Abstract Detail

Phylogenomics

Cooper, Benjamin [1], Moore, Michael [1], Wickett, Norman [1], Wagner, Warren [1], Johnson, Matthew [1], Overson, Rick [6], Skogen, Krissa [1].

The power of population sampling, splash-zone introns, and summary coalescent methods in targeted enrichment: untangling species relationships in Oenothera sect. Calylophus.

Phylogenetic signal can be obscured by processes such as incomplete lineage sorting (ILS) and gene flow. In addition, recent, rapid radiations can result in short branch lengths, conflicting gene tree topologies, and overlapping morphological variation in traits used to delimit species. There is a growing consensus that more accurate representations of phylogenetic relationships can be achieved, despite ILS, by sampling a large number of loci and multiple accessions per taxon, and using coalescent-based methods for species tree estimation. Target enrichment, a method that "captures" genes of interest from genomic libraries allowing for multiplexed, high-throughput sequencing of hundreds of loci across hundreds of samples, has emerged as a cost effective and computationally tractable approach for producing highly informative data sets for phylogenetics. In addition, although coalescent methods remain computationally challenging, summary coalescent methods have arisen as statistically consistent alternative for estimating species trees using hundreds or thousands of loci from many samples in a fraction of the time. Here, we use target enrichment, summary coalescent methods, and morphometric analyses to reconstruct a phylogenetic hypothesis, test taxon boundaries, and resolve the history of pollinator shifts, gypsum endemism, and permanent translocation heterozygosity in Oenothera sect. Calylophus, a group of 13 recognized taxa in the evening primrose family, Onagraceae. Importantly, sect. Calylophusis a well-circumscribed clade with a relatively restricted geographic range in the northern Chihuahuan Desert of North America making it feasible to comprehensively sample across the range of geographic and morphological diversity in the group. By combining comprehensive, population level taxon sampling, Target Enrichment with hundreds of genes and intron containing "splash" zones, and summary coalescent methods for tree estimation, this approach provides resolution of evolutionary relationships despite conflicting gene tree topologies where more traditional approaches using strictly morphological based analysis, relatively few genes, or supermatrix tree estimation methods, were unsuccessful.

1 -
2 - Oberlin College, Department Of Biology, 119 Woodland St., Science Center K111, Oberlin, OH, 44074, United States
3 - Chicago Botanic Garden, 1000 Lake Cook Rd., Glencoe, IL, 60022, United States
4 - Smithsonian Institution, Department Of Botany, MRC-166, P. O. Box 37012, Washington, DC, 20013, United States
5 - Texas Tech University, Biological Sciences, 2901 Main Street, Ms3131, Lubbock, TX, 79409, United States
6 - Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, United States
7 - Chicago Botanic Garden, Conservation Scientist, 1000 Lake Cook Road, Glencoe, IL, 60022, United States

Keywords:
target enrichment
HybPiper
multispecies coalescent
Onagraceae
Oenothera
Calylophus
Pollinator Shifts
gypsum.

Presentation Type: Oral Paper
Session: PHYL1, Phylogenomics I
Location: San Ignacio/Starr Pass
Date: Monday, July 29th, 2019
Time: 11:00 AM
Number: PHYL1012
Abstract ID:678
Candidate for Awards:None