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Abstract Detail

Phylogenomics

Hipp, Andrew L. [1], Manos, Paul [2], McVay, John D. [3], Cavender-Bares, Jeannine [4], Gonzalez Rodriguez, Antonio [5], Romero-Severson, Jeanne [6], Hahn, Marlene [7], Brown, Bethany H. [8], Budaitis, Breane [9], Deng, Min [10], Grimm, Guido [11], Fitzek, Elisabeth [1], Cronn, Richard C. [12], Jennings, Tara L. [13], Avishai, Michael [14], Simeone, Marco C. [15].

A phylogeny of the world’s oaks.

Oaks (Quercus: Fagaceae) are dominant species of temperate and subtropical forests throughout North America and Eurasia. Ecologically, culturally, and economically, oaks are among the most important trees in the world. Yet hybridization and lineage sorting have long dogged efforts to reconstruct phylogeny in the oaks. We have in the past few years had a great deal of success inferring species-level phylogenetic relationships in oaks using two genome-scanning methods, amplified fragment length polymorphisms (AFLP) and restriction-site associated DNA sequencing (RADseq). In this talk, we present a PstI RADseq phylogeny of the oaks that includes more than 200 of the world’s estimated 425 species. The Eurasian sections Cerris and Cyclobalanopsis are sister to each other, and these two are sister to the American oak clade. The Eurasian white oaks of section Quercus are embedded within the American oak clade, and we discuss evidence regarding alternative placements for the group. We compare RADseq data for a subset of North American white oaks to complete chloroplast sequences for the same individuals to investigate the relative contribution of phylogeny and geography to the chloroplast topology. We also evaluate the performance of RADseq compared to AFLP data for a subset of approximately 120 individuals sampled from across the American oak clade. Both methods recover phylogenetic signal that is distinguishable from the signal of localized gene flow, and both strongly support the notion that the entities we refer to as oak species are genetically coherent, species in a relatively traditional sense. Remarkably, numerous SNPs in the RADseq dataset appear to be fixed or nearly fixed between species, a finding that stands at odds with most previous population-level studies. We present preliminary work in using the RADseq data to develop a SNP set that can be used as an inexpensive DNA barcode for the eastern North American white oaks. We also present an R package and workflows for manipulating and analyzing clustered RADseq data.

1 - The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532-1293, USA, 630-725-2094
2 - Duke
3 - Duke University
4 - University Of Minnesota, 100 Ecology Bldg, 1987 Upper Buford Circle, Saint Paul, MN, 55108, USA
5 - UNAM, Universidad Nacional Autónoma de México, Centro de Investigaciones en Ecosistemas, , ., Morelia, Michoacán
6 - Notre Dame University
7 - The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
8 - The Morton Arboretum, Herbarium, 4100 Illinois Route 53, Lisle, IL, 60532-1293, USA
9 - University of Michigan
10 - Shanghai Chenshan Plant Science Research Center, 3888 Chenhua Road, Songjian, Shanghai, 201602, China
11 - University of Vienna
12 - USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR, 97330, USA
13 - PNW Research Station, USDA Forest Service
14 - The Hebrew University of Jerusalem
15 - Tuscia University

Keywords:
AFLP
Cyclobalanopsis
Fagaceae
next-generation sequencing
phylogenomics
Quercus
RADseq
restriction site associated DNA.

Presentation Type: Oral Paper:Papers for Topics
Session: 73
Location: Salon 9/The Shaw Conference Centre
Date: Wednesday, July 29th, 2015
Time: 4:45 PM
Number: 73012
Abstract ID:1305.
Candidate for Awards:Margaret Menzel Award