Category: Articles

A new test for ‘killer bees’

By , May 20, 2015

Happy to report that we played an important role in an international effort to develop a new diagnostic test for africanized ‘killer’ bees. Africanized bees invaded the southern US where Canadian beekeepers like to import queen bees. Older tests for telling if a bee is africanized or not are not reliable. We worked closely with Nadine Chapman and Ben Oldroyd from the University of Sydney’s famed social insect lab to develop a very accurate genetic  test. PhD candidate Brock Harpur used our database of over 12 million mutations in the honey bee  to pick diagnostic mutations that differ between African and European bees.

The study was recently published online in Molecular Ecology Resources. Also see the York U and UoSydney press releases too!

Chapman, N.C., Harpur, B.A., Lim, J., Rinderer, T.E., Allsopp, M.H., Zayed, A., Oldroyd, B.P. (2015) A SNP test to identify Africanized honey bees via proportion of ‘African’ ancestry. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12411

Two new reviews published

By , April 8, 2015

Happy to report the publication of two new reviews.

The first is titled Beyond fruit-flies: population genomic advances in non-Drosophila arthropods which just published in Briefings in Functional Genomics. I co-authored this review with Martin Hasselmann (University of Hohenheim, Germany) and Luca Ferretti (Université Pierre et Marie Curie, France). I am a big fan of Martin H.’s work on bee genetics – He and Martin Beye discovered and studied the honey bee’s sex determination gene, csd – and so i was very happy when he asked me to work with him on the review. We review how next generation sequencing has opened the door to answering some long-standing questions about insect evolution and adaptation.

The next review also published last week in Volume 48 of Advances in Insect Physiology. It is titled Population Genomic and Phylogenomic Insights into the Evolution of Physiology and Behaviour in Social Insects, and is co-authored with former-postdoc and now Senior Scientist at the HHMI’s Janelia Farm Campus, Clement Kent. The review focuses on how population genomics is helping us understand how and why social insects came to be(e).

New edited book on Sociogenomics!

By , April 8, 2015

Happy to report the publication of a new volume of Advances in Insect Physiology that i co-edited with Dr. Clement Kent, titled Genomics, Physiology and Behaviour of Social Insects. The book launched last week, and contains ten fantastic (in my slightly humble and obviously very biased opinion!) chapters on genomics-empowered research on the biology of social insects.  Clement and I strived for diversity and so we got honey bees, bumble bees, wasps, ants (ok… partial coverage on the ants) termites, and aphids… oh my! Check out the nice cover and table of contents here and below.AIP 48 front and back

It was a lot of work, but we had a group of fabulous and dedicated authors that really helped with meeting the very tight deadlines… Many of us worked over the December break and new years ; I remember doing some last min. editing on Christmas day, before the turkey!  Clement and I are very proud of the result, and we hope you enjoy it too!

Amro

New paper on the immune system of honey bees

By , August 29, 2014

Happy to announce a new publication from the lab on the immune system of honey bees in PLoS ONE. The study explored the genetic relationship between the honey bee’s innate and social immune system. The study was authored by PhD candidate Brock Harpur, with strong contributions from Anna Chernyshova and Arash Soltani – two honours thesis students in my lab (2012). MSc Candidate Nadia Tsvetkov and NSERC USRA students Mohammad and Jack (Zhixing) were instrumental in completing the field-work .

A general summary of the research will follow in a few days…

Amro

Population genomics study highlighted by Nature/Middle East

By , February 26, 2014

Happy to announce that a regional portal of the Journal Nature, Nature Middle East, published a Research highlight story on our recent honey bee population genomics study.

New Paper: Population Genomics of the Honey Bee in PNAS

By , February 26, 2014

Hi All,

harpur2014_coverI am very happy to announce the publication of a new paper from the lab, which appeared last week in the Proceedings of the National Academy of Sciences (PNAS) – a top journal in the field.  The study was featured on the cover of PNAS, and received a highlight in the “In This Issue” section of the journal.  Also see York U’s press release on the article.

The article was co-first authored by PhD Candidate Brock Harpur and postdoctoral fellow Dr. Clement Kent, with further contributions from MSc candidate Daria Molodostova, former Research at York undergraduate Jonathan Lebon, and two collaborators from King Saud University, Drs. Abdualziz Alqarni and Ayman Owayss.

The study involved sequencing the genomes of 39 European honey bees (Apis mellifera) from their native range in Africa, Asia, and Europe. We also sequenced the genome of the Asiatic honey bee Apis cerana.  We were able to identify over 12 million mutations in the European honey bee and this allowed us to identify DNA regions that have experienced positive ‘Darwinian’ selection. Positive selection refers to the evolutionary process that increase the frequency of beneficial mutations in a population, because such mutations confer an advantage to the individuals carrying them (e.g. such individuals can survive better, or reproduce more relative to others in the population).

Studying selection in social insects is not straight forward because worker honey bees are effectively sterile – they do not have offspring of their own, so they can only experience positive selection indirectly; mutations that affect a worker’s helping behaviour can only spread through the population if the helping behaviour allows their mother queen to produce more queens and drones (reproductive male bees); this is called kin-selection.  We set out to look for evidence of kin selection by searching for signs of positive selection on genes and proteins that affect worker traits.  We find very strong evidence that genes associated with worker behaviour experience high rates of positive selection. These included Royal Jelly proteins, which are produced in specialized worker glands to feed their sisters. Indeed, the gene for royalactin, the royal jelly that workers feed to young larva to make them queens, shows very high rates of positive selection.

We also found that worker biased proteins (i.e. proteins that are expressed at higher levels in workers relative to queens) experience stronger positive selection than queen-biased proteins.

