DOI: 10.5061/dryad.c2fqz617s
title: Alignement and phylogenetic tree of 106 Lepidoptera

description: We used both published and de novo sequences from one
 mitochondrial gene and seven nuclear genes, representing a
 total length of 7433 bp to infer a molecular phylogeny for 106
 lepidopteran species. Müllerian mimicry is a positive interspecific
 interaction, whereby co-occurring defended prey species share a common
 aposematic signal. In Lepidoptera, aposematic species typically harbour
 conspicuous opaque wing colour patterns with convergent optical properties
 among co-mimetic species. Surprisingly, some aposematic mimetic species
 have partially transparent wings, raising the questions of whether optical
 properties of transparent patches are also convergent, and of how
 transparency is achieved. Here we conducted a comparative study of wing
 optics, micro and nanostructures in neotropical mimetic clearwing
 Lepidoptera, using spectrophotometry and microscopy imaging. We show that
 transparency, as perceived by predators, is convergent among co-mimics.
 Underlying micro- and nanostructures are also convergent despite a large
 structural diversity. We reveal that while transparency is primarily
 produced by microstructure modifications, nanostructures largely influence
 light transmission, maybe enabling additional fine-tuning in transmission
 properties. This study shows that transparency might not only enable
 camouflage but can also be part of aposematic signals.
description: We used 106 Lepidoptera
 species listed at the end of this section. We used published sequences from
 eight gene regions to infer a molecular phylogeny: the mitochondrial
 cytochrome oxidase c subunit 1 (COI) gene and the nuclear genes
 carbamyl-phosphate synthase II (CAD), malate dehydrogenase (MDH),
 elongation factor 1 alpha (EF-1a), tektin (TKT), ribosomal protein S5
 (RpS5), isocitrate dehydrogenase (IDH) and Glyceraldehyde 3-phosphate
 dehydrogenase (GAPDH), which represent a total length of 7433 bp. To
 improve phylogeny topology, we added 35 species representing 8 additional
 families to the dataset. When no sequence was available for a particular
 species on Genbank, we sequenced <i>de novo</i> the COI, CAD
 and MDH genes of that species. We have missing data for some species, but
 we had at least the COI sequence for each species considered.
 For
 <i>de novo</i> sequencing, DNA was extracted from butterfly
 legs with a DNeasy® Blood & Tissue Kit (QIAGEN laboratory) and
 targeted genes were amplified with PCR conditions adapted from Wahlberg
 and Wheat (2008). COI, CAD and MDH were amplified in two pieces with the
 primers described in Wahlberg and Wheat (2008). PCR were performed in a
 volume of 25 µL with 2 to 4 µL of genomic DNA, 1 µL of each primer at a
 concentration of 100 pmol/µL, 1 µL of nucleotides at a concentration of 2
 mM, 2.5 µL of DreamTaq buffer, 0.125 µL of DreamTaq polymerase. The
 elongation phase was reduced to 70 seconds. For CAD and MDH, the annealing
 temperature was reduced to 50°C for most specimens. Eurofins Genomics
 sequenced the PCR products with Sanger method. Sequences were aligned with
 CodonCodeAligner (version 3.7.1.1, CodonCode Corporation,
 http://www.codoncode.com/) and concatenated with PhyUtility (version 2.2,
 Smith and Dunn 2008). The dataset was then partitioned by gene and codon
 positions and the best models of substitution were selected over all
 models implemented in BEAST, using the ‘greedy’ algorithm and linked rates
 implemented in Partition Finder 1.0.1 (Lanfear et al. 2012). We performed
 a Bayesian inference of the phylogeny using BEAST 1.8.3 (Baele et al.,
 n.d.) on the Cipres server (Miller et al., 2010). We constrained some
 clades to be monophyletic (notably Ithomiini, Danainae, Nymphalidae,
 Riodinidae, Pieridae, Papilionidae, Erebidae, Notodontidae, Geometridae,
 Noctuoidae, Papilionoidae) and we calibrated the crown age and divergence
 time of some groups, following Kawahara et al. (2019). Four independent
 analyses were run for 50 million generations, with one Monte Carlo Markov
 chain each and a sampling frequency of one out of 50 000 generations
 (resulting in 1000 posterior trees). After checking for convergence of the
 two best analyses, the posterior distributions of these two runs were
