Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves
Abstract
:1. Introduction
2. Materials and Methods
2.1. Phylogenetic Structure of Example Plant Communities
2.2. Calculation of Community Phylogenetic Distance Metrics
2.3. Examination of Phylogenetic Distances from Focal Species in a Community
2.4. Calculation of the AUPhyDC: Area under the Phylogenetic Distance Curve
2.5. Abundance Weighting of PD10 or AUPhyDC Metrics
3. Results
3.1. Distributions of Phylogenetic Distances in Communities Are Skewed toward Long Distances
3.2. Limitations of Standard Phylogenetic Metrics for Focal-Species Analyses
3.3. AUPhyDC: Area under the Phylogenetic Distance Curve
3.4. PD10: The 10th Quantile Phylogenetic Distance
3.5. Abundance Weighting of AUPhyDC and PD10
4. Discussion
4.1. Distributions of Phylogenetic Distances in Communities Are Skewed toward Long Distances
4.2. Cumulative Phylogenetic Distance Curves for Analysis of Focal Species
4.3. Uses and Contextual Limits of the AUPhyDC
4.4. Ecological Value of the 10th Quantile Phylogenetic Distance PD10
4.5. Abundance Weighting of AUPhyDC and PD10 Permits Inclusion of Conspecific Interactions
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Cavender-Bares, J.; Kozak, K.H.; Fine, P.V.A.; Kembel, S.W. The merging of community ecology and phylogenetic biology. Ecol. Lett. 2009, 12, 693–715. [Google Scholar] [CrossRef] [PubMed]
- Vamosi, S.M.; Heard, S.B.; Vamosi, J.C.; Webb, C.O. Emerging patterns in the comparative analysis of phylogenetic community structure. Mol. Ecol. 2009, 18, 572–592. [Google Scholar] [CrossRef] [PubMed]
- Harvey, P.H.; Pagel, M.D. The Comparative Method in Evolutionary Biology; Oxford University Press: Oxford, UK, 1991. [Google Scholar]
- Blomberg, S.P.; Garland, T.; Ives, A.R. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 2003, 57, 717–745. [Google Scholar] [CrossRef] [PubMed]
- Revell, L.J.; Harmon, L.J.; Collar, D.C. Phylogenetic signal, evolutionary process, and rate. Syst. Biol. 2008, 57, 591–601. [Google Scholar] [CrossRef]
- Losos, J.B. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecol. Lett. 2008, 11, 995–1003. [Google Scholar] [CrossRef]
- Alcantara, S.; Lohmann, L.G. Contrasting phylogenetic signals and evolutionary rates in floral traits of Neotropical lianas. Biol. J. Linn. Soc. 2011, 102, 378–390. [Google Scholar] [CrossRef] [Green Version]
- Baraloto, C.; Hardy, O.J.; Paine, C.E.T.; Dexter, K.G.; Cruaud, C.; Dunning, L.T.; Gonzalez, M.A.; Molino, J.F.; Sabatier, D.; Savolainen, V.; et al. Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities. J. Ecol. 2012, 100, 690–701. [Google Scholar] [CrossRef]
- Gilbert, G.S.; Webb, C.O. Phylogenetic signal in plant pathogen-host range. Proc. Natl. Acad. Sci. USA 2007, 104, 4979–4983. [Google Scholar] [CrossRef] [Green Version]
- Wiens, J.J.; Ackerly, D.D.; Allen, A.P.; Anacker, B.L.; Buckley, L.B.; Cornell, H.V.; Damschen, E.I.; Jonathan Davies, T.; Grytnes, J.A.; Harrison, S.P. Niche conservatism as an emerging principle in ecology and conservation biology. Ecol. Lett. 2010, 13, 1310–1324. [Google Scholar] [CrossRef]
- Cavender-Bares, J.; Keen, A.; Miles, B. Phylogenetic structure of Floridian plant communities depends on taxonomic and spatial scale. Ecology 2006, 87, S109–S122. [Google Scholar] [CrossRef] [Green Version]
- Willis, C.G.; Halina, M.; Lehman, C.; Reich, P.B.; Keen, A.; McCarthy, S.; Cavender-Bares, J. Phylogenetic community structure in Minnesota oak savanna is influenced by spatial extent and environmental variation. Ecography 2010, 33, 565–577. [Google Scholar] [CrossRef]
- Cavender-Bares, J.; Ackerly, D.D.; Baum, D.A.; Bazzaz, F.A. Phylogenetic overdispersion in Floridian oak communities. Am. Nat. 2004, 163, 823–843. [Google Scholar] [CrossRef]
