Immune System Evolution

Evolution of Insect Immune Systems

Immune systems can exhibit rapid evolutionary dynamics due to continuous interaction with ever-changing suites of pathogens, which themselves are evolving to evade or suppress host immunity. Additionally, optimal immunological focus may shift if the host evolves to exploit a new ecological niche that exposes the host to novel pathogens. We use population genetic, quantitative genetic, and molecular evolutionary analyses to understand the short-term and long-term selective pressures on insect immune systems, and to identify the genes that explain phenotypic variation in immune competence.

Quantitative Genetic Variation in Defense

Like other animals, wild D. melanogaster are genetically variable in their ability to resist infection (above). Genotype and environment can interact to determine resistance. Some genotypes that are resistant to infection on a low-sugar diet become highly susceptible on a high-sugar diet (left).

Individuals in natural populations are highly genetically variable in their ability to fight infection. We use both genome-wide association studies (GWAS) and candidate-gene based studies to identify the genes that underlie this variability. In some cases, we focus explicitly on genes in the immune system, as it is reasonable to suppose that DNA polymorphism in immune-related genes could cause differences in resistance to infection. Not all phenotypic variation in immunity will be due to classical immune genes, though. The immune system is integrated into whole-organism physiology, and variation in many physiological traits can impact defense against infection. Thus any gene with variation that alters a relevant physiology could correspondingly affect immune defense. Determining how much phenotypic variation maps to genes in the immune system versus other organismal processes is crucial to understanding the genetic basis for health and how natural selection will shape defense.

The genetic architecture of defense changes depending on the pathogen. This makes sense because distinct pathogens interact with the host in different ways, and therefore different genes may come into play. The architecture also changes in different environments, illustrating the role genotype-by-environment interactions (GxE) in determining defense quality. These interactions complicate natural selection on immunity because environmental variation erodes consistency in the connection between genotype and phenotype.

Molecular Evolution of Insect Immune Systems

We analyze genetic diversity within populations and genetic differences between species to reveal evolutionary pressures on the immune system. The mode of evolution differs across genes that encode different functions. The core signaling pathways that regulate immune systems are highly conserved across insect species, and in fact are homologous to inflammatory signaling pathways of vertebrates. However, the surveillance proteins that recognize pathogens and the antibiotic peptides that kill pathogens evolve much more quicky. These proteins are frequently encoded in multigene families that rapidly expand or contract in different species, presumably depending on the exact pathogens that most commonly afflict each species. We observe these patterns with comparative genomic analyses between insect species.

At the DNA and amino acid sequence level, some proteins show evidence of adaptive diversification. In antimicrobial peptides (AMPs), we also see intriguing evidence of polymorphisms that are adaptively maintained within D. melanogaster populations and convergent evolution of the same amino acid variants in different Drosophila species. In some cases, AMP alleles encoding variant amino acids are associated with altered resistance to particular bacterial infections. Our lab is currently recruiting a postdoc to study the molecular evolution of D. melanogaster AMP genes and link that variability to antibacterial resistance.

Molecular evolutionary and population genetic analyses reveal evolutionary pressures on immune response genes. For example, novel antimicrobial peptide (AMP) gene families evolve frequently, and AMP gene duplication and deletion is common (left, Cecropin cluster in 12 species of Drosophila). At the amino acid sequence level, we see adaptive maintenance of polymorphism and convergent evolution of amino acid sequences between species (right, residue 69 of Diptericin A).

Mosquitoes and Other Insects

Population genetic and comparative genomic analyses of diverse insects reveals common evolutionary patterns as well as idiosyncrasies that are specific to particular taxa. Evolutionary analyses of Anopheles and other mosquitoes provides foundational knowledge that can contribute to controlling disease transmission.

Although most of our experimental work is performed with Drosophila melanogaster as the insect host, we are extremely interested in comparisons and contrasts to other insect species. We have contributed to evolutionary genetic and comparative genomic analyses in several other species including house flies and honey bees. Although we do not currently have active projects in this area, our lab group has previously examined genetic evolution of mosquitoes that vector malaria in the genus Anopheles. This included documentation of extreme genetic diversity of the APL1 genes of Anopheles gambaie and An. coluzzii, as well as a pre-genome transcriptomic assembly of Anopheles funestus. Our work on population differentiation and genetic signatures of demographic history contributed to the eventual designation of Anopheles coluzzii as a distinct species from Anopheles gambie sensu stricto and suggests potential constraints on the efficacy of population interventions like transgenic gene drives to control mosquito populations.

