Phylogenetic clustering of unlinked markers.

<p>Neighbour-Joining tree of mitochondrial COI haplotypes and alleles at the nuclear loci <i>GAPDH</i> and <i>Hsp90</i>. Numbers above branches are the values for bootstrap support. Species and colour codes are as specified in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002752#pgen-1002752-g001" target="_blank">Figure 1</a>, with <i>H. melpomene</i> (circles) and <i>H. cydno</i> (triangles), <i>H. timareta</i> (squares) and <i>H. heurippa</i> (diamonds). <i>H. numata</i> (black) was used as the outgroup. Size of shapes represents haplotype frequency. Taxa with a rayed phenotype are coloured orange, red-banded phenotypes are red and those taxa lacking a dorsal red wing phenotype are yellow.</p

Phylogenetic clustering at HmB453k inferred by Maximum Likelihood.

<p>A phenotypic association regardless of species relationships is observed. Three major monophyletic clades (red, rays and no-red) are formed. Representative phenotypes of each clade are shown at the right (for full array of phenotypes and species see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002752#pgen-1002752-g001" target="_blank">Figure 1</a>). (i) <i>H. m. malleti</i>, (ii) <i>H. m. plesseni</i>, (iii) <i>H. t. timareta</i>, (iv) <i>H. c. cydnides</i>, (v) <i>H. c. weymeri</i> f. <i>gustavi</i>, (vi) <i>H. timareta</i> subsp. nov, (vii) <i>H. c. weymeri</i> f. <i>weymeri</i>, (viii) <i>H. c. chioneus</i>, (ix) <i>H. c. cordula</i>, (x) <i>H. c. zelinde</i>, (xi) <i>H. c. warningery</i>, (xii) <i>H. c. lisethae</i>, (xiii) <i>H. m. cythera</i>, (xiv) <i>H. m. melpomene</i>, (xv) <i>H. m. rosina</i>, (xvi) <i>H. m. vulcanus</i>, (xvii) <i>H. heurippa</i>, (xix) <i>H. m. amandus</i>, (xx) <i>H. m. amaryllis</i>, (xxi) <i>H. timareta</i> subsp. nov, (xxii) <i>H. m. aglaope</i>, (xxiii) <i>H. t. florencia</i>, (xxiv) <i>H. t. contigua</i>, (xxv) <i>H. m. thelxiopeia</i>, (xxvi) <i>H. m. ecuadoriensis</i>. Numbers above branches are the values for bootstrap support. <i>H. m. plesseni</i> and some of <i>H. m. malleti</i> (rayed phenotype) do not cluster within the three major phenotypic clades.</p

Rates of interspecies introgression between <i>H. melpomene</i>, <i>H. heurippa</i>, and <i>H. timareta</i>.

<p>Migration rates were inferred using IM, with estimated values converted into effective units of population migration rate per generation assuming 10 generations per year. <i>m₁</i> refers to migration from <i>H. timareta</i> to <i>H. melpomene</i> and <i>m₂</i> refers to the migration from <i>H. melpomene</i> to <i>H. timareta</i>. The 2Nm values are the effective number of gene migrations received by a population per generation. Values of 2Nm greater than or equal to one can prevent populations from accumulating divergence <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002752#pgen.1002752-Strasburg1" target="_blank">[37]</a>.</p><p>Values of 2Nm in migrants per generation.</p

Linkage disequilibrium test of historical gene flow.

<p>Observed and simulated values of <i>x = DSS-DSX</i> across four loci in <i>H. melpomene</i> and <i>H. timareta</i>. Positive values of <i>x</i> are indicative of gene flow and the recipient species displays the highest positive value. Simulated values of <i>x</i> were obtained with 30,000 simulations.</p

Population structure as inferred by Analysis of Molecular Variance (AMOVA).

<p>Percentage of variance explained by phenotype, species and geography is presented for markers both unlinked (shadowed) and linked (non-shadowed) to red colour pattern.</p><p>p-value is indicated below each percentage of variation.</p>*<p>p<0.05,</p>**<p>p 0.05<0.000001,</p>***<p>p = 0.000001.</p

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