What is Phylogenetic Comparative Analysis? › uploads › 7 › 5 › 3 › 6 › ... · Questions...

What is Phylogenetic Comparative Analysis?

Jinlong Zhang

[email protected]

7 NOV 2016

Jinlong Zhang ([email protected]) What is Phylogenetic Comparative Analysis? 7 NOV 2016 1 / 65

Outline

Contents

1 Questions to answer once the phylogeny is ready

2 Active Researchers in PCM

3 Basics of phylogenetic Trees

4 Phylogenetic Comparative Methods in R


Questions to answer once the phylogeny is ready

Contents








1. The phylogenetic relationship between taxa

2. Speciation rate is affected by: how old the lineage is? SpeciesRichness under this clade, the latitude of the taxa, or special habiatthe taxa belong to?

3. How geological events affect the speciation and extinction rates?

4. Should conservation priority base on evolutionary distinctiveness?

5. Does phylogenetic closely related species tend to have similarcharacters or habitat preference?




6. Given the trait status for all the taxa in a phylogeny, how to inferthe status of the ancestors?

7. Given the current distribution range, how to infere the range of theancestors?

8. How the adaptation evovled?

9. Are species within a community randomly occurred or beingfiltered by the enviromental factors?


Active Researchers in PCM

Contents








J. Felsenstein The Univeristy of Washington

M. Donoghue, Yale

A. Purvis, Imperial College

A. Rambaut, Edinburgh

D. Schluter UBC，

J. Weir Toronto

R. E. Ricklefs Missouri

L. Harmon, Idaho

J. J. Wiens, Arizona

J. Losos, Harvard


http://evolution.genetics.washington.edu/felsenstein.html

http://donoghuelab.yale.edu/

http://www.imperial.ac.uk/people/a.purvis

http://tree.bio.ed.ac.uk/people/arambaut/

https://www.zoology.ubc.ca/~schluter/wordpress/

http://www.utsc.utoronto.ca/~jweir/

http://www.umsl.edu/~ricklefsr/

https://www.uidaho.edu/sci/biology/people/faculty/lukeh

http://www.wienslab.com/Home.html

http://lososlab.oeb.harvard.edu/



R. A. Pyron, George Washington U

W. Jetz, Yale

J.L. Gittleman, George

T. Garland UC Riverside, S. Blomberg

D. Ackerly, UC Berkeley

Cam Webb, Arnold Arboretum, Harvard

D. Maddison, Oregon

W. Maddison, UBC

N. Swenson, U Maryland,

N. Kraft, UCLA

Marc Cadotte, Toronto


http://www.colubroid.org/

http://jetzlab.yale.edu

http://gittleman.ecology.uga.edu/

http://www.ackerlylab.org/

http://www.arboretum.harvard.edu/people/campbell-webb/

http://ib.oregonstate.edu/faculty/maddisod/David-Maddison

http://www.swensonlab.com/

https://sites.lifesci.ucla.edu/eeb-kraft/



R. Freckleton, Sheffield

M. Pagel, Reading

E. Paradis, U montpellier

D. Radobsky, Michigan

R. FitzJohn & Mark Westoby, Macquarie University

Rick Ree, Chicago

S. Smith, Michigan

Liam J. Revell, University of Massachusetts Boston

Brian O’Meara, Tennessee


https://www.shef.ac.uk/aps/staff-and-students/acadstaff/freckleton

http://www.evolution.rdg.ac.uk/

http://ape-package.ird.fr/ep/

http://www-personal.umich.edu/~drabosky/Home.html

https://richfitz.github.io/

http://bio.mq.edu.au/research/groups/ecology//westoby/mark.htm

http://www.reelab.net/home/

http://blackrim.org/

https://www.researchgate.net/researcher/14060729_Liam_J_Revell

http://brianomeara.info/

Basics of phylogenetic Trees

Contents







Working Flow for Building a Phylogeny

Processing of Nucleotide Sequenes

Alignment

Phylogenetic Inferences

Molecular Clocks / Dating



Tools for Building Phylogeny and Conducting theSubsequence Analysis

工欲善其事，必先利其器

OS: Windows, MacOS, Linux

Programming Language: R, Python (C, C++, FORTRAN, ...)

