PhD positions available in the Zayedlab

By , December 17, 2015

Multiple PhD positions in honey bee genomics and sociobiology at York University, Toronto.

Are you interested in genomics, population genetics, social insects and a Ph.D.?

The Zayed lab (http://zayedlab.apps01.yorku.ca/wordpress/) in the Department of Biology at York University (Toronto, Canada) is looking for enthusiastic new doctoral candidates in 2016 to work on one of several exciting projects:

1) BeeOMICs – Genome-Wide Association Studies – several positions

Funded by Genome Canada, the BeeOMICs team will apply genome-wide-association mapping and population genomic tools to study the genetics of 12 colony-level traits in honey bees. This will involve sequencing and analysis of 1,000 colony ‘genomes’. We seek applicants who bring interest and experience in SOME of the following fields: genomics, population genetics, and computing. There will be lots of opportunities to interact with members of the BeeOMICs team. Read more about the BeeOMICs project here:  http://www.genomebc.ca/news-events/news-releases/2015/canadian-queens-sustaining-and-securing-canadas-honey-bees-using-omic-tools/

 2) BeeOMICs – Modeling genetic load in social insects – 1 PhD position

We are looking for a PhD student that will work closely with Dr. Amro Zayed and Dr. Jianhong Wu (at York University’s Center for Disease Modeling) http://www.cdm.yorku.ca/wujh/content/about) to develop theory and models for understanding the genetic load in social insects. This will build upon some of our earlier work– see Zayed and Packer, 2005, PNAS 102:10742-10746.

 3) BeeOMICs – Population genomics of African honey bees – 1 PhD position

We plan to sequence multiple genomes of all honey bee subspecies found in Africa. The dataset will provide a wealth of knowledge about patterns of natural selection in bee genomes and will help us understand the enigmatic biogeographic history of honey bees. It will also allow us to refine a diagnostic tool for detecting Africanized honey bees. Representative pubs include:

Harpur, B.A., Chapman, N.C., Krimus, L., Maciukiewicz, P., Sandhu, V., Sood, K., Lim, J., Rinderer, T.E., Allsopp, M.H., Oldroyd, B.P. and Zayed, A. (2015). Assessing patterns of admixture and ancestry in Canadian honey bees. Insectes Sociaux. 62:479-489.

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.

4) Comparative population genomics of social insects – multiple positions

Funded by an NSERC discovery grant, we plan on carrying comparative population genomic studies across 24 different species that represent different stages of social evolution. Lots of interesting questions to ask, including: What is the relationship between social evolution and genome evolution? Are there common patterns of adaptive evolution associated with the origin of castes and sociality – Hamilton’s proverbial ‘genes for altruism’ ? What kind of mutations underlie adaptive evolution in social insects ? (e.g. coding vs. regulatory, taxonomically-restricted genes vs. conserved genes), and so on…

Representative publications include:

Kapheim, K. M. et al. including Kent, C.F. and Zayed, (2015) A. Genomic signatures of evolutionary transitions from solitary to group living. Science, 348:1139-1143.

Kent, C.F. and Zayed, A. (2015). Population Genomic and Phylogenomic Insights into the Evolution of Physiology and Behaviour in Social Insects. Advances in Insect Physiology. 48:293-342.

Molodtsova, D., Harpur, B.A., Kent, C.F., Seevananthan, K., and Zayed, A. (2014). Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviours. Frontiers in Genetics, 5:431.

Harpur, B.A., Kent, C.F., Molodtsova, D., Lebon, J.M.D., Alqarni, A.S., Owayss, A.A., Zayed, A. 2014. Population genomics of the honey bee reveals strong signatures of positive selection on worker traits. PNAS. 111:2614-2619

Kent, C.F., Minaei, S., Harpur, B.A., and Zayed, A. 2012. Recombination is associated with the evolution of genome structure and worker behavior in honey bees. PNAS. 109:18012-18017.

 

Successful candidates will receive training in genomics, bioinformatics and sociobiology in a very collaborative environment. Toronto is a great city to live and work in. Funding if available for Canadian students; international students are welcome to apply provided they have access to scholarships from their home country. If interested in applying, please send your c.v., contacts for references, and a 1 page cover letter to zayed@yorku.ca

 

Best,!

Amro

Erica sweeps bio undergrad awards

By , August 18, 2015

Very happy that Erica Shenfeld, who carried out her honours thesis research on Bee Genetics, won the Department of Biology’s C.W. Fowle and B. Rozario  prize, as well as the Mainguy Genetics Award.

The Fowel and Rozario prize is awarded to the most outstanding graduating student in Honours Biology as determined by the department. The award is based on grades, research potential and leadership activities within the department.

The Mainguy Genetics award is given to a 3rd or 4th year biology students who show extreme proficiency in Genetics, both in the laboratory and in the classroom.

Congrats Erica … you made us very proud!

Erica presenting her research on bee genetics at the Toronto Entomological Society, 2015

Erica presenting her research on bee genetics at the Toronto Entomological Society, 2015

New cohort of Undergrads join lab

By , May 22, 2015

May is a very fun time of the year. Spring is in full swing and the bees are happy. It is also a time when a fresh cohort of YorkU undergrads join the lab. This year we have two new summer NSERC USRA scholarship winners joining the lab, Danny and Pratik. We also have zayedlab veterans Harshil (research assistant, summer 2014, and Honors thesis 2014/15) and Research at York student Sani (bioinformatics research assistant) who will continue to work with us this summer.
Welcome and hoping for a very productive summer.

