Data from: Is permanent parasitism reversible? – Critical evidence from early evolution of house dust mites

Long-term specialization may limit the ability of a species to respond to new environmental conditions and lead to a higher likelihood of extinction. For permanent parasites and other symbionts, the most intriguing question is whether these organisms can return to a free-living lifestyle and, thus, escape an evolutionary 'dead end'. This question is directly related to Dollo's law, which stipulates that a complex trait (such as being free-living vs. parasitic) cannot re-evolve again in the same form. Here we present conclusive evidence that house dust mites, a group of medically important free-living organisms, evolved from permanent parasites of warm-blooded vertebrates. A robust, multigene topology (315 taxa, 8,942 nt), ancestral character state reconstruction, and a test for irreversible evolution (Dollo's law) demonstrate that house dust mites have abandoned a parasitic lifestyle, secondarily becoming free-living, and then speciated in several habitats. Hence, as exemplified by this model system, highly specialized permanent parasites may drastically de-specialize to the extent of becoming free-living and, thus escape from dead-end evolution. Our phylogenetic and historical ecological framework explains the limited cross-reactivity between allergens from the house dust mites and 'storage' mites and the ability of the dust mites to inhibit host immune responses. It also provides insights into how ancestral features related to parasitism (frequent ancestral shifts to unrelated hosts, tolerance to lower humidity, and preexisting enzymes targeting skin and keratinous materials) played a major role in reversal to the free-living state. We propose that parasitic ancestors of pyroglyphids shifted to nests of vertebrates. Later the nest-inhabiting pyroglyphids expanded into human dwellings to become a major source of allergens.Table S1. Taxa, collection data, and GenBank idsS1_Suppl_Table_Taxa_and_GenBank_ids_short.docTable S2. Partition selection based on four measures of relative goodness of fit of a statistical model. The lowest values (bold face) identify the 'best' model, which is used in our subsequent analysesS2_Suppl_Table_Partition_selection.docFig. S3. Total evidence and individual partition analysesS3_Suppl_Fig-Combined_and_individual_partition_analyses.pdfFig. S4. Outgroup sensitivity analysesS4_Suppl_Fig-Outgroup_sensitivity.pdfFig. S5. Species tree analysesS5_Suppl_Fig_Species_tree_analyses_summary.pdfTable S6. Evaluation of morphological, molecular, and immunological hypotheses of pyroglyphid dust mite relationships using an approximately unbiased test (AU) and three other common measures: bootstrap (BP), weighted versions of Kishino-Hasegawa (WKH) and Shimodaira-Hasegawa (WSH) tests. For these tests, p-values are reported; significant values (p>0.05) are marked by an asterisk and given in bold. The proportions of trees sampled from the posterior (BTP) of our preferred Bayesian analysis are also given. All 16 hypotheses assuming close relationships of pyroglyphids and storage mite (20, 21, 43-51, 53-55, 60, 62) were rejected.S6_Suppl_Table_Hypothesis_testing.docTable S7. Probabilities of being parasitic in ancestors of the dust mitesS7_Table_Probabilities_of_Parasitism.docxFig. S8. Host specificity in Psoroptidian mitesS8_Suppl_Fig_Host_Specificity_Graphs.pdfTable S8. Number of species and averaged host ranges in families of psoroptidian mites (exclusive of Pyroglyphidae)S9_Suppl_Table_Number_species_host_ranges_by_family.doc