@unpublished {22378, title = {Anti-bat ultrasound production in moths is globally and phylogenetically widespread}, year = {2021}, month = {09/2021}, pages = {1-31}, type = {bioRxiv preprint}, abstract = {

\"Warning signals are well known in the visual system, but rare in other modalities. Some moths produce ultrasonic sounds to warn bats of noxious taste or to mimic unpalatable models. Here we report results from a long-term study across the globe, assaying moth response to playback of bat echolocation. We tested 252 genera, spanning most families of large-bodied moths, and outline anti-bat ultrasound production in 52 genera, with eight new subfamily origins described. Based on acoustic analysis of ultrasonic emissions and palatability experiments with bats, it seems that acoustic warning and mimicry are the raison d\&$\#$39;etre for sound production in most moths. However, some moths use high-density ultrasound capable of jamming bat sonar. In fact, we find preliminary evidence of independent origins of sonar jamming in at least six subfamilies. Palatability data indicates that jamming and warning are not mutually exclusive strategies. To explore the possible organization of anti-bat warning sounds into acoustic mimicry rings, we intensively studied a community of moths in Ecuador and found five distinct acoustic clusters using machine learning algorithms. While these data represent an early understanding of acoustic aposematism and mimicry across this megadiverse insect order, it is likely that ultrasonically-signaling moths comprise one of the largest mimicry complexes on earth.\"

}, keywords = {ACOUSTICS, APOSEMATISM, BATS, DEFENCE, DIVERSITY, EREBIDAE, EVOLUTION, HEARING, JAMMING, LEPIDOPTERA, MIMICRY, PREDATOR AVOIDANCE, SPHINGIDAE, STRIDULATION, TYMBAL ORGANS, ULTRASONICS}, doi = {10.1101/2021.09.20.460855}, url = {https://doi.org/10.1101/2021.09.20.460855}, author = {Barber, J.R. and Plotkin, D. and Rubin, J.J. and Homziak, N.T. and Leavell, B.C. and Houlihan, P. and Miner, K.A. and Breinholt, J.W. and Quirk-Royal, B. and Padr{\'o}n, P.S. and Nunez, M. and Kawahara, A.Y.} } @article {22026, title = {Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives.}, journal = {BMC Evolutionary Biology}, volume = {19}, year = {2019}, month = {09/2019}, pages = {182 [1-13]}, chapter = {182}, abstract = {

\"Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.
Results: The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).
Conclusions: Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth \“arms race\”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.\"

}, keywords = {ANCHORED HYBRID ENRICHMENT, APATELODIDAE, AROTROS, BOMBYCIDAE, BOMBYCOIDEA, DNA, PHYLOGENOMICS, PHYLOGENY, TARGETED SEQUENCE CAPTURE}, doi = {10.1186/s12862-019-1505-1}, url = {https://doi.org/10.1186/s12862-019-1505-1}, author = {Hamilton, C.A. and St Laurent, R.A. and Dexter, K. and Kitching, I.J. and Breinholt, J.W. and Zwick, A. and Timmermans, M.J.T.N. and Barber, J.R. and Kawahara, A.Y.} } @article {21525, title = {Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for anchored phylogenomics}, journal = {Systematic Biology}, year = {2017}, type = {Early view}, abstract = {

\"The advent of next-generation sequencing technology has allowed for the collection 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 combineAHEand 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 shallowtaxonomic level, phylogenetic analyseswere 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.\"

}, keywords = {ANCHORED HYBRID ENRICHMENT, HEMARINI, HIGHER CLASSIFICATION, LEPIDOPTERA, METHODOLOGY, PHYLOGENOMICS, PHYLOGENY, PIPELINE, SATURNIIDAE, SPHINGIDAE}, doi = {10.1093/sysbio/syx048}, author = {Breinholt, J.W. and Earl, C. and Lemmon, A.R. and Moriarty_Lemmon, E. and Xiao, L. and Kawahara, A.Y.} } @article {21183, title = {Body size affects the evolution of eyespots in caterpillars}, journal = {Proceedings of the National Academy of Sciences}, volume = {112}, year = {2015}, month = {05/2015}, pages = {6664-6669}, chapter = {6664}, abstract = {

