- Open Access
Repeated horizontal transfers of four DNA transposons in invertebrates and bats
© Tang et al.; licensee BioMed Central. 2015
Received: 17 October 2014
Accepted: 30 December 2014
Published: 17 January 2015
Horizontal transfer (HT) of transposable elements (TEs) into a new genome is considered as an important force to drive genome variation and biological innovation. However, most of the HT of DNA transposons previously described occurred between closely related species or insects.
In this study, we carried out a detailed analysis of four DNA transposons, which were found in the first sequenced twisted-wing parasite, Mengenilla moldrzyki. Through the homology-based strategy, these transposons were also identified in other insects, freshwater planarian, hydrozoans, and bats. The phylogenetic distribution of these transposons was discontinuous, and they showed extremely high sequence identities (>87%) over their entire length in spite of their hosts diverging more than 300 million years ago (Mya). Additionally, phylogenies and comparisons of transposons versus orthologous gene identities demonstrated that these transposons have transferred into their hosts by independent HTs.
Here, we provided the first documented example of HT of CACTA transposons, which have been so far extensively studied in plants. Our results demonstrated that bats had continuously acquired new DNA elements via HT. This implies that predation on a large quantity of insects might increase bat exposure to HT. In addition, parasite-host interaction might facilitate exchanging of their genetic materials.
DNA-mediated or class 2 transposons were one class of transposable elements (TEs). Most DNA transposons transpose via a ‘cut and paste’ mechanism implemented by transposases. They were generally characterized by terminal inverted repeats (TIRs) and target site duplication (TSD) . Based on their transposases, DNA transposons could be classified into 19 superfamilies, including Tc1/mariner, hAT, PiggyBac, CACTA, MuDR, Merlin, Transib, P, PIF/Harbinger, Mirage, Zator, Ginger, Kolobok, Chapaev, Novosib, Rehavkus, PHIS, Sola, and Academ [2,3].
Although the possibility of stochastic loss suggests that TEs should be a seemingly inevitable vertical extinction in their original host genomes, TEs are widespread in organisms [1,4-6]. Horizontal transfer (HT) is a process of genetic material exchanging among non-mating species or isolated species. HT of a transposon into a new genome allows the element to evade inevitable extinction, suggesting that HT plays important roles in the persistence of TEs . In addition, HT of TEs into a new genome is also regarded as important forces to drive genome variation and biological innovation.
Generally, there are three criteria used to infer HT events: (1) high sequence similarity of TEs from divergent taxa, (2) incongruence between TE and host phylogeny, and (3) a patchy TE distribution within a group of taxa [7,8]. The first documented example of HT of TEs was the P element of Drosophila . More than 330 cases (188 cases for DNA transposons and 142 cases for RNA transposons) of eukaryote-to-eukaryote HT events of TEs were described so far . However, no documented example of HT has been described for the CACTA superfamily of DNA transposons, which so far has extensively been studied in plants [6,11]. In addition, most of HT of DNA transposons (122 out of 188) previously described occurred between closely related species or insects .
In this study, we described four DNA transposons which were present in diverse invertebrate and vertebrate animals. The combination of high identity levels between TEs despite deep divergence times of their host taxa, patchy TE taxonomic distribution, and lower genetic distances for TEs than for host genes clearly demonstrated that they had horizontally transferred into their hosts.
