Lepidoptera_v2

Phylogenomics backbone of 115 tips, built from transcriptomes mined from NCBI (mostly produced by the 1KITE project; Misof et al., 2014, Science 346, 763-767). Analyzed 101 published sourcetrees, from 54 of these (listed below), backbone extended through 113 grafts (Chesters et al. 2023, Molecular Ecology Resources 23, 1556-1573). Extended backbone then integrated with multigene alignment (Chesters 2020, Systematic Entomology 45, 540-551); complete for COI mined from BOLD 
(Ratnasingham and Hebert, 2007, Molecular Ecology Notes 7, 355-364) and with sequences of 16 additional markers mined from NCBI (profiled on Regier et al. 2013). Synthesis result is totally 11001 species including single outgroup Micropterna_lateralis.

Subtrees grafted from the following:
Alipanah et al. (2011) Phylogenetic relationships in the tribe Oxyptilini (Lepidoptera, Pterophoridae, Pterophorinae) based on morphological data of adults. Zoological Journal of the Linnean Society, 163, 484–547.
Basso et al. (2017) A total evidence phylogeny for the processionary moths of the genus Thaumetopoea (Lepidoptera: Notodontidae: Thaumetopoeinae). Cladistics, 33, 557-573
Boyle et al. (2015) Phylogeny of the Aphnaeinae: myrmecophilous African butterflies with carnivorous and herbivorous life histories. Syst Entomol, 40, 169-182.
Cognato et al. (2022) Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex. Cladistics, 0, 1–17
Doorenweerd et al. (2017) Phylogeny, classification and divergence times of pygmy leaf-mining moths (Lepidoptera: Nepticulidae): the earliest lepidopteran radiation on Angiosperms?. Syst Entomol, 42, 267-287.
Earl et al. (2021) Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America. iScience 24, 102239.
Hamilton et al. (2019) Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives. BMC Evol Biol, 19, 182.
Hardy and Otto (2014) Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses. Proc. R. Soc. B., 281, 20132960.
Heikkilä et al. (2014) Morphology reinforces proposed molecular phylogenetic affinities: a revised classification for Gelechioidea (Lepidoptera). Cladistics, 30, 563-589.
Heikkilä et al. (2015) Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera). BMC Evol Biol, 15, 260.
Hu et al. (2023) Molecular phylogeny, divergence time, biogeography and trends in host plant usage in the agriculturally important tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Olethreutinae). Cladistics, https://doi.org/10.1111/cla.12543
Imada et al. (2011) Allopatric distribution and diversification without niche shift in a bryophyte-feeding basal moth lineage (Lepidoptera: Micropterigidae). Proceedings. Biological Sciences, 278, 3026-3033.
Jiang et al. (2017) A molecular phylogeny of the Palaearctic and Oriental members of the tribe Boarmiini (Lepidoptera : Geometridae : Ennominae). Invertebrate Systematics, 31, 427–441.
Karsholt et al. (2013) A molecular analysis of the Gelechiidae (Lepidoptera, Gelechioidea) with an interpretative grouping of its taxa. Systematic Entomology, 38, 334-348
Kaliszewska et al. (2015) When caterpillars attack: Biogeography and life history evolution of the Miletinae (Lepidoptera: Lycaenidae). Evolution, 69, 571-588.
Kawahara et al. (2009) Phylogeny and Biogeography of Hawkmoths (Lepidoptera: Sphingidae): Evidence from Five Nuclear Genes. PLoS ONE, 4, e5719.
Kawahara et al. (2017) A molecular phylogeny and revised higher-level classification for the leaf-mining moth family Gracillariidae and its implications for larval host-use evolution. Syst Entomol, 42, 60-81.
Kawahara et al. (2023) A global phylogeny of butterflies reveals their evolutionary history, ancestral hosts and biogeographic origins. Nat Ecol Evol, https://doi.org/10.1038/s41559-023-02041-9
Keegan et al. (2021) Toward a Stable Global Noctuidae (Lepidoptera) Taxonomy. Insect Systematics and Diversity, 5, 1.
Kergoat et al. (2021) A novel reference dated phylogeny for the genus Spodoptera Guenée (Lepidoptera: Noctuidae: Noctuinae): new insights into the evolution of a pest-rich genus. Mol Phylogenet Evol., 161, 107161.
Kodandaramaiah et al. (2010) Phylogenetics and biogeography of a spectacular Old World radiation of butterflies: the subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrini). BMC Evol Biol, 10, 172.
Léger et al. (2020) Refining the phylogeny of Crambidae with complete sampling of subfamilies (Lepidoptera, Pyraloidea). Zool. Scr., 50, 84–99.
Lin et al. (2019) Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae). Ecol Evol., 9, 9827– 9840.
Mally et al. (2019) The phylogenetic systematics of Spilomelinae and Pyraustinae (Lepidoptera: Pyraloidea: Crambidae) inferred from DNA and morphology.Arthropod Systematics and Phylogeny. 77(1): 141–204.
Meng et al. (2022) The first complete mitochondrial genome of the hawkmoth Marumba saishiuana (Lepidoptera: Sphingidae) and insights into its phylogenetic position. Mitochondrial DNA Part B, 7, 1525-1527.
