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DETERMINING LOW LEVELS OF AFRICANIZATION
IN UNMANAGED HONEY BEE COLONIES
USING THREE DIAGNOSTIC TECHNIQUES
by
Katherine Darger
A thesis submitted to the Faculty of the University of Delaware in partial
fulfillment of the requirements for the degree of Master of Science in Entomology
Spring 2013
Copyright 2013 Katherine Darger
All Rights Reserved


ABSTRACT
“Killer bees†arrived in the United States in the year 1990. Questions have
arisen regarding low levels of Africanization in regions bordering the locations with
established, Africanized bees. Honey bees were collected and examined using three
methods of testing to determine levels of Africanization. With morphometrics,
mitochondrial DNA, and nuclear DNA tested with the use of microsatellites we found
that the known Africanized bees collected by the Florida Department of Agriculture
did not exhibit Africanization other than in the preliminary, morphometric test
performed by the Department of Agriculture.

Fast Africanized Bee Identification System (FABIS) is the field test for
preliminary identification of suspected Africanized honey bees (Rinderer 1986).
FABIS measures forewing length, fresh weight, dry weight, and femur length. This
process takes approximately twenty minutes per colony (Sylvester and Rinderer 2009).
Once the colony is identified with FABIS, the sample is analyzed with USDA-ID.
Universal System for Detecting Africanization (USDA-ID) (Sanford 2006) is
the test necessary to officially declare a case of Africanization in the Unites States.
This process is laborious due to the obligation to accuracy. Twenty-five mounted
parts of each specimen are needed to determine whether a colony is Africanized. This
requires thorough training to insure accuracy, as it includes miniscule measurements,
like the number of hamuli on the hindwing, the length and width of the basitarsus, and
the distance between wax mirrors (Rinderer et al. 1993).
Two newly established morphometric methods of analysis are less expensive
and faster than the well-established methods. The Automatic Bee Identification
System (ABIS) uses a comparison of plotted wing-vein junctions with a digital image
of the forewing of the specimen. The process takes two minutes per sample and the
accuracy rate is estimated to be 98.05% among bee species and 94% among honey bee
subspecies (Francoy et al. 2008). Geometric morphometric analysis is used to
delineate between honey bee subspecies. The test takes five minutes (Francoy et al.
2006) and has a 99.2% estimated accuracy rate looking at the wing venation angles
(Francoy et al. 2008, Francoy et al. 2009). Due to its precision and short preparation
time, this test was used on the samples in this study.

USDA-ARS Carl Hayden Honey Bee Research Center and the Florida Department of Agriculture and Consumer Services; Bureau of Plant and Apiary Inspection,
respectively. The samples from the Florida Department of Agriculture were collected in Alabama, Georgia, and Florida but were grouped together for this study. The samples from Jerry Hayes, formerly of the Florida Department of Agriculture, were grouped together to increase the samples size. Known Africanized samples from South America as well as African samples from Pretoria and Kenya were provided by Dr. Walter S. Sheppard’s personal collection from Washington State University. Forty known Africanized honey bee samples were sent from Belize by Brenna Traver. Altogether, there are 82 samples of known African/Africanized honey bees.
Morphometrics
For our morphometric diagnoses, ten right forewings per colony from an
assortment of colonies among our sampling collection were removed (Table 5). Our
samples and the control samples were diagnosed in Brazil by Dr. David De Jong using
the geometric morphometric technique of comparing wing venation (Francoy et al.
2006, Francoy et al. 2008, Francoy et al. 2009). The results are displayed in Principle
Component Analysis figures to exhibit the clustering of populations according to
morphometric restrictions.
Total DNA Extraction
A hind leg from two bees per sample, totaling in 188 unmanaged bees and 81
known Africanized bees, were cut into 4 to 6 pieces and placed in 150 μl of 10%

Results
The collection contained limited samples from certain states due to the time
constraints of this project affecting the number of collecting seasons.
Morphometrics
Through the geometric wing analysis performed by Dr. David De Jong, several
patterns emerged. The unmanaged and managed samples clustered together,
separately from the representative type of each subspecies (A. m. liguctica, A. m.
mellifera, A.m. carnica and A. m. caucasica) (Figure 2), showing that the bees in the
US are a distinct hybrid. The known Africanized samples separated from each other, however the samples from Florida, Georgia, and Alabama all clustered together but outside the range of Africanized bees (Figure 3). The Africanized bees from Arizona clustered separately from the known Africanized bees from Florida as well as the bees from Africa and Brazil (Figure 3). Based on morphological characters, the bees from Florida may not be fully Africanized.