- Maherali, H.; Klironomos, J.N. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 2007, 316, 1746–1748. [Google Scholar] [CrossRef] [Green Version]
- Webb, C.O.; Gilbert, G.S.; Donoghue, M.J. Phylodiversity-dependent seedling mortality, size structure, and diseases in a Bornean rain forest. Ecology 2006, 87, S123–S131. [Google Scholar] [CrossRef] [Green Version]
- Gilbert, G.S.; Parker, I.M. The evolutionary ecology of plant disease: A phylogenetic perspective. Annu. Rev. Phytopathol. 2016, 54, 549–578. [Google Scholar] [CrossRef]
- Daehler, C.C. Darwin’s naturalization hypothesis revisited. Am. Nat. 2001, 158, 324–330. [Google Scholar] [CrossRef]
- Duncan, R.P.; Williams, P.A. Darwin’s naturalization hypothesis challenged. Nature 2002, 417, 608–609. [Google Scholar] [CrossRef]
- Strauss, S.Y.; Webb, C.O.; Salamin, N. Exotic taxa less related to native species are more invasive. Proc. Natl. Acad. Sci. USA 2006, 103, 5841–5845. [Google Scholar] [CrossRef] [Green Version]
- Ma, C.; Li, S.-p.; Pu, Z.; Tan, J.; Liu, M.; Zhou, J.; Li, H.; Jiang, L. Different effects of invader–native phylogenetic relatedness on invasion success and impact: A meta-analysis of Darwin’s naturalization hypothesis. Proc. Soc. B Biol. Sci. 2016, 283, 20160663. [Google Scholar] [CrossRef] [Green Version]
- Gilbert, G.S.; Magarey, R.; Suiter, K.; Webb, C.O. Evolutionary tools for phytosanitary risk analysis: Phylogenetic signal as a predictor of host range of plant pests and pathogens. Evol. Appl. 2012, 5, 869–878. [Google Scholar] [CrossRef]
- Gilbert, G.S.; Briggs, H.M.; Magarey, R. The impact of plant enemies shows a phylogenetic signal. PLoS ONE 2015, 10, e0123758. [Google Scholar] [CrossRef]
- Pearse, I.S.; Hipp, A.L. Phylogenetic and trait similarity to a native species predict herbivory on non-native oaks. Proc. Natl. Acad. Sci. USA 2009, 106, 18097–18102. [Google Scholar] [CrossRef] [Green Version]
- Liu, X.B.; Liang, M.X.; Etienne, R.S.; Wang, Y.F.; Staehelin, C.; Yu, S.X. Experimental evidence for a phylogenetic Janzen-Connell effect in a subtropical forest. Ecol. Lett. 2012, 15, 111–118. [Google Scholar] [CrossRef]
- Parker, I.M.; Saunders, M.; Bontrager, M.; Weitz, A.P.; Hendricks, R.; Magarey, R.; Suiter, K.; Gilbert, G.S. Phylogenetic structure and host abundance drive disease pressure in communities. Nature 2015, 520, 542–544. [Google Scholar] [CrossRef] [Green Version]
- Yguel, B.; Bailey, R.; Tosh, N.D.; Vialatte, A.; Vasseur, C.; Vitrac, X.; Jean, F.; Prinzing, A. Phytophagy on phylogenetically isolated trees: Why hosts should escape their relatives. Ecol. Lett. 2011, 14, 1117–1124. [Google Scholar] [CrossRef]
- Cirtwill, A.R.; Dalla Riva, G.V.; Baker, N.J.; Ohlsson, M.; Norström, I.; Wohlfarth, I.M.; Thia, J.A.; Stouffer, D.B. Related plants tend to share pollinators and herbivores, but strength of phylogenetic signal varies among plant families. New Phytol. 2020, 226, 909–920. [Google Scholar] [CrossRef]
- Jacquemyn, H.; Merckx, V.; Brys, R.; Tyteca, D.; Cammue, B.P.A.; Honnay, O.; Lievens, B. Analysis of network architecture reveals phylogenetic constraints on mycorrhizal specificity in the genus Orchis (Orchidaceae). New Phytol. 2011, 192, 518–528. [Google Scholar] [CrossRef]
- Tucker, C.M.; Cadotte, M.W.; Carvalho, S.B.; Davies, T.J.; Ferrier, S.; Fritz, S.A.; Grenyer, R.; Helmus, M.R.; Jin, L.S.; Mooers, A.O.; et al. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol. Rev. 2017, 92, 698–715. [Google Scholar] [CrossRef]
- Pavoine, S. A guide through a family of phylogenetic dissimilarity measures among sites. Oikos 2016, 125, 1719–1732. [Google Scholar] [CrossRef] [Green Version]
- Washburne, A.D.; Morton, J.T.; Sanders, J.; McDonald, D.; Zhu, Q.; Oliverio, A.M.; Knight, R. Methods for phylogenetic analysis of microbiome data. Nat. Microbiol. 2018, 3, 652–661. [Google Scholar] [CrossRef]
