Deep mitochondrial divergence within a Heliconiusbutterfly species is not explained by cryptic speciation or endosymbiotic bacteria
© Muñoz et al; licensee BioMed Central Ltd. 2011
Received: 1 August 2011
Accepted: 12 December 2011
Published: 12 December 2011
Cryptic population structure can be an indicator of incipient speciation or historical processes. We investigated a previously documented deep break in the mitochondrial haplotypes of Heliconius erato chestertonii to explore the possibility of cryptic speciation, and also the possible presence of endosymbiont bacteria that might drive mitochondrial population structure.
Among a sample of 315 individuals from 16 populations of western Colombia, two principal mtDNA clades were detected with 2.15% divergence and we confirmed this structure was weakly associated with geography. The first mtDNA clade included 87% of individuals from northern populations and was the sister group of H. erato members of Andes western, while the second clade contained most individuals from southern populations (78%), which shared haplotypes with an Ecuadorian race of H. erato. In contrast, analysis using AFLP markers showed H. e. chestertonii to be a genetically homogeneous species with no association between mitochondrial divergence and AFLP structure. The lack of congruence between molecular markers suggests that cryptic speciation is not a plausible explanation for the deep mitochondrial divergence in H. e chestertonii. We also carried out the first tests for the presence of endosymbiontic bacteria in Heliconius, and identified two distinct lineages of Wolbachia within H. e. chestertonii. However, neither of the principal mitochondrial clades of H. e. chestertonii was directly associated with the patterns of infection.
We conclude that historical demographic processes are the most likely explanation for the high mitochondrial differentiation in H. e. chestertonii, perhaps due to gene flow between Cauca valley H. e. chestertonii and west Pacific slope populations of H. erato.
Sequences derived from the mitochondrial genome are commonly used both in species delimitation and historical phylogeography. For example, deep divergence in mitochondrial DNA sequences (mtDNA) between related individuals is often taken as evidence for the existence of cryptic species [1–4]. The discovery of cryptic species-level variation has important implications for characterising biodiversity and for studies of speciation. Nonetheless, it is now well recognised that inference of evolutionary processes and species boundaries from mitochondrial sequences alone can be problematic [5, 6]. For example, similar patterns of divergence can be due to host-parasite interactions, whereby selection leads different molecular markers to show different histories . Mitochondrial lineages may also be retained through admixture between divergent species or populations , or perhaps due to unusual population structures [9, 10]. Indeed, in diverse tropical radiations, mtDNA 'barcoding' may perform rather poorly as a species identification tool . It is therefore of general interest to pursue individual cases of deep mtDNA divergence in order to determine how often such divergence is indeed an indicator of cryptic species-level variation.
Heliconius butterflies are an excellent ecological and genetic system for studying speciation. These unpalatable butterflies are recognized for their diversity of wing color patterns associated with mimicry [11, 12]. The classical example of this adaptive radiation occurs between the comimetic species H. erato and H. melpomene. These butterflies co-occur in Central and South America and show convergent changes in their color pattern. They are represented by more than 20 different geographic forms which are considered subspecies . Neutral molecular markers show geographic structure among subspecies of H. erato and H. melpomene, and most named races fall within a particular geographic clade [13–16]. However, in H. erato two forms: H. e. hydara and H. e. chestertonii are polyphyletic in the mitochondrial phylogeny [13, 16]. Individuals of H. e. chestertonii fall into two distinct mtDNA clades that show over 2% divergence, with no clear biogeographic explanation . H. e. chestertonii is found in the western Colombian Andes on disturbed, dry habitats and forms a hybrid zone with the geographically closest subspecies: H. e. venus. Although H. e. chestertonii is a member of the erato clade, it has an unusual wing color pattern compared with the characteristic red/yellow/black pattern of H. erato. H. e. chestertonii has an iridescent and melanic forewing while the hindwing displays a broad yellow band. The co-mimic for this wing color pattern is H. cydno weymeri f. gustavi, a member of the H. melpomene clade.
Rapid evolution in the early stages of the speciation process is expected to lead to incongruence between morphological and molecular markers [14, 18, 19]. However, in H. e. chestertonii the deep divergence in the mitochondrial haplotypes is not readily explained through ancestral polymorphism or hybridization. Such mtDNA division has not been observed in any other Heliconius taxon to date. One possible explanation might be that structure is due to the presence of endosymbiotic bacteria [19–21]. Wolbachia are intracellular bacteria and infect numerous species of arthropods and nematodes . Interactions between these microorganisms and their eukaryotic hosts often has consequences for host reproduction, leading in some cases to breaks between populations or species [23, 24]. Wolbachia are inherited maternally, so their evolutionary fate is tightly linked to that of the mitochondrion . Furthermore, hybridization between H. e. chestertonii and its nearby relative, H. e. venus, produces partially infertile eggs . Hybrid sterility of this form can also be generated by endosymbionts where parental populations are infected by different strains.
