One of the most striking examples of sexual dimorphism is sex-limited mimicry in butterflies, a phenomenon in which one sex--usually the female--mimics a toxic model species, whereas the other sex displays a different wing pattern. Sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio, in which it is often associated with female mimetic polymorphism. In multiple polymorphic species, the entire wing pattern phenotype is controlled by a single Mendelian 'supergene'. Although theoretical work has explored the evolutionary dynamics of supergene mimicry, there are almost no empirical data that address the critical issue of what a mimicry supergene actually is at a functional level. Using an integrative approach combining genetic and association mapping, transcriptome and genome sequencing, and gene expression analyses, we show that a single gene, doublesex, controls supergene mimicry in Papilio polytes. This is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci. Analysis of gene expression and DNA sequence variation indicates that isoform expression differences contribute to the functional differences between dsx mimicry alleles, and protein sequence evolution may also have a role. Our results combine elements from different hypotheses for the identity of supergenes, showing that a single gene can switch the entire wing pattern among mimicry phenotypes but may require multiple, tightly linked mutations to do so.

Abstract Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]

Hybrid speciation, or the formation of a daughter species due to interbreeding between two parental species, is a potentially important means of diversification, because it generates new forms from existing variation. However, factors responsible for the origin and maintenance of hybrid species are largely unknown. Here we show that the North American butterfly Papilio appalachiensis is a hybrid species, with genomic admixture from Papilio glaucus and Papilio canadensis. Papilio appalachiensis has a mosaic phenotype, which is hypothesized to be the result of combining sex-linked traits from P. glaucus and P. canadensis. We show that P. appalachiensis' Z-linked genes associated with a cooler thermal habitat were inherited from P. canadensis, whereas its W-linked mimicry and mitochondrial DNA were inherited from P. glaucus. Furthermore, genome-wide AFLP markers showed nearly equal contributions from each parental species in the origin of P. appalachiensis, indicating that it formed from a burst of hybridization between the parental species, with little subsequent backcrossing. However, analyses of genetic differentiation, clustering, and polymorphism based on molecular data also showed that P. appalachiensis is genetically distinct from both parental species. Population genetic simulations revealed P. appalachiensis to be much younger than the parental species, with unidirectional gene flow from P. glaucus and P. canadensis into P. appalachiensis. Finally, phylogenetic analyses, combined with ancestral state reconstruction, showed that the two traits that define P. appalachiensis' mosaic phenotype, obligatory pupal diapause and mimicry, evolved uniquely in P. canadensis and P. glaucus, respectively, and were then recombined through hybridization to form P. appalachiensis. These results suggest that natural selection and sex-linked traits may have played an important role in the origin and maintenance of P. appalachiensis as a hybrid species. In particular, ecological barriers associated with a steep thermal cline appear to maintain the distinct, mosaic genome of P. appalachiensis despite contact and occasional hybridization with both parental species.

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Summary1. In generalist nectar-feeding insects such as butterflies, body size and proboscis length show an allometric relationship. Butterflies that deviate from this relationship and have disproportionately long proboscides can access nectar from deep flowers, which is inaccessible to species of similar or larger body size but with shorter proboscides. 2. Despite this selective advantage, few species possess disproportionately long proboscides for their body size, which indicates that there may be developmental, functional or other ecological constraints on very long proboscides. I hypothesized that species with disproportionately long proboscides had a functional cost in terms of higher handling time (amount of time spent per flower); therefore, they were at a competitive disadvantage compared to butterflies that had shorter proboscides and lower handling times. 3. I tested this hypothesis using Costa Rican butterflies. I measured body length, proboscis length and handling time on Lantana and Wedelia , two nectar plants with generalist pollination systems which attract large numbers of nectar-feeding butterfly species. 4. There was a strong positive relationship between 'relative proboscis length' (proboscis length in relation to body size) and handling time per flower on both nectar plants. Species with greater relative proboscis length had up to three times longer handling time per flower. Thus, butterflies with relatively long proboscides should harvest less nectar per unit time from the same flower than butterflies with normal proboscides. 5. Reduced foraging efficiency in the face of competition from other nectarivores may thus be a functional constraint that limits the evolution of disproportionately long proboscides in generalist nectar-feeding butterflies.

In animal-pollinated flowers, the pollinators cannot detect the presence of nectar before entering flowers, and therefore flowers may cheat by not producing nectar. An earlier model suggested that a mixed strategy of producing nectarful and nectarless flowers would be evolutionarily stable. Here we compare nectarless flowers as a cheating strategy with three competing hypotheses namely "visit-more-flowers", "cross-pollination enhancement" and "better contact". We collected field data on 28 species of plants to test some of the differential predictions of the hypotheses. Nectarless flowers were detected in 24 out of 28 plant species. Correlations of percent nectarless flowers with floral and ecological variables support the cheater flower hypothesis. We further model the cost-benefits of cheating and show that an evolutionary stable ratio of nectarless to nectarful flowers can be reached. The equilibrium ratio is mainly decided by factors associated with pollinator density and pollinator learning.