- Clarke, K.R.; Warwick, R.M. A taxonomic distinctness index and its statistical properties. J. Appl. Ecol. 1998, 35, 523–531. [Google Scholar] [CrossRef]
- Cadotte, M.W.; Davies, T.J.; Peres-Neto, P.R. Why phylogenies do not always predict ecological differences. Ecol. Monogr. 2017, 87, 535–551. [Google Scholar] [CrossRef]
- Shaner, G.; Finney, R. The effect of nitrogen fertilization on the expression of slow-mildewing resistance in Knox wheat. Phytopathology 1977, 67, 1051–1056. [Google Scholar] [CrossRef] [Green Version]
- Cadotte, M.W.; Dinnage, R.; Tilman, D. Phylogenetic diversity promotes ecosystem stability. Ecology 2012, 93, S223–S233. [Google Scholar] [CrossRef] [Green Version]
- Cobb, R.C.; Meentemeyer, R.K.; Rizzo, D.M. Apparent competition in canopy trees determined by pathogen transmission rather than susceptibility. Ecology 2010, 91, 327–333. [Google Scholar] [CrossRef] [Green Version]
- Cary, K.L. Physiology and Community Assembly in Mendocino’s Pygmy Forest; University of California: Santa Cruz, CA, USA, 2019. [Google Scholar]
- Godoy, O.; Kraft, N.J.B.; Levine, J.M. Phylogenetic relatedness and the determinants of competitive outcomes. Ecol. Lett. 2014, 17, 836–844. [Google Scholar] [CrossRef]
- Keck, F.; Rimet, F.; Franc, A.; Bouchez, A. Phylogenetic signal in diatom ecology: Perspectives for aquatic ecosystems biomonitoring. Ecol. Appl. 2016, 26, 861–872. [Google Scholar] [CrossRef] [Green Version]
- Naisbit, R.E.; Kehrli, P.; Rohr, R.P.; Bersier, L.-F. Phylogenetic signal in predator–prey body-size relationships. Ecology 2011, 92, 2183–2189. [Google Scholar] [CrossRef]
- Lynch, S.C.; Eskalen, A.; Gilbert, G.S. Host evolutionary relationships explain tree mortality caused by a generalist pest-pathogen complex. Evol. Appl. 2020, 14, 1083–1094. [Google Scholar] [CrossRef]
- Honorio Coronado, E.N.; Dexter, K.G.; Pennington, R.T.; Chave, J.; Lewis, S.L.; Alexiades, M.N.; Alvarez, E.; Alves de Oliveira, A.; Amaral, I.L.; Araujo-Murakami, A. Phylogenetic diversity of Amazonian tree communities. Divers. Distrib. 2015, 21, 1295–1307. [Google Scholar] [CrossRef]
- Liendo, D.; Biurrun, I.; Campos, J.A.; García-Mijangos, I.; Pearman, P.B. Effects of disturbance and alien plants on the phylogenetic structure of riverine communities. J. Veg. Sci. 2021, 32, e12933. [Google Scholar] [CrossRef]
- Montaño-Centellas, F.A.; Loiselle, B.A.; Tingley, M.W. Ecological drivers of avian community assembly along a tropical elevation gradient. Ecography 2020, 44, 574–588. [Google Scholar] [CrossRef]
- Redding, D.W.; Mooers, A.Ø. Incorporating evolutionary measures into conservation prioritization. Conserv. Biol. 2006, 20, 1670–1678. [Google Scholar] [CrossRef]
- Isaac, N.J.; Turvey, S.T.; Collen, B.; Waterman, C.; Baillie, J.E. Mammals on the EDGE: Conservation priorities based on threat and phylogeny. PLoS ONE 2007, 2, e296. [Google Scholar] [CrossRef] [Green Version]
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Gilbert, G.S.; Parker, I.M. Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves. Diversity 2022, 14, 521. https://doi.org/10.3390/d14070521
Gilbert GS, Parker IM. Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves. Diversity. 2022; 14(7):521. https://doi.org/10.3390/d14070521
Chicago/Turabian StyleGilbert, Gregory S., and Ingrid M. Parker. 2022. "Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves" Diversity 14, no. 7: 521. https://doi.org/10.3390/d14070521
APA StyleGilbert, G. S., & Parker, I. M. (2022). Phylogenetic Distance Metrics for Studies of Focal Species in Communities: Quantiles and Cumulative Curves. Diversity, 14(7), 521. https://doi.org/10.3390/d14070521