However, an alternative hypothesis for the mtDNA break within the continuous distribution of H. e. chestertonii is cryptic reproductive isolation, unrelated to endosymbionts. Given the emphasis on wing color pattern in Heliconius speciation, a potential case of cryptic speciation would be of considerable interest. To investigate these possibilities we first extend previous mtDNA sampling to better document the distribution of mtDNA lineages. In order to test for cryptic speciation, we have then complemented these data with nuclear Amplified Fragment Length Polymorphisms (AFLP) markers, to provide a comparison with nuclear biparentally inherited markers. Finally, we have tested for a variety of endosymbiotic bacteria to investigate whether mtDNA structure could be a result of patterns of infection among populations.
Description of mtDNA polymorphism among populations of H. e. chestertonii
H. e. venus
H. e. chestertonii
Buenos Aires (BA)
La Cumbre (CU)
Villa Colombia (VC)
Calima River valley (CV)
H. e. chestertonii (CV)
H. e. venus (CV)
Of the 327 loci examined, we found that 318 were polymorphic, representing 97% of loci. Genetic diversity statistics estimated from AFLP data showed that populations are differentiated within and among species (Additional file 3, P < 0.001). Both H. e. venus and H. e. chestertonii had values of genetic diversity of 27.6%, while the hybrid zone populations (Calima River Valley) were more diverse than in any allopatric locality (H. e. chestertonii (CV) = 29% and H. e. venus (CV) = 30%).
Interactions with endosymbionts
Distribution of Wolbachia within populations of H. e. chestertonii and H. e. venus
Buenos Aires (22)
La cumbre (14)
Villa Colombia (19)
Calima River valley (44)
It is generally accepted that genetic differentiation between subpopulations can lead to the formation of new reproductively isolated species over time . Phylogeographic analysis can be useful in identifying both cryptic species and incipient subpopulations on the way to becoming new species [2, 3]. The analysis of this cryptic population structure can show how genetic, behavioral and ecological processes have acted during the earliest stages of speciation . Studies that include independent sources of evidence, such as morphological comparisons, reproductive biology and phylogenetics, are necessary to understand the history of diverging lineages and to resolve species identification .
In this study, we first confirmed the unusual degree of mitochondrial divergence within H. e. chestertonii. Our analysis was based on a broad sampling of H. e. chestertonii which enabled the confirmation of two principal groups of mitochondrial haplotypes (Figure 1 and Additional file 1). Our broader sampling showed that these clades are not completely associated with the geographic distribution of the populations, as had been suspected previously (Figure 2b) . The principal haplotype groups (Figure 1 and Additional file 1) were on average 2.15% divergent, similar to that estimated in previous studies [13, 15, 17]. This is considerably more divergent than within any other race of H. erato, apart from the trans-Andean biogeographic break which occurs within the distribution of the race H. e. hydara as described above. However, here there is no clear biogeographic context for this population structure. Nonetheless, the haplotypes do show some geographic structure, with 87% of northern individuals being Clade 1 and 78% of southern individuals Clade 2.
If cryptic speciation was occurring, whereby two species are considered as one based on wing pattern morphology, we would expect the mtDNA haplotypes to be associated with a detectable level of genetic differentiation at nuclear markers. Such cryptic species have been identified in a diversity of organisms such as bryophytes, fungi, elasmobranches and arthropods [1, 4, 27, 29–32]. Within Heliconius, a case of cryptic speciation has been recently discovered in two closely related species: H. timareta and H. melpomene . However, in H. e. chestertonii we have found that despite deep divergence in mtDNA between two principal clades (2.15%), the AFLP analysis shows H. e. chestertonii to be a genetically homogeneous species (Figure 2).
Discordance between maternally inherited genetic markers and those transmitted biparentally, can often be explained by the spread of endosymbionts such as Wolbachia, Spiroplasma, Rickettsia, Arsenophonus, Cardinium, and others [34–37]. In most of the cases, these parasites are transmitted together with the mitochondrial genome through the egg cytoplasm, so associations over time can be detected when the mitochondrial genome is analyzed . Some of these endosymbiont microorganisms can lead to reproductive alterations in their arthropod hosts and will lead to divergence between populations [19, 39]. This is the first published study in which the presence of endosymbionts is tested in Heliconius, and we have identified two distinct lineages of Wolbachia within H. e. chestertonii. However, neither of the principal mitochondrial clades of H. e. chestertonii is directly associated with the infection (Table 2). We did not find evidence of presence of other endosymbionts in populations of H. e. chestertonii. We should add a caveat to our results, which is that our PCR assay might not have detected all possible infected individuals. Indeed, the stage of development of the host can lead to over or underestimates of the real density of Wolbachia within populations . This study was limited to adult butterflies, and future analysis might include other stages such as egg, larvae and pupae. Nonetheless, the density of Wolbachia estimated within H. e. chestertonii populations (7%) would be considered "very low" according to a recent classification . In the future it would be interesting to further investigate the phenotypic effects of this infection. It is also of course possible that another endosymbiont is present, which was not sampled with the PCR assays described here. However, for the moment there is no evidence that the mitochondrial structure in H. e. chestertonii is a result of endosymbiont infection. In summary, we have provided no evidence that mtDNA structure in H. e. chestertonii is due to either cryptic speciation or endosymbiotic bacteria. This leaves historical processes within the species as the most likely cause for the pattern.