Mitochondrial Testing
The unmanaged and managed honey bee colonies were tested and found to
have European mitotypes (Table 7). The Africanized samples from Florida and Belize
contained European mitotypes. The Africanized samples from Arizona had a variety
of mitotypes from the African lineage: A26, A26c, A1e predominantly, and A1. The
Africanized samples from Belize had four European mitotypes that were C1 while the


rest of the mitotypes were mostly A1 and A1e. The samples from Africa and Brazil
had no European mitotypes. They had mitotypes of A4, A47, A26a, and A26c (Table
1).
T Tests were performed in Microsoft Excel to test for significant differences
between the Africanized populations according to mitotypes. The p values for each
comparison were well below the significance level of 0.05, suggesting that the
Africanized samples from Belize, Arizona, Brazil, and Africa had significantly more
mtDNA of African origin compared to the mitotypes of Africanized samples collected from Florida, Alabama, and Georgia. In the comparison of Africanized bees from Florida versus Arizona significant differences were found (p value less than 0.0001,60 degrees of freedom). The comparison of the bees from Florida versus Brazil and Africa was also significant (p value less than 0.0001, 31 degrees of freedom). The p
value for the comparison of Florida versus Belize was 0.001 (96 degrees of freedom).
Even the bees from Arizona, Brazil, Africa, and Belize were significantly different
from each other based on mitotype. The p value for Arizona versus Brazilian and
African samples was 0.000991 (53 degrees of freedom), while the comparison of
Arizona versus Belize was 0.0075038 (118 degrees of freedom). The bees from Brazil
and Africa were different from the bees from Belize (p value = 0.0000509, 89 degrees
of freedom).


Microsatellites
The average number of alleles in each population tested ranged from 5.23
±2.12 in Africanized bees from Florida to 7.85 ± 3.25 in unmanaged populations
(Table 2). Allelic richness was the lowest in the Africanized bees from Florida while the Africanized bees from Arizona had the highest allelic richness measured (Table 2).
The expected heterozygosity was very similar with the largest range being between
0.79±0.1 (in samples from Africa and Brazil) and 0.62±0.2 (from the Africanized in
Florida/Alabama/Georgia and Managed populations) (Table 2).
The STRUCTURE output consistently provided two populations: Unmanaged
and managed clustering with the Africanized samples from Florida/Alabama/Georgia
versus Africanized from Arizona, Africanized from Belize, and samples from Africa
and Brazil (Figure 4). STRUCTURE is a program that uses multi-locus data to infer
population structure, assign individuals to populations, and is often used to study
hybrid areas.
FST stands for fixation index and shows population differentiation due to
structure variation as measured by Single Nucleotide Polymorphisms (SNPs) or
microsatellites. According to the FST results (Table 3), there was a significant
difference between the managed and unmanaged populations. There was also
significance between the African and managed samples. Highly significant FST values
were noted between Africanized bees from Arizona and managed bees and also
between Africanized bees from Arizona and the unmanaged bees. Importantly, the
Africanized samples were not significantly different from each other.
Through the use of Genepop, Hardy Weinberg equilibrium was tested using
Fis, or inbreeding coefficient, estimates to compare each locus for every population. In
each instance, using the Fisher’s Method, the results were highly significant, thus the
populations are not in equilibrium. Allele frequency data, which is the proportion of
alleles compared to the number of genes, can be found in Table 6 in the Appendix.
Discussion
Currently, Africanized bees are officially diagnosed through morphometric
methods only. The genetics of a honey bee are not often utilized in official
determinations of Africanization. Should we combine morphometric and molecular
data to identify the level of Africanization? Determining the process of Africanization
as either incomplete or absolute can be done with the use of mitochondrial and nuclear
DNA, as was performed in this study, and will serve as a good tool for tracking the
introgression of Africanized genes into commercial and unmanaged honey bee
populations in North America.
Morphometrically, the data shows that there is an American bee, an amalgam
that is distinctive from the originating, European subspecies (Figure 2). The GWV
morphometric study further distinguishes between Africanized bees from Arizona and
those from Africa and Brazil. Interestingly, the samples from
Florida/Alabama/Georgia which were originally diagnosed as Africanized by the
USDA-ID technique were found to have European ancestry using mtDNA markers,


