2.4.5. Haplogroup and haplotype identification

The varroa cox1 gene marker is also useful for identifying mites of large discreet populations within a species (such as island populations) (Anderson and Trueman, 2000). As smaller populations within these larger populations can be identified by concatenated (joined) sequence data obtained from the mtDNA cox3, atp6 and cytb genes, the larger discreet populations have been referred to as ‘haplogroups’ and the smaller populations within them ‘haplotypes’ (Navajas et al., 2010).  The primer sequences for amplifying all these fragments, together with the size of fragments amplified, are shown in Table 1.

As the varroa cox1 gene marker has proved useful for resolving mites from haplogroups to a particular species it has also been useful in phylogenetic studies. A phylogenetic tree of the all the currently known and published haplogroups with species is shown in Fig. 5 (see the section ‘Phylogenetic analysis of sequence data’ of the BEEBOOK paper on molecular methods (Evans et al., 2013) for methods to perform phylogenetic analyses).

Table 1. Primer sequences (and their names) used in varroa research to amplify fragments of a particular size (base pairs) of mtDNA genes. From Anderson and Fuchs (1998); Navajas et al. (2010).

mtDNA

Gene

Fragment

Size (bp)

 

Primer Sequence

 

Primer Name

Cox1

458

GG(A/G) GG(A/T) GA(C/T) CC(A/T) AAT (C/T)T(A/T)  TAT CAAC

COXF

 

 

CCT GT(A/T) A(A/T)A ATA GCA AAT AC

COXRa

Cox1

929

CTT GTA ATC ATA AGG ATA TTG GAAC

10KbCOIF1

 

 

AAT ACC AGT GGG AAC CGC

6,5KbCOIR

Atp6-cox3

818

GAC ATA TAT CAG TAA CAA TGAG

16KbATP6F

 

 

GAC TCC AAG TAA TAG TAA AACC

16KbCOIIIR

Cytb

985

GCA GCT TTA GTG GAT TTA CCT AC

10KbCytbF-1

 

 

CTA CAG GAC ACG ATC CCA AG

10KbCytbPRIM

 

Fig. 5.  A phylogenetic tree of the all the currently known and published haplogroups.

Figure 5