Climatic changes during glacial and interglacial periods can lead to contractions, expansions and fragmentations of populations [41–44]. The 2% divergence between lineages within H. e. chestertonii suggests divergence within approximately the last million years. Even without such vicariance, isolation by distance can lead to genetic structure within species. Intriguingly, recent work on H. cydno has shown that this species similarly has a marked genetic break in the center of its Cauca Valley range (Arias and Salazar, pers. comm.). In both species, southern Cauca populations are more closely related to subspecies on the Pacific coast than those in the North. A plausible scenario is that the Cauca Valley has been subject to a double colonization first from the central Andean valleys and subsequently from the Pacific populations in the west. Nonetheless, we are not aware of any geological evidence that would support this hypothesis.
Our genetic analysis shows that northern and southern populations of H. e. chestertonii are genetically differentiated, but with only frequency differences in mtDNA clades, and no corresponding genetic structure at nuclear markers, despite the deep divergence (2.15%) between the two principal mtDNA clades. Our results support the assertion that mtDNA evidence alone should be used with caution in delimiting species boundaries. In this case, divergent haplotype groups within populations could not be explained by either cryptic speciation or endosymbiont infections.
Populations collected and individuals used in each analysis
H. e. chestertonii
Buenos Aires (BA)
La Cumbre (CU)
Villa Colombia (VC)
H. e. chestertonii/Calima River Valley
H. e. venus /hybrids
H. e. venus
Rio Piedras (RP)†
DNA Butterflies extraction
Genomic DNA was extracted from one-third of thorax or the end of the abdomen using DNeasy Blood & Tissue kit (Qiagen) following the manufacturer's tissue-extraction protocol. The thorax extractions were used for mitochondrial and AFLPs analysis and abdomen extractions for endosymbiont assays (Table 3).
Sequencing and phylogenetic analysis of mitochondrial markers
At least six individuals of each population, three of each sex when possible (Table 3), were used to amplify a total of 1551 bp of a mitochondrial region, which covered the subunits I and II of Cytocrome Oxidase (CO I_II) and leucine-tRNA. We used published primers and PCR conditions from Beltran et al. 2002 for our amplifications. Subsequently, all the PCR products were purified for sequencing with Exonuclease I and Shrimp Alkaline Phosphatase enzymes (Fermentas) and sent to Macrogen Sequencing Service (Macrogen, Korea). Sequence editing was performed using Geneious Ver. 5.4 . Sequences were aligned using Clustal W Ver. 2.0  and checked for reading-frame errors in protein-coding regions with MacClade Ver. 4.08 . Sequences were deposited in GenBank (Access numbers: JF912810-JF912880). To complement our analysis, we included publicly available sequences of H. erato [13, 16, 17] and sequences of H. hecalesia and H. clysonimus were used as outgroups (GenBank access numbers in Additional file 5). Phylogenetic analyses were performed using two different approaches: Maximum-Parsimony (MP) and Bayesian inference (BI).
Maximum-parsimony (MP) methods were implemented in PAUP 4.0b8 , using a heuristic search and tree bisection-reconnection (TBR) branch swapping option. A majority rule consensus tree was computed whenever multiple equally parsimonious trees were obtained. Parsimony bootstrap support values were estimated through 1000 bootstrap replicates. A Bayesian analysis was conducted with GTR + I + G nucleotide substitution model, which was the best-fit model obtained in JModel Test Ver. 0.1.1  based on a Hierarchical Likelihood Ratio Test (HLRT). Bayesian inference (BI) was carried out using four simultaneous chains for ten million generations of Markov Chain Montecarlo (MCMC), sampling every 100 generations. The consensus tree and posterior probability of the nodes was estimated with Mr Bayes Ver. 3.1 [50, 51].
