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Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics.
Syst Biol. 2018 Jan 01; 67(1):78-93.SB

Abstract

The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.

Links

Publisher Full Text (DOI)

Authors+Show Affiliations

Breinholt JW
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. RAPiD Genomics, Gainesville, FL 32601, USA.
Earl C
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
Lemmon AR
Department of Scientific Computing.
Lemmon EM
Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
Xiao L
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
Kawahara AY
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.

MeSH

AnimalsButterfliesClassificationMothsPhylogenySequence Analysis, DNA

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

28472519

Citation

Breinholt, Jesse W., et al. "Resolving Relationships Among the Megadiverse Butterflies and Moths With a Novel Pipeline for Anchored Phylogenomics." Systematic Biology, vol. 67, no. 1, 2018, pp. 78-93.
Breinholt JW, Earl C, Lemmon AR, et al. Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics. Syst Biol. 2018;67(1):78-93.
Breinholt, J. W., Earl, C., Lemmon, A. R., Lemmon, E. M., Xiao, L., & Kawahara, A. Y. (2018). Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics. Systematic Biology, 67(1), 78-93. https://doi.org/10.1093/sysbio/syx048
Breinholt JW, et al. Resolving Relationships Among the Megadiverse Butterflies and Moths With a Novel Pipeline for Anchored Phylogenomics. Syst Biol. 2018 Jan 1;67(1):78-93. PubMed PMID: 28472519.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics. AU - Breinholt,Jesse W, AU - Earl,Chandra, AU - Lemmon,Alan R, AU - Lemmon,Emily Moriarty, AU - Xiao,Lei, AU - Kawahara,Akito Y, PY - 2016/07/01/received PY - 2017/04/28/accepted PY - 2017/5/5/pubmed PY - 2018/2/21/medline PY - 2017/5/5/entrez KW - Exon KW - hybrid enrichment KW - phylogenetics KW - sequence capture KW - target capture KW - transcriptomics KW - ultraconserved elements SP - 78 EP - 93 JF - Systematic biology JO - Syst Biol VL - 67 IS - 1 N2 - The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community. SN - 1076-836X UR - https://www.unboundmedicine.com/medline/citation/28472519/Resolving_Relationships_among_the_Megadiverse_Butterflies_and_Moths_with_a_Novel_Pipeline_for_Anchored_Phylogenomics_ DB - PRIME DP - Unbound Medicine ER -