Key Publications

Natural Genetic Variation in Defense

Shahrestani, P., M. Phillips, E. King, R. Ramezan, M. Riddle, M. Thornburg, Z. Greenspan, Y. Estrella, K. Garcia, P. Chowdhury, G. Malarat, M. Zhu, S.M. Rottshaefer, S. Wraight, M. Griggs, J. Vandenberg, A.D. Long, A.G. Clark and B.P. Lazzaro (2021) The genetic basis of Drosophila melanogaster defense against Beauveria bassiana explored through two approaches: experimental evolution with resequencing and quantitative trait locus mapping. G3: Genes, Genomes, Genetics 11:jkab324 [pdf]

Howick, V.M. and B.P. Lazzaro (2017) The genetic architecture of defense as resistance to and tolerance of bacterial infection in Drosophila melanogaster. Molecular Ecology 26:1533-1546. [pdf]

Unckless, R.L., S.M. Rottschaefer and B.P. Lazzaro (2015) The complex contributions of genetics and nutrition to immunity in Drosophila melanogaster. PLoS Genetics 11(3): e1005030. [pdf]

Sackton, T.B., B.P. Lazzaro and A.G. Clark (2010) Genotype and gene expression associations with immune function in Drosophila. PLoS Genetics, 6:e1000797 [pdf]

Lazzaro, B.P., T.B. Sackton and A.G. Clark (2006) Genetic variation in Drosophila melanogaster resistance to infection: a comparison across bacteria. Genetics 174:1539-1554 [pdf]

Lazzaro, B.P., B.K. Sceurman and A.G. Clark (2004) The genetic basis of natural variation in D. melanogaster antibacterial immunity. Science 303:1873-1876 [pdf]

Antimicrobial Peptide (AMP) Evolution

Lazzaro, B.P. (2025) The promise of antimicrobial peptides. Open Access Government October 2025 issue, pp 40-41. https://doi.org/10.56367/OAG-048-11766 [pdf]

Lazzaro, B.P., M. Zasloff, and J. Rolff (2020) Antimicrobial peptides: application informed by evolution. Science 368:eaau5480 [pdf]

Unckless, R.L. and B.P. Lazzaro The potential for adaptive maintenance of diversity in insect antimicrobial peptides. Philosophical Transactions of the Royal Society, Biology, 371:20150291 [pdf]

Unckless, R.L.*, V.M. Howick*, and B.P. Lazzaro (2016) Convergent balancing selection on an antimicrobial peptide in Drosophila. Current Biology 26:257-262 [pdf]

Lazzaro, B.P. and A.G. Clark (2003) Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster. Molecular Biology and Evolution 20:914-923 [pdf]

Lazzaro, B. P. and A.G. Clark (2001) Evidence for recurrent paralogous gene conversion and exceptional allelic divergence in the Attacin genes of Drosophila melanogaster. Genetics 159:659-671 [pdf]

Molecular Evolution of Insect Immune Systems

Waterhouse, R.M., B.P. Lazzaro, and T.B. Sackton (2020) Characterization of insect immune systems from genomic data. In Immunity in Insects, Springer Protocols Handbooks. Ch 1, pp 3-34 [pdf]

Im, J.H. and B.P. Lazzaro (2018) Population genetic analysis of autophagy and phagocytosis genes in Drosophila melanogaster and D. simulans. PLoS One 13:e0205024 [pdf]

Sackton, T.B., B.P. Lazzaro, and A.G. Clark (2017) Rapid expansion of immune-related gene families in the house fly, Musca domestica. Molecular Biology and Evolution 34:857-872. [pdf]

Unckless, R.L.*, V.M. Howick*, and B.P. Lazzaro (2016) Convergent balancing selection on an antimicrobial peptide in Drosophila. Current Biology 26:257-262 [pdf]