Topology test and population genetics analysis
The Shimodaira-Hasegawa (SH) log-likelihood test, as implemented in PAUP 4.0b8 [48, 52], was used to test the monophyly of H. e. chestertonii. To test this a priori hypothesis, BI analysis was first performed using the same parameters as described earlier but this time by enforcing the monophyly of the complex as a topological constraint. The SH test was then used to compare trees obtained from both constrained and unconstrained analysis.
We described DNA polymorphism in populations of H. e. chestertonii and H. e. venus (Table 1) with DnaSP Ver. 5.10.01 . The measures employed were: 1) number of segregating sites (S), 2) number of haplotypes (h), 3) average pairwise number of differences between sequences (k) and genetic diversity (θ). An analysis of molecular variance (AMOVA) and F ST values were obtained in ARLEQUIN Ver. 3.5 to determine genetic structure between populations from mtDNA markers . To investigate relationships between populations a haplotype network was constructed using NETWORK Ver. 22.214.171.124 .
AFLPs, cluster analysis and genetic distance
Genomic DNA from 185 individuals from all the populations, was used for DNA fingerprinting with AFLP markers (Table 3). The DNA quality was quantified by spectrophotometry and only samples with an A260/A280 ratio between 1.8 and 2.0 were used. For AFLP generation, we applied the general method of Vos et al.  with minor modifications. The AFLP® Core Reagent Kit (Invitrogen) was used for the digestion of 125 ng of DNA for samples with EcoRI and MseI restriction endonucleases and the ligation with EcoRI/MseI adaptors, following the manufacturers protocol. The best primer combinations (high variation and fragments between 50 to 400 bp) for pre- and selective amplifications were selected by comparing the final sequencing of eight different primer mixtures for 48 individuals (Additional file 6). Sixteen samples chosen at random were run in duplicate during the screening process to ensure reproducibility of selected markers. As result, primers carrying a single selective nucleotide at the 3-end: EcoRI+A (5-GAC TGC GTA CCA ATT CA-3) and MseI+C (5-GAT GAG TCC TGA GTA AC-3) were chosen for the pre-amplification cycle. The conditions in this first PCR were: denaturation at 94°C for 60s, followed by 20 cycles with denaturation at 94°C for 30s, annealing at 56°C for 60s and extension at 72°C for 120s. Subsequently, selective amplifications were performed using four pairs of primers that contained three selective bases and EcoRI primers were labelled with the fluorescent dyes: EcoRI (FAM)+ACA/MseI+CGT, EcoRI (VIC)+ACC/MseI+CGT, EcoRI (PET)+ACT/MseI+CGT and EcoRI (NED)+ACG/MseI+CAC. For these amplifications we applied a touchdown PCR of 12 cycles with denaturation at 94°C for 30s, an annealing temperature with 0.7°C stepwise reduction from 65°C to 56°C for 60s and extension at 72°C for 120s, after which 23 additional cycles were run with fixed annealing temperature of 56°C for 30s. AFLP reaction products were labelled with an internal size standard (GeneScan™-500 LIZ™) and run on an ABI 3730 automated DNA sequencer (Applied Biosystems). Fragment data were collected and analysed with GeneMapper Ver. 4.0 (Applied Biosystems). All bands were visually confirmed and only unambiguous loci between 50 and 400 bp were included in the analysis. Each individual genotype was manually assessed. A binary data matrix of presence (1) or absence (0) of bands of each size by sample was generated.
We used the presence/absence matrix of AFLP fragments to differentiate all individuals and populations using a Bayesian clustering algorithm implemented in the program Structure Ver. 2.3.3 [57, 58]. The number of clusters (K) was determined by comparing the likelihood ratios for K values between 1 and 6. Previous runs including more than 6 clusters were done and the likelihood values were lower and are not shown in this analysis. Each likelihood value was estimated with runs that involved a burn-in of between 104 and 107 MCMC generations with 10 interactions. An admixture model under the assumption of Hardy-Weinberg equilibrium was implemented in the runs. The best number of clusters was confirmed with the ad hoc statistic ΔK . Additionally we implemented a principal component analysis (PCA) using the software Genetix Ver. 4.05.  to confirm the results and variation of our data. Measures of heterozygosity and variation were estimated with AFLP-SURV Ver.1.0  and with an AMOVA in Arlequin .
Determination of the presence of endosymbionts
Primers for mtDNA and endosymbionts genes
Beltran et al. 2002
Beltran et al. 2002
Zhou et al. 1998
von der Schulenburg
et al. 2001
Hurst et al. 1999
Van kuppeveld et al.1992
AGM was supported by COLCIENCIAS, Facultad de Ciencias and Vicerrectoria de Investigaciones, Universidad de los Andes. ML and AGM were funded by Banco de la República (Project 2582), and private donations (Continautos S.A., Proficol El Carmen S.A. and Didacol S.A). CDJ was fund by Funding from a Leverhulme Research Leadership grant.
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