title	author	date
Resources for Ecology, Evolution and Phylogenetic Comparative Methods	Jinlong Zhang	2018-08-24

Please visit https://github.com/helixcn/EcoEvoLinks for more update.

Welcome to the curated list for Phylogenetic Comparative Methods.

Research Teams

• Phylodiversity network

• Evolutionary Community Ecology Group - Université Montpellier II

• Ackerly D.

• Anderson, Marti Jane

• Angert A. - at the interface of ecology and evolutionary biology

• Araújo M. - PREDICTING THE EFFECTS OF ENVIRONMENTAL CHANGE ON BIODIVERSITY

• Arroyo‐Rodríguez

• Beaumount L. - Department of Biological Sciences, Macquarie University, Australia, Niche Modeling

• Bokma F. Umeå University, Sweden

• Bolnick D. - BOLNICK LAB AT THE UNIVERSITY OF TEXAS AT AUSTINE

• Brown J. - Interdisciplinary Biology, Community Ecology, Biogeography, Allometry

• Bruelheide,H

• Buckley L. - The University of Washington

• Butler M. University of Hawaii

• Cadotte M. University of Toronto

• Cahill J. - University of Alberta

• Cao Kunfang - Guangxi University

• Cavender-Bares J. University of Minnesota

• Chase J. M. - Process Governing species assembly over various scales

• Chave J.

• Chazdon, Robin

• Chen Shengbin - Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection

• Comita, Liza Tropical Forest Ecology, Yale University

• Condit, Richard

• Coomes, David A.

• Corlett R. - Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences

• Cornwell W.

• Crisp M.

• Davies, Kendi UNIVERSITY OF COLORADO BOULDER

• [Davies, JONATHAN] (https://phyloecology.wordpress.com/) at the University of Columbia

• Devictor V.

• Dexter, KG

• Diniz-Filho A. F. - Brazil

• Dormann, Carsten F.

• Drummond A.

• Duarte, LDS

• Enquist B.

• Felsenstein J. - University of Washington

• Feng Gang - Inner Mongolia University

• Freckleton R. - Plant population ecology, modelling plant populations, modelling weed populations. Evolutionary ecology, phylogenetic comparative methodology and its application to ecological problems.

• Fukami, Tadashi

• Garland T. -UC Riverside

• Gaston K. - Conservation at University of Exeter

• Ge Xuejun South China Botanical Garden

• Gilbert, Benjamin

• Gittleman J. - INSTITUTE OF ECOLOGY, ECOLOGY BUILDING, UNIVERSITY OF GEORGIA, ATHENS, GA 30602-2202

• Glor R.

• Graham C. - Stony Brook University

• Green J.

• Guisan A. - Univerisite de Lausanne

• Hardy O.

• Harmon, Luke

• Harms, Hyle

• Hawkins B. - University of California, Irvine

• He Fangliang Univerisity of Alberta, Canada

• Heard S. - Understanding ecological controls on the evolution of biodiversity

• Heibl C.

• Helmus, Matthew R

• Holl, Karon

• Holyoak M.

• Hu Junhua - Chengdu Institute of Biology, Chinese Academy of Sciences

• Huang Jihong - Chinese Academy of Forestry

• Hulbert, Allen

• Hunt G.

• Hurbert A.

• Ingram T. Otago University

• Isaac, Nick

• Ives A.

• Jetz W. - Yale University, USA

• Kattge, Jens

• Kembel S.

• Kerr J. - University of Ottawa

• Kraft N. - UCLA

• Kreft H. - University of Goettingen

• Kress J.

• Lasky, JR

• Lavergne S. - Laboratoire d'Ecologie Alpine (LECA) CNRS - Université Grenoble Alpes (UMR 5553)

• Legendre P.

• Letcher, Susan

• Levine, J. M.

• Li Rong Kunming Institute of Botany, Chinese Academy of Sciences

• Lin Luxiang Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences

• Liu Xiaojuan Institute of Botany, Chinese Academy of Sciences

• Loreau M.

• Losos J. - Evolution of Lizards, Havard University

• Lovette I.

• Ma Keping -IBCAS

• Maddison W.

• Mao Lingfeng - Nanjing Forestry University

• Mayfield, M.M.

• McPeek M. - how communities of organisms are assembled and structured across the landscape

• Meynard C.

• Mi Xiangcheng -IBCAS

• Moles A.

• Mooers A.

• Morlon H.

• Mouquet N.

• Muller-Landau, Helene

• Muscarella, R

• Norden, Natalia

• Oakley T.

• O'Meara B.

• Pavoine S.

• Pei Nancai - Research Institute of Tropical Forestry, the Chinese Academy of Forestry

• Peres-Neto P. - Community and Quantitative Ecology

• Primack R. - Boston University

• Purschke,O

• Purvis A. - Natural History Museum, London, UK

• Pyšek P. - Department of invasion ecology Botanický ústav Akademie věd ČR/Institute of Botany, Academy of Sciences of the Czech Republic

• Qian Hong - Illinois State Museum, USA

• Qiao Huijie

• Queenborough S. A.

• Rabosky D. University of Michigan

• Rahbek C. - Univerisity of Copenhagen, Denmark

• Redding, David W

• Rosauer, Dan

• Sanders, Nathan

• Schluter D. - University of British Columbia

• Slik, JWF

• Smith Stacy

• Smith Stephan

• Soininen J. University of Helsinki

• Svenning J. -The Arhus University, Denmark

• Swenson N. University of Maryland

• Sykes M.

• Thuiller W. Lab -Chez-Alice University, France

• Tucker, Caroline M.

• Tuomisto H.

• Ulrich, W

• Umaña, MN

• Uriarte, M

• Vamosi S. University of Calgary

• Vellend M.

• Violle, Cyrille

• Wainwright P.

• Wang Zhiheng - Peking University

• Wang Jianjun

• Warren, Dan

• Webb C. University of Alaska

• Weiblen, G. D.

• Weir J. - University of Toronto

• Whittaker R. - School of Geography and the Environment, University of Oxford

• Wiens J. - Evolution of adaptation of world's amphibians

• Willig M. University of Connecticut

• Wright I.

• Yang jie Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences

• Zahawi, Rakan A.

• Zang Runguo

• Zhang Jian - East China Normal University

• Zimmermann, Niklaus E.

Journals

Journal	Website
Advances in Botanical Research	https://www.sciencedirect.com/bookseries/advances-in-botanical-research
American Journal of Botany	https://bsapubs.onlinelibrary.wiley.com/journal/15372197
Annals of Botany	https://academic.oup.com/aob
Annual Review of Ecology, Evolution, and Systematics	https://www.annualreviews.org/journal/ecolsys
Applications in Plant Sciences (APPS)	https://bsapubs.onlinelibrary.wiley.com/journal/21680450#
Austral Ecology	https://onlinelibrary.wiley.com/journal/14429993
Basic and Applied Ecology	https://www.journals.elsevier.com/basic-and-applied-ecology
Biodiversity and Conservation	https://link.springer.com/journal/10531
Bioinformatics	https://academic.oup.com/bioinformatics
Biological Conservation	https://www.journals.elsevier.com/biological-conservation
Biology Letters	https://royalsocietypublishing.org/journal/rsbl
Biotropica	https://onlinelibrary.wiley.com/journal/17447429
BMC Plant Biology	https://bmcplantbiol.biomedcentral.com/
Botanical Journal of the Linnean Society	https://onlinelibrary.wiley.com/journal/10958339
Cladistics	https://onlinelibrary.wiley.com/journal/10960031
Conservation Biology	https://onlinelibrary.wiley.com/journal/15231739
Conservation Letters	https://onlinelibrary.wiley.com/journal/1755263x
Current Opinion in Plant Biology	https://www.journals.elsevier.com/current-opinion-in-plant-biology
Diversity and Distributions	https://onlinelibrary.wiley.com/journal/14724642
Ecography	https://onlinelibrary.wiley.com/journal/16000587
Ecological Applications	https://esajournals.onlinelibrary.wiley.com/journal/19395582
Ecological Indicators	https://www.journals.elsevier.com/ecological-indicators
Ecological Modelling	https://www.journals.elsevier.com/ecological-modelling
Ecological Monographs	https://esajournals.onlinelibrary.wiley.com/journal/15577015
Ecological Research	https://esj-journals.onlinelibrary.wiley.com/journal/14401703
Ecology	https://esajournals.onlinelibrary.wiley.com/journal/19399170
Ecology and Evolution	https://onlinelibrary.wiley.com/journal/20457758
Ecology Letters	https://onlinelibrary.wiley.com/journal/14610248
Ecosphere	https://esajournals.onlinelibrary.wiley.com/journal/21508925
Evolution	https://onlinelibrary.wiley.com/journal/15585646
Frontiers in Ecology and Evolution	https://www.frontiersin.org/journals/ecology-and-evolution
Frontiers in Plant Science	https://www.frontiersin.org/journals/plant-science
Frontiers of Biogeography	https://escholarship.org/uc/fb
Functional Ecology	https://besjournals.onlinelibrary.wiley.com/journal/13652435
Giga Science	https://academic.oup.com/gigascience
Global Change Biology	https://onlinelibrary.wiley.com/journal/13652486
Global Ecology and Biogeography	https://onlinelibrary.wiley.com/journal/14668238
Global Ecology and Conservation	https://www.journals.elsevier.com/global-ecology-and-conservation
Heredity	https://www.nature.com/hdy/
International Journal of Plant Sciences	https://www.journals.uchicago.edu/toc/ijps/current
Journal of Animal Ecology	https://besjournals.onlinelibrary.wiley.com/journal/13652656
Journal of Applied Ecology	https://besjournals.onlinelibrary.wiley.com/journal/13652664
Journal of Biogeography	https://onlinelibrary.wiley.com/journal/13652699
Journal of Ecology	https://besjournals.onlinelibrary.wiley.com/journal/13652745
Journal of Plant Ecology	https://academic.oup.com/jpe
Journal of Plant Research	https://link.springer.com/journal/10265
Journal of Systematics and Evolution	https://onlinelibrary.wiley.com/journal/17596831
Journal of Threatened Taxa	https://threatenedtaxa.org/
Landscape Ecology	https://link.springer.com/journal/10980
Methods in Ecology and Evolution	https://besjournals.onlinelibrary.wiley.com/journal/2041210x
Molecular Ecology	https://onlinelibrary.wiley.com/journal/1365294x
Molecular Phylogenetics and Evolution	https://www.journals.elsevier.com/molecular-phylogenetics-and-evolution
National Science Review (NSR)	https://academic.oup.com/nsr
Nature	https://www.nature.com/
Nature Ecology and Evolution	https://www.nature.com/natecolevol
Nature Plants	https://www.nature.com/nplants/
New Phytologist	https://nph.onlinelibrary.wiley.com/journal/14698137
Nordic Journal of Botany	https://onlinelibrary.wiley.com/journal/17561051
NOVON	https://novon.mobot.org/
Oecologia	https://link.springer.com/journal/442
Oikos	https://onlinelibrary.wiley.com/journal/16000706
Perspectives in Plant Ecology, Evolution and Systematics	https://www.journals.elsevier.com/perspectives-in-plant-ecology-evolution-and-systematics
Phytotaxa	https://www.mapress.com/phytotaxa/
Plant Diversity	https://www.sciencedirect.com/journal/plant-diversity
PLoS Biology	https://journals.plos.org/plosbiology/
PLOS ONE	http://journals.plos.org/plosone
Proceedings of the National Academy of Sciences	https://www.pnas.org/
Proceedings of the Royal Society B: Biological Sciences recent issues	https://royalsocietypublishing.org/journal/rspb
Science	http://science.sciencemag.org
Science Advances	https://advances.sciencemag.org/
Science of the Total Environment	https://www.journals.elsevier.com/science-of-the-total-environment
Scientific Reports	https://www.nature.com/srep/
Systematic Biology	https://academic.oup.com/sysbio
Systematic Botany	https://bioone.org/journals/systematic-botany/issues
TAXON	https://onlinelibrary.wiley.com/journal/19968175
The American Naturalist	https://www.journals.uchicago.edu/toc/an/current
The Plant Journal	https://onlinelibrary.wiley.com/journal/1365313x
Theoretical Ecology	https://link.springer.com/journal/12080
Trends in Ecology and Evolution	https://www.cell.com/trends/ecology-evolution/home

I would like to thank Dr. Yu Xiaoya and Prof. Ge Xuejun for comments

Software

• Joe Felsenstein's comprehensive list for Phylogenetic software

• Tree Thinkers

• Seqtrace Extracting DNA sequences from ab1 files.

