ML_tree_Dennis

Maximum likelihood tree generated from the dennis region multiple alignmen

Dennis BEAST dated FigTree file

Compiled Tree Annotator file for Dennis with dated node numerical values. Opens with FigTree program

Dennis_BEAST

BEAST input file for generating dennis region dated tre

Dennis and Ray Alignments

Multiple alignment fasta files for dennis and ray regions composed of full versions (including flanking regions and alleles with very poor coverage) and 'tree' versions (poor coverage rogue alleles removed) used to generate ML and BEAST trees

Ray BEAST dated TreeFig file

Compiled Tree Annotator file for Ray with dated node numerical values. Opens with FigTree program

Schematic overview of the <i>dennis</i> region alignment architecture.

<p>Each group of alleles is characterised by a complex structure of insertion and deletion variation. Horizontal bars represent aligned allele sequences for the outgroups (A), silvaniforms (B), <i>H</i>. <i>elevatus</i> (C), dennis morph melpomene/timareta (D), non-dennis morph melpomene/timareta (E), and the cydno/heurippa/pachinus clade (F). There are three general forms of the region: an “outgroup” allele (X) with many indels and lacking large sections of sequence; a silvaniform/dennis allele (Y), which possesses indel 1 and lacks indel 2; and a non-dennis/cydno allele (Z), which lacks indel 1 and possesses indel 2. Dotted lines and blue colouration indicate the point where dennis-morph melpomene/timareta alleles become silvaniform like (left) and where the dennis-only morph, <i>H</i>. <i>m</i>. <i>meriana</i>, recombines with the other non-rayed melpomene (right). Fixed SNPs in perfect association with the dennis phenotype are indicated by yellow asterisks and form two clusters. See Dryad depository for alignment [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002353#pbio.1002353.ref032" target="_blank">32</a>].</p