> "Eastern European and Western European lineages " What is meant by this?

Honey bees are divided into four or five lineages, called M, C, A, O and sometimes Y.

M = Western European (references samples used in the study = A. m. mellifera and A. m. iberiensis)
C = Eastern European (samples used = A.m. carnica and A. m. ligustica)
A = African ( used = A. m. scutellata)

These lineages are identified by genetic markers which have nothing to do with any behavioral qualities or coloration factors. While the M lineage is generally dark, the C lineage can range from black to yellow (carnica vs ligustica) and these differences are not reflected in the DNA markers that are used to determine lineages.

What I was pointing out was that the study showed that the ancestry of feral and domestic populations was essentially the same. I never meant nor implied that there were _no_ differences. Whatever differences exist are not reflected in the genetic markers used to classify lineages. There are millions of genetic markers (unique base pair sequences). 

Trevor said: "we do notice a big difference between the feral and our domestic stock." This is to be expected because the feral bees are a subset that has been naturally selected for survival traits, while the domestic population is a subset which has been artificially selected for behavior and coloration. 

* * *

Phylogeographical studies using morphology, allozymes, mitocondrial DNA (mtDNA), microsatellites, and more recently SNPs have grouped this wide-ranging diversity into five lineages (A, M, C, O, Y).

Different genetic markers may capture different parts of an organism’s history. While mtDNA can only reveal the maternal component, biparentally inherited markers may capture genome-wide effects (e.g. admixture, expansions, and contractions) or locus-specific effects (e.g. selection). 

Maria Alice Pinto, & al. (2011) EVOLUTIONARY HISTORY OF THE IBERIAN HONEY BEE (APIS MELLIFERA IBERIENSIS): A GENOME-WIDE APPROACH

* * *

At least 29 subspecies of A. mellifera have been delineated on the basis of morphometry (Ruttner 1988; Engel 1999; Sheppard et al. 2003). These subspecies are now typically divided into four major groupings, supported by morphometric and genetic studies in addition to analyses of ecological, physiological, and behavioral traits: group A, which includes subspecies throughout Africa; group M, which includes subspecies from western and northern Europe; group C, which includes subspecies from eastern Europe; and group O, which includes species from Turkey and the Middle East. However, some studies do not distinguish between groups C and O (labeling them both as C) and the existence of a fifth lineage (Y) in north-east Africa has been proposed

Based on comparisons of mtDNA loci, the A. mellifera lineage split from other extant honeybees at least 6 million years ago, and the subspecies began diverging around 1 million years ago. These estimates are based on a commonly used rate of mtDNA sequence divergence in insects of 2% per million years. The reliability of this estimate is not certain and in the absence of recent fossils it is not possible to refine specifically for honeybee clades. 

Han, F., Wallberg, A., & Webster, M. T. (2012). From where did the Western honeybee (Apis mellifera) originate?. Ecology and evolution, 2(8), 1949-1957.

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