Papers

2012
Heliconius_Genome_Consortium,. (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature , 487, 94-98.Abstract

The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.

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doi: 10.1038/nature11041

Boenigk, J., Ereshefsky, M., Hoef-Emden, K., Mallet, J., & Bass, D. (2012). Concepts in protistology: species definitions and boundaries. European Journal of Protistology , 48, 96-102.Abstract

This paper summarises the Symposium 'Concepts in Protistology', during the VI European Congress of Protistology, Berlin, 25-29 July 2011. There is an increasing focus on cataloguing the number of species on earth, species barcoding initiatives, and the increasing need to reconcile molecular with morphological data in protists within a taxonomic framework. We identify several obstructions to defining species in protists, including the high incidence of asexuality, high levels of both morphological conservation and evolutionary convergence, high levels of genetic diversity that cannot so far be correlated with phenotypic characters, conflicting signals between both genetic and phenotypic taxonomic markers, and different requirements and challenges of species definition in different protist groups. We assert that there is no species 'category' for protists, and recommend that a working definition of species is clarified on a case-by-case basis. Thus, a consensus approach may emerge within protist groups, but any one approach is unlikely to encompass a wide phylogenetic range. However, as long as clarity of intent and method is maintained, the utility of the term 'species' in protists will also be maintained as a reproducible and convenient (if artificial) way of referring to particular lineages within a tightly defined context.

REPRINT Suppl. text 1 Mallet & Dasmahapatra Suppl. text 2 Ereshefsky Suppl. text 3 Hoef-Emden & Bass

doi: 10.1016/j.ejop.2011.11.004

Merrill, R. M., Wallbank, R. W., Bull, V., Salazar, P. C., Mallet, J., Stevens, M., & Jiggins, C. D. (2012). Disruptive ecological selection on a mating cue. Proceedings of the Royal Society B: Biological Sciences , 279, 4907-4913.Abstract

Adaptation to divergent ecological niches can result in speciation. Traits subject to disruptive selection that also contribute to non-random mating will facilitate speciation with gene flow. Such 'magic' or 'multiple-effect' traits may be widespread and important for generating biodiversity, but strong empirical evidence is still lacking. Although there is evidence that putative ecological traits are indeed involved in assortative mating, evidence that these same traits are under divergent selection is considerably weaker. Heliconius butterfly wing patterns are subject to positive frequency-dependent selection by predators, owing to aposematism and Mullerian mimicry, and divergent colour patterns are used by closely related species to recognize potential mates. The amenability of colour patterns to experimental manipulation, independent of other traits, presents an excellent opportunity to test their role during speciation. We conducted field experiments with artificial butterflies, designed to match natural butterflies with respect to avian vision. These were complemented with enclosure trials with live birds and real butterflies. Our experiments showed that hybrid colour-pattern phenotypes are attacked more frequently than parental forms. For the first time, we demonstrate disruptive ecological selection on a trait that also acts as a mating cue.

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doi: 10.1098/rspb.2012.1968

Nadeau, N. J., Whibley, A., Jones, R. T., Davey, J. W., Dasmahapatra, K. K., Baxter, S. W., Quail, M. A., et al. (2012). Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philosophical Transactions of the Royal Society B , 367, 343-53.Abstract

Heliconius butterflies represent a recent radiation of species, in which wing pattern divergence has been implicated in speciation. Several loci that control wing pattern phenotypes have been mapped and two were identified through sequencing. These same gene regions play a role in adaptation across the whole Heliconius radiation. Previous studies of population genetic patterns at these regions have sequenced small amplicons. Here, we use targeted next-generation sequence capture to survey patterns of divergence across these entire regions in divergent geographical races and species of Heliconius. This technique was successful both within and between species for obtaining high coverage of almost all coding regions and sufficient coverage of non-coding regions to perform population genetic analyses. We find major peaks of elevated population differentiation between races across hybrid zones, which indicate regions under strong divergent selection. These 'islands' of divergence appear to be more extensive between closely related species, but there is less clear evidence for such islands between more distantly related species at two further points along the 'speciation continuum'. We also sequence fosmid clones across these regions in different Heliconius melpomene races. We find no major structural rearrangements but many relatively large (greater than 1 kb) insertion/deletion events (including gain/loss of transposable elements) that are variable between races.

