Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0-2000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors. DNA barcoding -the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species -was added to the taxonomic identification process in 2003.

Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]. Most data were generated with a new anchored hybrid enrichment (AHE) [5] gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g., [6]) informative loci, enabling direct comparison and future dataset merging with previous studies. Butterflies originated around 119 million years ago (mya) in the late Cretaceous, but most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses support swallowtails (Papilionidae) as sister to all other butterflies, followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae) as sister to the remainder, indicating a secondary reversal from diurnality to nocturnality. The whites (Pieridae) were strongly supported as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks (Lycaenidae and Riodinidae). Ant association independently evolved once in Lycaenidae and twice in Riodinidae. This study overturns prior notions of the taxon's evolutionary history, as many long-recognized subfamilies and tribes are para- or polyphyletic. It also provides a much-needed backbone for a revised classification of butterflies and for future comparative studies including genome evolution and ecology.

DNA 'barcoding' relies on a short fragment of mitochondrial DNA to infer identification of specimens. The method depends on genetic diversity being markedly lower within than between species. Closely related species are most likely to share genetic variation in communities where speciation rates are rapid and effective population sizes are large, such that coalescence times are long. We assessed the applicability of DNA barcoding (here the 5' half of the cytochrome c oxidase I) to a diverse community of butterflies from the upper Amazon, using a group with a well-established morphological taxonomy to serve as a reference. Only 77% of species could be accurately identified using the barcode data, a figure that dropped to 68% in species represented in the analyses by more than one geographical race and at least one congener. The use of additional mitochondrial sequence data hardly improved species identification, while a fragment of a nuclear gene resolved issues in some of the problematic species. We acknowledge the utility of barcodes when morphological characters are ambiguous or unknown, but we also recommend the addition of nuclear sequence data, and caution that species-level identification rates might be lower in the most diverse habitats of our planet.

Ecological communities are structured in part by evolutionary interactions among their members. A number of recent studies incorporating phylogenetics into community ecology have upheld the paradigm that competition drives ecological divergence among species of the same guild. However, the role of other interspecific interactions, in particular positive interactions such as mutualism, remains poorly explored. We characterized the ecological niche and inferred phylogenetic relationships among members of a diverse community of neotropical Müllerian mimetic butterflies. Müllerian mimicry is one of the best studied examples of mutualism, in which unpalatable species converge in wing pattern locally to advertize their toxicity to predators. We provide evidence that mutualistic interactions can drive convergence along multiple ecological axes, outweighing both phylogeny and competition in shaping community structure. Our findings imply that ecological communities are adaptively assembled to a much greater degree than commonly suspected. In addition, our results show that phenotype and ecology are strongly linked and support the idea that mimicry can cause ecological speciation through multiple cascading effects on species' biology.

Global biodiversity peaks in the tropical forests of the Andes, a striking geological feature that has likely been instrumental in generating biodiversity by providing opportunities for both vicariant and ecological speciation. However, the role of these mountains in the diversification of insects, which dominate biodiversity, has been poorly explored using phylogenetic methods. Here we study the role of the Andes in the evolution of a diverse Neotropical insect group, the clearwing butterflies. We used dated species-level phylogenies to investigate the time course of speciation and to infer ancestral elevation ranges for two diverse genera. We show that both genera likely originated at middle elevations in the Andes in the Middle Miocene, contrasting with most published results in vertebrates that point to a lowland origin. Although we detected a signature of vicariance caused by the uplift of the Andes at the Miocene-Pliocene boundary, most sister species were parapatric without any obvious vicariant barrier. Combined with an overall decelerating speciation rate, these results suggest an important role for ecological speciation and adaptive radiation, rather than simple vicariance.

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We present a higher-level phylogenetic hypothesis for the diverse neotropical butterfly subfamily Ithomiinae, inferred from one of the largest non-molecular Lepidoptera data sets to date, including 106 species (105 ingroup) and 353 characters (306 informative) from adult and immature stage morphology and ecology. Initial analyses resulted in 1716 most parsimonious trees, which were reduced to a single tree after successive approximations character weighting. The inferred phylogeny was broadly consistent with other past and current work. Although some deeper relationships are uncertain, tribal-level clades were generally strongly supported, with two changes required to existing classification. The tribe Melinaeini is polyphyletic and Athesis + Patricia require a new tribe. Methona should be removed from Mechanitini into the restored tribe Methonini. Dircennini was paraphyletic in analyses of all data but monophyletic based on adult morphology alone, and its status remains to be confirmed. Hypothyris, Episcada, Godyris, Hypoleria and Greta are paraphyletic. A simulation analysis showed that relatively basal branches tended to have higher partitioned Bremer support for immature stage characters. Larval hostplant records were optimized on to a reduced, generic-level phylogeny and indicate that ithomiines moved from Apocynaceae to Solanaceae twice, or that Tithoreini re-colonized Apocynaceae after a basal shift to Solanaceae. Ithomiine clades have specialized on particular plant clades suggesting repeated colonization of novel hostplant niches consistent with adaptive radiation. The shift to Solanum, comprising 70% of neotropical Solanaceae, occurs at the base of a clade containing 89% of all ithomiines, and is interpreted as the major event in the evolution of ithomiine larval hostplant relationships.

We compiled a large database of 58 059 point locality records for 70 species and 434 subspecies of heliconiine butterflies and used these data to test evolutionary hypotheses for their diversification. To study geographical patterns of diversity and contact zones, we mapped: (1) species richness; (2) mean molecular phylogenetic terminal branch length; (3) subspecies richness and the proportion of specimens that were subspecific hybrids, and (4) museum sampling effort. Heliconiine species richness is high throughout the Amazon region and peaks near the equator in the foothills and middle elevations of the eastern Andes. Mean phylogenetic terminal branch length is lowest in the eastern Andes and tends to be low in species-rich areas. By contrast, areas of high subspecies richness, where subspecies overlap in range and/or hybridize, are concentrated along the course of the Amazon River, with the eastern Andes slopes and foothills relatively depauperate in terms of local intraspecific phenotypic diversity. Spatial gradients in heliconiine species richness in the Neotropics are consistent with the hypothesis that species richness gradients are driven at least in part by variation in speciation and/or extinction rates, resulting in observed gradients in mean phylogenetic branch length, rather than via evolutionary age or niche conservatism alone. The data obtained in the present study, coupled with individual case studies of recently evolved Heliconius species, suggest that the radiation of heliconiine butterflies occurred predominantly on the eastern slopes of the Andes in Colombia, Ecuador, and Peru, as well as in the upper/middle Amazon basin.