Gene trees for the <i>Ldh</i>A and <i>Rab4</i> haplotypes.

<p>The trees are maximum-likelihood topologies with branches coloured to indicate the mtDNA clades carried by the individuals in which the haplotypes were samples. Clade acronyms are the same as those used in Fig. 1. The two- or three-letter code names correspond to the individuals’ sampling localities (Table S1) and the numbers following the underline character to different alleles within heterozygotes. Only one individual is listed for each haplotype to save space and the number of individuals carrying that haplotype is noted in parentheses when higher than one (for trees showing all individuals, branch length estimates and bootstrap frequencies, see Figs S1 and S2; Supporting Information). Amino acid substitutions distinguishing the pond (S) and lake (F) alleles of <i>Ldh</i>A are indicated as follows: *, charge-changing Gln229Glu substitution; †, charge-conservative Asp6Glu substitution.</p

Schematic scenario reconciling the discordance of the mtDNA gene tree with the species tree.

<p>Grey bars represent the species tree, thick black lines the mtDNA gene tree, and black wedges denote mtDNA clades within each species. The cross symbolises the hypothesized disappearance of the autochthonous <i>Daphnia pulicaria</i>’s mtDNA in North America due to its replacement with that of <i>Daphnia pulex</i>. The arrows indicate the direction of this ancient mtDNA introgression as well as of a more recent introgression of the haplotypes from the NAPX clade.</p

Bayesian species tree.

<p>Species tree for the European and North American <i>Daphnia pulicaria</i> (EPC and NAPC) and <i>Daphnia pulex</i> (EPX and NAPX) inferred from the nuclear gene data by the multispecies coalescent in *BEAST. The tree is a maximum clade credibility tree with clade probabilities indicated above branches. Nodes bars are the 95% highest posterior density intervals for the node ages with median values within the bars. Inset: The 99% credible set of trees containing three topologies with the indicated frequencies.</p

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