> The commercially-managed population is genetically bottlenecked, as are other livestock animals

We heard statements like this when people were first casting about for causes of large scale losses. I thought the notion was pretty much put to rest by this work:

The process of domestication often brings about profound changes in levels of genetic
variation in animals and plants. The honey bee, Apis mellifera, has been managed by
humans for centuries for both honey and wax production and crop pollination. Human
management and selective breeding are believed to have caused reductions in genetic
diversity in honey bee populations, thereby contributing to the global declines
threatening this ecologically and economically important insect.

We found that managed honey bees actually have higher levels
of genetic diversity compared with their progenitors in East and West Europe, providing
an unusual example whereby human management increases genetic diversity by
promoting admixture. The relationship between genetic diversity and honey bee
declines is tenuous given that managed bees have more genetic diversity than their
progenitors and many viable domesticated animals.

Management increases genetic diversity of honey bees via admixture
BROCK A. HARPUR, SHERMINEH MINAEI , CLEMENT F. KENT and AMRO ZAYED, 2012

¶

* One problem with these studies which look for genetic diversity is that they are essentially combing through billions of data points trying to make sense of it. There has to be some sort of criteria, some sort of screening. If the criteria are wrong to begin with the conclusions will also be wrong. 

Another recurrent challenge for researchers
is accounting for systematic biases that may
be present in genomic data. The majority of
selection studies to date have utilized SNP
data, which is collected using genotyping arrays
designed to detect known polymorphisms.
The practical limitations of SNP discovery
protocols mean that low-frequency alleles
may go undetected, in which case they are
excluded from these arrays. These arrays can
therefore generate data that may be unrepresentative
of the full extent of genetic diversity,
a phenomenon known as ascertainment bias
(23). This sampling of the data can artificially
distort allele frequency measures as well as
derivative statistics that include LD. When the
SNP discovery protocol is known, statistical
measures can be taken to counteract the effect
of ascertainment bias


Detecting Natural Selection in Genomic Data
Joseph J. Vitti, Sharon R. Grossman, and Pardis C. Sabeti, 2013

¶

Finally, the honey bee seems to have evolved ways of combating the reduction of diversity that can occur in small inbreeding populations which may be geographically isolated for long periods of time

Social insects in general, and the honey bee in particular, have very high rates of recombination. 
Kent et al. (2012) using population genetic analysis of randomly
chosen genes, demonstrated a link between recombination, genome
structure and the evolution of social behaviour; genes with worker-biased
expression were enriched in parts of the honey bee genome with the highest
rates of recombination and genetic diversity and where natural selection is
most efficient. Kent and Zayed (2013) later suggested that high recombination
rates may have been selected for during the evolution of sociality

Population Genomic and Phylogenomic Insights into the Evolution of Physiology and Behaviour in Social Insects
Clement F. Kent*, Amro Zayed 2015


PLB

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