Background similarity test. Tutorial

Tutorial:
Background similarity test: overcoming common errors
(Originally published in: https://www.youtube.com/watch?v=z1W95MLH2U8)

By:
Daniel Romero-Álvarez (@vakdaro)
[email protected]

Luis E. Escobar (@luiseecobar)
[email protected]

Introduction

According to the authors, the test 'tries to compare if two species are more or less similar than expected based on differences in the environmental background in which they occur’(Warren, ENMTools software tutorial, link below).
At first, to perform the test seemed to be an easy task, however it took some time to figure out some important steps…we found some help in internet but it was scarce... that is why we are sure this tutorial will come in handy.
So, let’s do it! The video will explain all the steps to perform the test and then how to overcome the common errors in the process. One more thing, the tutorial is made for windows.
Good modelling!


Programs to install:

ENMTools: http://goo.gl/Xhnaxg
Pearl: http://goo.gl/at7CMy
Maxent: https://goo.gl/eMVZvd
Java: https://java.com/en/download/

References to review the theoretical principles behind the Backgound similarity test:
Warren DL, Glor RE, Turelli M. ENMTools: a toolbox for comparative studies of environmental niche models. Ecography (Cop). 2010:607-611. doi:10.1111/j.1600-0587.2009.06142.x.
Warren DL, Glor RE, Turelli M. Environmental niche equivalency versus conservatism: Quantitative approaches to niche evolution. Evolution (N Y). 2008;62(11):2868-2883. doi:10.1111/j.1558-5646.2008.00482.x.
Errors solved:

1.- ENMTools:
Error 5032. Corrected by specifying the correct path directory of java.exe file (minute 10:40)

Can't open G:/Research/Maxent_results/WorldClim/Fremont_genetics/8ClimVar_current/ENMTools/NicheIdentityTest_2/Populus california_rep0.asc!!

while executing
"::perl::CODE(0x45c95a8)"
invoked from within
".b5 invoke "
invoked from within
".b5 instate !disabled { .b5 invoke } "
invoked from within
".b5 instate pressed { .b5 state !pressed; .b5 instate !disabled { .b5 invoke } } "
(command bound to event)

2.- Maxent:
Fatal Error: Java.lang.NullPointerException. Corrected by creating the folder ‘plots’ inside the output directory folder for results (minute 11:58)

Useful webs discussing this problems:
Warren tutorial of ENMTools: http://www.danwarren.net/enmtools/builds/Release/ENMTools_User_Manual%201.1.pdf
Java error: http://enmtools.blogspot.com/2013/09/fixed-error-in-resampling-in-enmtools.html
Maxent error: https://groups.google.com/forum/#!topic/maxent/6RuAqOj54ew

You can also make this test using the ‘Phyloclim’ package in R (http://artax.karlin.mff.cuni.cz/r-help/library/phyloclim/html/hypothesis.tests.html) developed by Christoph Heibl.