Molecular Phylogenetics and Evolution 42 (2007) 756–775 www.elsevier.com/locate/ympev 1055-7903/$ - see front matter Published by Elsevier Inc. doi:10.1016/j.ympev.2006.12.018 Phylogenetic relationships within the leaf-mining Xies (Diptera: Agromyzidae) inferred from sequence data from multiple genes Sonja J. ScheVer a,¤ , Isaac S. Winkler b , Brian M. Wiegmann c a Systematic Entomology Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705, USA b Department of Entomology, University of Maryland, College Park, MD 20740, USA c Department of Entomology, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC 27695, USA Received 9 January 2006; revised 29 November 2006; accepted 18 December 2006 Available online 31 December 2006 Abstract The leaf-mining Xies (Diptera: Agromyzidae) are a diverse group whose larvae feed internally in leaves, stems, Xowers, seeds, and roots of a wide variety of plant hosts. The systematics of agromyzids has remained poorly known due to their small size and morphological homogeneity. We investigated the phylogenetic relationships among genera within the Agromyzidae using parsimony and Bayesian anal- yses of 2965 bp of DNA sequence data from the mitochondrial COI gene, the nuclear ribosomal 28S gene, and the single copy nuclear CAD gene. We included 86 species in 21 genera, including all but a few small genera, and spanning the diversity within the family. The results from parsimony and Bayesian analyses were largely similar, with major groupings of genera in common. SpeciWcally, both analy- ses recovered a monophyletic Phytomyzinae and a monophyletic Agromyzinae. Within the subfamilies, genera found to be monophyletic given our sampling include Agromyza, Amauromyza, Calycomyza, Cerodontha, Liriomyza, Melanagromyza, Metopomyza, Nemorimyza, Phytobia, and Pseudonapomyza. Several genera were found to be polyphyletic or paraphyletic including Aulagromyza, Chromatomyia, Phytoliriomyza, Phytomyza, and Ophiomyia. We evaluate our Wndings and discuss host-use evolution in light of current agromyzid taxon- omy and two recent hypotheses of relationships based on morphological data. Published by Elsevier Inc. Keywords: Phytophagy; Acalypterate; Opomyzoidea; Host-use evolution; Endophagy 1. Introduction The leaf-mining Xies (Diptera: Agromyzidae) are small Xies having phytophagous larvae that feed within leaves, stems, roots, Xowers, or seeds. Agromyzids attack a broad diversity of plant hosts, including more than 140 plant fam- ilies representing all major terrestrial plant groups, with the exception of mosses and most gymnosperms (Spencer, 1990; Benavent-Corai et al., 2005). These Xies are distrib- uted worldwide with their greatest diversity in northern temperate regions (Spencer, 1977). Despite the broad diet breadth exhibited by agromyzids as a group, most agro- myzid species are remarkably specialized, feeding on only one or a few closely related plant species (Spencer, 1990; ScheVer and Wiegmann, 2000). Host-use evolution within the Agromyzidae is a subject of great interest because diversiWcation in this group appears to be largely associated with host shifts and dietary specialization (Spencer, 1990; Kulp, 1968; ScheVer and Wiegmann, 2000). However, mod- ern phylogenetic analyses necessary for elaborating the his- tory of agromyzid/host associations have only recently been applied to studies of these Xies (ScheVer and Wieg- mann, 2000; Dempewolf, 2001). Despite their near ubiquity and interesting larval habits, the systematics of agromyzids has remained rather poorly understood due to their small size and morphological homogeneity. Species identiWcation generally requires dis- section of the male genitalia, and it is diYcult to identify some female specimens even to genus using only morpho- logical characters. Currently, the Agromyzidae contains * Corresponding author. Fax: +1 301 504 6482. E-mail address: sscheVe@sel.barc.usda.gov (S.J. ScheVer).