European morphology based on GWV and grouped with managed and unmanaged
honey bee colonies in a population structure analysis using microsatellite markers.
A panmictic population is one in which all forms of recombination are possible
due to a lack of restriction caused by genetics and behavior, and all fertile individuals
are potential partners. We hypothesized that the samples would separate into distinct
populations delineated by lines of latitude. The samples tested in our study are not in
Hardy Weinberg equilibrium, as shown through the use of the Fisher’s test in
Genepop, which is indicative that they are not separate and distinct populations as
would be expected based on geographic collecting locations. Essentially, our study
indicates that bees on the east coast are not in distinct populations as would be
surmised based on collection latitude. Northern bees were not differentiated from
southern bees.
Studies in Europe showed the M lineage, consisting of western and northern
European bees, is genetically much more similar to A, or the African lineage than to C
(eastern Europe) or O lineages (near East and central Asia) (Whitfield et al. 2006).
Our data shows that two populations could be discerned based on microsatellite allele
frequency. The Africanized samples from Arizona and Belize were genetically similar
to the African bees from Africa and Brazil based on allele frequency data on the tested
microsatellites. Furthermore, the unmanaged, managed, and Africanized bees from
Florida/Alabama/Georgia shared enough alleles to be considered one population.
These low levels of introgression can be seen in the Africanized samples collected
from Florida/Alabama/Georgia (STRUCTURE output Figure 4) from the known


African and Africanized populations from Arizona, Belize and Brazil. However, the
Africanized samples from Florida/Alabama/Georgia still grouped with unmanaged and
managed samples collected along the east coast. This could be due to the very recent
Africanization of Florida (2010) or could be due to an incomplete Africanization of
the entire east coast as supplanted by the migratory queen rearing and caged bee trade.
High linkage disequilibrium in A. m. ligustica and A. m. mellifera accounts for the
potential for high genetic variation and recombination (Whitfield et al. 2006). The
opposite is true for A. m. scutellata and A. m, intermissa (Whitfield et al. 2006),
accounting for infiltration of A. m. scutellata into European genetics and not the other
way around.
The mtDNA data supplants this conclusion, as the samples of Africanized
bees from Florida/Alabama/Georgia did not exhibit Africanized mitotypes in the
majority of the samples, rather they had European maternal influences, which were also found in the managed and unmanaged samples.
According to Whitfield et al. (2006), New World bees in Brazil were highly
Africanized, yet individuals had alleles from the M lineage. Our data shows bees from
Florida had low levels of Africanization. Mid to late infiltration time showed
substantially, but not exclusively, Africanized genes (Whitfield et al. 2006) which is
substantiated by our data; the Africanized bees from Arizona, one of the earliest states
declared Africanized, were determined to be Africanized based on morphometrics,
mitochondrial DNA, and when tested with microsatellites.


During the process of Africanization in Latin America, bees have historically
had African nuclear and mitochondrial markers become the majority after the first five
to ten years following the invasion (Schneider et al. 2004). This increase of African
nuclear and mitochondrial genes over time is supported by our findings: the samples
from Florida/Alabama/Georgia have European mtDNA and low levels of Africanized
alleles while samples from Arizona consist of mostly African mitotypes and are
accompanied by African nuclear alleles. The onset of the invasion into the
southeastern U.S. as opposed to the desert southwest is supported by the observed
differences in genetic composition between the two sets of samples and is due to the
fact that Arizona was one of the earliest states colonized by Africanized bees due to
the proximity to Central America. It stands to reason that this amount of time allowed
for more complete introgression to occur, making Arizona further along in the
Africanization process. All of the managed and unmanaged honey bees had European
mitotypes (Table 7).
In Texas, the first state to have Africanized bees, it was suggested that the rate
of Africanization was enhanced by the decimation of European feral and managed
colonies by the Varroa destructor mite (Pinto et al. 2005). The Varroa mite created a
selection pressure as Africanized bees survive infestation. It was also suggested that
Texas may be the northernmost range of Africanization possible (Pinto et al. 2005),
while the most recent map of Africanization in the United States shows that as being a
false prediction. This map, however, was constructed using USDA-ID as the
diagnostic tool. If molecular tools were used diagnostically, as in our study, Florida
would not be included. It is possible that the diagnostic techniques (USDA-ID) for
determining Africanized swarms may be sensitive only to phenotype that is not yet
linked to genotype and could find a diagnosis in bees with few genetically African
indicators.
Genetics should also not be used alone diagnostically. Through the use of
mtDNA testing along with microsatellite data it was shown that the forefront of the
Africanized bee movement is caused by Africanized drones mating with European
queens (Pinto et al. 2005). The resulting hybrid drones were tested and found to be at
a competitive disadvantage (Hall 1991) because of reduced flight speed, eventually
leading to direct competition between European and Africanized queens (Pinto et al.
2005). Our data shows that the Africanized bees from Florida/Alabama/Georgia were morphometrically Africanized only using USDA-ID not the GWV technique, and not necessarily genetically similar enough to the African bee to be considered an Africanized bee.
The Africanized bees from Florida/Alabama/Georgia were different from the
other Africanized samples from other locations using each of the three testing
methods. Using GWV morphometric techniques, the Africanized samples from
Florida/Alabama/Georgia clustered together as being identical to the managed and
unmanaged samples from the north, central, and southern aspects of the eastern
seaboard of the United States and not within the same populations as the Africanized
bees from Arizona, Brazil, or Africa. No clinal gradient in the degree of
Africanization was observed in the unmanaged samples collected along the eastern