Distribution patterns of four DNA transposons
Characteristics of four DNA transposons in this study
Average divergence ± SE
8.22 ± 5.66
1.45 ± 0.65
1.45 ± 0.75
2.16 ± 3.75
9.94 ± 2.83
0.86 ± 1.49
1.82 ± 0.85
2.32 ± 1.38
13.5 ± 2.16
4.74 ± 1.51
4.81 ± 1.48
4.63 ± 1.87
9.88 ± 3.95
2.74 ± 3.87
10.6 ± 3.69
5.94 ± 3.48
13.2 ± 5.49
9.91 ± 3.84
2.82 ± 2.24
2.16 ± 0.60
2.46 ± 0.20
The third DNA transposon, called Spongebob, was found in insects (M. moldrzyki, R. prolixus, and Bombyx mori) and hydrozoans (Hydra magnipapillata). Only partial consensus sequences of Spongebob could be reconstructed for insects (Table 1 and Figure 1C). In the hydrozoans, Spongebob was present in multiple full-length copies (>50), which allowed the reconstruction of a consensus sequence of 5,836 in length. However, it is difficult for us to find the exact transposase encoding by Spongebob_ HMa due to stop codons or frameshifts. The first three bases in the TIRs of Spongebob_ HMa were CCC, and their copies were flanked by 2 bp target site duplication (TSD) (Additional file 2: Figure S1), suggesting that it was a member of TRC elements of the CACTA (also called En/Spm) superfamily of DNA transposons . A pairwise comparison of Spongebob consensus sequences from the above four species revealed that the elements were more than 89.7% identical over about 430 bp (Figure 1C), suggesting that they should belong to the same family.
The last DNA transposon named as Kenshin was shared by the twisted-wing parasite, alfalfa leafcutting bee Megachile rotundata and bat Myotis davidii (Table 1 and Figure 2). We found one copy of Kenshin in the twisted-wing parasite and alfalfa leafcutting bee, which had an intact open reading frame (ORF) encoded a 584- and 581-amino acid (aa) long transposase, respectively. This suggests that the element had an ability of transposition in both species. This element might be also responsible for the amplification of non-autonomous elements in these species. We identified one non-autonomous element in the alfalfa leafcutting bee and two non-autonomous elements in the bat (Table 1). These non-autonomous elements had experienced successful amplification and largely outnumbered their autonomous masters (Table 1). One explanation might be that non-autonomous elements could avoid defense system of their hosts as a result of short sequence length . Kenshin elements identified in these species were very similar to each other and diverged by 5.0%–11.1% (Figure 1D). Phylogenetic analysis based on transposases of autonomous elements demonstrated that it was a member of the piggyBac superfamily (Figure 4B).
Evidence for repeated horizontal transfers
Four DNA transposons described here showed extremely high identities (>87%) over the full length at the nucleotide level despite their hosts diverged more than 300 Mya (Figures 1 and 2, respectively). This provided us with convincing evidence to support that these transposons had repeatedly invaded into these species by HTs. However, we should note that these results might result from other evolutionary processes, such as purifying selection acting on transposons or variable rates of the evolution of transposons [24,25]. Therefore, making HT conclusion of these transposons should be cautious.
To obtain more evidence for HTs of these transposons, we investigated the phylogenetic distribution of these transposons. The results indicated that they were discontinuous distribution in species (Table 1 and Figure 2). For example, both Buster2 and Kenshin were only present in two invertebrates and one vertebrate, and they were not identified in all other vertebrate and invertebrate species for which a complete or nearly complete genome is available in the National Center for Biotechnology Information (NCBI) database (>102) . Similar patterns were also observed for Buster1 and Spongebob (Figure 2).
Additionally, in many cases, the sequence identities of these four DNA transposons were extremely high compared with the divergence time of their hosts. For example, there was more than 87% between Buster2 in the insects and the freshwater planarian, which diverged more than 792 Mya  (Figures 1 and 2). Similarly, Buster2 and Kenshin identified in the insects and mammals, which shared the last common ancestor about 782 Mya , showed more than 89% identities. Besides, we also found that Spongebob in the insects and hydrozoans shared high sequence identities (>89%) at the nucleotide level.
We also observed that phylogenies for Buster1 and Buster2 showed a striking lack of structure. For example, phylogenetic analysis based on transposases of Buster1 showed that this element identified in the twisted-wing parasite was much closer to the freshwater planarian than to another insect, the triatomine bug (Figure 4A). Besides, an unrooted tree based on copies of Buster2 suggested that Buster2 elements in the triatomine bug and evening bat were much closer with each other compared with that in the twisted-wing parasite (Additional file 3: Figure S2). All these results were not consistent with vertical inheritance of these transposons.
