Microsatellite data

This MSExcel file contains the microsatellite data used to run the clustering analyses

Four developmental stages of <i>Hirtella physphora</i> leaves.

<p>(a) Juvenile leaves: less than 5 cm long, positioned vertically; the domatia are not fully developed. (b) Expanding leaves: have fully developed domatia, but the blade is still immature. (c) Young leaves: from 15 to 25 cm long; positioned horizontally, mature but still relatively tender, and light green in color. (d) Old leaves: older, non-senescent, mature leaves of up to 30 cm in length, positioned horizontally, stiff, and dark green in color. Scale bars represent 5 cm.</p

<i>Hirtella physophora</i> leaves, flowers and fruits.

<p>(a) Leaves bear leaf pouches (left arrow) at the base of their laminas. <i>Allomerus decemarticulatus</i> workers capture a green locust thanks to their trap: a gallery made using severed host plant trichomes and the mycelium of an Astomycota fungus that the ants manipulate to create a composite material pierced by numerous holes (from under which the workers ambush prey). A wasp is seen robbing a piece of the locust abdomen; the wasp was also captured in turn as was the red Reduviid (right arrow). (b) At the distal position of the branch, flowers are segregated on racemous inflorescences at different stages of maturation from flower buds to fully open flowers. (c) Development of young, green (i.e. unripe) drupes. (d) A dark purple (i.e. ripe) drupe. Scale bars represent 1 cm.</p

Electronic Supplementary Material for Male et al. 2017 from An ant–plant mutualism through the lens of cGMP-dependent kinase genes

Additional information on genome sequencing, PKG assembly, and phylogenetic history of PKG genes in arthropods

script_chloro

UNIX script used for plastid reconstruction. The following tools must be installed: VELVET, PLAST, COPE, OBITOOL

alignments

Plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only. Alignments were performed using MAFFT and cleaned using Gblocks. Files are in fasta format

trees

Trees obtained with plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only, using RAxML and MrBayes. Files are in NEXUS format

Information about individuals included in the GBS VCF file

Morph and localities for each individual included in the GBS study

Supplementary Methods and TablesThis file includes details about methods and parameters used, as well as supplementary results on analyses ofphenotype and whole genome analyses. from A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the <i>Zosterops borbonicus</i> white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex <i>cis</i>-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a ‘brown’ ancestral population, the dominant ‘grey’ allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection