The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology's "Phylogenetic Beta Diversity" Framework

被引:69
作者
Faith, Daniel P. [1 ]
Lozupone, Catherine A. [2 ]
Nipperess, David [3 ]
Knight, Rob [2 ]
机构
[1] Australian Museum, Sydney, NSW 2010, Australia
[2] Univ Colorado, Dept Chem & Biochem, Boulder, CO 80309 USA
[3] Macquarie Univ, Dept Biol Sci, N Ryde, NSW 2109, Australia
关键词
bacteria; UniFrac; feature diversity; ordination; PD calculus; evolutionary features; GEO BON; climate change; COMMUNITY; BACTERIAL; BIODIVERSITY; PATTERNS; CONSERVATION; DISSIMILARITY; BIOGEOGRAPHY; CONVERGENCE; SPACE;
D O I
10.3390/ijms10114723
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional species-level ecological indices to the features level. The "phylogenetic beta diversity" framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework's success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.
引用
收藏
页码:4723 / 4741
页数:19
相关论文
共 59 条
[1]   Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin [J].
Alexander, Eva ;
Stock, Alexandra ;
Breiner, Hans-Werner ;
Behnke, Anke ;
Bunge, John ;
Yakimov, Michail M. ;
Stoeck, Thorsten .
ENVIRONMENTAL MICROBIOLOGY, 2009, 11 (02) :360-381
[2]  
[Anonymous], ASSESSING ECOLOGICAL
[3]  
[Anonymous], GEO BIODIVERSITY OBS
[4]   CONTINUUM CONCEPT, ORDINATION METHODS, AND NICHE THEORY [J].
AUSTIN, MP .
ANNUAL REVIEW OF ECOLOGY AND SYSTEMATICS, 1985, 16 :39-61
[5]   DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius [J].
Balakirev, Evgeniy S. ;
Pavlyuchkov, Vladimir A. ;
Ayala, Francisco J. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (42) :16218-16223
[6]   A COMPARISON OF 2 APPROACHES TO BETA-FLEXIBLE CLUSTERING [J].
BELBIN, L ;
FAITH, DP ;
MILLIGAN, GW .
MULTIVARIATE BEHAVIORAL RESEARCH, 1992, 27 (03) :417-433
[7]   Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity [J].
Bryant, Jessica A. ;
Lamanna, Christine ;
Morlon, Helene ;
Kerkhoff, Andrew J. ;
Enquist, Brian J. ;
Green, Jessica L. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 :11505-11511
[8]   The merging of community ecology and phylogenetic biology [J].
Cavender-Bares, Jeannine ;
Kozak, Kenneth H. ;
Fine, Paul V. A. ;
Kembel, Steven W. .
ECOLOGY LETTERS, 2009, 12 (07) :693-715
[9]  
Chave J., 2007, Scaling biodiversity, P150
[10]   Biodiversity and biogeography of phages in modern stromatolites and thrombolites [J].
Desnues, Christelle ;
Rodriguez-Brito, Beltran ;
Rayhawk, Steve ;
Kelley, Scott ;
Tran, Tuong ;
Haynes, Matthew ;
Liu, Hong ;
Furlan, Mike ;
Wegley, Linda ;
Chau, Betty ;
Ruan, Yijun ;
Hall, Dana ;
Angly, Florent E. ;
Edwards, Robert A. ;
Li, Linlin ;
Thurber, Rebecca Vega ;
Reid, R. Pamela ;
Siefert, Janet ;
Souza, Valeria ;
Valentine, David L. ;
Swan, Brandon K. ;
Breitbart, Mya ;
Rohwer, Forest .
NATURE, 2008, 452 (7185) :340-U5