Elias M, Hill RI, Willmott KR, Dasmahapatra KK, Brower AV, Mallet J, Jiggins CD. Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proceedings of the Royal Society. 2007;274 :2881-9.Abstract

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.

Mallet J, Beltran M, Neukirchen W, Linares M. Natural hybridization in heliconiine butterflies: the species boundary as a continuum. BMC Evolutionary Biology [Internet]. 2007;7 :28. Heliconiine hybrid databaseAbstract

BACKGROUND: To understand speciation and the maintenance of taxa as separate entities, we need information about natural hybridization and gene flow among species. RESULTS: Interspecific hybrids occur regularly in Heliconius and Eueides (Lepidoptera: Nymphalidae) in the wild: 26-29% of the species of Heliconiina are involved, depending on species concept employed. Hybridization is, however, rare on a per-individual basis. For one well-studied case of species hybridizing in parapatric contact (Heliconius erato and H. himera), phenotypically detectable hybrids form around 10% of the population, but for species in sympatry hybrids usually form less than 0.05% of individuals. There is a roughly exponential decline with genetic distance in the numbers of natural hybrids in collections, both between and within species, suggesting a simple "exponential failure law" of compatibility as found in some prokaryotes. CONCLUSION: Hybridization between species of Heliconius appears to be a natural phenomenon; there is no evidence that it has been enhanced by recent human habitat disturbance. In some well-studied cases, backcrossing occurs in the field and fertile backcrosses have been verified in insectaries, which indicates that introgression is likely, and recent molecular work shows that alleles at some but not all loci are exchanged between pairs of sympatric, hybridizing species. Molecular clock dating suggests that gene exchange may continue for more than 3 million years after speciation. In addition, one species, H. heurippa, appears to have formed as a result of hybrid speciation. Introgression may often contribute to adaptive evolution as well as sometimes to speciation itself, via hybrid speciation. Geographic races and species that coexist in sympatry therefore form part of a continuum in terms of hybridization rates or probability of gene flow. This finding concurs with the view that processes leading to speciation are continuous, rather than sudden, and that they are the same as those operating within species, rather than requiring special punctuated effects or complete allopatry. Although not qualitatively distinct from geographic races, nor "real" in terms of phylogenetic species concepts or the biological species concept, hybridizing species of Heliconius are stably distinct in sympatry, and remain useful groups for predicting morphological, ecological, behavioural and genetic characteristics.

Joron M, Papa R, Beltran M, Chamberlain N, Mavarez J, Baxter S, Abanto M, Bermingham E, Humphray SJ, Rogers J, et al. A conserved supergene locus controls colour pattern diversity in Heliconius butterflies. PLoS Biology . 2006;4 :e303.Abstract

We studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Mullerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a "supergene", determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic "supergene" polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions.

Dasmahapatra KK, Mallet J. DNA barcodes: recent successes and future prospects. Heredity . 2006;97 :254-255. REPRINT
Bull V, Beltran M, Jiggins CD, McMillan WO, Bermingham E, Mallet J. Polyphyly and gene flow between non-sibling Heliconius species. BMC Biology. 2006;4 :11.Abstract

BACKGROUND: The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae), whose distributions overlap in Central and Northwestern South America. RESULTS: In these taxa, we sequenced 30-45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII), and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi), mannose-6-phosphate isomerase (Mpi) and cubitus interruptus (Ci) genes. A fifth gene, dopa decarboxylase (Ddc) produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. CONCLUSION: Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Mullerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

Mallet J. What does Drosophila genetics tell us about speciation?. Trends in Ecology and Evolution. 2006;21 :386-93.Abstract

Studies of hybrid inviability, sterility and 'speciation genes' in Drosophila have given insight into the genetic changes that result in reproductive isolation. Here, I survey some extraordinary and important advances in Drosophila speciation research. However, 'reproductive isolation' is not the same as 'speciation', and this Drosophila work has resulted in a lopsided view of speciation. In particular, Drosophila are not always well-suited to investigating ecological and other selection-driven primary causes of speciation in nature. Recent advances have made use of far less tractable, but more charismatic organisms, such as flowering plants, vertebrates and larger insects. Work with these organisms has complemented Drosophila studies of hybrid unfitness to provide a more complete understanding of speciation.

Lamas G, Mallet JLB. Case 3320. Papilio sapho Drury, 1782 (currently Heliconius sapho; Insecta, Lepidoptera): proposed conservation of the specific name. Bulletin of Zoological Nomenclature. 2005;62 :21-24. REPRINT
Gourbiere S, Mallet J. Has adaptive dynamics contributed to the understanding of adaptive and sympatric speciation?. Journal of Evolutionary Biology. 2005;18 :1201-1204. REPRINT
Mallet J. Hybridization as an invasion of the genome. Trends in Ecology and Evolution. 2005;20 :229-237.Abstract

Hybridization between species is commonplace in plants, but is often seen as unnatural and unusual in animals. Here, I survey studies of natural interspecific hybridization in plants and a variety of animals. At least 25% of plant species and 10% of animal species, mostly the youngest species, are involved in hybridization and potential introgression with other species. Species in nature are often incompletely isolated for millions of years after their formation. Therefore, much evolution of eventual reproductive isolation can occur while nascent species are in gene-flow contact, in sympatry or parapatry, long after divergence begins. Although the relative importance of geographic isolation and gene flow in the origin of species is still unknown, many key processes involved in speciation, such as 'reinforcement' of post-mating isolation by the evolution of assortative mating, will have ample opportunity to occur in the presence of continuing gene flow. Today, DNA sequence data and other molecular methods are beginning to show that limited invasions of the genome are widespread, with potentially important consequences in evolutionary biology, speciation, biodiversity, and conservation.

