Phylogenomic reconstruction of transcriptome data confirms the basal position of Prodoxidae moths within the order Lepidoptera

Clive T. Darwell, Saravanaraj Ayyampalayam, James Leebens-Mack, Chris I. Smith, Kari Segraves, David M Althoff

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Yucca moths (Prodoxidae) have long been considered by taxonomists to be basally positioned within the Lepidoptera in the superfamily Adeloidea. Recently, phylogenomic reconstructions of ordinal lepidopteran relationships using transcriptome data confirmed the basal position of the Adeloidea and the positioning of the Tegeticula pollinating yucca moths within the superfamily. However, to date, no phylogenetic studies have been conducted attempting to position the Prodoxus bogus yucca moths using whole genome data. We incorporated our own transcriptome libraries into publicly available lepidopteran data in order to phylogenetically confirm the evolutionary position of the Prodoxidae within the Lepidoptera and to assess the position of Prodoxus relative to Tegeticula. Our phylotranscriptomic reconstruction verified the Prodoxidae as the sister taxa to the basal Adelidae (Adeloidea), and Prodoxus as sister to Tegeticula. However, topological relationships among our four focal Tegeticula species contradicted recent findings from RAD-seq analyses. We show that this apparent paradox is in fact an artefact of the phylogenetic methods employed in building the ordinal level phylogeny (i.e. sequence alignment based on the first two nucleotide positions only) and that the true Tegeticula relationships are recovered by using all three nucleotide base positions to correctly infer more recent evolutionary events. Our work shows the utility of next-generation sequencing (NGS) technologies whilst highlighting some technical considerations that may confound phylogenetic interpretation according to taxonomic scale. We add to the growing consensus that NGS techniques offer a prime opportunity to elucidate previously challenging questions in evolutionary biology.

Original languageEnglish (US)
Pages (from-to)59-64
Number of pages6
JournalArthropod Systematics and Phylogeny
Volume76
Issue number1
StatePublished - Jan 1 2018

Fingerprint

Tegeticula
Prodoxidae
Yucca
Lepidoptera
Moths
Transcriptome
transcriptome
moths
Nucleotides
Sequence Alignment
phylogeny
Phylogeny
Artifacts
nucleotides
Genome
Technology
sequence alignment
pollination
Biological Sciences
genome

Keywords

  • Lepidoptera
  • Phylogenomics
  • Prodoxidae
  • Prodoxus
  • Tegeticula
  • Transcriptomics
  • Yucca moths

ASJC Scopus subject areas

  • Genetics
  • Insect Science

Cite this

Phylogenomic reconstruction of transcriptome data confirms the basal position of Prodoxidae moths within the order Lepidoptera. / Darwell, Clive T.; Ayyampalayam, Saravanaraj; Leebens-Mack, James; Smith, Chris I.; Segraves, Kari; Althoff, David M.

In: Arthropod Systematics and Phylogeny, Vol. 76, No. 1, 01.01.2018, p. 59-64.

Research output: Contribution to journalArticle

@article{819a6b7e2d26420289f582f1daf18153,
title = "Phylogenomic reconstruction of transcriptome data confirms the basal position of Prodoxidae moths within the order Lepidoptera",
abstract = "Yucca moths (Prodoxidae) have long been considered by taxonomists to be basally positioned within the Lepidoptera in the superfamily Adeloidea. Recently, phylogenomic reconstructions of ordinal lepidopteran relationships using transcriptome data confirmed the basal position of the Adeloidea and the positioning of the Tegeticula pollinating yucca moths within the superfamily. However, to date, no phylogenetic studies have been conducted attempting to position the Prodoxus bogus yucca moths using whole genome data. We incorporated our own transcriptome libraries into publicly available lepidopteran data in order to phylogenetically confirm the evolutionary position of the Prodoxidae within the Lepidoptera and to assess the position of Prodoxus relative to Tegeticula. Our phylotranscriptomic reconstruction verified the Prodoxidae as the sister taxa to the basal Adelidae (Adeloidea), and Prodoxus as sister to Tegeticula. However, topological relationships among our four focal Tegeticula species contradicted recent findings from RAD-seq analyses. We show that this apparent paradox is in fact an artefact of the phylogenetic methods employed in building the ordinal level phylogeny (i.e. sequence alignment based on the first two nucleotide positions only) and that the true Tegeticula relationships are recovered by using all three nucleotide base positions to correctly infer more recent evolutionary events. Our work shows the utility of next-generation sequencing (NGS) technologies whilst highlighting some technical considerations that may confound phylogenetic interpretation according to taxonomic scale. We add to the growing consensus that NGS techniques offer a prime opportunity to elucidate previously challenging questions in evolutionary biology.",
keywords = "Lepidoptera, Phylogenomics, Prodoxidae, Prodoxus, Tegeticula, Transcriptomics, Yucca moths",
author = "Darwell, {Clive T.} and Saravanaraj Ayyampalayam and James Leebens-Mack and Smith, {Chris I.} and Kari Segraves and Althoff, {David M}",
year = "2018",
month = "1",
day = "1",
language = "English (US)",
volume = "76",
pages = "59--64",
journal = "Arthropod Systematics and Phylogeny",
issn = "1863-7221",
publisher = "Staatliche Naturhistorische Sammlungen Dresden",
number = "1",

