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Abstract Detail



Phylogenomics

Granados Mendoza, Carolina [1], Salazar, Gerardo A. [1], Hagsater, Eric [2], van der Berg, Cassio [3], Magallón, Susana [4], Moriarty Lemmon, Emily [5], Lemmon, Alan R. [5].

Enhanced phylogenetic resolution of the highly-diverse Neotropical genus Epidendrum (Orchidaceae) using Anchored Hybrid Enrichment.

Large-scale sequence data collection for macro- and micro-evolutionary studies has recently been boosted by the application of novel genomic partitioning strategies (GPS), a set of methods focused on simultaneously sequencing selected portions of the genome that are expected to be highly informative for specific phylogenetic scopes. Anchored Hybrid Enrichment (AHE; Lemmon et al. 2012) is a novel and highly efficient GPS for phylogenomics. Its probe design targets the capture of hundreds of loci with different proportions of conserved vs. non-conserved regions, therefore capturing loci that are potentially useful for a range of evolutionary depths. Although AHE was first tested in vertebrates, a newly-developed plant-capture probe set was recently applied to angiosperm lineages. The present work demonstrates the application of the AHE method in Epidendrum (Orchidaceae, Asparagales), a highly diverse Neotropical genus whose relationships have not been resolved. Our aims were to evaluate the effectiveness of gene capture and sequencing of the AHE in Epidendrum and estimate the performance of the obtained loci in resolving and supporting phylogenetic relationships along a range of taxonomical depths. For this we used a representative taxon sampling including 18 species of Epidendrum and one species each of the genera Caularthron, Barkeria, Broughtonia and Arpophyllum (Subtribe Laeliinae). Pleurothallis cardiothallis of subtribe Pleurothallidinae was used to root the phylogenetic tree. The method captured and sequenced 335 loci with an average copy number ranging from 0.66 to 0.89 and an average length of 581 bp (ranging from 163 to 1495 bp). A maximum likelihood analysis of all the loci concatenated retrieved a fully resolved and highly supported phylogenetic tree (all nodes with bootstrap support ≥92). The feasibility of applying AHE to plants is here corroborated for Epidendrum. The loci obtained were highly informative along the full range of taxonomical depths herein tested, including relationships of closely related species and genera of Tribe Epidendreae.


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Related Links:
Center for Anchored Phylogenomics
Personal website


1 - National Autonomous University of Mexico, Institute of Biology, Botany Department, Departamento de BotÁnica, Instituto de Biología, U.N.A.M. Circuito Exterior s/n, Ciudad Universitaria, Copilco, CoyoacÁn A.P. 70-367 México, Ciudad de México, Mexico City, Mexico City, 04510, Mexico
2 - HERBARIO AMO, Montanas Calizas 490, Lomas De Chapultepec, MEXICO, N/A, 11000, Mexico
3 - Universidade Estadual De Feira De Santana, Av. Transnordestina S/n, Ed. Labio, Sala 13, FEIRA DE SANTANA-BA, N/A, 44036-900, Brazil
4 - Instituto De Biologia, Universidad Nacional Autonoma De Mexico, 3er Circuito De Ciudad Universitaria, Del. Coyoacan, A.P. 70-233, Mexico City, Mexico D.F., N/A, 04510, Mexico
5 - Florida State University, Department of Biological Science, 319 Stadium Dr., P.O. Box 3064295, Tallahassee, FL, Tallahassee, FL, 4295, USA

Keywords:
Epidendrum
Orchidaceae
anchored phylogenomics
Genomic Partitioning Strategies.

Presentation Type: Oral Paper
Session: 1, Phylogenomics I
Location: 101/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 10:45 AM
Number: 1011
Abstract ID:411
Candidate for Awards:None


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