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Abstract Detail



Phylogenomics

Pham, Kasey Khanh [1], Hipp, Andrew [2], Cronn, Richard [3], Manos, Paul [4].

A Time and a Place for Everything: Phylogenetic history and geography as joint predictors of oak plastome phylogeny.

Due to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation cause topology to reflect geographic structure, while deeper branches reflect population and lineage divergence history. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales. Our study compares pairwise phylogenetic distances based on complete plastome sequences, pairwise phylogenetic distances from nuclear restriction site-associated DNA sequences (RADseq), and pairwise geographic distances from provenance data for 34 individuals of the white oak clade representing 24 North American and Eurasian species. Within the North American white oak clade alone, phylogenetic history has essentially no effect on plastome variation, while geography explains 11–21% of plastome phylogenetic variance. However, across multiple continents and clades, phylogeny predicts 30–41% of plastome variation, geography 3–41%. Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, it has little use in solving phylogenetic questions, but can still be a useful barcoding / phylogenetic marker for resolving questions among major clades, especially when used in tandem with nuclear data.


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1 - Michigan State University, Plant Biology, 612 Wilson Rd, East Lansing, MI, 48824, USA
2 - The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532-1293, USA
3 - USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR, 97330, USA
4 - Duke University, Biology, 330 Bio Sci Bldg, Durham, NC, 27708, USA

Keywords:
gene flow
Hybridization
partial Mantel test
RADseq.

Presentation Type: Oral Paper
Number: 29005
Abstract ID:179
Candidate for Awards:None


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