Open Access Highly Accessed Research article

Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study

Jerome C Regier1, Andreas Zwick1, Michael P Cummings3, Akito Y Kawahara2, Soowon Cho24, Susan Weller5, Amanda Roe56, Joaquin Baixeras7, John W Brown8, Cynthia Parr9, Donald R Davis10, Marc Epstein11, Winifred Hallwachs12, Axel Hausmann13, Daniel H Janzen12, Ian J Kitching14, M Alma Solis8, Shen-Horn Yen15, Adam L Bazinet3 and Charles Mitter2*

Author Affiliations

1 Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA

2 Department of Entomology, University of Maryland, College Park, Maryland 20742, USA

3 Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA

4 Department of Plant Medicine, Chungbuk National University, Cheongju 361-763, Korea

5 Department of Entomology, University of Minnesota, St. Paul, Minnesota 55455, USA

6 Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada

7 Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Apartat de correus 2085, 46071 Valencia, Spain

8 Systematic Entomology Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, USA

9 Encyclopedia of Life, Smithsonian Institution, Washington, D.C. 20013-7012, USA

10 Department of Entomology, Smithsonian Institution, Washington, D.C. 20013-7012, USA

11 Plant Pest Diagnostics Branch, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, California 95832-1448, USA

12 Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA

13 Bavarian State Collection of Zoology, Münchhausenstrasse 21, D-81247 München, Germany

14 Department of Entomology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK

15 Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan

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BMC Evolutionary Biology 2009, 9:280  doi:10.1186/1471-2148-9-280

Published: 2 December 2009

Additional files

Additional file 1:

Specimen information and Genbank numbers. For each specimen sequenced we list superfamily, family, genus and species name, code name, collection locality, GenBank accession numbers for all sequences, and missing and partial sequences. Numbers after the superfamily name indicate number of families sampled/number of families total. An L in parentheses after the species name means the specimen sequenced was a larva; a P in parentheses means it was a pupa. All other specimens were adults. An 'X' in the Genbank number table means that no sequence was obtained for that gene in that taxon.

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Additional file 2:

Data matrix. The final sequence alignment, excluding alignment-ambiguous regions, is presented in sequential Nexus format. The file includes charsets for different genes, nucleotides and LR/noLR. Taxon names are the code names given in Additional file 1.

Format: TXT Size: 813KB Download file

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Additional file 3:

Single-gene bootstrap analyses. We present a table of bootstrap values obtained from a separate analysis of all nucleotides for each gene, for all nodes on the all-nt ML tree plus all other nodes supported by BP of 50% or greater by any gene. We summarize the evidence on bootstrap-supported groupings that conflict with those found for other individual genes, with the all-gene result, and with conventional understanding of relationships, and examine the two instances of strong conflict.

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Additional file 5:

Nt123 Bayesian analysis, partitioned noLRall2 + nt2 vs. LR + nt3. Majority rule consensus of trees sampled from partitioned Bayesian analysis of nt123 with partitions noLRall2 + nt2 versus LRall2 + nt3. Two runs, 10106 trees sampled from each, with standard deviation of split frequencies < 0.01.

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Additional file 6:

123-taxon ML tree & bootstrap for noLRall2 + nt2. Part A: noLRall2 + nt2 best ML tree found in 10,000 replicate GARLI searches, GTR + G + I model, phylogram format. Part B: noLR2all + nt2 bootstrap majority rule consensus tree, generated in PAUP, from 1000 GARLI ML bootstrap replicates, GTR + G + I model.

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Additional file 7:

123-taxon ML tree & bootstrap consensus tree for nt12. Part A: nt12 best ML tree found in 10,000 replicate GARLI searches, GTR + G + I model, phylogram format. Part B: nt12 bootstrap majority rule consensus tree, generated in PAUP, from 1000 GARLI ML bootstrap replicates, GTR + G + I model.

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Additional file 8:

Effects of compositional heterogeneity on inferred relationships, compared between nt3 and noLRall2 + nt2. Part A. Analysis of variable nt3 characters. Part B. Analysis of noLRall2 + nt2 characters.

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Additional file 9:

123-taxon ML tree & bootstrap consensus tree for nt3. Part A. nt3 best ML tree found in 10,000 replicate GARLI searches, GTR + G + I model, phylogram format. Part B. nt3, bootstrap 50% majority rule consensus tree, generated in PAUP, from 1000 GARLI ML bootstrap replicates, GTR + G + I model.

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Additional file 4:

123-taxon ML tree & bootstrap consensus tree for nt123. Part A: nt123, best ML tree found in 10,000 replicate GARLI searches, GTR + G + I model, phylogram format. Part B: nt123, majority rule consensus tree from 1000 GARLI ML bootstrap replicates, generated in PAUP.

Format: PDF Size: 2.4MB Download file

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