenen5, Colin E. Hughes5 (1Dept of Biology, New Mexico State University, Las Cruces, NM, USA;2Crop and Soil Sciences, University of Georgia, Athens, GA, USA;3Benson Hill Biosystems, St. Loius, MO;4Information and Communication Technologies, New Mexico State University, Las Cruces, NM, USA;5University of Zurich, Institute of Systematic Botany, Zurich, Switzerland )

6. Inga: using a next-generation hybrid capture phylogenomics method in a case study of evolutionary radiation in tropical rain forest trees
James Nicholls1, Catherine Kidner2, Phyllis Coley4, Thomas Kursar4, Graham Stone3, Kyle Dexter3, Toby Pennington*5 (1CSIRO, Australia;2Royal Botanic Garden Edinburgh, UK;3University of Edinburgh, UK;4University of Utah, USA;5University of Exeter, UK )

7. Pleistocene glacial cycles, species pumps, explosive species diversification and rapid adaptive evolutionary radiation of Lupinus (Leguminosae) in the high elevation Andes
Bruno Nevado1, Guy Atchison2, Natalia Contreras-Ortiz3, Dmitry Filatov1, Colin Hughes*2 (1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K.;2Department of Systematic & Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland;3Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Apartado Aéreo 4976, Bogotá, Colombia )

8. Target-enrichment phylogenomics improves the resolution of legume lineages at generic, tribal, and subfamily levels.
Ashley N Egan*1, Mohammad Vatanparast2 (1The George Washington University, Computational Biology Institute, Washington, DC, USA;2University of Copenhagen, Dept of Geoscience & Natural Resource Management, Copenhagen, Denmark )

9. Comparison of three methods for targeted enrichment bait design in legumes
Mohammad Vatanparast*1, Adrian Powell2, Jeff J Doyle3, Ashley N Egan4 (1Department of Geosciences and Natural Resource Management, Rolighedsvej 23, 1958 Frederiksberg C., University of Copenhagen, Denmark;2Boyce Thompson Institute, 533 Tower Road, Ithaca, New York 14853, USA;3Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, 512 Mann Library, Ithaca, New York 14853, USA;4Department of Botany, National Museum of Natural History, Smithsonian Institution, 37012, Washington, DC 20560, USA )

10. A genus-level phylogenetic tree of legumes: preliminary results using an angiosperm-wide targeted enrichment approach
Felix Forest*1, William J Baker1, Abigail Barker1, Grace Brewer1, Anne Bruneau2, Steven Dodsworth3, Niroshini Epitalawage1, Manuel de la Estrella4, Elyse-Ann Faubert2, Jan Kim1, Ilia Leitch1, Olivier Maurin1, Lisa Pokorny1, Gwilym P Lewis1 (1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom;2Institut de recherche en biologie végétale, 4101 Sherbrooke E., Montréal (Québec), H1X 2B2, Canada;3School of Life Sciences, University of Bedfordshire, Luton LU1 3JU, United Kingdom;4Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de Córdoba, Spain )