Software: R, Python, Mesquite



R CRAN Task View：Phylogenetics I

https://cran.r-project.org/web/views/Phylogenetics.html

R Getting trees into R

Tree Manipulation

Tree Visualization

Ancestral state reconstruction

Diversification Analysis

Divergence Times

Tree Simulations


https://cran.r-project.org/web/views/Phylogenetics.html


R CRAN Task View：Phylogenetics II

Trait evolution

Trait Simulations

Community/Microbial Ecology

Phyloclimatic Modeling

Phylogeography/Biogeography

Species/Population Delimitation

Taxonomy



What is phylogenetic tree?

Phylogenetic trees are dendrograms representing the relationship betweenthe taxa. The meaning of branch length depends on the the type of thetree, eg. substitution rate, time, etc.



Milestones in Phylogenetic Reconstruction

In 1859, Darwin drew the first phylogenetic tree

E. Haeckel started to use trees to represent the relationships betweenthe species at the end of 19th century.

In 1964, Cavalli-Sforza and Edwards proposed the possibility to usethe Maximum Parsimony and Maximum Likelihood in phylogeneticinferences conceptually.

Hennig proposed the Theory of cladistics

In 1977, Fitch first applied parsimony methods in tree infrerences

In 1978, Felsenstein for the first time, realized the maximumlikelihood in phylogenetic inferences

In 1996, Rannala and Yang introduced the Bayes inferences in treereconstruction.



Phylogenetic Trees



Newick Format

adopted by James Archie, William H. E. Day, Joseph Felsenstein, WayneMaddison, Christopher Meacham, F. James Rohlf, and David Swofford, attwo meetings in 1986, the second of which was at Newick’s restaurant inDover, New Hampshire, US. PHYLIP, RAxML use Newick format.



Nexus File

NEXUS Format is an upgrade to the Newick format，by adding a numberof code blocks . NEXUS is used by BEAST，PAUP*, MrBayes,Mesquite，r8s etc。



Other formats

New Hampshire eXtended format (NHX)（http://home.cc.umanitoba.ca/ psgendb/doc/atv/NHX.pdf）Jplace（http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0031009）



How to Obtain Nucleotide Sequences

How to obtain Nucleotide sequences from GenBank

1. DNA barcoding Sequences AB1 file > Fasta File

2. Genebank Fasta File

3. Next Generation Sequencing (Genome)



FASTA Files

FASTA files are plain text files designed for storaging nucleotide sequences.

1. Name for Each sequence start with >

2. Nucleotide sequence are in the next row

3. A semicolon is appended between sequences

3. - is for missing sites, aligned sequences also allowed.



Alignment

Compare the sequences, and find out the informative site.

Nucleotide Sequences before alignmentJinlong Zhang ([email protected]) What is Phylogenetic Comparative Analysis? 7 NOV 2016 23 / 65


Alignment

Compare the sequences, and find out the informative site.

Nucleotide Sequences after alignment



Substitution Models

ATCG

Prob[kevents] =µtke−µt

k!

transition matrix。



Transition Matrix



Jukes-Cantor (JC69) Model 1969



GTR: General Time Reversible Model



The relationship between Nucleotide substitution models



Gamma Distribution and the variation of substitution rates

Different sites tend to have different rate of substitution, Gammadistribution has been introduced to account for this variation.



Selection of the Substitution Models

Software: Modeltest, Jmodeltest, mainly based on Akaike InformationCriterion or Likelihood Ration Test

If the nucleotide is very short, the information site could be verylimited, in these cases, the most complex models (eg. GTR) wouldover estimated the parameters. Therefore the models must beselected.

However, for the sequences with enough variation, GTR + Gammaare alway suggested.



Distance Based Methods

Compute the genetic distance between each pair of sequences， eg,RAW, Transition , Tranversion，or based on other substitutionmodels。

Clustering, usually using UPGMA (Unweighted Pair-Group Methodwith Arithmetic means)

or Neighbour Joining

or Minumum Evolution

Distance based methods are of old fashion and rarely used nowadays.



Parsimony

The Phylosophy behind Parsimony:Number of change during the evolutionary history should be as minumumas possible. The advantages of Parsimony Methods

Easy to understand

Fast

Generally, the topology of the phylogeny is stable and accurate.

Parsimony trees are widely used as starting trees for the MaximumLikelihood based methods



Maximum Likelihood 1

The general idea of Maximum Likelihood:

Assume a phylogenetic tree T is available,

and the transition matrix Q is avialble,

What is the likelihood for the existing aligment pattern?