REPRINT SUPPLEMENTARY MATERIAL

doi: 10.1098/rstb.2011.0198

Cook, L. M., Grant, B. S., Saccheri, I. J., & Mallet, J. (2012). Selective bird predation on the peppered moth: the last experiment of Michael Majerus. Biology Letters , 8 609-612.Abstract

Colour variation in the peppered moth Biston betularia was long accepted to be under strong natural selection. Melanics were believed to be fitter than pale morphs because of lower predation at daytime resting sites on dark, sooty bark. Melanics became common during the industrial revolution, but since 1970 there has been a rapid reversal, assumed to have been caused by predators selecting against melanics resting on today's less sooty bark. Recently, these classical explanations of melanism were attacked, and there has been general scepticism about birds as selective agents. Experiments and observations were accordingly carried out by Michael Majerus to address perceived weaknesses of earlier work. Unfortunately, he did not live to publish the results, which are analysed and presented here by the authors. Majerus released 4864 moths in his six-year experiment, the largest ever attempted for any similar study. There was strong differential bird predation against melanic peppered moths. Daily selection against melanics (s approximately 0.1) was sufficient in magnitude and direction to explain the recent rapid decline of melanism in post-industrial Britain. These data provide the most direct evidence yet to implicate camouflage and bird predation as the overriding explanation for the rise and fall of melanism in moths.

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(Open Access) doi: 10.1098/rsbl.2011.1136

Kronforst, M. R., Barsh, G. S., Kopp, A., Mallet, J., Monteiro, A., Mullen, S. P., Protas, M., et al. (2012). Unraveling the thread of nature's tapestry: the genetics of diversity and convergence in animal pigmentation. Pigment Cell and Melanoma Research , 25, 411-433.Abstract

Animals display incredibly diverse color patterns yet little is known about the underlying genetic basis of these phenotypes. However, emerging results are reshaping our view of how the process of phenotypic evolution occurs. Here, we outline recent research from three particularly active areas of investigation: melanin pigmentation in Drosophila, wing patterning in butterflies, and pigment variation in lizards. For each system, we highlight (i) the function and evolution of color variation, (ii) various approaches that have been used to explore the genetic basis of pigment variation, and (iii) conclusions regarding the genetic basis of convergent evolution which have emerged from comparative analyses. Results from these studies indicate that natural variation in pigmentation is a particularly powerful tool to examine the molecular basis of evolution, especially with regard to convergent or parallel evolution. Comparison of these systems also reveals that the molecular basis of convergent evolution is heterogeneous, sometimes involving conserved mechanisms and sometimes not. In the near future, additional work in other emerging systems will substantially expand the scope of available comparisons.

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(Open Access) doi: 10.1111/j.1755-148X.2012.01014.x

2011
Mallet, J. & Dasmahapatra, K. (2011). Catfish mimics (News and Views on Alexandrou et al. article in same issue). Nature , 469, 41-42.Abstract

Mutualism can be a double-edged sword if the animals concerned also competefor food. This may explain the discovery that mimic catfish in the Amazon rarelyengage in mimicry with related species.

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Mallet, J., Wynne, I. R., & Thomas, C. D. (2011). Hybridisation and climate change: brown argus butterflies in Britain (Polyommatus subgenus Aricia). Insect Conservation and Diversity , 4 192-199. REPRINT
De-Silva, D. L., VÁSquez, A. S., & Mallet, J. (2011). Selection for enemy-free space: eggs placed away from the host plant increase survival of a neotropical ithomiine butterfly. Ecological Entomology , 36, 667-672.Abstract

1. The selection of an oviposition site by a phytophagous insect can depend
on many factors, including the risk of predation. Many species avoid predators by laying eggs where enemies searching host plants are unlikely to find them.
2. Females of the Peruvian butterfly, Oleria onega Hewitson (Lepidoptera:
Nymphalidae: Danainae: Ithomiini) lay most of their eggs (76 ± 9%) off the host plant, Solanum mite Ruiz & Pav. These off-host eggs may be laid up to 0.5 m from the nearest host-plant individual, on twigs or leaf litter, as well as on living plants of species unsuitable for larval food.
3. Disappearance of eggs on and off the host plant was recorded by transferring eggs laid in captivity to known locations in the wild and recording rates of disappearance before the larvae emerged. After 2 days, eggs on the host were significantly more likely to have disappeared compared to eggs laid elsewhere.
4. We conclude that a high risk of predation is a likely trigger that caused O. onega to evolve a behaviour of laying eggs off its host plant.