• Rentrez R package Downloading Nucleotide Sequences from Genbank

• Geneious An integrated system for phylogenetic analysis

• CLUSTAL Alignment

• MUSCLE

• PartitionFinder

• ModelFinder

• jModelTest

• RAxML Builing phylogenies

• FastTree Approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences for very large dataset.

• MrBayes

• PAUP*

• BEAST, FigTree, PhyloGen and Tracer

• MEGA

• r8s Dating using Penalized likelihood

• PATHd8 Dating

• TreePL Dating for Large Trees

• multidivtime

• TimeTree - The divergence Time between two taxa, widely used in molecular dating.

• Mesquite

• Phylocom

• APE Analysis of Phylogenetics and Evolution

• diversitree

• RASP Reconstruction of Ancestral Area

• Lagrange Reconstruction of Ancestral Area using Maximum Likelihood

• BioGeoBEARS Reconstruction of Ancestral Area

• BAMM Bayesian Analysis of Macroevolutionary Mixtures

• SAM

• Biodiverse Phylogenetic Diversity and Conservation

• EcoSim

• PAST

• Lifemapper

• DIVA-GIS

• MAXENT Species Distribution Modelling using Maxim Entropy

• WALLACE

• SSDM R package Species Distribution Modelling

• BIOMOD R package Species Distribution Modelling

• SDMtoolbox A Python Library for Species Distribution Modelling

• A curated list for species distribution modelling

Resources for R

• R project

• Quick R

• The R Graphical Manual

• R Examples

• R Resources at NCEAS

• R-phylo Wiki

• Comparative methods in R - Ilhabela

• R Hackathon

• Analysis of Community data using R

• F. Farrell's R resources

• R Programming for APTS Students at Oxford University by R. Ripley

• Statistics with R

• R-Tips

• Create Maps with R geographical Classes

• Applied Spatial Statistics in R

• Spatial Analysis by Robert Hijmans

• r-popgen-hackathon

• Analysis of Discret Data

• Data Mining by Dr, Michael Hahsler

• Prof. Bolker's Rpub

• Prof. Bolker's Mixed Models Github Page

Data

• gbif

• Genbank

• The Plantlist

• Tropicos

• DRYAD

• CTFS

• CFBIO

• Gentry's Transect Dataset

• TimeTree The divergence Time between two taxa

• TRY A global database of plant traits

• CHELSA, Climatologies at high resolution for the earth’s land surface areas

• WorldClim

• Global Soil at 1km resolution ftp://ftp.soilgrids.org/

Online Courses

• Bayesian Methods

• Machine Learning

• Doing Bayesian Data Analysis

• Doing Bayesian Data Analysis

• Stat 295 Bayesian Inferences

• Integrative Biology at UC Berkeley, Principles of Phylogenetics: Ecology and Evolution

• Principles of Phylogenetics: Systematics

• EEB courses on Ecology

• Phylogenetics (EEB)

• Principles and Methods in Systematic Biology

• Quantitative methods in Ecology and Evolution by Schluter (UBC)

• Principles and Practice of Phylogenetic Systematics

• Phylogenetic Comparative Methods

• Biodiversity analysis by He Fangliang

• Statistical Methods in Ecology

• Statistics for Ecology and Evolution 2008 By Jack Weiss

• An Introduction to R: Software for statistical modelling and Computing, Course Notes

• Biostatistics-Statistical Computing by Gonçalo

• [Coalescent Theory and Applications] (http://web.eve.ucdavis.edu/pbg298/)

Videos

• NIMBioS Species Distribution Modelling Course

• Species distribution modelling by Richard Pearson at the University College London in November 2014

• Methods in Experimental Botany