Finally, our results showed that the nucleotide sequence divergence among four DNA transposons (about 1.5%–13%) was much lower than that observed for three conserved host nuclear genes (about 22%–30%), heat shock cognate 70, Tubulin beta-3, and elongation factor 1 alpha, which were described in our previous study . Therefore, HTs of these transposons might be the only logical explanation for high sequence identities among these transposons in distantly related species.
Here, we performed a detailed analysis of characteristics and evolutionary history of four DNA transposons in diverse species. The combination of high identity levels between TEs despite deep divergence times of their host taxa, patchy TE taxonomic distribution, and lower genetic distances for TEs than for host genes clearly demonstrated that these elements had transferred into these species by independent HTs. We also noted that the phenomenon of HT of Buster1 had previously been reported . However, the detail information about this transposon remains unknown. In this study, both non-autonomous elements and its autonomous partners were found in the twisted-wing parasite, triatomine bug, and freshwater planarian (Table 1), which would provides us with a better understanding for the evolutionary history of Buster1. In addition, structural and phylogenetic analyses showed that Buster1 was a novel member of the Buster family.
Although the distribution of these four DNA transposons in species was patchy, their transfer did not randomly happen since the same species have been independently invaded by different, unrelated TEs but others appear to be immune to HT (Figure 2). For example, three transposons are present in the twisted-wing parasite and triatomine bug, but they are not found in other insects (>30) for which genomic sequences are available. This pattern implies that some taxa might be prone to exchanging of genetic materials or are more hospitable to TEs than others. It is reasonable that species which are vulnerable to HT have a weakened response to TE invasion, which would lead them to lose control of the amplification of the new invader. However, species with a strong resistance would not allow the TEs to amplify in the genome. Similar phenomena have been observed in vertebrates .
DNA transposons exist in a wide variety of organisms. However, it was believed that DNA transposons existing in mammals were fossils, and they did not have any ability for mobility in the last 40 Mya [29-31]. This situation has changed when recent DNA transposon activity was discovered in the bats [32-34]. Here, the low average divergence (2.16%–4.81%) between copies of Buster2 and Kenshin and their consensus sequences in the bats strongly suggested that they had been inserted recently (Table 1). Besides, Buster2 and Kenshin were apparently absent from all other mammals (>80) including other seven closely related bats (Figure 2), for which genome sequences are available. Interestingly, Kenshin is only present in the genome of the bat M. davidii but is not in the other three Myotis genomes sequenced, suggesting that it might be mobilized within the last 10 Mya . These results also implied that bats had continuously acquired new DNA elements via HT. Interestingly, bats belonging to Vespertilionidae family that were the only mammals reported to have recent DNA transposon activity [32-34]. Meanwhile, many of DNA transposons were also horizontally transferred into their hosts [28,35]. However, we should note that HT provides a delivery system for the re-colonization of TEs of genomes and we cannot exclude that DNA transposons might be active in many mammals for which genomes are not sequenced.
Four DNA transposons were found in a wide range of organisms including insects, freshwater planarian, hydrozoans, and bats, suggesting that multiple mechanisms might be involved in their HTs. One interesting finding is the identification of these elements to be present and transferred between insects and bats. The evening bats feed heavily on beetles (Coleoptera), but they also eat moths (Lepidoptera), small flies (Diptera), and other insects . This suggested that predation on a large quantity of insects might increase bat exposure to HT. Another interesting finding is the identification of near identical DNA transposons in insects and the twisted-wing parasite. M. moldrzyki is a species of Strepsiptera (Mengenillidae), which infects at least 35 families of insects belonging to seven orders . During the process of parasitism, these parasites obtained nutrients from their hosts . Therefore, parasite-host interaction might facilitate exchanging of their genetic materials.
In this study, we provided the first documented example of HT of CACTA transposons. Our results demonstrated that bats had continuously acquired new DNA elements via HT. This implies that predation on a large quantity of insects might increase bat exposure to HT. In addition, parasite-host interaction might facilitate exchanging of their genetic materials.
