RNA extraction

Lab work

RNA extraction for the 12 temperature-treated samples of 3 ants from Andrew’s putative A. rudis colony. Followed two-step step RNAzol RT and Qiagen RNeasy protocol as before, with two elutions of the RNA column. The first elution was with a volume of 20ul and the second was with 14ul

RNA concentration from Nanodrop (also showing results from A22 colony, which we extracted RNA from yesterday):

Sample	Temp	Elution	Concentratinon (ng/ul)	volume (ul)	RNA (ng)	combined RNA (ng)
A22	0	1	66.15	16	1058.4	1259.52
A22	0	2	12.57	10	201.12	.
A22	3.5	1	26.63	16	426.08	654.88
A22	3.5	2	14.3	10	228.8	.
A22	7	1	20.29	16	324.64	532.64
A22	7	2	13	10	208	.
A22	10.5	1	82.79	16	1324.64	1780.48
A22	10.5	2	28.49	10	455.84	.
A22	14	1	73.57	16	1177.12	1383.2
A22	14	2	12.88	10	206.08	.
A22	17.5	1	43.64	16	698.24	986.56
A22	17.5	2	18.02	10	288.32	.
A22	21	1	57.69	16	923.04	1215.2
A22	21	2	18.26	10	292.16	.
A22	24.5	1	57.97	16	927.52	1283.04
A22	24.5	2	22.22	10	355.52	.
A22	28	1	57.29	16	916.64	1170.56
A22	28	2	15.87	10	253.92	.
A22	31.5	1	46.93	16	750.88	1035.36
A22	31.5	2	17.78	10	284.48	.
A22	35	1	108.51	16	1736.16	2019.84
A22	35	2	17.73	10	283.68	.
A22	38.5	1	55.29	16	884.64	1065.28
A22	38.5	2	11.29	10	180.64	.
Ar	0	1	52.4	16	838.4	1064
Ar	0	2	14.1	10	225.6	.
Ar	3.5	1	119.7	16	1915.2	2078.4
Ar	3.5	2	10.2	10	163.2	.
Ar	7	1	35	16	560	811.2
Ar	7	2	15.7	10	251.2	.
Ar	10.5	1	70.5	16	1128	1561.6
Ar	10.5	2	27.1	10	433.6	.
Ar	14	1	96.4	16	1542.4	2510.4
Ar	14	2	60.5	10	968	.
Ar	17.5	1	77.2	16	1235.2	1734.4
Ar	17.5	2	31.2	10	499.2	.
Ar	21	1	42.8	16	684.8	1446.4
Ar	21	2	47.6	10	761.6	.
Ar	24.5	1	112.3	16	1796.8	1961.6
Ar	24.5	2	10.3	10	164.8	.
Ar	28	1	49.6	16	793.6	1513.6
Ar	28	2	45	10	720	.
Ar	31.5	1	93.9	16	1502.4	1737.6
Ar	31.5	2	14.7	10	235.2	.
Ar	35	1	135.9	16	2174.4	2475.2
Ar	35	2	18.8	10	300.8	.
Ar	38.5	1	75.1	16	1201.6	1396.8
Ar	38.5	2	12.2	10	195.2	.

For all samples except Ar7, well over 1ug of RNA with both elutions combined, and for most samples can use only the first elution and save the second elution for qPCR validation or another analyses.

Reading

Garud et al. (2013) Soft selective sweeps are the primary mode of recent adaptation in Drosophila melanogaster. arXiv:1303.0906

authors present an interesting new statistic (H12) that can detect both hard and soft sweeps with equal power. the basic idea is quite simple - calculate homozygosity with the first and second most abundant haplotypes combined - yet appears quite powerful. Power of this test is high for hard and soft sweeps that are young and strong. This test is followed up by a second test (H2/H1), contingent on a significant results from the first test, that determines whether the sweep was soft or hard based on the ratio of all haplotypes excluding the most frequent (H2) to all haplotypes (H1). Main finding of the paper is that all recent sweeps in Drosophila are soft sweeps. This is plausible if mutation is not limiting adaptation, but the effective population size of Drosophila is on the order of 10^8 instead of 10^6 as estimated from heterozygosity at neutral sites.