Notes for week of June 24

2013-06-24

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…

2013-06-25

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.

2013-06-26

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.

2013-06-27

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

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

Finished 3 colonies in about 2 hours

2013-06-28

Lab

Finished preparing composite colonies.

Notes:

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.

Protocol:

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

Labeling

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

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