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Hines, H. M., Counterman, B. A., Papa, R., Albuquerque de Moura P,, Cardoso, M. Z., Linares, M., Mallet J,, et al. (2011). A wing patterning gene redefines the mimetic history of Heliconius butterflies. Proceedings of the National Academy of Sciences, USA , 108, 19666-19671.Abstract

The mimetic butterflies Heliconius erato and Heliconius melpomenehave undergone parallel radiations to form a near-identical patchworkof over 20 different wing-pattern races across the Neotropics.Previous molecular phylogenetic work on these radiations has suggestedthat similar but geographically disjunct color patterns arosemultiple times independently in each species. The neutral markersused in these studies, however, can move freely across color patternboundaries, and therefore might not represent the history ofthe adaptive traits as accurately as markers linked to color patterngenes. To assess the evolutionary histories across different loci, wecompared relationships among races within H. erato and within H.melpomene using a series of unlinked genes, genes linked to colorpattern loci, and optix, a gene recently shown to control red colorpatternvariation.We found that although unlinked genes partitionpopulations by geographic region, optix had a different history,structuring lineages by red color patterns and supporting a singleorigin of red-rayed patterns within each species. Genes closelylinked (80–250 kb) to optix exhibited only weak associations withcolor pattern. This study empirically demonstrates the necessity ofexamining phenotype-determining genomic regions to understandthe history of adaptive change in rapidly radiating lineages. Withthese refined relationships, we resolve a long-standing debateabout the origins of the races within each species, supporting thehypothesis that the red-rayed Amazonian pattern evolved recentlyand expanded, causing disjunctions of more ancestral patterns.

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2010
Dasmahapatra, K. K., Lamas, G., Simpson, F., & Mallet, J. (2010). The anatomy of a 'suture zone' in Amazonian butterflies: a coalescent-based test for vicariant geographic divergence and speciation. Molecular Ecology , 19, 4283-4301.Abstract

Attempts by biogeographers to understand biotic diversification in the Amazon have often employed contemporary species distribution patterns to support particular theories, such as Pleistocene rainforest refugia, rather than to test among alternative hypotheses. Suture zones, narrow regions where multiple contact zones and hybrid zones between taxa cluster, have been seen as evidence for past expansion of whole biotas that have undergone allopatric divergence in vicariant refuges. We used coalescent analysis of mutilocus sequence data to examine population split times in 22 pairs of geminate taxa in ithomiine and heliconiine butterflies. We test a hypothesis of simultaneous divergence across a suture zone in NE Peru. Our results reveal a scattered time course of diversification in this suture zone, rather than a tight cluster of split times. Additionally, we find rapid diversification within some lineages such as Melinaea contrasting with older divergence within lineages such as the Oleriina (Hyposcada and Oleria). These results strongly reject simple vicariance as a cause of the suture zone. At the same time, observed lineage effects are incompatible with a series of geographically coincident vicariant events which should affect all lineages similarly. Our results suggest that Pleistocene climatic forcing cannot readily explain this Peruvian suture zone. Lineage-specific biological traits, such as characteristic distances of gene flow or varying rates of parapatric divergence, may be of greater importance.

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(Open Access) doi: 10.1111/j.1365-294X.2010.04802.x

Gourbiere, S., & Mallet, J. (2010). Are species real? The shape of the species boundary with exponential failure, reinforcement, and the "missing snowball". Evolution , 64, 1-24.Abstract

Under simple assumptions, the evolution of epistatic "Dobzhansky-Muller" incompatibilities between a pair of species should yield an accelerating decline of log overall reproductive compatibility--a "snowball" effect that might rapidly provide new species with "reality." Possible alternatives include: (1) simple exponential failure, giving a linear rate of log compatibility loss, and (2) "slowdown," likely during reinforcement in which mate choice evolves to prevent deleterious hybridization, yielding a decelerating log compatibility loss. In analyses of multiple datasets, we find little support for the snowball effect, except possibly in Lepidoptera hybrid viability. The snowball predicts a slow initial rate of incompatibility acquisition, with low initial variance; instead, highly variable compatibility is almost universally observed at low genetic distances. Another deviation from predictions is that reproductive isolation usually remains incomplete until long after speciation. These results do not disprove snowball compatibility decay, but can result if large deleterious effects are due to relatively few genetic changes, or if different types of incompatibility evolve at very different rates. On the other hand, data on Bacillus and Saccharomyces, as well as theories of chromosomal evolution, suggest that some kinds of incompatibility accumulate approximately linearly, without Dobzhansky-Muller effects. In microorganisms, linearity can result from direct negative effects of DNA sequence divergence on compatibility. Finally, a decelerating slowdown model is supported for sympatric Leptasterias starfish, and in Drosophila prezygotic isolation in sympatry but not allopatry, providing novel comparative evidence for reinforcement.

