README for Dryad

This README file refers to the data reported in manuscript JEB-2016-00399.R2
published in Journal of Evolutionary Biology

Authors: Christoph Vorburger, Jenny Herzog & Romain Rouchet

Title: Aphid specialization on different summer hosts is associated with strong genetic differentiation and unequal symbiont communities despite a common mating habitat

The study design is explained in the publication. For queries please contact christoph.vorburger@eawag.ch

1) The file 'microsat_data_for_dryad.txt' contains the genotype data for 698 aphids that were genotyped at 8 microsatellite loci. The file has 17 columns. The first column contains individual identifiers that also contain the information about the site and host plant each individual was collected from. These identifiers follow the format:
[3-letter code for site]_[3-letter code for host plant][running number of 2009 field collection]

To give an example:
The first entry has the identifier aes_cir2223. This individual was collected at site 'Aesch' on the host plant 'Cirsium', and it was assigned the running number 2223 in the 2009 field sampling campaign.

Site codes (geographic locations for each site are provided in the paper):
aes = Aesch; alp = Alpnach; chu = Chur; gen = Geneva; grm = Grosses Moos; lan = Langnau; mag = Magadino; mar = Martigny; men = Mendrisio; mon = Mont�limar; neu = Neunkirch; orb = Orbe, rem = Remoulins; sie = Sierre; stm = St. Margrethen; zur = Zurich

Host plant codes:
che = Chenopodium; cir = Cirsium

The remaining 16 columns contain the allele calls for each of the 8 microsatellite loci (aphids are diploid, hence two alleles per locus). Missing allele data are represented by 000. Locus names are indicated in the header line above the first allele for each locus.

2) The file 'endo_data_for_dryad.txt' contains the results of a diagnostic PCR screen for the presence of six bacterial endosymbionts in individual aphids collected from the field. It has 12 columns:
id_09: Running number of aphid individuals collected in 2009 (corresponding to running numbers in file 'microsat_data_for_dryad.txt'
date: Collection date of aphid
site: Collection site of aphid
plant: Host plant species from which the aphid was collected
host: Genus of the host plant from which the aphid was collected (either Cirsium or Chenopodium)
aphid: The aphid species each individual belonged to
buchnera: Result of PCR screen for the obligate endosymbiont Buchnera aphidicola. 1 = present, 0 = absent 
hamiltonella: Result of PCR screen for the facultative endosymbiont Hamiltonella defensa. 1 = present, 0 = absent 
rickettsia: Result of PCR screen for the facultative endosymbiont Rickettsia sp. 1 = present, 0 = absent
regiella: Result of PCR screen for the facultative endosymbiont Regiella insecticola. 1 = present, 0 = absent
serratia: Result of PCR screen for the facultative endosymbiont Serratia symbiotica. 1 = present, 0 = absent
x-type: Result of PCR screen for the facultative endosymbiont called X-type or PAXS. 1 = present, 0 = absent