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Phylocom

This document provides an overview of using the software phylocom to analyze community phylogenetic structure and trait dispersion. It discusses different null models for comparing observed community phylogenetic patterns to random expectations. Specifically, it explains null models 0, 1, and 2, which randomize phylogenies or species membership in different ways. The document also outlines commands in phylocom to calculate various metrics like Net Relatedness Index, determine locations of phylogenetic signal in communities, and analyze trait dispersion patterns compared to null expectations.

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Guilherme Landgraf
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261 views27 pages

Phylocom

This document provides an overview of using the software phylocom to analyze community phylogenetic structure and trait dispersion. It discusses different null models for comparing observed community phylogenetic patterns to random expectations. Specifically, it explains null models 0, 1, and 2, which randomize phylogenies or species membership in different ways. The document also outlines commands in phylocom to calculate various metrics like Net Relatedness Index, determine locations of phylogenetic signal in communities, and analyze trait dispersion patterns compared to null expectations.

Uploaded by

Guilherme Landgraf
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Using phylocom to answer questions about community assembly

Jean H. Burns and Sharon Y. Strauss Center for Population Biology

Community assembly

Terrestrial plants

Inquiline communities in pitcher plants

Marine sponges

Cattle tanks

Phylogeny in community assembly


Underdispersed/Clumped A B A B C D Habitat filtering Overdispersed/Even A C A B C D Competition

Measures of Community Phylogenetic Structure

Vamosi et al. 2009

Options for analysis for community phylogenetic dispersion patterns


Phylocom R packages: picante, (ape, vegan) Matlab code

Technical stuff to think about


Effects of polytomies (Swenson 2009) Effects of branch length (Holzman et al. in prep.) Size of community relative to regional pool (Kraft et al. 2007) Method of phylogeny estimation (e.g. phylomatic for angiosperms)

File structure
NO extra hard returns
They will be read as empty species or samples

newick phylogeny tabs must line up in text file

Start phylocom
cd /Users/Jean/Desktop/phylocom-4.1 Run the community phylogenetic dispersion command ./phylocom comstruct > results.xls

Null model 2: species randomized with respect to the phylogeny pool

Interpreting the output


NRI = Net Relatedness Index
+ = underdispersed/clumped - = overdispersed/even

Calculate p-value:
p = (MPD.rankHi/1000) Make sure that the # of counts in .rankHi + .rankLow ~ number of runs (If not there are many ties. Interpret with caution.)

Null model 0, phylogeny shuffle

figure from Hardy 2008

null model 0
Maintains local species diversity per site Maintains among site abundance distribution per species Maintains spatial autocorrelation of local abundances per species

Null model 1: Species in sample are random draws from sample pool

null model 1
Maintains local species diversity per site

Null model 2: species are a random draw from the phylogeny pool

null model 2
Maintains species diversity per site reduces to null model 1 if the species in the phylogeny pool = the species in the sample pool This is the Default model

Null model 3: Independent shuffle/ Checkerboard

Independent swap
constrains swapped matrix to have same row and col totals as sample matrix preserves species richness per site and # sites in which each species occurs very time consuming

Try using a different null model and comparing results


./phylocom comstruct -m 0 -r 999 > results.xls

Incorporate abundance
./phylocom comstruct -m 0 -a > results.xls Open the resulting text file in excel.

Abundance evenness or clumping


Regional Pool A 10 B 10 C 10 D 10 A C A A C C B A A B A C B Even Clumped

Calculate the distance from each species to its nearest native neighbor
./phylocom icomdist > results.xls

Determine the position of phylogenetic clumping or evenness in a community sample


./phylocom nodesig > results.nex Open the resulting nexus file in mesquite.

At what nodes is there significant clumping/evenness?


*(5): SIGMORE *(12): SIGMORE *(4): SIGMORE *(3): SIGMORE *(34): SIGLESS

Interpretation in light of trait evolution/dispersion

from Webb et al. 2002

Comtrait calculates the trait dispersion within a file and compares to a null model
./phylocom comtrait -m 0 -r 999 -x 1 > results.xls The trait B in clump2b has a SESMetric of 2.83, which is significantly lower than expected by chance (p < 0.0001) -underdispersed/clumped. The trait is thus interpreted as conserved.

Trait B is conserved at clump 1

from Webb et al. 2002

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