seaboard using microsatellite markers. Using mitochondrial testing, the mitotypes
found in the Africanized bees from Florida/Alabama/Georgia proved to be of
European ancestry which differed from the mostly pure African ancestry of the
African and Africanized samples collected from Arizona, Belize, and Brazil. The
difference in mitotypes found in the samples from Arizona, Belize and Africa warrant
further research into possible routes of entry of Africanized colonies.
Using microsatellite analysis to reconstruct actual population dynamics, the
Africanized bees from Florida/Alabama/Georgia clustered into a population with the
unmanaged and managed bees from the east coast while the populations from Arizona,
Belize, Brazil, and Africa clustered together into another separate population. The
lack of definitiveness in the three diagnostic tools leads us to the conclusion that
sensitivity of genetic markers may not be the most useful factor in determining
desirable stock for managing honey bees. Perhaps the best way to evaluate a hive is
by phenotypic traits, such as aggressive tendencies, and other undesirable traits such
as swarming and absconding, and not by genotypic traits. Containing a blend of
markers denotes a level of Africanization but perhaps negative behavior should be the
first line of diagnosis. Excessive stinging and swarming indicates a need for further
tools to be used, but even without the negative diagnoses these traits should be
discouraged.
In conclusion, I hypothesized that unmanaged honey bee colonies have blends
of genes from European and African influences and low levels of Africanization occur
throughout the United States, and can be detected using microsatellite markers. This


blend of genes was made evident by comparing morphometric and mitochondrial test
results. The results from the USDA-ID technique conflicted with the results of the
geometric wing venation, which depicted the Africanized samples from
Florida/Alabama/Georgia as non-Africanized.
Future Plans
For future analysis of our data, more software using Bayesian analysis will
further indicate population structure and degree of admixture. Bayesian Analysis of
Population Structure (BAPS) is one program that shows population structure and
information on introgression. Before processing the samples, we will prepare the data
by forming “group-wise clustering†of the individuals from each population (Corander
et al. 2009). All of the data will be pre-processed through the BAPS program prior to
analysis of genetic information (Corander et al. 2009). Format is the key to successful
analysis. In the future, the reasoning for the difference in sensitivity of the tests
should be explored. Perhaps the diagnoses do not necessitate genotype, as
morphologically and behaviorally the colonies are being confirmed to be Africanized.
The USDA-ID test is performed after a colony is deemed overly aggressive in the
field. With those two delineations, a need for genotypic examination may be
unnecessary. Three of the tools used: geometric wing analysis, mtDNA testing, and microsatellites showed the Africanized bees from Florida, already confirmed
Africanized by USDA-ID, to be incompletely or not at all Africanized.
The probable Africanized drone front is a possibility in the Africanized
counties in Florida, leading to the incomplete genetic introgression. The possibility of


exchanging the morphometric program with a purely molecular diagnostic program is
appealing in that it is more precise, less expensive, and less time consuming, but the
sensitivity may under-estimate the aggressiveness of the hive due to incomplete
introgression.


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