Resources for Ecology, Evolution and Phylogenetic Comparative Methods

Welcome to the curated list for Phylogenetic Comparative Methods.

Research Teams

• Phylodiversity network

• Evolutionary Community Ecology Group - Université Montpellier II

• Ackerly D.

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

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

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

• Bokma F. Umea, Sweden

• Bolnick D. - BOLNICK LAB AT THE UNIVERSITY OF TEXAS AT AUSTINEco-Evo-Immuno Dynamics

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

• 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.

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

• Comita L.

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

• Cornwell W.

• Crisp M.

• Davies J.

• Davies K. F.

• Devictor V.

• Diniz-Filho A. F. - Brazil

• Drummond A.

• 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.

• Garland T. -UC Riverside

• Gaston K. - Conservation at University of Exeter

• Ge Xuejun South China Botanical Garden

• 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.

• Hawkins B. - University of California, Irvine

• He Fangliang Univerisity of Alberta, Canada

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

• Heibl C.

• Holyoak M.

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

• Huang Jihong - Chinese Academy of Forestry

• Hunt G.

• Hurbert A.

• Ingram T.

• Ives A.

• Jetz W. - Yale University, USA

• Kembel S.

• Kerr J. - University of Ottawa

• Kraft N. - UCLA

• Kreft H. - University of Goettingen

• Kress J.

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

• Legendre P.

• 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 - University of Alberta

• 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.

• 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

• 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

• Schluter D. - University of British Columbia

• Smith Stephan

• Smith Stacy

• 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

• Tuomisto H.

• Vamosi S. University of Calgary

• Vellend M.

• Wainwright P.

• Wang Zhiheng - Peking University

• Webb C. University of Alaska

• 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

• Zhang Jian - East China Normal University

Journals

• American Journal of Botany

• Annual Review of Ecology and Systematics

• Biodiversity Science

• Botanical Journal of the Linnean Society

• Conservation Biology

• Diversity and Distributions

• Ecography

• Ecological Monographs

• Ecology Letters

• Ecology

• Evolution

• Global Ecology and Biogeography

• Guihaia

• Journal of Biogeography

• Journal of Ecology

• Journal of Systematics and Evolution

• Methods in Ecology and Evolution

• Molecular Ecology

• Nature

• New Phytologist

• Oecologia

• Oikos

• Plant Diversity

• PLoS ONE

• Proc. Nat. Acad. Sci.

• Proc. Royal. Soc. Biolog.

• Science

• Scientific Reports

• Taxon

• The American Naturalist

• Trends in Ecology and Evolution

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

• SSDM R package Species Distribution Modelling

• BIOMOD R package Species Distribution Modelling

• SDMtoolbox A Python Library 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

Online Courses

• Review Course: Markov Chains and Monte Carlo Methods

• Bayesian Methods

• Machine Learning

• Doing Bayesian Data Analysis

• Doing Bayesian Data Analysis

• Stat 295 Bayesian Inferences

• Bayesian Analysis for the Social Sciences

• 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

• Basic Population Genetics (and a plenty of resources)

• Biology Textbook

• Coalescent Theory and Applications

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/

Contact

Please contact Jinlong Zhang if you find any mistake.