Why finding out the right phylogenetic tree is supercomputationally intensive？

Ntaxa： N possible trees3: 15: 1510: 202702515: 790585358062516: 21345804667687517: 619028335362937418: 19189878396251062419: 633265987076285030420: 2.216430954767e+2030: 8.687364e+3650: 2.838063e+74



Heuristic Search

Since there are too many possible trees, obtaining the phylogeny withMaximum Likelihood could not be possible.

Heuristic search start to search the phylogeny with a higherlikelihood, and only keep the phylogeny with higher likelihood whenadding the taxa randomly to an existing tree.

Pruning and grafting, eg TBR (tree bisection reconnection)

staring from multiple random trees will also help to find the globaloptimal tree.



Software for building phylogenies using MaximumLikelihood

PHYLIP, developed by J. Felsenstein, the first software that adoptsthe Maximum Likelihood in inferencing the phylogenies.

PAUP*, by David Swoford, and is extremly well known for theParsimony Methods, but also ML. It provides a number of tests too.

PHYML, by Guidon, suitable for large number of sequences, allowingthe selection of different substitution models.

RAxML, by Stamatakis, for very large dataset of nucleotidesequences, providing rapid bootstrap. Very Popular



The Supporting Value from Bootstrap

Introduced by J. Felsenstein.Jinlong Zhang ([email protected]) What is Phylogenetic Comparative Analysis? 7 NOV 2016 38 / 65


Differences between ML and Bayesian Methods for treeconstruction



Bayesian Trees

BEAST and MrBayes are the two most important software forreconstructing phylogenetic trees.



Branch length in a phylogenetic tree

The meaning of branch length depends on how the tree was built:

Distance based method: genetic distance

Maximum parsimony: Number of sites changed

Maximum likelihood and Bayesian：likelihood of mutation betweentwo sequences

Long branch length could be resulted from: high mutation rates, timesince divergence, but the branch lengh could not reflect time.



Dating of phylogenies

Left：before dating / Right：after datingJinlong Zhang ([email protected]) What is Phylogenetic Comparative Analysis? 7 NOV 2016 42 / 65


Software for molecular dating

r8s: Non parametric rate smoothing (NPRS); Penalized Likelihood(PL).

PATHd8: suitable for large phylogenies, but might not be thataccurate.

BEAST：for phylogenetic reconstruction as well as dating based onBayesian Inferences.

APE package in R：Penalized Likelihood and more (relatively simple).


Phylogenetic Comparative Methods in R

Contents







APE: Analysis of Phylogenetics and Evolution

APE was developed by Dr. E. Paradis specifically for conductingphylogenetic comparative analysis in R

http://ape-package.ird.fr/ape authors.html

APE defined the class phylo, and it is the basis for most of the otherR packages.



Main funtionalities of APE

reading and manipulating phylogenetic trees and DNA sequences,

computing DNA distances,

estimating trees with distance-based methods,

a range of methods for comparative analyses and analysis ofdiversification.

Functionalities are also provided for programming new phylogeneticmethods.

Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (SecondEdition). New York: Springer.



Getting trees into R: read.tree()

Function read.tree() reads newick trees into R, and save the trees in phyloobjects. phylo objects are actually lists that containing four vectors,namely:

edge: Topological relationship between different branches;

Nnode： number of internal nodes;

tip.label： names for the taxa on the terminal;

edge.length： Branch length



How to save a phylogenetic tree from APE

### An extract from Sibley and Ahlquist (1990)tiff(filename = "tree.tiff", width = 2400, height = 2400,

units = "px", pointsize = 12, res = 600, compression

="lzw")

cat("(((Strix_aluco:4.2,Asio_otus:4.2):3.1,",

"Athene_noctua:7.3):6.3,Tyto_alba:13.5);", file = "ex.tre",

sep = "

n")

tree.owls < − read.tree("ex.tre")

plot(tree.owls)

dev.off()



The most important functions in APE I

ace() reconstruct the ancestral status

ladderize() Ladderizing the internal nodes of phylogenies.

