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      A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies

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          Abstract

          Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of “slender-bodied Oenochrominae” that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively.

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          Genomic outposts serve the phylogenomic pioneers: designing novel nuclear markers for genomic DNA extractions of lepidoptera.

          Increasing the number of characters used in phylogenetic studies is the next crucial step towards generating robust and stable phylogenetic hypotheses - i.e., strongly supported and consistent across reconstruction method. Here we describe a genomic approach to finding new protein-coding genes for systematics in nonmodel taxa, which can be PCR amplified from standard, slightly degraded genomic DNA extracts. We test this approach on Lepidoptera, searching the draft genomic sequence of the silk moth Bombyx mori, for exons > 500 bp in length, removing annotated gene families, and compared remaining exons with butterfly EST databases to identify conserved regions for primer design. These primers were tested on a set of 65 taxa primarily in the butterfly family Nymphalidae. We were able to identify and amplify six previously unused gene regions (Arginine Kinase, GAPDH, IDH, MDH, RpS2, and RpS5) and two rarely used gene regions (CAD and DDC) that when added to the three traditional gene regions (COI, EF-1alpha and wingless) gave a data set of 8114 bp. Phylogenetic robustness and stability increased with increasing numbers of genes. Smaller taxanomic subsets were also robust when using the full gene data set. The full 11-gene data set was robust and stable across reconstruction methods, recovering the major lineages and strongly supporting relationships within them. Our methods and insights should be applicable to taxonomic groups having a single genomic reference species and several EST databases from taxa that diverged less than 100 million years ago.
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            A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

            Background Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies. Methodology / Principal Findings 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity. Conclusions / Significance Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.
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              Order Lepidoptera Linnaeus, 1758. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness

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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                27 August 2019
                2019
                : 7
                : e7386
                Affiliations
                [1 ]Grupo Biología Evolutiva, Department of Biology, Universidad de Sucre , Sincelejo, Sucre, Colombia
                [2 ]Systematic Biology Group, Department of Biology, Lund University , Lund, Sweden
                [3 ]Institut für Zoologie und Evolutionsbiologie, Phyletisches Museum , Jena, Germany
                [4 ]Finnish Museum of Natural History, University of Helsinki , Helsinki, Finland
                [5 ]Staatliche Naturwissenschaftliche Sammlungen Bayerns , München, Germany
                [6 ]Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu , Tartu, Estonia
                [7 ]Estonian University of Life Sciences, Institute of Agricultural and Environmental Sciences , Tartu, Estonia
                [8 ]Natural History Museum, University of Tartu , Tartu, Estonia
                [9 ]LepsocAfrica , Magaliesburg, South Africa
                [10 ]Berghoffsweg 5 , Jena, Germany
                Author information
                http://orcid.org/0000-0003-2237-9325
                http://orcid.org/0000-0003-1029-4236
                http://orcid.org/0000-0002-1259-3363
                Article
                7386
                10.7717/peerj.7386
                6716565
                31523494
                0f50fd65-0dc8-4a57-b33a-81d179d128bf
                © 2019 Murillo-Ramos et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 6 February 2019
                : 1 July 2019
                Funding
                Funded by: Academy of Finland
                Award ID: 265511
                Funded by: Swedish Research Council
                Award ID: 2015-04441
                Funded by: Colciencias
                Award ID: 756-2016
                Funded by: Universidad de Sucre, Colombia
                Funded by: European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 642241 (BIG4)
                Funded by: Estonian Ministry of Education and Research
                Award ID: IUT20-33
                Funded by: Funding for fieldwork in Peru
                Award ID: DFG grant Br 2280/6-1) and for visits to the NHM: SYNTHESYS grant GB TAF1048 and 6817
                Niklas Wahlberg received funding from the Academy of Finland (Grant No. 265511) and the Swedish Research Council (Grant No. 2015-04441). Leidys Murillo-Ramos received funding from Colciencias, 756-2016 and Universidad de Sucre, Colombia. Hamid Reza Ghanavi was funded from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 642241 (BIG4). Sille Holm, Erki Õunap, Andro Truuverk and Toomas Tammaru were supported by institutional research funding IUT (IUT20-33) of the Estonian Ministry of Education and Research. Gunnar Brehm received funding for fieldwork in Peru (DFG grant Br 2280/6-1) and for visits to the NHM (SYNTHESYS grant GB TAF1048 and 6817). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Entomology
                Evolutionary Studies
                Taxonomy
                Zoology

                new subfamily,phylogeny,moths,epidesmiinae,taxonomy,loopers
                new subfamily, phylogeny, moths, epidesmiinae, taxonomy, loopers

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