Mixed effect models and SEMs

I’m increasingly convinced of the value of structural equation models (SEMs)in ecology – particularly if random effects and phylogenetic relationships can be incorporated. That is exactly what has been achieved in the new R package ‘Piecewise SEM’ by Jonathan Lefcheck recently published Methods in Ecology and Evolution.  Before this if your model variables were not normally distributed or independent this was a big problem for SEM models. This limited the use of this type of modelling in ecology as ecological data, for the most part, violates these assumptions readily. This package extends SEMs to include mixed effect models, all sorts of other data distributions (Poisson etc) and phylogentic generalized least-squares (PGLS). This seems like a really nice extension of the idea and the package looks relatively easy to implement. There are limitations, of course, such as not being able to account for bidirectional relationships, but  as Jon suggests, future work will rectify these. Nonetheless this is a useful extension of the SEM idea which I’m sure will lead to greater uptake of this useful modelling approach.

Here is the link: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12512/full

Journal club as a blog

After  a busy week running  a workshop on using phylogenetic community ecology to better understand influenza I had a chance to catch up on everything and read a blog that one of the workshop attendees (Will Pearse) contributes to: https://pegejournalclub.wordpress.com/.

A journal club in the form of a blog is truly an excellent idea – maybe something we should do with our wildlife epidemiology journal club.

Anyway definitely an interesting read for anyone interested in in how phylogenetics can be applied to ecology.

Field trip notes: Habitat connectivity in SoCal

Why did the big cat cross the road? What impact does a 16 lane highway have on disease transmission for bobcat and puma? Answering questions like these are central to  the NSF project I’m working on, and was the reason that I went on a trip to one of the most fragmented landscapes in the U.S. – Southern California. It was fun after staring at maps  of the area for so long to actually get the chance to visit, see the landscape and talk big cat biology and trapping with a friendly set of field biologists. I feel like modelers should do this more often wherever possible…. Another Tasmanian on the project (Chis Kozakiewicz) joined me for the trip.

Below is a series of images from San Diego to Ventura county (north of LA) taken from the trip with some field notes.

San Diego bobcat habitat

We started off the trip down in Sand Diego in some beautiful and relatively undisturbed bobcat habitat in the Sycamore Canyon. Straight away we found bobcat scats which  was promising (but no sightings of course). Then we met our San Diego Collaborator (Meggan Jennings) and went touring around her bobcat sites in the hills behind Ramona helping check camera traps along the way. Then she took us to the more urbanized coast and some of the canyon preserves where she trapped many a bobcat including three in one place which is rare! For a heavily urbanized place, Sand Diego has real potential to build habitat connectivity as there are numerous canyons running west-east that remain reasonably undeveloped. The urban-to-developed gradient is nearly set up like a natural experiment which is nice.

Next was on to Orange County to quite a different landscape, but one I know quite well from maps (I have written a paper on feline immunodeficiency virus (FIV) transmission in the area). We met up with Erin Boydston (from the USGS) and her crew and went on a back hills tour of the OC. The scale of the Santa Ana mountains (the mountain range behind the OC) and the San Joaquin Hills (on the coast) surprised me – they were much bigger than I imagined. They were also more fragmented than I imagined. The 91 (featured above) and I5 are vast highways and I’m surprised any mammal could cross. The ‘famous’ Coal Canyon wildlife underpass (above) that links the Santa Ana Mountains to the Chino Hills makes this possible and we spotted clusters of bobcat scats at the entrance which was nice. Apparently the rocks placed randomly in the underpass made it more effective for deer at least. That said, if animals use the underpass they still have to cross the Santa Ana river and  a golf course to connect to the Chino Hills.

The it was back towards the coast and through the San Joaquin Hills to Laguna Beach. This is really nice part of the OC  – but the connection to here from the Santa Ana’s crossing the I5 and some very urban areas would be difficult to say the least. Yet FIV data has clearly demonstrated that this can happen (see Lee et al’s paper below). Golf courses and celebrity gated communities strangely may make this easier as both provide good habitat for bobcat at least. The theory goes that, in drought conditions the grass is still watered which means that prey populations (e.g. rabbits) are more stable. We went through a gated community  and the amount of open ‘natural’ space was surprising. To finish the day we went to watch a bobcat be released into a urban fragment also on the coast after being being a victim of some form of attack (perhaps a dog). It was great to actually see a bobcat in the flesh and here is hoping that this female bobcat doesn’t become another road casualty.

Lee et al: http://www.ncbi.nlm.nih.gov/pubmed/22335296

Santa Monicas

We finished the trip north of LA in Ventura county with Seth Riley and discussed the puma part of the project. The Santa Monica mountains are truly beautiful and the photo doesn’t do them much justice. This area is habitat for ~8 puma and the issue is how to keep this small fragmented population from falling into an inbreeding depression. There are larger populations to the north but allowing connectivity is stymied by (you guessed it) one massive highway (101) and a few smaller ones. There is only one real spot that makes sense to put an under or over pass, but building it is going to be in the order of $35 million. Obviously this would provide connectivity for other species too – hopefully there are enough wealthy donors that can help with this – there are sure many of them in the area (we went passed Will Smiths house in a gated community close by). We finished our trip checking out the Hollywood Hills habitat of the infamous puma P22 that recently ate a Koala from the the LA zoo. His range is small and very very isolated but he has been there for years after crossing two of the largest highways in America…

I’m really excited to pushing forward with this project in the coming months. We will be getting host/viral genomic data from these areas and the data will tell will no doubt be an interesting one.