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doi: 10.1111/j.1558-5646.2009.00844.x

Baxter, S. W., Nadeau, N. J., Maroja, L. S., Wilkinson, P., Counterman, B. A., Dawson, A., Beltran, M., et al. (2010). Genomic hotspots for adaptation: the population genetics of Mullerian mimicry in the Heliconius melpomene clade. PLoS Genetics , 6(2), e1000794.Abstract

Wing patterning in Heliconius butterflies is a longstanding example of both Mullerian mimicry and phenotypic radiation under strong natural selection. The loci controlling such patterns are "hotspots" for adaptive evolution with great allelic diversity across different species in the genus. We characterise nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium, and candidate gene expression at two loci and across multiple hybrid zones in Heliconius melpomene and relatives. Alleles at HmB control the presence or absence of the red forewing band, while alleles at HmYb control the yellow hindwing bar. Across HmYb two regions, separated by approximately 100 kb, show significant genotype-by-phenotype associations that are replicated across independent hybrid zones. In contrast, at HmB a single peak of association indicates the likely position of functional sites at three genes, encoding a kinesin, a G-protein coupled receptor, and an mRNA splicing factor. At both HmYb and HmB there is evidence for enhanced linkage disequilibrium (LD) between associated sites separated by up to 14 kb, suggesting that multiple sites are under selection. However, there was no evidence for reduced variation or deviations from neutrality that might indicate a recent selective sweep, consistent with these alleles being relatively old. Of the three genes showing an association with the HmB locus, the kinesin shows differences in wing disc expression between races that are replicated in the co-mimic, Heliconius erato, providing striking evidence for parallel changes in gene expression between Mullerian co-mimics. Wing patterning loci in Heliconius melpomene therefore show a haplotype structure maintained by selection, but no evidence for a recent selective sweep. The complex genetic pattern contrasts with the simple genetic basis of many adaptive traits studied previously, but may provide a better model for most adaptation in natural populations that has arisen over millions rather than tens of years.

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(Open Access) doi: 10.1371/journal.pgen.1000794.

Counterman, B. A., Araujo-Perez, F., Hines, H. M., Baxter, S. W., Morrison, C. M., Lindstrom, D. P., Papa, R., et al. (2010). Genomic hotspots for adaptation: the population genetics of Mullerian mimicry in Heliconius erato. PLoS Genetics , 6(2), e1000796.Abstract

Wing pattern evolution in Heliconius butterflies provides some of the most striking examples of adaptation by natural selection. The genes controlling pattern variation are classic examples of Mendelian loci of large effect, where allelic variation causes large and discrete phenotypic changes and is responsible for both convergent and highly divergent wing pattern evolution across the genus. We characterize nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium (LD), and candidate gene expression patterns across two unlinked genomic intervals that control yellow and red wing pattern variation among mimetic forms of Heliconius erato. Despite very strong natural selection on color pattern, we see neither a strong reduction in genetic diversity nor evidence for extended LD across either patterning interval. This observation highlights the extent that recombination can erase the signature of selection in natural populations and is consistent with the hypothesis that either the adaptive radiation or the alleles controlling it are quite old. However, across both patterning intervals we identified SNPs clustered in several coding regions that were strongly associated with color pattern phenotype. Interestingly, coding regions with associated SNPs were widely separated, suggesting that color pattern alleles may be composed of multiple functional sites, conforming to previous descriptions of these loci as "supergenes." Examination of gene expression levels of genes flanking these regions in both H. erato and its co-mimic, H. melpomene, implicate a gene with high sequence similarity to a kinesin as playing a key role in modulating pattern and provides convincing evidence for parallel changes in gene regulation across co-mimetic lineages. The complex genetic architecture at these color pattern loci stands in marked contrast to the single casual mutations often identified in genetic studies of adaptation, but may be more indicative of the type of genetic changes responsible for much of the adaptive variation found in natural populations.