Moraes and Duarte (2014) Phylogeny of Neotropical Castniinae (Lepidoptera: Cossoidea: Castniidae): testing the hypothesis of the mimics as a monophyletic group and implications for the arrangement of the genera. Zoological Journal of the Linnean Society, 170, 362–399.
Murillo-Ramos et al. (2021) Molecular phylogeny, classification, biogeography and diversification patterns of a diverse group of moths (Geometridae: Boarmiini). Mol Phylogenet Evol., 162, 107198.
Nazari et al. (2007) Phylogeny, historical biogeography, and taxonomic ranking of Parnassiinae (Lepidoptera, Papilionidae) based on morphology and seven genes. Molecular Phylogenetics and Evolution, 42, 131-156.
Pinna et al. (2021) Mimicry can drive convergence in structural and light transmission features of transparent wings in Lepidoptera. eLife, 10, e69080.
Ponomarenko (2006) Subfamily Dichomeridinae (Lepidoptera, Gelechiidae): Phylogeny, classification, and position in the system of gelechiid moths. Entmol. Rev. 86, 449–456.
Regier et al. (2008) Phylogenetic relationships of wild silkmoths (Lepidoptera: Saturniidae) inferred from four protein-coding nuclear genes. Systematic Entomology, 33, 219-228.
Regier et al. (2012) A Molecular Phylogeny for the Leaf-Roller Moths (Lepidoptera: Tortricidae) and Its Implications for Classification and Life History Evolution. PLoS ONE, 7, e35574.
Regier et al. (2013) A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLoS ONE, 8, e58568.
Regier et al. (2015) A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution. Syst Entomol, 40, 671-704.
Regier et al. (2015) A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia. Syst Entomol, 40, 409-432. 
Robinson and Tuck (1997) Phylogeny and composition of the Hieroxestinae (Lepidoptera: Tineidae). Systematic Entomology, 22, 363-396.
Roe et al. (2014) Phycitinae Phylogeny Based on Two Genes, with Implications for Morphological Trait Evolution and Heinrich's Tribal Classification (Lepidoptera: Pyralidae). The Journal of the Lepidopterists' Society, 69, 157-173.
Rönkä et al. (2016) Putting Parasemia in its phylogenetic place: a molecular analysis of the subtribe Arctiina (Lepidoptera). Syst Entomol, 41, 844-853.
Seifert et al. (2022) Dietary specialization mirrors Rapoport’s rule in European geometrid moths, Dryad, Dataset, https://doi.org/10.5061/dryad.k3j9kd58f.
Sihvonen et al. (2011) Comprehensive molecular sampling yields a robust phylogeny for geometrid moths (Lepidoptera: Geometridae). PLoS One, 6, e20356.
Sihvonen et al. (2020) Molecular phylogeny of Sterrhinae moths (Lepidoptera: Geometridae): towards a global classification. Syst Entomol, 45, 606-634.
Sohn et al. (2013) A Molecular Phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and Its Implications for Classification, Biogeography and the Evolution of Host Plant Use. PLoS ONE, 8, e55066.
St Laurent et al. (2018) Museum specimens provide phylogenomic data to resolve relationships of sack-bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae). Systematic Entomology, 43, 729-761.
St Laurent et al. (2023) Phylogenetic systematics, diversification, and biogeography of Cerurinae (Lepidoptera: Notodontidae) and a description of a new genus. Insect Systematics and Diversity, 7, 1–25.
Talavera et al. (2013) Establishing criteria for higher-level classification using molecular data: the systematics of Polyommatus blue butterflies (Lepidoptera, Lycaenidae). Cladistics, 29, 166-192.
Valencia-Montoya et al. (2021) Evolutionary trade-offs between male secondary sexual traits revealed by a phylogeny of the hyperdiverse tribe Eumaeini (Lepidoptera: Lycaenidae). Proc Biol Sci., 288, 20202512. 
Wang et al. (2015) Molecular phylogeny of Lymantriinae (Lepidoptera, Noctuoidea, Erebidae) inferred from eight gene regions. Cladistics, 31, 579-592.
Wang and Li (2020) Phylogeny of the superfamily Gelechioidea (Lepidoptera: Obtectomera), with an exploratory application on geometric morphometrics. Zool Scr., 49, 307–328.
Wiemers et al. (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124.
Wu et al. (2010) A pilot study on the molecular phylogeny of Drepanoidea (Insecta: Lepidoptera) inferred from the nuclear gene EF-1α and the mitochondrial gene COI. Bulletin of Entomological Research, 100, 207-216.
Yang et al. (2021) The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance. BMC Genomics, 22, 755.
Zaspel et al. (2014) Phylogeny and Evolution of Pharmacophagy in Tiger Moths (Lepidoptera: Erebidae: Arctiinae). PLoS ONE, 9, e101975.
Zenker et al. (2017) Systematics and origin of moths in the subfamily Arctiinae (Lepidoptera, Erebidae) in the Neotropical region. Zoologica Scripta, 46, 348–362.
Zwick et al. (2011) Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera). Systematic Entomology, 36, 31-43.