The silkworm (Bombyx mori) assembled genomic sequences were downloaded from Silkworm Genome Database  (http://www.silkdb.org/silkdb/). The triatomine bug, Rhodnius prolixus, genomic supercontig sequences were downloaded from VectorBase  (https://www.vectorbase.org/). Survey sequences from the genomes of five bats (Myotis austroriparius, Lasiurus borealis, Corynorhinus rafinesquii, Perimyotis subflavus, and Nycticeius humeralis) were downloaded from Dryad Digital Repository  (http://datadryad.org/). The postman butterfly (Heliconius melpomene) genomic sequences were downloaded from Butterfly Genome Database  (http://www.butterflygenome.org/). All of the rest of the genome sequences used in this study were downloaded from the National Center for Biotechnology Information.
Identification of four DNA transposons in Mengenilla moldrzyki and other surveyed genomes
Four DNA transposons were identified from the genome of the twisted-wing parasite, M. moldrzyki, and they were designated as Buster1, Buster2, Spongebob, and Kenshin, respectively. Their consensus sequences were reconstructed using the software DAMBE . Then, their consensus sequences were used as queries to search against Repbase  (http://www.girinst.org/) to classify them into known superfamilies. To identify related elements in other species, Blastn  searches were performed using nucleotide sequences of the above four DNA transposons query against all GenBank databases and Repbase. Significant hits (>85%) were collected and aligned. Their consensus sequences were also reconstructed and compared among species.
Next, we used these respective consensus sequences to mask each genome to estimate copy number. If one autonomous element and its derivatives coexisted in many studied species genomes (Table 1), their copy numbers were calculated using the following criteria. Fragments that were longer than 600 bp were calculated as copies of autonomous elements as miniature inverted-repeat transposable elements are generally shorter than 600 bp . For MITEs or other non-autonomous elements, all fragments with more than 80% identity and coverage to their consensus sequences were calculated as their copies. Meanwhile, fragments were considered to be a single insertion when they were separated by less than 50 bp. If only one autonomous or non-autonomous element was present in one species, all blast hits with more than 100 bp and 80% identity were used to calculate copy number .
ORF of transposons used in this study was predicted using getorf in EMBOSS-6.3.1 package . These elements were aligned using MUSCLE . Shading and minor manual refinements of multiple alignments were deduced using Genedoc  and Illustrator CS5. Then, we used the software Bioedit  to calculate each pairwise identity of their consensus sequences after all ambiguous and gapped sites were removed. Sequence logos of Buster1_NA1_SM and Buster2_NA2_NH were created by WebLogo  using 30 bp (15 upstream and 15 downstream) flanking their insertion sites.
To determine the relationship of Buster1 and Kenshin with known DNA transposons, transposase sequences of the hAT and piggybac superfamilies were downloaded from GeneBank and Repbase. Phylogenies were performed with the neighbor-joining method (NJ) using MEGA 4  (pairwise deletion, Poisson correction model, 1,000 bootstrap replicates) based on their transposase sequences. Besides, we also investigated the relationship of Buster2 from different species. MEGA 4  (pairwise deletion, maximum composite likelihood, 1,000 bootstrap replicates) was used to build phylogenetic trees based on nucleotide sequences of their full-length or nearly full-length copies.
This work is supported by the Hi-Tech R&D Program (863) of China (2013AA102507-2 to ZZ), the National Natural Science Foundation of China (No. 31260632 to XGZ, No. 31401106 to MJH, and No. 31471197 to ZZ), and the National Natural Science Foundation in Jiangxi Province of China (20122BAB204018 to XGZ).
- Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 2007;41:331–68.PubMed CentralPubMedView ArticleGoogle Scholar
- Jurka J. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet. 2000;16:418–20.PubMedView ArticleGoogle Scholar
- Han MJ, Xu HE, Zhang HH, Feschotte C, Zhang Z. Spy: a new group of eukaryotic DNA transposons without target site duplications. Genome Biol Evol. 2014;6:1748–57.PubMed CentralPubMedView ArticleGoogle Scholar
- Schaack S, Gilbert C, Feschotte C. Promiscuous DNA: horizontal transfer oftransposable elements and why it matters for eukaryotic evolution. Trends Ecol Evol. 2010;25:537–46.PubMed CentralPubMedView ArticleGoogle Scholar
- Hartl DL, Lohe AR, Lozovskaya ER. Modern thoughts on an ancyent marinere: function, evolution, regulation. Annu Rev Genet. 1997;31:337–58.PubMedView ArticleGoogle Scholar
- Roberston HM. Evolution of DNA transposons in eukaryotes. In: Craig NL, Craigie M, Lambowitz A, editors. Mobile DNA II. Herndon, VA: ASM; 2002. p. 1093–110.Google Scholar
- Kidwell MG. Horizontal transfer of P elements and other short inverted repeat transposons. Genetica. 1992;86:275–86.PubMedView ArticleGoogle Scholar
- Silva JC, Loreto EL, Clark JB. Factors that affect the horizontal transfer of transposable elements. Curr Issues Mol Biol. 2004;6:57–71.PubMedGoogle Scholar
- Daniels SB, Peterson KR, Strausbaugh LD, Kidwell MG, Chovnick A. Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics. 1990;124:339–55.PubMed CentralPubMedGoogle Scholar
- Wallau GL, Ortiz MF, Loreto EL. Horizontal transposon transfer in eukarya: detection, bias, and perspectives. Genome Biol Evol. 2012;4:689–99.PubMedView ArticleGoogle Scholar
- Capy P, Bazin C, Higuet D, Langin T. Dynamics and evolution of transposable elements (Molecular Biology Intelligence Unit). New York: Springer; 1998.Google Scholar
- Niehuis O, Hartig G, Grath S, Pohl H, Lehmann J, Tafer H, et al. Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Curr Biol. 2012;22:1309–13.PubMedView ArticleGoogle Scholar
- Lavoie CA, Platt 2nd RN, Novick PA, Counterman BA, Ray DA. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera. Mob DNA. 2013;4:21.PubMed CentralPubMedView ArticleGoogle Scholar
- Hedges SB, Dudley J, Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics. 2006;22:2971–2.PubMedView ArticleGoogle Scholar
- Stadelmann B, Lin LK, Kunz TH, Ruedi M. Molecular phylogeny of New World Myotis (Chiroptera, Vespertilionidae) inferred from mitochondrial and nuclear DNA genes. Mol Phylogenet Evol. 2007;43:32–48.PubMedView ArticleGoogle Scholar
- Zhang HH, Shen YH, Xu HE, Liang HY, Han MJ, Zhang Z. A novel hAT element in Bombyx mori and Rhodnius prolixus: its relationship with miniature inverted repeat transposable elements (MITEs) and horizontal transfer. Insect Mol Biol. 2013;22:584–96.PubMedView ArticleGoogle Scholar
- Lack JB, Van Den Bussche RA. Identifying the confounding factors in resolving phylogenetic relationships in Vespertilionidae. J Mammal. 2010;91:1435–48.View ArticleGoogle Scholar
- Moreno-Vazquez S, Ning J, Meyers BC. hATpin, afamily of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures. Plant Mol Biol. 2005;58:869–86.PubMedView ArticleGoogle Scholar
- Tu Z. Molecular and evolutionary analysis of two divergent subfamilies of a novel miniature inverted repeat transposable element in the yellow fever mosquito, Aedes aegypti. Mol Biol Evol. 2000;17:1313–25.PubMedView ArticleGoogle Scholar
- Arensburger P, Hice RH, Zhou L, Smith RC, Tom AC, Wright JA, et al. Phylogenetic and functional characterization of the hAT transposon superfamily. Genetics. 2011;188:45–57.PubMed CentralPubMedView ArticleGoogle Scholar
- Datzmann T, von Helversen O, Mayer F. Evolution of nectarivory in phyllostomid bats (Phyllostomidae Gray, 1825, Chiroptera: Mammalia). BMC Evol Biol. 2010;10:165.PubMed CentralPubMedView ArticleGoogle Scholar
- Yang G, Nagel DH, Feschotte C, Hancock CN, Wessler SR. Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE. Science. 2009;325:1391–4.PubMedView ArticleGoogle Scholar
- DeMarco R, Venancio TM, Verjovski-Almeida S. SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamily. BMC Evol Biol. 2006;6:89.PubMed CentralPubMedView ArticleGoogle Scholar
