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. exhibited ten singletons and three COI rare variants (i.e. 0.05). exhibited three singletons, nine rare variants, and one qi Cytb ≤ minor variant (qi = 0.08). exhibited only one singleton and five rare variants. ATPsα Genealogical tests for recombination with branch-and-bound method detected no evidence for recombination within these genes. We also tested for recombination between and and as expected for mitochondrial genes, found no evidence for COI Cytb, recombination. The network was more complex (Fig. 3C). The allele dominated the HSP HSP*1 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 genes are highly duplicated in some marine invertebrates HSP (Zhang et al. 2012), we cannot that the homoplasy resulted from paralogous genes. Alternatively, if the observed variation resulted from homologous alleles, HSP 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
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
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