28 June 2013

Aphaenogaster and Medicago

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Notes for week of June 24


Finished edits to ‘Genomic estimation of heritability’ manuscript and sent to co-authors.

Had planned to collect colonies at Red Rocks but afternoon thunderstorms got in the way…


Drove to Harvard Forest. Arrived about 1pm and quickly begin searching for Aphaenogaster colonies with goal of collecting 50.

Aphaenogaster very common! Found 25 colonies in 4 hours of searching with help from Monica Davis.


Collecting at Harvard Forest - 25 additional colonies for a total of 50!

Only found 1 more queen, though was working quickly to get quantity of colonies.

Plans for sampling local sites with Kerri and Skyler.


Early morning went out collecting for common garden colonies at Red Rock. Difficult to find colonies – too wet. Found 2 small colonies in about an hour before going to East Woods (Stonehedge access). Much better! Found 2 colonies within 15 minutes, and 9 colonies in 90 minutes. In the last colony, finally found a queen!

Preparation of common garden ‘composite’ colonies

  1. Empty colony into Fluon-lined container. Look for queen
  2. Aspirate about 32 workers and transfer to glass dish on ice
  3. When workers are still, individually mark gaster with Testers paint pen. Yellow shows up best. Small dot, trying to avoid legs
  4. Let paint dry for about 5 minutes. Transfer 30 workers to next colony
  5. Collect an additional 10-15 workers into 95% EtOH in eppendorf for genotyping.

Finished 3 colonies in about 2 hours



Finished preparing composite colonies.


  • found queen for EW04! two queens for this site
  • EW02 had few workers. while got 30 for colony, only a few stored in EtOH
  • RR02 was completely dead. very wet in container…too wet? slugs also present and slimy. replaced this colony with a lab colony collected by Andrew and crew at East Woods. This was ALSO called EW3. Need to rename (see below).
  • EW08, RR01 were small and no extra workers
  • Not enough larvae in HF014 so host colony EW02 did not get a larvae
  • Not enough larvae in HF015 so host colonies RR01, EW08 and EW3-AN (#11) did not get a larvae

** Thought - should get CTmax/min for each of the host colonies as well. **

Joel, Kerri and Skyler helped with transfer of larvae to composite colonies.


  1. Dump colony into Fluon-lined tupperware. Look for queen. If present, collect!
  2. **Carefully* collect 13 larvae with soft forceps.
  3. Using paintbrush, brush larvae in front of water tube for each colony.


A damn tricky issue. Mentioned to Sara and she commented that one strategy (her PhD advisor?) was to just label ALL samples collected sequentially and keep one big log file. As in

JSG0001 | Chamaecrista | Date | Location | Lat | Long | Description JSG0002 | Chamaecrista | Date | Location | Lat | Long | Description JSG0102 | Aphaenogaster | Date | Location | Lat | Long Description

For lack of better ideas, I think I’ll adopt this. But how to label samples in experiment? Seems I could also label all experiments sequentially. In fact, I actually started to do this with Chamaecrista

ID Short Name Year Started Description
JSG-E01 CfComp 2007 Effect of competition of Chamae fitness
JSG-E02 CfHab 2008 Effect of soil type and range location on Chamae fitness
JSG-E03 CfRL2 2009 Chamae range limit experiment
JSG-E04 CfRhiz 2009 Chamaecrista - rhizobia range limit experiment
JSG-E05 CfPopGen 2009 Chamaecrista population genetics
JSG-E06 CfBe 2010 Geographic variation in Chamaecrista-Bradyrhizobium symbiosis
JSG-E07 BelkGenome 2011 Bradyrhizobium genomics
JSG-E08 MtGWAS 2011 Medicago GWAS
JSG-E09 MtGCTA 2011 Medicago genomic estimation of heritability
JSG-E10 MxE 2012 Medicago Experimental Evolution
JSG-E11 AphaenoTranscriptome 2013 Aphaenogaster transcriptome
JSG-E12 GxL 2013 Aphaenogaster Gene eXpression by Latitude
JSG-E13 AphAdaPt 2013 Aphaenogaster Adaptive Potential

Label composite colonies

JSG-E13-01, JSG-E13-02, etc

Maintain csv file with information for each colony in /project/climate-cascade/APt/planning directory

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