Skip to main content
SpringerLink
Log in

Selection for Antimicrobial Peptide Diversity in Frogs Leads to Gene Duplication and Low Allelic Variation

  • Published:
Journal of Molecular Evolution Aims and scope Submit manuscript

Abstract

Antimicrobial peptides are highly diverse pathogen-killing molecules. In many taxa, their evolution is characterized by positive selection and frequent gene duplication. It has been proposed that genes encoding antimicrobial peptides might be subject to balancing selection and/or an enhanced mutation rate, but these hypotheses have not been well evaluated because allelic variation has rarely been studied at antimicrobial peptide loci. We present an evolutionary analysis of novel antimicrobial peptide genes from leopard frogs, Rana. Our results demonstrate that a single genome contains multiple homologous copies, among which there is an excess of nonsynonymous nucleotide site divergence relative to that expected from synonymous site divergence. Thus, we confirm the trends of recurrent duplication and positive selection. Allelic variation is quite low relative to interspecies divergence, indicating a recent positive selective sweep with no evidence of balancing selection. Repeated gene duplication, rather than a balanced maintenance of divergent allelic variants at individual loci, appears to be how frogs have responded to selection for a diverse suite of antimicrobial peptides. Our data also support a pattern of enhanced synonymous site substitution in the mature peptide region of the gene, but we cannot conclude that this is due to an elevated mutation rate.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Ali MF, Lips KR, Knoop FC, Fritzsch B, Miller C, Conlon JM (2002) Antimicrobial peptides and protease inhibitors in the skin secretions of the crawfish frog, Rana areolata. Biochim Biophys Acta 1601:55–63

    PubMed  CAS  Google Scholar 

  • Altizer S, Harvell D, Friedle E (2003) Rapid evolutionary dynamics and disease threats to biodiversity. Trends in Ecology and Evolution 18:589–596

    Article  Google Scholar 

  • Bakker EG, Toomajian C, Kreitman M, Bergelson J (2006) A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell 18:1803–1818

    Article  PubMed  CAS  Google Scholar 

  • Basir YJ, Knoop FC, Dulka J, Conlon JM (2000) Multiple antimicrobial peptides and peptides related to bradykinin and neuromedin N isolated from skin secretions of the pickerel frog, Rana palustris. Biochim Biophys Acta 1543:95–105

    PubMed  CAS  Google Scholar 

  • Bergelson J, Kreitman M, Stahl EA, Tian D (2001) Evolutionary dynamics of plant R-genes. Science 292:2281–2285

    Article  PubMed  CAS  Google Scholar 

  • Bulmer MS, Crozier RH (2004) Duplication and diversifying selection among termite antifungal peptides. Mol Biol Evol 21:2256–2264

    Article  PubMed  CAS  Google Scholar 

  • Chen T, Farragher S, Bjourson AJ, Orr DF, Rao P, Shaw C (2003) Granular gland transcriptomes in stimulated amphibian skin secretions. Biochem J 371:125–130

    Article  PubMed  CAS  Google Scholar 

  • Chen T, Zhou M, Rao P, Walker B, Shaw C (2006) The Chinese bamboo leaf odorous frog (Rana (Odorrana) versabilis) and North American Rana frogs share the same families of skin antimicrobial peptides. Peptides 27:1738–1744

    Article  PubMed  CAS  Google Scholar 

  • Chinchar VG, Bryan L, Silphadaung U, Noga E, Wade D, Rollins-Smith L (2004) Inactivation of viruses infecting ectothermic animals by amphibian and piscine antimicrobial peptides. Virology 323:268–275

    Article  PubMed  CAS  Google Scholar 

  • Clark AG, Wang L (1997) Molecular population genetics of Drosophila immune system genes. Genetics 147:713–724

    PubMed  CAS  Google Scholar 

  • Conlon JM, Halverson T, Dulka J, Platz JE, Knoop FC (1999) Peptides with antimicrobial activity of the brevinin-1 family isolated from skin secretions of the southern leopard frog, Rana sphenocephala. J Peptide Res 54:522–527

    Article  CAS  Google Scholar 

  • Conlon JM, Sonnevend Á, Patel M, Davidson C, Nielsen PF, Pál T, Rollins-Smith LA (2003) Isolation of peptides of the brevinin-1 family with potent candidacidal activity from the skin secretions of the frog Rana boylii. J Peptide Res 62:207–213