Pratik, Harshil and Danny

Pratik, Harshil and Danny

 

Science: Bee genomes take flight!

By , May 20, 2015

The bee community’s answer to the 12 fruit fly genomes…. The 10 bee genomes…. all the ACGT’s plus methylation and very cool social behaviour… take that Drosophila!  :) [who has Drosophila envy —> me]

My former postdoc Dr. Clement Kent and I were part of a large international effort, spearheaded by the Karen Kapheim and Gene Robinson from the University of Illinois, to sequence and study the genomes of 10 bee species that vary in terms of their social organization. The study was published in the journal Science last week. Our role was to study patterns of molecular evolution as a function of social organization and genome structure.

It was a lot of fun! The added bonus (in addition to a paper in Science) is that i am now a co-author with 50+ of my favourite bee researchers from around the world… Neat!

Anyways, check out the nice little write up on the article by TheScientist’s Ruth Williams

 

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

Anatomy of a pollinator garden

By , March 9, 2015

Some of you know that i love bees. I also generally dislike grass. I don’t like mowing it. I don’t like watering it. I don’t find manicured fields of green grass beautiful.

So, when the snow thawed off the ground – in that first spring in our new home in Woodbridge Ontario in 2010 – my wife and i did something fun… we put a layer of newspaper on our front lawn (neighbours thought we were crazy), put about 2 inches of soil on top of the news paper, and planted several species of hardy native perennials that are attractive to bees, butterflies and birds. I had a lot of help, former postdoc and master gardner Clement Kent provided me with most of the plants (from his garden) and good instructions about how to keep my plants happy.

I was doing a google search on our home and was pleased to see that google maps snapped a nice picture of our pollinator garden in mid bloom last summer. Here is the full list of plants in my garden… in case you want to build your own.

Amro

I spy with my little eye, something that is full of bees

I spy with my little eye, something that is full of bees

Garden with 30+ species of plants, mostly native

Garden with 30+ species of plants, mostly native. See Plant list below… I used pea gravel and some slate stones on the edges.

Plant List
Some of the plants below are not native, but look pretty and still attract pollinators. Some I removed from the garden bed for some reason or another.

1. Violets
2. Amsonia tabernaemontana [blue star]
3. Rudbeckia hirta – Black-eyed Susan
4. Rudbeckia laciniata – Cutleaf Coneflower
5. Wild strawberries (spc ?)
6. Filipendula rubra – Queen of the Prairie
7. Physostegia virginiana [obedient plant]
8. Monarda (bee balm) (purple; red = M. didyma – jacob cline; c = fistulosa blue)
9. Iris versicolor – Northern Blue Flag
10. Veronica longifolia – white speedwell
11. Sanguisorba canadensis – Canadian burnet
12. Baptisia australis – Blue false indigo
13. Penstemon hirsutus – hairy beardtongue
14. Gaillardia aristata – blanketflower
15. Asclepias incarnata – Swamp Milkweed
16. Agastache foeniculum – Golden Anise Hyssop
17. Liatris spicata – gayfeather
18. Helenium hoopesii – orange helenium
19. Echinacea purpurea (2 from C. Kent; 1 bright star, 1 Magnus); purple coneflower
20. Liatris ligulistylis – Meadow Blazingstar
21. Echinacea purpurea ‘baby white swan’
22. Veronica spicata (speedwell – sunny border blue)
23. Creeping thyme (mother of thyme)
24. Sage (spc ?)
25. Tiarella cordifolia – heartleaved foamflower
26. Phlox stolonifera blue ridge – Phlox
27. Oenothera tetragona – sundrops
28. Phlox subulata Emerald blue creeping Phlox
28b. Phlox subulata Emerald pink creeping Phlox
29. Coreopsis verticillata – threadleaf coreopsis golden showers
30. Viola labradorica – Labrador Violet
TT. Tarda Tulips
BR. Sanguinaria canadensis – bloodroot
31. Aster novae-angliae -New England Aster
32. Erigeron speciosus – Showy Fleabane
33. Eupatorium purpureum – Sweet Joe-Pye weed
34. Heliopsis helianthoides
35. Phlox paniculata a.David b. Nicky c. purple flame – Summer Phlox
36. French Lavender (spc. ?)
36a. Pincushion flower Scabiosa pink mist
37. Wolly thyme jeepers creepers thymus pseudolanuginousus
38. Lamium maculatum “white nancy”
39. Hen and chicks Crassulaceae

Upcoming Seminars: Back to Cali & Treehouse!

By , February 3, 2015

Hi Folks,

two seminar next week, in California and Toronto,

1st: I am giving a seminar on bee genomics at the UC Davis’ Department of Entomology and Nematology , Feb 11.

2nd: I am giving a public talk on bees, as part of the Treehouse talks, Friday Feb 13th, 6:30 pm at the Toronto Reference Library.  Title is: Bees are the bee’s knees! [dancing is not optional]

Drop by and say hi!

Amro

The great canadian genome survey hits the road!

By , January 29, 2015

In Moncton New Brunswick! Drop by and see my talk on the great canadian genome survey at the Canadian Honey Council and Canadian Association of Professional Apiculturists’ Research Symposium tomorrow.

Amro, 5'9", Moncton NB Snow Bank 5' 8"

Amro, 5’9″, Moncton NB Snow Bank 5′ 8″