Virology for an ecologist

The virus world is a strange one and I feel like disease ecologists that patterns of viral infection at a macro-scale should have some understanding of whats going on at a cell level. I’ve recently come across a interesting virology blog that has definitely  helped me understand virus biology in a new (and more detailed) way.

Here is the link: http://www.virology.ws/2013/11/05/the-neuraminidase-of-influenza-virus/

 

MCMC GLMM in R

I’ve been finding Jarrod Hadfield’s MCMC GLMM package in R really useful for dealing with some pretty complicated data sets. It’s fast, easy to use and has an excellent tutorial for ecologists by Wilson et al to assist with interpretation. A really useful way in my case to get to bottom of some of the factors that shape pathogen diversity pattern across lion prides in the Serengeti.

Here is the link: http://www.wildanimalmodels.org/tiki-download_wiki_attachment.php?attId=24

 

The foundation stones of functional ecology

How sound are the fundamental concepts of trait-based ecology? The key ideas and historical context of functional trait-based ecology don’t get discussed as often as they should. Bill  Shipley et al explore arguably three of the most important ideas in the latest issue of Oecologia.  1. Functional traits are related to fitness, 2. Intraspecific trait variation doesn’t matter and 3. Traits respond to environmental gradients in a predictable way. They argue that these ideas are poorly developed and rarely tested mostly because a) exploring foundational concepts isn’t novel enough and b) it’s difficult to do so. For example , how can you measure fitness consequences of a functional trait for hundreds of species? The use plant-based perspective, but I think these points resonate even more for animal and parasite trait-based ecologists.

To my knowledge, for example, no one has looked into intraspecific variation of a functional trait  for any invertebrate group at least (please tell me if I’m wrong!). Understanding this variation, as the authors point out, could be critical for how communities respond to the environmental gradient e.g., trait plasticity enables a species to recolonize a disturbed habitat. This paper also calls for a more standardized approach to measuring environmental gradients, which is clearly lacking in all the trait databases. What is the point of standardized trait measurement approaches when we can’t link them to to environmental gradients measured in more or less the same way? I found this paper really useful reminder to just how tenuous the building blocks of functional ecology are. I would’ve liked to seen a section linking  in phylogenetic signal in traits as I really think this can help with understanding global trait patterns – I feel like phylogenetic information should be linked to trait databases also (worthy of another paper). Regardless, this is a really interesting article (and interesting issue!).

Shipley et al: http://link.springer.com/article/10.1007/s00442-016-3549-x

The issue: http://link.springer.com/journal/442/180/4/page/1