ChrisYesson_PhyloclimaticModellingExercise
Channel: A. Townsend Peterson
Date: 2012-10-24

PHYLOCLIMATIC MODELLING WORKSHOP
Dr. Christopher Yesson, Zoological Society of London

Presented in Xalapa, Veracruz, Mexico, on 8-9 October 2012
In English

This workshop presents methods to examine niche modelling from an evolutionary perspective.  By combining temporally calibrated phylogenies with environmental preferences we can reconstruct ancestral niches and project these into palaeoclimate reconstructions to estimate ancestral areas.  The methods discussed include temporal calibration of phylogenies, niche modelling, phylogenetic niche conservancy; the presentation culminates with a simple example of phyloclimatic modelling.

Materials to accompany the lectures in this workshop can be downloaded as .zip files from http://hdl.handle.net/1808/10358. 


TEMPORAL CALIBRATION

TemporalCalibrationLecture.pdf (slides from the lecture) 
TemporalCalibrationPractical.pdf (instructions for the practical) 
TemporalCalibrationPracticalData.zip (zip file of data for the practical)
 
These lectures provide an introduction to the temporal calibration of phylogenies using assumptions of strict and relaxed molecular clocks.  In the first part, I provide a brief background to the theory and introduce the methods employed to convert phylogenies to ultrametric trees.  Then I look at calibrating dates on the ultrametric trees, the uncertainty associated with these dates, and methods to present this uncertainty.

 
DATA QUALITY

DataQualityLecture.pdf (slides from the lecture)
 
These lectures discuss the data required for species distribution modelling and how issues concerning data quality may affect the models.  First, I introduce climate data and discuss uncertainty in past and future climate models.  Next, I look at species distribution data and its potential biases, and point out some common issues with this type of data.  Finally, I examine other issues with extracting distribution data from databases and summarize the importance of a rigorous examination of data quality prior to modelling.

 
NICHE CORRELATION

NicheCorrelationLecture
NicheCorrelationPractical
NicheCorrelationData

This segment looks at comparing niches of multiple species using correlation measures such as the D & I statistics.  Such measures of niche divergence are combined with dated phylogenies to test the phylogenetic conservancy of the niche.  An example of comparing age to most recent common ancestor with niche divergence is presented.


PHYLOCLIMATIC MODELING

PhyloclimaticModellingLecture
PhyloclimaticModellingPractical
PhyloclimaticModellingData

This segment looks at the ancestral state reconstruction of continuous environmental characteristics on a phylogeny.  By reconstructing the observed minimum and maximum values of multiple environmental characters we create a Bioclim niche model for ancestral nodes on the phylogeny.  An example model is projected into palaeoclimate reconstructions of the time period suggested by a dated phylogeny.  The areas selected by the model represent an estimate of ancestral areas.