TLR1LA_All AberthelotiiThis fasta file contains the TLR1LA genotypes of all Berthelot's pipits sampledTLR1LA_All AcampestrisThis file contains all the TLR1LA genotypes of tawny pipits sampledTLR1LB_All AberthelotiiThis file contains the TLR1LB genotypes of all Berthelot's pipits sampledTLR1LB_All AcampestrisThis file contains the TLR1LB genotypes of all tawny pipits sampled.TLR3_All AberthelotiiThis file contains the TLR3 genotypes of all Berthelot's pipits sampledTLR3_All AcampestrisThis file contains the TLR3 genotypes of all tawny pipits sampledTLR4_All AberthelotiiThis file contains the TLR4 genotypes of all Berthelot's pipits sampledTLR4 _All AcampestrisThis file contains the TLR4 genotypes of all tawny pipits sampledTLR21_All AberthelotiiThis file contains the TLR21 genotypes of all Berthelot's pipits sampledTLR21_All AcampestrisThis file contains the TLR21 genotypes of all tawny pipits sampledPipit TLR FSTThis file contains the pairwise Fst calculated for TLRsPipit pairwise FST per msat locusThis file contains the pairwise Fst calculated with microsatellitescode to get pairwise bottleneck distance between islandsThis file contains an R code to get pairwise bottleneck distancesCO1_Anthus_alignedThis file contains the alignment of the Cytochrome Oxidase subunit 1 haplotypes from Anthus campestris and Anthus berthelotiiTLR1LA_All_genotypes2015This is the output file with Phase results for TLR1LA in Berthelot's pipits. This is a fasta file but should be opened using a text editor such as NotepadTLR1LB_All_genotypes2015This is the output file with Phase results for TLR1LB in Berthelot's pipits. This is a fasta file but should be opened using a text editor such as NotepadTLR3_All_genotypes2015This is the output file with Phase results for TLR3 in Berthelot's pipits. This is a fasta file but should be opened using a text editor such as NotepadTLR4_All_genotypes2015This is the output file with Phase results for TLR4 in Berthelot's pipits. This is a fasta file but should be opened using a text editor such as NotepadTLR21_All_genotypes2015This is the output file with Phase results for TLR21 in Berthelot's pipits. This is a fasta file but should be opened using a text editor such as NotepadTLR1LA_ TREE SESSION 2015Tree file for the TLR1LA phylogenyTLR1LB_tree session 2015Tree file for the TLR1LB phylogenyTLR3_TREE SESSION 2015Tree file for the TLR3 phylogenyTLR4_new tree sessionTree file for the TLR4 phylogenyTLR21_new tree sessionTree file for the TLR21 phylogeny

Understanding the relative role of different evolutionary forces in shaping the level and distribution of functional genetic diversity among natural populations is a key issue in evolutionary and conservation biology. To do so accurately genetic data must be analyzed in conjunction with an unambiguous understanding of the historical processes that have acted upon the populations. Here we focused on diversity at toll-like receptor (TLR) loci, which play a key role in the vertebrate innate immune system and, therefore, are expected to be under pathogen-mediated selection. We assessed TLR variation within and among 13 island populations (grouped into three archipelagos) of Berthelot's pipit, Anthus berthelotii, for which detailed population history has previously been ascertained. We also compared the variation observed with that found in its widespread sister species, the tawny pipit, Anthus campestris. We found strong evidence for positive selection at specific codons in TLR1LA, TLR3 and TLR4. Despite this, we found that at the allele frequency level, demographic history has played the major role in shaping patterns of TLR variation in Berthelot's pipit. Levels of diversity and differentiation within and across archipelagos at all TLR loci corresponded very closely with neutral microsatellite variation, and with the severity of the bottlenecks that occurred during colonization. Our study shows that despite the importance of TLRs in combating pathogens, demography can be the main driver of immune gene variation within and across populations, resulting in patterns of functional variation that can persist over evolutionary timescales.