}

TY - JOUR

T1 - Phylogenomic reconstruction of transcriptome data confirms the basal position of Prodoxidae moths within the order Lepidoptera

AU - Darwell, Clive T.

AU - Ayyampalayam, Saravanaraj

AU - Leebens-Mack, James

AU - Smith, Chris I.

AU - Segraves, Kari

AU - Althoff, David M

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Yucca moths (Prodoxidae) have long been considered by taxonomists to be basally positioned within the Lepidoptera in the superfamily Adeloidea. Recently, phylogenomic reconstructions of ordinal lepidopteran relationships using transcriptome data confirmed the basal position of the Adeloidea and the positioning of the Tegeticula pollinating yucca moths within the superfamily. However, to date, no phylogenetic studies have been conducted attempting to position the Prodoxus bogus yucca moths using whole genome data. We incorporated our own transcriptome libraries into publicly available lepidopteran data in order to phylogenetically confirm the evolutionary position of the Prodoxidae within the Lepidoptera and to assess the position of Prodoxus relative to Tegeticula. Our phylotranscriptomic reconstruction verified the Prodoxidae as the sister taxa to the basal Adelidae (Adeloidea), and Prodoxus as sister to Tegeticula. However, topological relationships among our four focal Tegeticula species contradicted recent findings from RAD-seq analyses. We show that this apparent paradox is in fact an artefact of the phylogenetic methods employed in building the ordinal level phylogeny (i.e. sequence alignment based on the first two nucleotide positions only) and that the true Tegeticula relationships are recovered by using all three nucleotide base positions to correctly infer more recent evolutionary events. Our work shows the utility of next-generation sequencing (NGS) technologies whilst highlighting some technical considerations that may confound phylogenetic interpretation according to taxonomic scale. We add to the growing consensus that NGS techniques offer a prime opportunity to elucidate previously challenging questions in evolutionary biology.

AB - Yucca moths (Prodoxidae) have long been considered by taxonomists to be basally positioned within the Lepidoptera in the superfamily Adeloidea. Recently, phylogenomic reconstructions of ordinal lepidopteran relationships using transcriptome data confirmed the basal position of the Adeloidea and the positioning of the Tegeticula pollinating yucca moths within the superfamily. However, to date, no phylogenetic studies have been conducted attempting to position the Prodoxus bogus yucca moths using whole genome data. We incorporated our own transcriptome libraries into publicly available lepidopteran data in order to phylogenetically confirm the evolutionary position of the Prodoxidae within the Lepidoptera and to assess the position of Prodoxus relative to Tegeticula. Our phylotranscriptomic reconstruction verified the Prodoxidae as the sister taxa to the basal Adelidae (Adeloidea), and Prodoxus as sister to Tegeticula. However, topological relationships among our four focal Tegeticula species contradicted recent findings from RAD-seq analyses. We show that this apparent paradox is in fact an artefact of the phylogenetic methods employed in building the ordinal level phylogeny (i.e. sequence alignment based on the first two nucleotide positions only) and that the true Tegeticula relationships are recovered by using all three nucleotide base positions to correctly infer more recent evolutionary events. Our work shows the utility of next-generation sequencing (NGS) technologies whilst highlighting some technical considerations that may confound phylogenetic interpretation according to taxonomic scale. We add to the growing consensus that NGS techniques offer a prime opportunity to elucidate previously challenging questions in evolutionary biology.

KW - Lepidoptera

KW - Phylogenomics

KW - Prodoxidae

KW - Prodoxus

KW - Tegeticula

KW - Transcriptomics

KW - Yucca moths

UR - http://www.scopus.com/inward/record.url?scp=85047004797&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85047004797&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:85047004797

VL - 76

SP - 59

EP - 64

JO - Arthropod Systematics and Phylogeny

JF - Arthropod Systematics and Phylogeny

SN - 1863-7221

IS - 1

ER -