Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

Hamilton, Chris A.; Laurent, Ryan A. St; Dexter, Kelly M.; Kitching, Ian J.; Breinholt, Jesse W.; Zwick, Andreas; Timmermans, Martijn J. T. N.; Barber, Jesse R.; Kawahara, Akito Y.

doi:10.1186/s12862-019-1505-1

Cited by 66 publications

(81 citation statements)

References 84 publications

(144 reference statements)

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“…3 from Breinholt et al, 2018). Producing augmented probe sets that are focused on a lineage of interest (e.g., BUTTERFLY1.0, BUTTERFLY 1.1 and BOM1 derived from the more general Lep1) more efficiently recovers phylogenetically informative loci and/or loci capture efficiency (Espeland et al, 2018;Toussaint et al, 2018;Hamilton et al, 2019). Comparing the application of Lep1 within the Erebinae (Noctuoidea: Erebidae) to our results applying NOC1 to the Arctiinae, we recovered more loci (730 vs 658), longer mean locus length (575 bp vs 320 bp) and a longer concatenated total length (420 574 bp vs 210 484 bp) (Homziak et al, 2018).…”

Section: Sensitivity Analysismentioning

confidence: 99%

“…The BUTTER-FLY1.0 kit was further specialized for Hesperiidae in a later study ('BUTTERFLY1.1') (Toussaint et al, 2018). A similar approach was taken to produce the Bombycoidea-specific probe set 'BOM1' (Hamilton et al, 2019). This probe kit specialization has generally resulted in an increased number of captured loci as well as an overall improved view of evolutionary relationships within the targeted groups (Hamilton et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…A similar approach was taken to produce the Bombycoidea-specific probe set 'BOM1' (Hamilton et al, 2019). This probe kit specialization has generally resulted in an increased number of captured loci as well as an overall improved view of evolutionary relationships within the targeted groups (Hamilton et al, 2019). In this study, we produce a new AHE probe set (NOC1) to improve support at both deep and shallow taxonomic levels within an important group of Lepidoptera.…”

Section: Introductionmentioning

confidence: 99%

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A deeper meaning for shallow‐level phylogenomic studies: nested anchored hybrid enrichment offers great promise for resolving the tiger moth tree of life (Lepidoptera: Erebidae: Arctiinae)

Dowdy

Keating

Lemmon

et al. 2020

Systematic Entomology

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Anchored hybrid enrichment (AHE) has emerged as a powerful tool for uncovering the evolutionary relationships within many taxonomic groups. AHE probe sets have been developed for a variety of insect groups, though none have yet been shown to be capable of simultaneously resolving deep and very shallow (e.g., intraspecific) divergences. In this study, we present NOC1, a new AHE probe set (730 loci) for Lepidoptera specialized for tiger moths and assess its ability to deliver phylogenetic utility at all taxonomic levels. We test the NOC1 probe set with 142 individuals from 116 species sampled from all the major lineages of Arctiinae (Erebidae), one of the most diverse groups of noctuoids (>11 000 species) for which no well‐resolved, strongly supported phylogenetic hypothesis exists. Compared to previous methods, we generally recover much higher branch support (BS), resulting in the most well‐supported, well‐resolved phylogeny of Arctiinae to date. At the most shallow‐levels, NOC1 confidently resolves species‐level and intraspecific relationships and potentially uncovers cryptic species diversity within the genus Hypoprepia. We also implement a ‘sensitivity analysis’ to explore different loci combinations and site sampling strategies to determine whether a reduced probe set can yield results similar to those of the full probe set. At both deep and shallow levels, only 50–175 of the 730 loci included in the complete NOC1 probe set were necessary to resolve most relationships with high confidence, though only when the more rapidly evolving sites within each locus are included. This demonstrates that AHE probe sets can be tailored to target fewer loci without a significant reduction in BS, allowing future studies to incorporate more taxa at a lower per‐sample sequencing cost. NOC1 shows great promise for resolving long‐standing taxonomic issues and evolutionary questions within arctiine lineages, one of the most speciose clades within Lepidoptera.

