Supplementary Material A:

Known or Inferred Immunity Gene Functions

18w: Toll-related transmembrane receptor involved in gram-negative antibacterial humoral response pathway; also functions in larval development.

cact: Inhibitor of Dif and dorsal translocation to nucleus (IB domain) during antifungal and gram-positive antibacterial humoral response; also functions in larval development.

CG3212: Secreted scavenger receptor protein potentially involved in cellular immune response.

CG11833: Extracellular protein bears strong homology to mucin domain of Hmu.

crq: Macrophage receptor important for phagocytosis of apoptotic cells and, potentially, infected cells as part of cellular immune response.

Dif: Dorsal-related transcription factor involved in antifungal and gram-positive antibacterial humoral response pathway.

dorsal (isoform A): Transcription factor (NF-B domain) involved in antifungal and gram-positive antibacterial humoral response pathway; also functions in larval development.

Dredd: Caspase that cleaves the IB domain from NF-B domain, activating the Relish transcription factor during the gram-negative antibacterial humoral response; also functions in apoptosis.

GNBP1: Plasma membrane gram-negative-binding protein, initiates the gram-negative antibacterial humoral response pathway upon binding LPS.

Hmu: Hemocyte surface mucin that binds an inducer of the gram-negative antibacterial humoral response pathway.

IKK: Cytoplasmic protein kinase interacts with IKK, phosphorylates Relish, involved in the gram-negative antibacterial humoral response pathway.

IKK: Cytoplasmic protein interacts with IKK, involved in the gram-negative antibacterial humoral response pathway.

imd: Death domain protein involved in the gram-negative antibacterial humoral response pathway; potentially involved in apoptosis.

B-Ras: Regulates the rate of degredation of cactus, a necessary step during the activation of the antifungal and gram-positive antibacterial humoral response pathway.

Lectin-galC1: Plasma membrane lectin involved in defense response to gram-negative bacteria.

Mvl: Hemocyte membrane protein controls metal ion accessibility; bears strong homology to mammalian Nramp, a protein that confers resistance to intracellular bacterial parasites.

pelle: Cytoplasmic protein kinase phosphorylates Dif/dorsal, involved in antifungal and gram-positive antibacterial humoral response pathway; also functions in larval development.

PGRP-LA: Plasma membrane peptidoglycan (i.e. gram-positive bacteria) recognition protein expressed in hemocytes, potentially involved in cellular immune response.

PGRP-SA: Secreted peptidoglycan recognition protein expressed in hemocytes, pattern recognition receptor for gram-positive bacteria.

PGRP-SD: Secreted peptidoglycan recognition protein expressed in hemocytes, transcription upregulated during gram-positive bacterial infection.

ref(2)P: Transmembrane protein confers resistance to sigma virus.

Relish: Transcription factor (NF-B and IB domains) involved in gram-negative antibacterial humoral response pathway.

Ser7: Extracellular endopeptidase thatis upregulated during parasitoid wasp and bacterial infection.

Spn43Ac: Extracellular serpin inhibits unknown protease from activating spz as part of antifungal and gram-positive antibacterial humoral response pathway.

spz: Extracellular Toll ligand involved in antifungal and gram-positive antibacterial humoral response pathway; also functions in larval development.

Sr-CI: Plasma membrane scavenger receptor protein binds wide variety of microbial ligands, expressed in hemocytes, may also function in cell-cell adhesion.

Sr-CII: Plasma membrane scavenger receptor protein potentially involved in cellular immune response.

Sr-CIII: Secreted scavenger receptor protein potentially involved in cellular immune response, tandem duplicate of Sr-CI.

Tak1: Cytoplasmic kinase involved in gram-negative antibacterial humoral response pathway.

Tehao: Toll-related transmembrane receptor involved in antifungal immunity, suggested to act as a pattern recognition receptor.

Tep1: Extracellular complement-like protein upregulated after bacterial infection.

Thor: Cytoplasmic protein involved in translational regulation of innate immune system genes, transcription upregulated during bacterial infection.

Toll: Transmembrane receptor involved in antifungal and gram-positive antibacterial humoral response pathway; also functions in larval development.

tube: Cytoplasmic protein interacts with pelle, involved in antifungal and gram-positive antibacterial humoral response pathway; also functions in larval development.

Supplementary Material B:

Data from Individual Immunity and Non-immunity Genes



 = nucleotide diversity, = average pairwise difference per site for silent and replacement sites. D = divergence per site between D. simulans and D. melanogaster. RP = # replacement polymorphisms, SP = # silent polymorphisms in D. simulans. RF = # replacement fixations, SF = # silent fixations along the D. simulans lineage. Hd = haplotype diversity.

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