Crawford, J.E., S.M. Rottschaefer, B. Coulibaly, M. Sacko, O. Niare, M.M. Riehle, S.F. Traore, K.D. Vernick and B.P. Lazzaro (2013) No evidence for positive selection at two potential targets for malaria transmission-blocking vaccines in Anopheles gambiae s.s. Infection, Genetics, and Evolution 16:97-92 [pdf]

Lazzaro, B.P. and A.G. Clark (2012) “Rapid evolution of innate immune response genes.” In Rapidly Evolving Genes and Genetic Systems, R.S. Singh, J. Xu and R.J. Kulathinal, eds. Oxford University Press, Oxford, UK [pdf]

Crawford, J.E., E. Bischoff, T. Garnier, A. Gneme, K. Eiglmeier, I. Holm, M.M. Riehle, W.M. Guelbeogo, N. Sagnon, B.P. Lazzaro and K.D. Vernick (2012) Evidence for population-specific positive selection on immune genes of Anopheles gambiae. Genes, Genomes, Genetics 2:1505-1519 [pdf]

Rottschaefer, S.M., M.M. Riehle, B. Coulibaly, M. Sacko, O. Niare, I. Morlais, S.F. Traore, K.D. Vernick and B.P. Lazzaro (2011) Exceptional diversity, maintenance of polymorphism, and recent directional selection on the APL1 malaria resistance genes of Anopheles gambiae. PLoS Biology 9:e1000600 [pdf]

Juneja, P. and B.P. Lazzaro (2010) Haplotype structure and expression divergence at the Drosophila cellular immune gene eater. Molecular Biology and Evolution, 27:2284-2299 [pdf]

Juneja, P. and B.P. Lazzaro (2009) “Population genetics of insect immune responses.” In Insect Infection and Immunity, J. Rolff and S. Reynolds eds. [pdf]

Lazzaro, B.P. (2008) Natural selection on the Drosophila innate immune system. Current Opinion in Microbiology, 11:284-289 [pdf]

Sackton, T.B., B.P. Lazzaro, T.A. Schlenke, J.D. Evans, D. Hultmark and A.G. Clark (2007) Dynamic evolution of the innate immune system in Drosophila. Nature Genetics 39:1461-1468 [pdf]

Lazzaro, B.P. (2005) Elevated polymorphism and divergence in the class C scavenger receptors of Drosophila melanogaster and D. simulans. Genetics 169:2023-2034 [pdf]

Lazzaro, B.P. and A.G. Clark (2003) Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster. Molecular Biology and Evolution 20:914-923 [pdf]

Lazzaro, B. P. and A.G. Clark (2001) Evidence for recurrent paralogous gene conversion and exceptional allelic divergence in the Attacin genes of Drosophila melanogaster. Genetics 159:659-671 [pdf]

Mosquito Population Genetics and Immunity

Hollingsworth, B.D., N.D. Grubaugh, B.P. Lazzaro, and C.C. Murdock (2023) Leveraging the mosquito virome to understand mosquito ecology and mosquito-borne disease transmission. PLoS Pathogens 19:e1011588 [pdf]

Crawford, J.E., W.M. Guelbeogo, A. Sanou, A. Traore, K.D. Vernick, N. Sagnon and B.P. Lazzaro (2010) De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology. PLoS One, 5:314202 [pdf]

Crawford, J. and B.P. Lazzaro (2010) The demographic histories of the molecular forms of Anopheles gambiae s.s. Molecular Biology and Evolution, 27:1739-1744 [pdf]

Riehle, M.M., J. Xu, B.P. Lazzaro, S.M. Rottschaefer, B. Coulibaly, M. Sacko, O. Niare, I. Morlais, S.F. Traore and K.D. Vernick (2008) Anopheles gambiae APL1 is a family of variable LRR proteins required for Rel1-mediated protection from the malaria parasite, Plasmodium berghei. PLoS One 3:e3672 [pdf]

Vernick, K., F. Oduol, B.P. Lazzaro, J. Glazebrook, J. Xu, M. Riehle and J. Li (2005) Molecular genetics of mosquito resistance to malaria parasites. Current Topics in Microbiology and Immunology 295:383-415 [pdf]