The y-axis here is Y, a measure of the strength of selection (positive values indicate positive selection). We found that worker biased proteins have higher levels of selection relative to queen biased proteins, as well as proteins that are not differentially expressed between queens and workers (NDEG). Figure reproduced from our PNAS paper

The y-axis here is Y, a measure of the strength of selection (positive values indicate positive selection). We found that worker biased proteins have higher levels of selection relative to queen biased proteins, as well as proteins that are not differentially expressed between queens and workers (NDEG). Figure reproduced from our PNAS paper

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Our study shows that workers, through their helping behaviour, play a major role in environmental adaptation in the honey bee.  In other words, ‘survival of the fittest’ in honey bees is essentially survival of the colonies with the best workers!

Cheers,
Amro

PNAS Cake II

By , January 7, 2014

Very happy to report that, after months of hard work, we’ve just heard that our study will be published in PNAS – a top science journal. Can’t tell you much about the article now – it is embargoed until published – but it is very very neat in my humble and biased opinion. We had a little mini-celebration with PNAS cake… Yum! 🙂

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Hmmm, 40^3!

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[L to R]: Nadia, Alivia, Jen, Daria, Phil, Brock, Lior, Amro

Management and diversity in honey bees: comment and reply.

By , June 2, 2013

De la Rúa et al. raised some comments about our recent article showing that management enhances genetic diversity in honey bees. Their comments, along with our response have been published online in Molecular Ecology.  We stress that admixture does enhance genetic diversity in managed bees.

Conserving genetic diversity in the honeybee: Comments on Harpur et al. (2012)
Pilar De la Rúa, Rodolfo Jaffé, Irene Muñoz, José Serrano, Robin F. A. Moritz and F. Bernhard Kraus
Article first published online: 28 MAY 2013 | DOI: 10.1111/mec.12333

and

Admixture increases diversity in managed honey bees: Reply to De la Rúa et al. (2013)
Brock A. Harpur, Shermineh Minaei, Clement F. Kent and Amro Zayed
Article first published online: 9 MAY 2013 | DOI: 10.1111/mec.12332

New paper: the curious case of the disappearing immune genes in honey bees.

By , April 9, 2013

We have a new paper out in Molecular Biology and Evolution.  See the press release here.

When the honey bee Apis mellifera genome was sequenced in 2006, researchers found that the bee has fewer innate immune genes – the genes that recognize and destroy pathogens – than other solitary insects.  The bee had about 30% of the innate immune genes found in flies and mosquitos.  Wow! Why?

Dr. Jay Evans (USDA) and colleagues hypothesized that maybe bees have fewer pathogens, or that they can fight pathogens better with social behaviour; worker bees can groom themselves and their sisters, and they can recognize sick/dead larva and remove them from the colony.

Brock Harpur, a MSc (now PhD) student in the lab is very interested in immunity in social insects, and he decided to study the evolution of 13 innate immune genes in the honey bee.  We sequenced these genes in about 40 different honey bee workers, and in one worker of the closely related Asian honey bee Apis cerana.  This allowed us to discover mutations in innate immune genes within the European honey bee Apis mellifera, and between the European and the Asian honey bee (Apis mellifera vs. Apis cerana).  We compared the amount of mutations in innate immune genes to those found in 20 randomly chosen genes.

The DNA sequence of a given gene codes for a specific sequence of amino acids that get folded into a 3-dimensional protein that then preforms a specific function within the cell.  Mutations in a gene sequence come in two flavours: there are mutations that don’t change the amino acid sequence of the resulting protein (we call these silent mutations), and there are mutations that change the amino acid sequence of the resulting protein (we call these replacement mutations).  The silent mutations – because they do not affect the shape and structure of the resulting protein – do not often affect fitness and are not ‘weeded-out’ by natural selection; silent mutations accumulated within species, and between species.  However, replacement mutations will change the shape / structure of proteins, and often the resulting protein will not function optimally (if it works at all).  These mutations, because they are often bad, are then rapidly removed by natural selection (because bees with these mutations do not survival as well).

Now imagine a gene sequence that was functional in an ancestor but is now no longer necessary.  Replacement mutations in such genes will no longer be weeded-out by natural selection (because bees with these mutations survival normally), and these mutations can then accumulate similar to silent mutations; this process is called ‘relaxation of purifying selection or relaxation of constraint’.

 

When selection is relaxed (right), mutations accumulate at fast rates in gene sequences. Normally, mutations that alter the amino acid sequence of a protein will be removed by purifying selection as a large fraction of these mutations are bad (left)

 

 

 

 

 

 

 

 

 

 

 

This is exactly what we see when we look at most immune genes in the honey bee. When we examine silent mutations, immune genes and random genes have similar rates. However, if we examine replacement mutations, we find that immune genes have 3 to 4 higher mutations relative to random genes; this is consistent with a relaxation of purifying selection.  We reckon that the same process that resulted in massive loss of innate immune genes in the bee is still acting to erode some of the remaining innate immune genes in contemporary bee populations.  Our work supports Dr. Jay Evans’ idea that some aspect of social living makes an individual-based innate immune system less useful.

New paper: the evolution of recombination rates in social insects

By , March 25, 2013

We have a paper out this month in Communicative and Integrative Biology on the evolution of recombination rates in social insects.  This follows up on our recent PNAS paper showing a relationship between recombination, GC content, and worker biased genes in the honey bee.  We now present a conceptual paper on how high recombination could have been advantageous during the initial stages of the evolution of sociality, which in turn could have affected GC content in social insects.  The paper was authored by Dr Clement Kent – a postdoctoral fellow in the lab.  Its an open access article, so you can download it and read it for free!

Amro