bd.ext() Estimating the parameters of speciation based on birth-deathprocess

chronopl() Molecular clock calibrating based on penalized likelihood

consensus() Compute the consensus tree based on many trees

drop.tip() Delete taxa from the tree

gammaStat() Pybus-Harvey’s Gamma



The most important functions in APE II

ltt.plot() Lineages Through Time Plot

mrca() Find the most recent common ancestor

multi2di() processing polytomies

di2multi() processing polytomies

read.nexus() read Nexus file

root() setting the outgroup

rtree() generating random tree for simulation

write.tree() save phylo object to a text file



ggtree for visualizing phylogenies

The R package ggtree was developed by PhD candidate Yu Guangchuang(The University of Hong Kong) for visualizing phylogenies. It is a goodextension to the classes of the ggplot2 package. Manipulating andvisualizing trees within ggtree is easy and flexible. By changing a fewparameters, ggtree can draw very complex figures.ggtree reads various kinds of formats, including the outputs from r8s,RAxML.



Example from ggtree

trees <- lapply(c(10, 20, 40), rtree)

class(trees) <- "multiPhylo"

ggtree(trees) + facet_wrap(~.id, scale="free") +

geom_tiplab()

See: https://github.com/GuangchuangYu/ggtree

https://bioconductor.org/packages/release/bioc/html/ggtree.html



Lineages Through Time Plot

ltt plot



Laser：Estimating the Speciation and Extinction Rates

Laser was developed by Dan Rabosky, Likelihood Analysis ofSpeciation/Extinction Rates from PhylogeniesThree Models:

1. fitSPVAR() fits a model with an exponentially declining speciationrate through time and constant extinction.

2. fitEXVAR() fits a model with exponentially increasing extinctionand constant speciation.

3. fitBOTHVAR() fits a model where both speciation and extinctionrates can vary through time.



Laser: Likelihood Analysis of Speciation/Extinction Ratesfrom Phylogenies



Analysing the change in diversication rate duringspeciation process, MEDUSA

Modeling Evolutionary Diversification Using Stepwise AIC

geiger::medusaJinlong Zhang ([email protected]) What is Phylogenetic Comparative Analysis? 7 NOV 2016 56 / 65


Ancestral Status Estimation

ape::ace



Phylogenetic Diversity using Picante

Faith’s PD Phylogenetic Diversity (Faith 1992) is the sum of branchlength that connect all the taxa occurred in a region together.picante::pd()

Phylogenetic Signal（Blomberg’s K）: The more closer the speciesphylogenetically related, the more similar thetraits。picante::phylosignal()

Evolutionary Distinctiveness (ED): The unique evolutionaryinformation each species carries. picante::evol.distinct()



Phylogenetic beta Diversity

Phylogenetic beta diversity is how two different plots are phylogeneticallyrelated.comdist()& comdistnn() :MPD and MNTD (Webb 2000)phylosor() :Phylosor (Bryant et al. 2008)unifrac(): :Unifrac(Lozupone et al. 2006)rao() :Rao 1982, Jost 2007, Webb et al. 2008pcd() :PCD (Ives and Helmus 2010)



Null Models in Community Phylogenetics

Null model is an approach that could help to test the assembly of thecommunities under different randomization senarios, and help to assess therelative importance of environmental filtering, and the stochastic process.In community phylogenetics, four models are used for randomize thecommunity phylogenetic structure

Null 0 Phylogeny shuffle: This null model shuffles species labelsacross the entire phylogeny.

Null 1 Species in each sample become random draws from samplepool

Null 2 Species in each sample become random draws from phylogenypool

Null 3 Independent swap, the species pairs are kept, but swap acrosscommunities



Processing plant names using plantlist

taxize, taxonstand, plantlist

status(): Looking for the taxonomic status of species

data(acc dat): The accepted plant names from the Plant List

data(syn dat): Synonyms database from The Plant List

taxa.table(): Making a Taxa Table based on the result of functionTPL for Phylomatic

TPL(): Looking up Family, Family Number and Order in ModernClassification Systems.



Using the plantlist R package

plantlist::TPL



Summary

In this lesson, we focused on:

1. Questions could be answered once the phylogenetic tree isavailable.

2. The active researchers in Phylogenetic Comparative Methods.

3. Phylogenetic tree inferences and the molecular clocks.

4. Phylogenetic Comparative Methods



Take Home Message

1. The procedures and the principles underlying phylogenticinferences are very complicated.

2. Many questions related with evolution and ecology could beanswered with the help of Phylogenetic Comparative Analysis.

3. Skills in R is essential for conducting Phylogenetic ComaparativeAnalysis, and APE package lies in the center.



Thanks for your attention.!Question？


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