    Article  CAS  Google Scholar 

  • Conlon JM, Kolodziejek J, Nowotny N (2004) Antimicrobial peptides from ranid frogs: taxonomic and phylogenetic markers and a potential source of new therapeutic agents. Biochim Biophys Acta 1696:1–14

    PubMed  CAS  Google Scholar 

  • Cronn R, Cedroni M, Haselkorn T, Grover C, Wendel JF (2002) PCR-mediated recombination in amplification products derived from polyploidy cotton. Theor Appl Genet 104:482–489

    Article  PubMed  CAS  Google Scholar 

  • Crump D, Lean D, Trudeau VL (2002) Octylphenol and UV-B radiation alter larval development and hypothalamic gene expression in the leopard frog (Rana pipiens). Environ Health Perspect 110:277–284

    Article  PubMed  CAS  Google Scholar 

  • Daszak P, Cunningham AA, Hyatt AD (2000) Emerging infectious diseases of wildlife – threats to biodiversity and human health. Science 287:443–449

    Article  PubMed  CAS  Google Scholar 

  • Duda TF Jr, Vanhoye D, Nicolas P (2002) Roles of diversifying selection and coordinated evolution in the evolution of amphibian antimicrobial peptides. Mol Biol Evol 19:858–864

    PubMed  CAS  Google Scholar 

  • Garrigan D, Hedrick PW (2003) Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. Evolution 57:1707–1722

    PubMed  CAS  Google Scholar 

  • Goraya J, Wang Y, Li Z, O’Flaherty M, Knoop FC, Platz JE, Conlon JM (2000) Peptides with antimicrobial activity from four different families isolated from the skins of the North American frogs Rana luteiventris, Rana berlandieri, and Rana pipiens. Eur J Biochem 267:894–900

    Article  PubMed  CAS  Google Scholar 

  • Hillis DM, Wilcox TP (2005) Phylogeny of the New World true frogs (Rana). Mol Phylogenet and Evol 34:299–314

    Article  Google Scholar 

  • Hoffman EA, Blouin MS (2004) Evolutionary history of the northern leopard frog: reconstruction of phylogeny, phylogeography, and historical changes in population demography from mitochondrial DNA. Evolution 58:145–159

    PubMed  Google Scholar 

  • Horikawa R, Parka DS, Herring PL, Pisano JJ (1985) Pipinins: new mast cell degranulating peptides from Rana pipiens. Fed Proc 44:695

    Google Scholar 

  • Hudson RR, Kreitman M, Aguadé M (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116:153–159

    PubMed  CAS  Google Scholar 

  • Ironside JE, Filatov DA (2005) Extreme population structure and high interspecific divergence of the silene Y chromosome. Genetics 171:705–713

    Article  PubMed  CAS  Google Scholar 

  • Kwon SY, Carlson BA, Park JM, Lee BJ (2000) Structural organization and expression of the gaegurin 4 gene of Rana rugosa. Biochim Biophys Acta 1492:185–190

    PubMed  CAS  Google Scholar 

  • Lutz GJ, Cuizon DB, Ryan AF, Lieber RL (1998) Four novel myosin heavy chain transcripts define a molecular basis for muscle fibre types in Rana pipiens. J Physiol 508:667–80

    Article  PubMed  CAS  Google Scholar 

  • Lynn DJ, Higgs R, Gaines S, Tierney J, James T, Lloyd AT, Fares MA, Mulcahy G, O’Farrelly C (2004) Bioinformatic discovery and initial characterisation of nine novel antimicrobial peptide genes in the chicken. Immunogenetics 56:170–177

    Article  PubMed  CAS  Google Scholar 

  • Marenah L, Flatt PR, Orr DF, Shaw C, Abdel-Wahab YHA (2005) Characterization of naturally occurring peptides in the skin secretion of Rana pipiens frog reveal pipinin-1 as the novel insulin-releasing agent. J Pept Res 66:204–210

    Article  PubMed  CAS  Google Scholar 

  • Maxwell AI, Morrison GM, Dorin JR (2003) Rapid sequence divergence in mammalian β-defensins by adaptive evolution. Mol Immunol 40:413–421

    Article  PubMed  CAS  Google Scholar 

  • Maynard Smith JM (1992) Analyzing the mosaic structure of genes. J Mol Evol 34:126–129

    Google Scholar 

  • Morjan CL, Rieseberg LH (2004) How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles. Mol Ecol 13:1341–1356