\"Many caterpillars have conspicuous eye-like markings, called eyespots. Despite recent work demonstrating the efficacy of eyespots in deterring predator attack, a fundamental question remains: Given their protective benefits, why have eyespots not evolved in more caterpillars? Using a phylogenetically controlled analysis of hawkmoth caterpillars, we show that eyespots are associated with large body size. This relationship could arise because (i) large prey are innately conspicuous; (ii) large prey are more profitable, and thus face stronger selection to evolve such defenses; and/or (iii) eyespots are more effective on large-bodied prey. To evaluate these hypotheses, we exposed small and large caterpillar models with and without eyespots in a 2 \× 2 factorial design to avian predators in the field. Overall, eyespots increased prey mortality, but the effect was particularly marked in small prey, and eyespots decreased mortality of large prey in some microhabitats. We then exposed artificial prey to na\ïve domestic chicks in a laboratory setting following a 2 \× 3 design (small or large size \× no, small, or large eyespots). Predators attacked small prey with eyespots more quickly, but were more wary of large caterpillars with large eyespots than those without eyespots or with small eyespots. Taken together, these data suggest that eyespots are effective deterrents only when both prey and eyespots are large, and that innate aversion toward eyespots is conditional. We conclude that the distribution of eyespots in nature likely results from selection against eyespots in small caterpillars and selection for eyespots in large caterpillars (at least in some microhabitats).\"

}, keywords = {ANOVA, DEFENCE, EVOLUTION, EYESPOT, IMMATURE MORPHOLOGY, MIMICRY, PREDATION, SPHINGIDAE}, doi = {10.1073/pnas.1415121112}, author = {Hossie, T.J. and Skelhorn, J. and Breinholt, J.W. and Kawahara, A.Y. and Sherratt, T.N.} } @article {20886, title = {A molecular phylogeny of Eumorpha (Lepidoptera: Sphingidae) and the evolution of anti-predator larval eyespots}, journal = {Systematic Entomology}, volume = {40}, year = {2015}, pages = {401-408}, chapter = {401}, keywords = {BAYESIAN INFERENCE, BEHAVIOUR, BIOGEOGRAPHY, CAD, COI, DEFENCE, DNA, EF-1ALPHA, EUMORPHA, EYESPOT, IMMATURE STAGES, MAXIMUM LIKELIHOOD, MIMICRY, PHYLOGENY, RASP, RAXML, SPHINGIDAE, WINGLESS, WORLDMAP1}, doi = {10.1111/syen.12111}, url = {https://doi.org/10.1111/syen.12111}, author = {Ponce, F.V. and Breinholt, J.W. and Hossie, T. and Barber, J.R. and Janzen, D.H. and Hallwachs, W. and Kawahara, A.Y.} } @article {18694, title = {Evolution of Manduca sexta hornworms and relatives: biogeographical analysis reveals an ancestral diversification in Central America}, journal = {Molecular Phylogenetics and Evolution}, volume = {68}, year = {2013}, month = {2013}, pages = {381-386}, chapter = {381}, keywords = {BAYESIAN INFERENCE, BIOGEOGRAPHY, CAD, COI, DNA, EF-1ALPHA, MANDUCA, MAXIMUM LIKELIHOOD, PEST, RASP, SPHINGIDAE, WINGLESS}, doi = {10.1016/j.ympev.2013.04.017}, url = {https://doi.org/10.1016/j.ympev.2013.04.017}, author = {Kawahara, A.Y. and Breinholt, J.W. and Ponce, F.V. and Haxaire, J. and Lei, X. and Lamarre, G.P.A. and Rubinoff, D. and Kitching, I.J.} } @article {17015, title = {Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data}, journal = {Genome Biology and Evolution}, volume = {5}, year = {2013}, month = {10/2013}, pages = {2082-2092}, chapter = {2082}, abstract = {

\"Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (\∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions.\"

}, keywords = {ACTIAS, ANTHERAEA, BOMBYCIDAE, BOMBYX, CERATOMIA, DARAPSA, DNA, ENYO, HEMARIS, INCOMPLETE, MANDUCA, MAXIMUM LIKELIHOOD, PARSIMONY, PHYLOGENY, RADICAL, RAXML, SAMIA, SATURATION, SATURNIIDAE, SPHINGIDAE, SYNONYMOUS SUBSTITUTIONS, TRANSCRIPTOMICS}, doi = {10.1093/gbe/evt157}, url = {https://doi.org/10.1093/gbe/evt157}, author = {Breinholt, J.W. and Kawahara, A.Y.} }