Whinnett A, Willmott KR, Brower AVZ, Simpson F, Lamas G, Mallet J. Mitochondrial DNA provides an insight into the mechanisms driving diversification in the ithomiine butterfly Hyposcada anchiala (Lepidoptera: Nymphalidae, Ithomiinae). European Journal of Entomology . 2005;102 :633-639.Abstract

Geographic subspecies of several ithomiine butterflies on the lower east Andean slopes display a black and orange“melanic tiger” aposematic wing pattern that occurs from Colombia to Bolivia, while geographically adjacent lowland subspeciestypically bear a coloured, “tiger” pattern. However, it is not clear whether subspecies with similar wing patterns in different regionshave arisen through independent events of convergent adaptation, possibly through parapatric differentiation, or result from allopatricdifferentiation, as proposed by the refuge hypothesis. Here, we examine geographic patterns of divergence in the widespreadand common ithomiine butterfly Hyposcada anchiala. We present phylogenetic hypotheses for 5 subspecies of H. anchiala, basedon 1567 bp mitochondrial DNA. All topologies indicated that a single switch in mimetic pattern best explained the wing patterningof the H. anchiala studied here. This finding suggests that the subspecies of H. anchiala studied here result from at least two stagesof differentiation, and is consistent with a single colonisation into a novel altitudinal zone coincident with a wing pattern switch, followedby subsequent divergence within, rather than across altitudinal zones. The subspecies divergences indicated diversificationswere consistent with the Pleistocene. Furthermore, the lowland subspecies were more recently derived than the montane taxa, in contrastto predictions of the “Andean species pump” hypothesis.

Drès M, Mallet J. Molecular and behavioural evidence for gene flow between host races of the larch budmoth Zeiraphera diniana (Lepidoptera: Tortricidae). Proceedings of the Royal Society B. 2005;Submitted.Abstract

Larch and pine associated populations of Zeiraphera diniana (Lepidoptera: Tortricidae) differin a number of heritable traits, but pheromone-mediated cross-attraction occurs betweenthem in the wild. Using a quartet mate choice design (one male and one female of each typeper cage) we estimate that, following cross-attraction by pheromones, the subsequentprobability of hybridization is approximately 28%. We also examined molecular data, andwere unable to distinguish between the races on the basis of 695bp of mitochondrial COI,tRNA-leucine, and COII gene sequence. Both results support earlier field studies suggestingthat larch- and pine-feeding populations are host races that hybridize at an appreciable levelin the wild. The shared mitochondrial haplotypes we observed are also consistent withongoing and successful gene flow between the two host races.

Whinnett A, Brower AVZ, Lee M-M, Willmott KR, Mallet J. Phylogenetic utility of tektin, a novel region for inferring systematic relationships among Lepidoptera. Annals of the Entomological Society of America. 2005;98 :873-886.Abstract

Rapidly evolving nuclear coding sequences are highly desirable for phylogeneticstudies of closely related species. Here, we investigated an 807-bp region, homologous to the testisspeciÞcTektin gene from Bombyx mori (L.), in 34 nymphalid butterßy taxa in the subfamiliesIthomiinae, Danainae, and Heliconiinae. Within Ithomiinae, relationships inferred from Tektin sequencedata were remarkably similar to those in trees based on combined morphological andecological data. Partitioned Bremer analysis, with mitochondrial cytochrome oxidase I and II, andnuclear wingless and elongation factor 1- sequences, revealed Tektin to have the greatest utility forinferring relationships at the genus, tribe, and subfamily levels across the studied taxa.Wethink Tektinwill provide a useful source of molecular characters for inference of relationships among otherbutterßies, and perhaps among other insect taxa.

Mallet J, Isaac N, Mace G. Response to Harris and Froufe, and Knapp : Taxonomic inflation. Trends in Ecology and Evolution. 2005;20 :8-9. REPRINT
Mallet J. Speciation in the 21st Century. Review of "Speciation", by Jerry A. Coyne & H. Allen Orr. Heredity. 2005;95 :105-109. REPRINT
Whinnett A, Zimmermann M, Willmott KR, Herrera N, Mallarino R, Simpson F, Joron M, Lamas G, Mallet J. Strikingly variable divergence times inferred across an Amazonian butterfly 'suture zone'. Proceedings of the Royal Society B. 2005;272 :2525-2533.Abstract

'Suture zones' are areas where hybrid and contact zones of multiple taxa are clustered. Such zones have been regarded as strong evidence for allopatric divergence by proponents of the Pleistocene forest refugia theory, a vicariance hypothesis frequently used to explain diversification in the Amazon basin. A central prediction of the refugia and other vicariance theories is that the taxa should have a common history so that divergence times should be coincident among taxa. A suture zone for Ithomiinae butterflies near Tarapoto, NE Peru, was therefore studied to examine divergence times of taxa in contact across the zone. We sequenced 1619bp of the mitochondrial COI/COII region in 172 individuals of 31 species from across the suture zone. Inferred divergence times differed remarkably, with divergence between some pairs of widespread species (each of which may have two or more subspecies interacting in the zone, as in the genus Melinaea) being considerably less than that between hybridizing subspecies in other genera (for instance in Oleria). Our data therefore strongly refute a simple hypothesis of simultaneous vicariance and suggest that ongoing parapatric or other modes of differentiation in continuous forest may be important in driving diversification in Amazonia.