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doi: 10.1371/journal.pgen.1000796

Mallet, J. (2010). Group selection and the development of the biological species concept. Philosophical Transactions of the Royal Society , 365, 1853-1863.Abstract

The development of what became known as the biological species concept began with a paper by Theodosius Dobzhansky in 1935, and was amplified by a mutualistic interaction between Dobzhansky, Alfred Emerson and Ernst Mayr after the second world war. By the 1950s and early 1960s, these authors had developed an influential concept of species as coadapted genetic complexes at equilibrium. At this time many features of species were seen as group advantages maintained by selection to avoid breakdown of beneficial coadaptation and the 'gene pool'. Speciation thus seemed difficult. It seemed to require, more so than today, an external deus ex machina, such as allopatry or the founder effect, rather than ordinary within-species processes of natural selection, sexual selection, drift and gene flow. In the mid-1960s, the distinctions between group and individual selection were clarified. Dobzhansky and Mayr both understood the implications, but their views on species changed little. These group selectionist ideas now seem peculiar, and are becoming distinctly less popular today. Few vestiges of group selectionism and species-level adaptationism remain in recent reviews of speciation. One wonders how many of our own cherished views on evolution will seem as odd to future biologists.

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doi: 10.1098/rstb.2010.0040

Dasmahapatra, K. K., Elias, M., Hill, R. I., Hoffman, J. I., & Mallet, J. (2010). Mitochondrial DNA barcoding detects some species that are real, and some that are not. Molecular Ecology Resources , 10, 264-273.Abstract

Mimicry and extensive geographical subspecies polymorphism combine to make species in the ithomiine butterfly genus Mechanitis (Lepidoptera; Nymphalidae) difficult to determine. We use mitochondrial DNA (mtDNA) barcoding, nuclear sequences and amplified fragment length polymorphism (AFLP) genotyping to investigate species limits in this genus. Although earlier biosystematic studies based on morphology described only four species, mtDNA barcoding revealed eight well-differentiated haplogroups, suggesting the presence of four new putative 'cryptic species'. However, AFLP markers supported only one of these four new 'cryptic species' as biologically meaningful. We demonstrate that in this genus, deep genetic divisions expected on the basis of mtDNA barcoding are not always reflected in the nuclear genome, and advocate the use of AFLP markers as a check when mtDNA barcoding gives unexpected results.

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doi: 10.1111/j.1755-0998.2009.02763.x

de-Silva, D. L., Day, J. J., Elias, M., Willmott, K., Whinnett, A., & Mallet, J. (2010). Molecular phylogenetics of the neotropical butterfly subtribe Oleriina (Nymphalidae: Danainae: Ithomiini). Molecular Phylogenetics and Evolution , 55, 1032-1041.Abstract

The Oleriina is one of the most speciose subtribes of the neotropical nymphalid butterfly tribe Ithomiini. They are widely distributed across the Andes and Amazonian lowlands and like other ithomiines they are involved in complex mimicry rings. This subtribe is of particular interest because it contains the most diverse ithomiine genus, Oleria, as well as two genera, Megoleria and Hyposcada, that feed on hostplants not utilized elsewhere in the tribe. Here we present the first comprehensive species-level phylogeny for the Oleriina, representing 83% of recognised species in the group, and based on 6698bp from eight mitochondrial (mt) and nuclear (nc) genes. Topologies are largely congruent for ncDNA and the concatenated dataset and the genera Oleria, Hyposcada and Megoleria are recovered and well-supported, although strongly discordant genealogy between mtDNA and ncDNA suggest possible introgression among Hyposcada and Megoleria. A fourth clade containing the type species of Ollantaya is consistently recovered, and this recently synonymized name is resurrected. Clear subdivisions within Oleria separate the genus into four species groups, onega, amalda, makrena and aegle, which also correspond to differing biogeographic and elevation range characteristics. Unlike other ithomiine genera, the Oleriina show homogeneity in mimetic wing pattern, in sharp contrast to the emerging paradigm that mimetic shifts have enhanced diversification in the tribe. Our results show a potentially more important role for geographic isolation in the diversification of the Oleriina compared to other Ithomiini studied to date and provide a framework for more detailed biogeographical studies, in addition to a rare opportunity for comparative analyses with other neotropical groups.

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doi: 10.1016/j.ympev.2010.01.010

Mallet, J. (2010). Shift happens! Shifting balance and the evolution of diversity in warning colour and mimicry. Ecological Entomology , 35 (Suppl. 1), 90-104. REPRINT
Mallet, J. (2010). Why was Darwin’s view of species rejected by twentieth century biologists? Biology and Philosophy , 25, 497-527. REPRINT
2009
Sachs, J. D., Baillie, J. E. M., Sutherland, W. J., Armsworth, P. R., Ash, N., Beddington, J., Blackburn, T. M., et al. (2009). Policy forum: Biodiversity conservation and the Millennium Development Goals. Science , 325, 1502-1503.

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