Sampling of common dolphins for this study.

<p>White circles indicate new samples; black symbols refer to sequences from GenBank. Sample size is shown between parentheses. The square indicates sequences of the <i>tropicalis</i>-form and the triangle the only sequence available of the putative <i>D</i>. <i>d</i>. <i>ponticus</i>. SE Br: Southeastern Brazil (grouping samples from Rio de Janeiro, RJ and São Paulo, SP); RS: Rio Grande do Sul; ARG: Argentina; NW Atl: Northwestern Atlantic; NE Atl: Northeastern Atlantic; CE Atlantic: Central Eastern Atlantic; NE Pac: Northeastern Pacific; SW Pac: Southwestern Pacific. Dc: long-beaked common dolphins “<i>Delphinus capensis</i>”; Dd: short-beaked common dolphins <i>D</i>. <i>delphis</i>.</p

Common dolphin cytochrome b sequences used in this study.

<p>Sequences from other studies were obtained from GenBank. Except where noted and in the SE Atl, all specimens had or were assumed as the short-beaked morphotype. Samples from the SW Atl were assigned to morphotypes after skull measurements (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140251#pone.0140251.t001" target="_blank">Table 1</a>).</p

Phylogenetic tree (NJ/ML/BI) of common dolphin cytochrome b haplotypes.

<p>Values above nodes correspond to bootstrap (NJ), aLRT (ML) and posterior probability (BI), respectively, > 50%. Arrows indicate sequences generated in this study (SW Atlantic): specimens coded with RJ, RS ARG4 and ARG18 had the long-beaked morphotype, and the remaining specimens coded with ARG had the short-beaked haplotype (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140251#pone.0140251.t001" target="_blank">Table 1</a>). Grey circles indicate sequences of the <i>tropicalis</i>-form. The star indicates the haplotype shared by short and long-beaked common dolphins (from almost all localities, including the SW Atlantic) and the putative <i>D</i>. <i>d</i>. <i>ponticus</i> (Black Sea). Black circles mark the long-beaked morphotype from the NE Pacific (please note the paraphyly).</p

Collection and morphological data of the specimens genetically analysed.

<p>Osteological material from stranded and by-caught specimens are deposited in the following institutions: RJ–Laboratório de Mamíferos Aquáticos e Bioindicadores, Universidade do Estado do Rio de Janeiro; SP–Projeto Biopesca; RS–Laboratório de Ecologia e Conservação da Megafauna Marinha, Fundação Universitária do Rio Grande; ARG–Universidad Nacional de Mar del Plata.</p><p>Specimens marked with an asterisk were considered immature.</p

<i>Triatoma</i> samples used in the study.

1<p>D = domestic, P = peridomestic, S = sylvatic, ND = no data.</p>*<p>indicates cyt b haplotypes from Dorn <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070974#pone.0070974-Dorn2" target="_blank">[17]</a>.</p

DNA polymorphism and neutrality tests.

<p>Nseq: Number of sequences; Nhap: Number of haplotypes; S: Variable sites; P: Parsimony informative sites; h: Haplotype diversity; π: Nucleotide diversity; Tajima’s D (Tajima 1989);</p>a<p>P>0.70.</p

Sampling sites of representatives of the <i>Triatoma dimidiata</i> species complex. Numbers in the circles correspond to numbers of sampled locations listed in Table 1.

<p>Sampling sites of representatives of the <i>Triatoma dimidiata</i> species complex. Numbers in the circles correspond to numbers of sampled locations listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070974#pone-0070974-t001" target="_blank">Table 1</a>.</p

Principal component plots constructed from genetic similarity matrix based on cyt b sequences (<i>a</i>) and on cyt b and ND4 (<i>b</i>) combined data.

<p>Color codes for different groups of the <i>Triatoma dimidiata</i> complex coincide with colors used in Fig. 2.</p

This figure shows how the topology recovered for the <i>T.</i><i>dimidiata</i> species complex based on the phylogenetic analysis of ITS-2 sequence data of Bargues et al. [18]

<p>(a) compares to the one derived from the mtDNA sequence data (cytb+ND4) presented in this paper (b). Examination of this new figure shows that ITS-2 groups 1, 2, and 3 of Bargues et al. are essentially the same as our mtDNA groups I, II, and III (i.e. they include specimens collected from the same geographic areas). Branch color codes in “b” indicate each of the four different genetic groups (plus <i>T. hegneri</i>) that comprise the <i>T. dimidiata</i> species complex. See Discussion section for more details on the few incongruities between the two topologies and on how these were interpreted and discussed.</p

Median-joining haplotype network based on <i>T.</i><i>dimidiata</i> and <i>T. hegneri</i> cytochrome <i>b</i> haplotypes.

<p>The size of the circles on the network is proportional to haplotype frequency. Small red circles represent missing haplotypes. Network circle colors are the same as in Fig. 1. Circles with dotted red outlines denote the presence of haplotypes from Guatemala, Petén among groups I and II.</p