    Article  PubMed  CAS  Google Scholar 

  • Park JM, Jung J-E, Lee BJ (1994) Antimicrobial peptides from the skin of a Korean frog, Rana rugosa. Biochem Biophys Res Commun 205:948–954

    Article  PubMed  CAS  Google Scholar 

  • Perron GG, Zasloff M, Bell G (2006) Experimental evolution of resistance to an antimicrobial peptide. Proc Biol Sci 273:251–256

    Article  PubMed  CAS  Google Scholar 

  • Peschel A, Sahl H-G (2006) The co-evolution of host cationic antimicrobial peptides and microbial resistance. Nat Rev Microbiol 4:529–536

    Article  PubMed  CAS  Google Scholar 

  • Piertney SB, Oliver MK (2006) The evolutionary ecology of the major histocompatibility complex. Heredity 96:7–21

    PubMed  CAS  Google Scholar 

  • Rollins-Smith LA, Conlon JM (2005) Antimicrobial peptide defenses against chytridiomycosis, an emerging infectious disease of amphibian populations. Dev Comp Immunol 29:589–598

    Article  PubMed  CAS  Google Scholar 

  • Rollins-Smith LA, Carey C, Longcore J, Doersam JK, Boutte A, Bruzgal JE, Conlon JM (2002) Activity of antimicrobial skin peptides from ranid frogs against Batrachochytrium dendrobatidis, the chytrid fungus associated with global amphibian declines. Dev Comp Immunol 26:471–479

    Article  PubMed  CAS  Google Scholar 

  • Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497

    Article  PubMed  CAS  Google Scholar 

  • Schroder JM (1999) Epithelial peptide antibiotics. Biochem Pharmacol 57:121–134

    Article  PubMed  CAS  Google Scholar 

  • Schutte BC, Mitros JP, Bartlett JA, Walters JD, Jia HP, Welsh MJ, Casavant TL, McCray PB Jr (2002) Discovery of five conserved β-defensin gene clusters using a computational search strategy. Proc Natl Acad Sci USA 99:2129–2133

    Article  PubMed  CAS  Google Scholar 

  • Semple CAM, Rolfe M, Dorin JR (2003) Duplication and selection in the evolution of primate β-defensin genes. Genome Biol 4:R31

    Article  PubMed  Google Scholar 

  • Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.0b10. Sinauer Associates, Sunderland, MA

    Google Scholar 

  • Tennessen JA (2005a) Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. J Evol Biol 18:1387–1394

    Google Scholar 

  • Tennessen JA (2005b) Enhanced synonymous site divergence in positively selected vertebrate antimicrobial peptide genes. J Mol Evol 61:445–455

    Google Scholar 

  • Tiffin P, Hacker R, Gaut BS (2004) Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea. Genetics 168:425–434

    Article  PubMed  CAS  Google Scholar 

  • Wakeley J (1999) Nonequilibrium migration in human history. Genetics 153: 1863–1871

    PubMed  CAS  Google Scholar 

  • Won H-S, Kim SS, Jung S-J, Son W-S, Lee B, Lee B-J (2004) Structure-activity relationships of antimicrobial peptides from the skin of Rana esculenta inhabiting Korea. Mol Cells 17:469–476

    PubMed  CAS  Google Scholar 

  • Vanhoye D, Bruston F, Nicolas P, Amiche M (2003) Antimicrobial peptides from hylid and ranin frogs originated from a 150-million year old ancestral precursor with a conserved signal peptide but a hypermutable antimicrobial domain. Eur J Biochem 270:2068–2081

    Article  PubMed  CAS  Google Scholar 

  • Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555–556

    PubMed  CAS  Google Scholar 

  • Yeaman MR, Yount NY (2003) Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev 55:27–55

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank C. Criscione, E. Hoffman, and K. Field. This work was supported by a National Science Foundation Graduate Research Fellowship to J. Tennessen.

Author information

Authors and Affiliations

  1. Department of Zoology, Oregon State University, 3029 Cordley Hall, Corvallis, OR, 97331, USA

    Jacob A. Tennessen & Michael S. Blouin

Authors
  1. Jacob A. Tennessen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael S. Blouin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jacob A. Tennessen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tennessen, J.A., Blouin, M.S. Selection for Antimicrobial Peptide Diversity in Frogs Leads to Gene Duplication and Low Allelic Variation. J Mol Evol 65, 605–615 (2007). https://doi.org/10.1007/s00239-007-9045-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-007-9045-5

Keywords

Search

Navigation