Community Phylogenetic structure with R

1. Community Phylogenetic structure with R

2. Central question in community ecology • What processes are responsible for the identity and relative abundances of co-occurring species in local assemblages? • What is the relative importance of different ecological processes in structuring communities • Search for patterns in community structure that may reflect underlying processes

3. Phylogenetic data

4. Patterns of phylogenetic community structure • Phylogenetic clustering • Co-occurring species are more closely related than expected by chance • Phylogenetic over-dispersion/evenness • Co-occurring species are more distantly related than expected by chance • Random patterns

5. Community assembly processes • Many processes could influence phylogenetic community structure • Facilitation • Negative density dependent processes (e.g. herbivory, predation) • Indirect interactions mediated by herbivores, parasites, pathogens • Disturbance e.g. fire • Speciation • Two main processes are usually considered

6. Habitat filtering • Adaptation of species to abiotic conditions • Communities composed of ecologically similar species • Environment imposes a filter via abiotic conditions favoring species with similar adaptations Emerson & Gillepsie, 2008

7. Competitive exclusion • The principle of competitive exclusion: similar species cannot coexist indefinitely. • Related species are ecologically similar • Prediction: closely related species should co-occur less than would be expected • Early efforts tested this hypothesis using • species : genus ratios • Taxonomic community structure Emerson & Gillepsie, 2008

8. Phylogenetic signal Kembel, 2009

9. Community phylogenetic structure (Competitive exclusion) (or clustering) Kembel, 2009

10. Clustering: Co-occurring species are more closely related than expected by chance Over-dispersion: Co-occurring species are more distantly related than expected Clustering due to environmental filtering Trait conservatism Over-dispersion due to competitive exclusion Trait conservatism Clustering due to competitive exclusion Trait convergence Over-dispersion due to environmental filtering Trait convergence h

11. Emerging patterns • Communities structured by several processes acting in concert • Mediated by different sets of traits • Scale is important • Taxonomic scale (Cavender-Barres et al., 2004; 2006) • Oaks: phylogenetic over dispersion • Angiosperms: phylogenetic clustering • Spatial scales • Similar shift from smaller (overdispersion) to larger spatial scales (clustering)

12. Steps • Quantify the degree of relatedness among co-occurring species using a phylogeny • Define a broader pool of species from which communities have been assembled • Construct a null model which generates random communities from the broader species pool • Determine phylogenetic signal for functional traits that influence community assembly

13. Data • Phylogenetic tree for regional/broader species pool • Entire species in all the communities • Species list and presence/absence or abundance data for the different communities, plots or specific habitats within a community.

14. Getting a phylogenetic tree • Can use either sequence data or species list • Different formats: Newick, Nexus • Online tools available e.g. • Genbank (http://www.ncbi.nlm.nih.gov/): can obtain raw sequence data • ARB/Silva (http://www.arb-silva.de/): provides aligned sequence data free for academic use • RDP (http://rdp.cme.msu.edu/ ): provides sequence data and builds phylogenetic tree • Beast (http://beast.bio.ed.ac.uk/Main_Page): contains programs to create phylogenies with sequence data • Phylomatic (http://www.phylodiversity.net/phylomatic/): assembles phylogenies using species lists.

15. Quantifying degree of relatedness Vamosiet al., 2009

16. Within community measures • Faith’s phylogenetic diversity (PD) • Total branch length spanned by the tree including all species in a local community. • A lower value indicates that • Taxa are clumped on the phylogeny • Capture only a small part of the total phylogenetic diversity present in the entire phylogeny • Co-ocurring species are more closely related

17. MPD: Mean pair-wise distance between all species in a community • Measures whether species in a community are more closely related than expected by chance (using a null model and the regional species pool) • MPD is more sensitive to tree-wide phylogenetic patterns • MNTD: Mean distance to nearest taxon for each species in the community • Measures whether closely related species tend to co-occur or not (using a null model and the regional species pool). • MNTD is more sensitive to patterns of evenness and clustering closer to the tips of the phylogeny

18. Distance matrix Kembel, 2009

19. Null models • Randomize the phylogeny • Phylogeny shuffle: randomizes phylogenetic relationships among species by shuffling the taxa on the tips. • Randomize tree structure • Randomize community structure • Randomize draws from species pool • Species in each sample are random draws from the • Sample pool: maintains species richness of each sample but species are drawn without replacement from the list of all species actually occurring in the sample. • Regional species pool: maintains species richness, but species are drawn without replacement from a broader phylogeny pool. • Randomize community matrix • Independent swap: creates swapped versions of the sample/species matrix; only applicable with presence/absence data.

20. Randomization • Using null model • Generate a random community • Recalculate metrics i.e. MPD/MNTD • Repeat many times • Result: distribution of metric values for random communities

21. Standardized effect sizes (SES) • SES=(Observed value – Mean (random values))/SD(random values) • Net relatedness index (NRI): standardized metric obtained by comparing MPDobs and MPDexp • +NRI = phylogenetic clustering • -NRI = phylogenetic evenness • Calculated as standardized effect size (SES) in picante • SES = -1 x NRI

22. SES continued • Nearest taxon index (NTI): obtained by comparing MNTDobs and MNTDexp • + NTI = phylogenetic clustering • - NTI = phylogenetic evenness • Computed as standardized effect size (SES) in picante • SES = -1 x NTI

23. Phylogenetic Beta Diversity • Measures patterns of phylogenetic relatedness among communities • Among communities equivalent of MPD and MNTD using pairs of species drawn from different communities • can be used with any method based on among-community distances • e.g. cluster analysis, phyloordination, Mantel tests with spatial/environmental distances separating communities.

24. Today’s Data • Bird communities along 3 highways: 64, 44, and 55 • Gradient from urban (1) to rural (5) along those highways, with each community separated by 16 km • Ex. Communities: RD441, RD442, RD443, RD641, RD642, etc… 1 2 3 4 5 RD64 ???

25. Genetic data from Genbank using 2 mitochondrial genes • Cytochromeb (Cytb) and Cytochrome c oxidase subunit I (COI) • Made a phylogeny using Beast and Beauti (free online, easy to use, and comes with a short tutorial and good manual) • Question: What is the phylogenetic structure of communities as you go from rural to urban environments? 1 2 3 4 5 RD64 ???