Notes

ddRADseq

Bioanalyzer HS results in.

Each sample has a tiny peak at 68-69 bp. Are these the adapters? What happened to DNA???

ApTranscriptome

Meeting with Nick

global patterns of expression; compare among colonies
model ‘costs’ of gene expression when exposed to extreme temperatures

Robust regression

Concerned that simple lm maybe too liberal in detecting patterns. After some reading, decided that I should use robust regression for analysis of gene expression data. No default F statistic to assess overall model fit, but this page explains that fitting a full model and a minimal model with no covariates Y ~ 1 and then doing anova(full.model, minimal.model) is equivalent to an F test. I confirmed this for the simple lm case.

Error message where model doesn’t fit - need to continue ddply even with error. Using try as suggested here.

Reading

Hof, C., Rahbek, C. & Araújo, M.B. (2010). Phylogenetic signals in the climatic niches of the world’s amphibians. Ecography, 33, 242–250.

examined phylogenetic signal in climatic niche similarity at species, genus, subfamily and family groups
- is this really a fair test? no formal designation of levels above species
results show presence of phylogenetic signal at both genus and family levels
considerable variation across amphibian orders and biogeographic regions
“result lends support to the suggestion of the existence of considerable constancy in climatic niches for a period of time that reaches back to the late Cretaceous or even earlier”

Botkin, D., Saxe, H., Araujo, M.B., Betts, R., Bradshaw, R.H.W., Cedhagen, T., Chesson, P., Dawson, T.P., Etterson, J.R., Faith, D.P., Ferrier, S., Guisan, A., Hansen, A., Hilbert, D.W., Loehle, C., Margules, C., New, M., Sobel, M.J. & Stockwell, D.R.B. (2007). Forecasting the Effects of Global Warming on Biodiversity. BioScience, 57, 227–236.

Quaternary conundrum: predictions of great extinction, but few species went extinct during last ice age
- species survive in local ‘cryptic’ refugia
- genetic heterogeneity within species