four gene fragments, with seven polymorphic sites that distinguished eight haplotypes. None of the loci showed any evidence of selection (data not shown). All DNA sequences and alignments were deposited with GenBank (acc. nos. KM270879-KM271776) Haplotype networks were generated for each gene fragment (Fig. 3). The COI, Cytb and networks exhibited similar star-like phylogenies dominated by two sequences (allelic haplotypes *1 and *2). In each case, only one (ATPsα), two (COI), or three (Cytb) mutational steps separated the leading haplotypes. COI exhibited ten singletons and three rare variants (i.e. qi ≤ 0.05). Cytb exhibited three singletons, nine rare variants, and one minor variant (qi = 0.08). ATPsα exhibited only one singleton and five rare variants. Genealogical tests for recombination with branch-and-bound method detected no evidence for recombination within these genes. We also tested for recombination between COI and Cytb, and as expected for mitochondrial genes, found no evidence for recombination. The HSP network was more complex (Fig. 3C). The HSP*1 allele dominated the sample (qi = 0.41), four additional alleles (HSP*2, *3, *4 and *5) occurred at moderate frequencies (qi > 0.05), eleven were rare (qi ≤ 0.05), and four were singletons. The network exhibited considerable homoplasy (multiple mutation paths connecting the haplotypes). Because HSP genes are highly duplicated in some marine invertebrates (Zhang et al. 2012), we cannot that the homoplasy resulted from paralogous genes. Alternatively, if the observed HSP variation resulted from homologous alleles, homoplasy might result from intra-genic recombination. A test using the method detected possible recombination events at five nucleotide sites, four of which were located in the intron region of the amplicon. The putative recombinants are
Discussion Multilocus analyses revealed that T. jerichonana genotypes could be assigned to northern and southern lineages that occupied the NEPR and PAR regions of the southeastern Pacific ridge system. Connecting segments of the SEPR axis represented a region of and intergradation between the two lineages (Fig. 5). The significant cytonuclear disequilibrium (CND) observed between ATPsα and mtDNA genes at SEPR also indicated admixture in this region, although no significan was found at HSP. Latitudinal clines that produced an IBD-like signal were observed, as previously reported for COI (). Cytb exhibited an identical signal because the mitochondrial genes are coupled in the non-recombinant mitochondrial genome. In addition, two independent nuclear genes, HSP and ATPsα, also exhibited IBD-like signals, though the slopes of ΦST on latitude were shallower (Fig. 4). Stepping-stone dispersal (SSD) among discrete vent fields could create the IBD-like signals (). Strong selection gradients also could result in a convergence of clines among independent loci (), although there was no evidence of selection on any locus examined. The geochemical composition of vent effluents can vary greatly on very small spatial scales (), but the extremes of these local conditions are very broad. In contrast, the temperatures and salinities of ambient (non-vent) seawater are relatively homogeneous at depths occupied by T. jerichonana (2235–2747 m). The Refuge/re-invasion hypothesis A regional extinction event (or events) followed by secondary invasion of the SEPR axis with T. jerichonana colonists from NEPR and PAR refugia could have generated the observed patterns. According to the refuge/re-invasion hypothesis, the NEPR and PAR