@article{supple_hines_dasmahapatra_lewis_nielsen_lavoie_ray_salazar_owen mcmillan_counterman_2013, title={Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies}, volume={23}, ISSN={["1549-5469"]}, DOI={10.1101/gr.150615.112}, abstractNote={Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the evolutionary history of these adaptive alleles. We use whole genome resequencing from four hybrid zones between divergent color pattern races of Heliconius erato and two hybrid zones of the co-mimic Heliconius melpomene to examine genetic variation across 2.2 Mb of a partial reference sequence. In the intergenic region near optix, the gene previously shown to be responsible for the complex red pattern variation in Heliconius, population genetic analyses identify a shared 65-kb region of divergence that includes several sites perfectly associated with phenotype within each species. This region likely contains multiple cis-regulatory elements that control discrete expression domains of optix. The parallel signatures of genetic differentiation in H. erato and H. melpomene support a shared genetic architecture between the two distantly related co-mimics; however, phylogenetic analysis suggests mimetic patterns in each species evolved independently. Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius and gained important insights into the evolution of novel adaptive phenotypes in natural populations.}, number={8}, journal={GENOME RESEARCH}, author={Supple, Megan A. and Hines, Heather M. and Dasmahapatra, Kanchon K. and Lewis, James J. and Nielsen, Dahlia M. and Lavoie, Christine and Ray, David A. and Salazar, Camilo and Owen McMillan, W. and Counterman, Brian A.}, year={2013}, month={Aug}, pages={1248–1257} }
 @article{miko_friedrich_yoder_hines_deitz_bertone_seltmann_wallace_deans_2012, title={On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0030137}, abstractNote={A spectacular hypothesis was published recently, which suggested that the “helmet” (a dorsal thoracic sclerite that obscures most of the body) of treehoppers (Insecta: Hemiptera: Membracidae) is connected to the 1st thoracic segment (T1; prothorax) via a jointed articulation and therefore was a true appendage. Furthermore, the “helmet” was interpreted to share multiple characteristics with wings, which in extant pterygote insects are present only on the 2nd (T2) and 3rd (T3) thoracic segments. In this context, the “helmet” could be considered an evolutionary novelty. Although multiple lines of morphological evidence putatively supported the “helmet”-wing homology, the relationship of the “helmet” to other thoracic sclerites and muscles remained unclear. Our observations of exemplar thoraces of 10 hemipteran families reveal multiple misinterpretations relevant to the “helmet”-wing homology hypothesis as originally conceived: 1) the “helmet” actually represents T1 (excluding the fore legs); 2) the “T1 tergum” is actually the anterior dorsal area of T2; 3) the putative articulation between the “helmet” and T1 is actually the articulation between T1 and T2. We conclude that there is no dorsal, articulated appendage on the membracid T1. Although the posterior, flattened, cuticular evagination (PFE) of the membracid T1 does share structural and genetic attributes with wings, the PFE is actually widely distributed across Hemiptera. Hence, the presence of this structure in Membracidae is not an evolutionary novelty for this clade. We discuss this new interpretation of the membracid T1 and the challenges of interpreting and representing morphological data more broadly. We acknowledge that the lack of data standards for morphology is a contributing factor to misinterpreted results and offer an example for how one can reduce ambiguity in morphology by referencing anatomical concepts in published ontologies.}, number={1}, journal={PLOS ONE}, author={Miko, Istvan and Friedrich, Frank and Yoder, Matthew J. and Hines, Heather M. and Deitz, Lewis L. and Bertone, Matthew A. and Seltmann, Katja C. and Wallace, Matthew S. and Deans, Andrew R.}, year={2012}, month={Jan} }
 @article{hines_papa_ruiz_papanicolaou_wang_nijhout_mcmillan_reed_2012, title={Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation}, volume={13}, journal={BMC Genomics}, author={Hines, H. M. and Papa, R. and Ruiz, M. and Papanicolaou, A. and Wang, C. and Nijhout, H. F. and McMillan, W. O. and Reed, R. D.}, year={2012} }
 @article{hines_counterman_papa_moura_cardoso_linares_mallet_reed_jiggins_kronforst_et al._2011, title={Wing patterning gene redefines the mimetic history of Heliconius butterflies}, volume={108}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1110096108}, abstractNote={The mimetic butterfliesHeliconius eratoandHeliconius melpomenehave undergone parallel radiations to form a near-identical patchwork of over 20 different wing-pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries, and therefore might not represent the history of the adaptive traits as accurately as markers linked to color pattern genes. To assess the evolutionary histories across different loci, we compared relationships among races withinH. eratoand withinH. melpomeneusing a series of unlinked genes, genes linked to color pattern loci, andoptix, a gene recently shown to control red color-pattern variation. We found that although unlinked genes partition populations by geographic region,optixhad a different history, structuring lineages by red color patterns and supporting a single origin of red-rayed patterns within each species. Genes closely linked (80–250 kb) tooptixexhibited only weak associations with color pattern. This study empirically demonstrates the necessity of examining phenotype-determining genomic regions to understand the history of adaptive change in rapidly radiating lineages. With these refined relationships, we resolve a long-standing debate about the origins of the races within each species, supporting the hypothesis that the red-rayed Amazonian pattern evolved recently and expanded, causing disjunctions of more ancestral patterns.}, number={49}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Hines, Heather M. and Counterman, Brian A. and Papa, Riccardo and Moura, Priscila Albuquerque and Cardoso, Marcio Z. and Linares, Mauricio and Mallet, James and Reed, Robert D. and Jiggins, Chris D. and Kronforst, Marcus R. and et al.}, year={2011}, month={Dec}, pages={19666–19671} }
 @article{reed_papa_martin_hines_counterman_pardo-diaz_jiggins_chamberlain_kronforst_chen_et al._2011, title={optix Drives the Repeated Convergent Evolution of Butterfly Wing Pattern Mimicry}, volume={333}, ISSN={["1095-9203"]}, DOI={10.1126/science.1208227}, abstractNote={
            Heliconius
            butterfly wing pattern mimicry is driven by cis-regulatory variation of the
            optix
            gene.
          }, number={6046}, journal={SCIENCE}, author={Reed, Robert D. and Papa, Riccardo and Martin, Arnaud and Hines, Heather M. and Counterman, Brian A. and Pardo-Diaz, Carolina and Jiggins, Chris D. and Chamberlain, Nicola L. and Kronforst, Marcus R. and Chen, Rui and et al.}, year={2011}, month={Aug}, pages={1137–1141} }
 @article{counterman_araujo-perez_hines_baxter_morrison_lindstrom_papa_ferguson_joron_ffrench-constant_et al._2010, title={Genomic hotspots for adaptation: The population genetics of Mullerian mimicry in Heliconius erato}, volume={6}, number={4}, journal={PLoS Genetics}, author={Counterman, B. A. and Araujo-Perez, F. and Hines, H. M. and Baxter, S. W. and Morrison, C. M. and Lindstrom, D. P. and Papa, R. and Ferguson, L. and Joron, M. and Ffrench-Constant, R. H. and et al.}, year={2010} }
 @article{hines_cameron_2010, title={The phylogenetic position of the bumble bee inquiline Bombus inexspectatus and implications for the evolution of social parasitism}, volume={57}, number={4}, journal={Insectes Sociaux}, author={Hines, H. M. and Cameron, S. A.}, year={2010}, pages={379–383} }