- Volff JN. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays. 2006;28:913–22.PubMedView ArticleGoogle Scholar
- Loreto EL, Carareto CM, Capy P. Revisiting horizontal transfer of transposable elements in Drosophila. Heredity. 2008;100:545–54.PubMedView ArticleGoogle Scholar
- Gilbert C, Schaack S, Pace II JK, Brindley PJ, Feschotte C. A role for host parasite interactions in the horizontal transfer of transposons across phyla. Nature. 2010;464:1347–50.PubMed CentralPubMedView ArticleGoogle Scholar
- Zhang HH, Xu HE, Shen YH, Han MJ, Zhang Z. The origin and evolution of six miniature inverted-repeat transposable elements in Bombyx mori and Rhodnius prolixus. Genome Biol Evol. 2013;5:2020–31.PubMed CentralPubMedView ArticleGoogle Scholar
- Novick P, Smith J, Ray D, Boissinot S. Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene. 2010;449:85–94.PubMedView ArticleGoogle Scholar
- Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.PubMedView ArticleGoogle Scholar
- Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420:520–62.PubMedView ArticleGoogle Scholar
- Pace JK, Feschotte C, Feschotte C. The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage. Genome Res. 2007;17:422–32.PubMed CentralPubMedView ArticleGoogle Scholar
- Ray DA, Pagan HJ, Thompson ML, Stevens RD. Bats with hATs: evidence for recent DNA transposon activity in genus Myotis. Mol Biol Evol. 2007;24:632–9.PubMedView ArticleGoogle Scholar
- Ray DA, Feschotte C, Pagan HJ, Smith JD, Pritham EJ, Arensburger P, et al. Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res. 2008;18:717–28.PubMed CentralPubMedView ArticleGoogle Scholar
- Pagán HJ, Macas J, Novák P, McCulloch ES, Stevens RD, Ray DA. Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats. Genome Biol Evol. 2012;4:575–85.PubMed CentralPubMedView ArticleGoogle Scholar
- Thomas J, Schaack S, Pritham EJ. Pervasive horizontal transfer of rolling-circle transposons among animals. Genome Biol Evol. 2010;2:656–64.PubMed CentralPubMedView ArticleGoogle Scholar
- Simmons NB. Order chiroptera. In: Wilson DE, Reeder DM, editors. Mammal species of the world. 3rd ed. Johns Hopkins University; 2005. p.312-529.Google Scholar
- Kathirithamby J. Review of the order Strepsiptera. Syst Ent. 1989;14:41–92.View ArticleGoogle Scholar
- Kathirithamby J. Host-parasitoid associations in Strepsiptera. Annu Rev Ent. 2009;54:227–49.View ArticleGoogle Scholar
- Duan J, Li R, Cheng D, Fan W, Zha X, Cheng T, et al. SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology. Nucleic Acids Res. 2010;38(Database issue):D453–6.PubMed CentralPubMedView ArticleGoogle Scholar
- Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, et al. VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res. 2009;37(Database issue):D583–7.PubMed CentralPubMedView ArticleGoogle Scholar
- Pagán HJ, Macas J, Novák P, McCulloch ES, Stevens RD, Ray DA: Data from: Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats. 2012 Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.83164r7v.
- Dasmahapatra KK, Walters JR, Briscoe AD, Davey JW, Whibley A, Nadeau NJ, et al. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature. 2012;487:94–8.PubMed CentralGoogle Scholar
- Xia X, Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J Hered. 2001;92:371–3.PubMedView ArticleGoogle Scholar
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.PubMedView ArticleGoogle Scholar
- Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000;16:276–7.PubMedView ArticleGoogle Scholar
- Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.PubMed CentralPubMedView ArticleGoogle Scholar
- Nicholas KB, Nicholas HB, Deerfield DW. GeneDoc: analysis and visualization of genetic variation. EMBNEW News. 1997;4:14.Google Scholar
- Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.Google Scholar
- Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14:1188–90.PubMed CentralPubMedView ArticleGoogle Scholar
- Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9.PubMedView ArticleGoogle Scholar
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.