As many may know – I am pretty obsessed with the uses of phylogeny in biological studies. In fact, one could say this has driven almost all of my work. Thus when an email went around a little bit ago about an article for a journal club at UC Davis where the title begins with “Does phylogeny matter?”, well, I had to take a look. Alas, I was a bit worried when I saw the article was in Ecology Letters because I am at home and was not sure about access policies for this journal.
But I was pleasantly surprised to get full access without any library – VPN login to the following article: Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis – Chamberlain – 2012 – Ecology Letters – Wiley Online Library. I cannot figure out WHY it is freely available right now, nor how long it will be, but I took the chance to look the article over.
And I was even more pleasantly surprised to look over the article. Many meta-analyses can seem forced – if not almost unbearable to look through. But this one is very well done. Basically they did a massive comparison of conclusions that one could reach when one either does or does not take into account the phylogenetic non-independence of taxa when conducting meta-analyses in evo-eco studies. They searched published literature for meta-analyses and then .. well I will use their words here (from the end of their introduction):
Herein, we re-analyse datasets from previously published meta-analytic studies, comparing results of traditional and phylogenetic meta-analyses. In addition, we attempt to explain variation in the effect of phylogenetic information on meta-analytic outcomes by examining characteristics of phylogenies. We ask: (1) how does accounting for phylogenetic non-independence change results of individual meta-analyses? and (2) across datasets, what characteristics of phylogenies explain changes in effect size for phylogenetic vs. traditional meta-analyses? As a complement to our main questions, in Appendix A, we also ask (3) how does accounting for phylogenetic non-independence affect model fit of individual meta-analyses? and (4) across datasets, what characteristics of phylogenies explain variation in the relative fit of phylogenetic meta-analyses? Despite the many compelling reasons to incorporate phylogenetic information into meta-analyses that involve multiple species, investigators often use model comparison criteria, such as Akaike’s Information Criterion (AIC) to assess fit of phylogenetic vs. traditional meta-analytic models. We found a clear bias in relation to phylogeny size for one of the two methods currently used to quantify relative model fit (Q-based AIC), thus our findings have important implications for meta-analysts using such model comparisons (see Appendix A for details).
And the key conclusions are
Here, we have shown that incorporating phylogenies influences ecological meta-analysis outcomes, in many cases changing whether the observed effect size differs significantly from zero. We also show that the degree of difference between traditional and phylogenetic meta-analyses depends on key characteristics of phylogenies. Despite this potential complication, we strongly recommend incorporating phylogenetic information into ecological meta-analyses to account for species non-independence.
They also offer up three main recommendations for consideration
To conclude, we outline three recommendations for the use of phylogenetic meta-analyses in ecology and evolutionary biology:
- Use phylogenetic meta-analysis, but note that some response metrics are less likely to be affected by phylogenetic methods.
- Include as many species as possible.
- Be aware that phylogeny shape may influence meta-analytic outcomes.
Definitely worth a look …
Chamberlain, S., Hovick, S., Dibble, C., Rasmussen, N., Van Allen, B., Maitner, B., Ahern, J., Bell-Dereske, L., Roy, C., Meza-Lopez, M., Carrillo, J., Siemann, E., Lajeunesse, M., & Whitney, K. (2012). Does phylogeny matter? Assessing the impact of phylogenetic information in ecological meta-analysis Ecology Letters, 15 (6), 627-636 DOI: 10.1111/j.1461-0248.2012.01776.x
2 thoughts on “Does phylogeny matter? (In Eco-Evo meta-analyses) … Apparently, yes, but it depends.”
Hi Jonathan, From the Ecology Letters homepage, all “Reviews and Syntheses” papers are freely available. The “Phylogeny” article is classed as a review. –Karen A.
Thanks for the post about our paper. Just watched your TedMED talk – great stuff.