Does phylogeny matter? (In Eco-Evo meta-analyses) … Apparently, yes, but it depends.

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:

  1. Use phylogenetic meta-analysis, but note that some response metrics are less likely to be affected by phylogenetic methods.
  2. Include as many species as possible.
  3. 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

Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

2 thoughts on “Does phylogeny matter? (In Eco-Evo meta-analyses) … Apparently, yes, but it depends.”

  1. 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.


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