 combined (using logCombiner 1.8.2, Drummond and Rambaut 2007), with a
 burnin of 10%. The maximum clade credibility (MCC) tree with median node
 ages was computed using TreeAnnotator 1.8.2. Species not represented in
 our dataset were then pruned from the tree. The MCC tree was used for
 subsequent phylogenetic analyses. List of species : 
 
 Genus species ssp Tip label in MCCtree Bombyx  mori   Bombyx_mori Cyclotorna sp.   Cyclotorna_sp Drepana curvatula   Drepana_curvulata Epicopeia hainesii   Epicopeia_hainesii Calodesma albiapex   Calodesma_albiapex Dysschema leucophaea   Dysschema_leucophaea Dysschema sp.   ME15_88_DYSSSP1 Episcea extravagans   Episcea_extravagans Euchlaenidia transcisa   Euchlaenidia_transcisa Hyalurga egeon   ME16_67_HYALEGE Hyalurga fenestrata   Hyalurga_fenestrata Hyalurga grandis   TR17_17_HYALGRA Hypocrita confluens   Hypocrita_confluens Hypocrita strigifera   ME16_58_HYPOSTRI Hypocrita strigifera   ME16_44_HYPOSTR Hypocrita strigifera   ME16_64_HYPOSTR Notophyson tiresias   ME16_63_NOTOTIR Notophyson tiresias   TR17_9_NOTOTIRE Notophyson tiresias   TR17_8_NOTOTIR Notophyson tiresias   TR17_4_NOTOTIRE Pseudophaloe troetschi   Pseudophaloe_troetschi Sthenognatha gentilis   Sthenognatha_gentilis Metastatia pyrrhorhoea   Metastatia_pyrrhorhoea       ME16_16_METASP2       TR17_13_CHTEN2       11_996_CHTEN1   Arctiinae1   TR17_7_MOTH1   Arctiinae2   11_1065_MOTH2   Arctiinae3   ME16_15_METASP1       ME16_91_MOTH3 Inurois fumosa   Inurois_fumosa Biston panterinaria   Biston_panterinaria Plutodes costatus   Plutodes_costatus   Geo1   11_1002_GEO1   Geo2   ME16_100_GE02 Hagnagora mortipax   Hagnagora_mortipax Operophtera brumata   Operophtera_brumata   Geo9   TR17_16_GEO9   Geo12   ME16_105_GEO1   Geo3   11_1879_GEO3       ME16_87_GEO1       11_1001_GEO2 Tolype velleda   Tolype_velleda Phalera bucephala   Phalera_bucephala   Noto1   ME16_92_GEO4   Noto2   TR17_1_GEO11       11_994_GEO5       11_1064_GEO6       TR17_15_GEO4 Vila azeca   LS11_2414_ERES1 Vila emilia   ME16_56_ERESCLI Lycorea ilione   Lycorea_ilione Callithomia lenea zelie Callithomia_lenea_zelie Godyris hewitsoni   Godyris_hewitsoni Godyris panthyale panthyale Godyris_panthyale_panthyale Heterosais nephele   Heterosais_nephele_nephele Hyalenna paradoxa praestigiosa Hyalenna_paradoxa_praestigiosa Hypomenitis enigma pseudortygia Hypomenitis_enigma Hypomenitis lydia   Hypomenitis_lydia Hypomenitis oneidodes   Hypomenitis_oneidodes Hypomenitis ortygia ortygia Hypomenitis_ortygia_ortygia Hypomenitis theudelinda zalmunna Hypomenitis_theudilinda_zalmunna Ithomia agnosia agnosia Ithomia_agnosia_agnosia Ithomia amarilla   Ithomia_amarilla Ithomia avella epona Ithomia_avella Mcclungia cymo   Mcclungia_cymo Megoleria orestilla orestilla Megoleria_orestilla Methona curvifascia   Methona_curvifascia Napeogenes harbona   Napeogenes_harbona Napeogenes inachia   Napeogenes_inachia Napeogenes larilla   Napeogenes_larilla Napeogenes sylphis corena Napeogenes_sylphis_corena Oleria athalina banjana Oleria_athalina_banjana Oleria onega   Oleria_onega Oleria sexmaculata sexmaculata Oleria_sexmaculata_sexmaculata Ollantaya olerioides   Oleria_olerioides Pseudoscada florula aureola Pseudoscada_florula_aureola Pseudoscada timna utilla Pseudoscada_timna_utilla Pteronymia oneida oneida Pteronymia_oneida_oneida Veladyris pardalis   Veladyris_pardalis Eresia nauplius plagiata Eresia_nauplius_plagiata   Nymp1   ME16_46_NYMP1 Papilio glaucus   Papilio_glaucus Parides hahneli   Parides_iphidamas Dismorphia teresa   TR17_18_DISMSP1 Dismorphia theucharila leucone TR17_14_DISMTHEU Dismorphia theucharila orange tip TR17_6_DISMTHEU Dismorphia theucharila yolanda LS11_2240_DISTH Dismorphia zathoe   Dismorphia_zathoe Moschoneura pinthous   TR17_3_MOSCPINT Moschoneura pinthous   Moschoneura_pinthous_GB Patia orise   Patia_orise Itaballia demophile   Itaballia_demophile Itaballia pandosia   ME16_62_ITAPAND Itaballia pandosia   Itaballia_pandosia Perrhybris ? Pier1   MECN_140_PIER1 Pyralis farinalis   Pyralis_farinalis Ithomiola callixena   Ithomiola_callixena Ithomiola floralis orange tip 11-1116_ITHOFLO Ithomiola floralis white-band 11_1127_ITHOFLO Stalachtis euterpe   TR17_5_STALEUT Stalachtis euterpe   Stalachtis_euterpe_GB   Riodin2   TR17_12_GEO7   Riodin1   MECN_133_BUT1   Riodin3   TR17_11_GEO8 Aglia tau   Aglia_tau