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Section: Sensitivity Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A deeper meaning for shallow‐level phylogenomic studies: nested anchored hybrid enrichment offers great promise for resolving the tiger moth tree of life (Lepidoptera: Erebidae: Arctiinae)

Dowdy

Keating

Lemmon

et al. 2020

Systematic Entomology

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“…It also shows that subfamilies Oberthuriinae and Prismostictinae are far from Bombycinae (Figure 1), agreeing that former subfamilies should be treated under Endromidae (Wang et al 2019). Sphingidae, however, is clustered with Bombycidae s.str not Saturniidae (Figure 1), which is also incongruent to former phylogenomic study (Hamilton et al 2019) with relatively low bootstrap values and posterior priority (Figure 1). Our results address the question why trees of mitochondrial and nucleic genes present difference phylogenetic relationships at the level of higher taxa.…”

mentioning

confidence: 75%

The complete mitochondrial genome of Rotunda rotundapex (Miyata & Kishida, 1990) (Lepidoptera: Bombycidae)

Park¹,

Xi²,

Park³

2019

Mitochondrial DNA Part B

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Rotunda rotundapex (Miyata & Kishida, 1990) is a silk moth identified in Korea. We completed its mitochondrial genome which is 15,298 bp long and the shortest mitogenome of Bombycidae s.str. It includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNAs, and a control region. Comparison with COI sequence of Taiwan isolate suggests the Korean population of this species can be a novel species. Gene order of R. rotundapex mitogenome is conserved as in other Bombycidae species. Phylogenetic trees show that R. rotundapex is closely related to genus Rondotia.

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“…This protocol was published in Hamilton et al . (). Downstream DNA extraction protocol was the same as for molecular samples from MGCL (see Cho et al ., ).…”

Section: Methodsmentioning

confidence: 97%

A new target capture phylogeny elucidates the systematics and evolution of wing coupling in sack‐bearer moths

Laurent

Mielke²,

Herbin

et al. 2020

Systematic Entomology

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The frenulum is a wing coupling structure that is found on the wings of most families of Lepidoptera. It is a single bristle or set of bristles that originate from the base of the hindwing that often interlocks with the forewing during flight. This wing coupling mechanism is thought to have been a major evolutionary innovation that allowed for enhanced flight in Lepidoptera. The sack-bearer moths (Mimallonidae) are unusual among Lepidoptera in that not all species within the family have a frenulum. We test the hypothesis that the frenulum is not necessary and is therefore lost in mimallonids that have longer male forewings, because such wings are perhaps better suited to be coupled by other means. To understand the evolution of the frenulum, we inferred the most taxonomically and genetically sampled anchored hybrid enrichment-based phylogeny of Mimallonidae, including 604 loci from all 41 genera and from 120 species, covering about 40% of the described species in the family. The maximum likelihood tree robustly supports major relationships within the family, and ancestral state reconstruction clearly recovers the frenulum as the plesiomorphic condition in Mimallonidae. Our results show that the frenulum is more often observed in species that have shorter, rather than longer, male forewings. The frenulum has historically been used as an important character for intrafamilial classification in Mimallonidae, but our results conclusively show that this character system is more variable than previously thought. Based on our results, we erect two new subfamilies, Roelofinae St Laurent & Kawahara, subfam.n. and Meneviinae St Laurent, Herbin, & Kawahara, subfam.n., for four genera previously considered incertae sedis. In the predominantly frenulum-lacking clade Cicinninae, we describe a new genus, Cerradocinnus St Laurent, Mielke, & Kawahara, gen.n., and the genus Gonogramma stat. rev. is revalidated to include many species previously placed in Cicinnus sensu lato. With these changes, Cicinnus can now be considered monophyletic. Thirty-three species are transferred to Gonogramma from Cicinnus sensu lato.This published work has been registered on Zoobank, http://zoobank.org/urn:lsid: zoobank.

show abstract

Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

Cited by 66 publications

References 84 publications

A deeper meaning for shallow‐level phylogenomic studies: nested anchored hybrid enrichment offers great promise for resolving the tiger moth tree of life (Lepidoptera: Erebidae: Arctiinae)

A deeper meaning for shallow‐level phylogenomic studies: nested anchored hybrid enrichment offers great promise for resolving the tiger moth tree of life (Lepidoptera: Erebidae: Arctiinae)

The complete mitochondrial genome of Rotunda rotundapex (Miyata & Kishida, 1990) (Lepidoptera: Bombycidae)

A new target capture phylogeny elucidates the systematics and evolution of wing coupling in sack‐bearer moths

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