1
|
Henao-Diaz LF, Pennell M. The Major Features of Macroevolution. Syst Biol 2023; 72:1188-1198. [PMID: 37248967 DOI: 10.1093/sysbio/syad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/02/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.
Collapse
Affiliation(s)
- L Francisco Henao-Diaz
- Department of Ecology and Evolution, University of Chicago, Chicago, USA
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, USA
| |
Collapse
|
2
|
Measuring tree balance using symmetry nodes - A new balance index and its extremal properties. Math Biosci 2021; 341:108690. [PMID: 34433072 DOI: 10.1016/j.mbs.2021.108690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 11/22/2022]
Abstract
Effects like selection in evolution as well as fertility inheritance in the development of populations can lead to a higher degree of asymmetry in evolutionary trees than expected under a null hypothesis. To identify and quantify such influences, various balance indices were proposed in the phylogenetic literature and have been in use for decades. However, so far no balance index was based on the number of symmetry nodes, even though symmetry nodes play an important role in other areas of mathematical phylogenetics and despite the fact that symmetry nodes are a quite natural way to measure balance or symmetry of a given tree. The aim of this manuscript is thus twofold: First, we will introduce the symmetry nodes index as an index for measuring balance of phylogenetic trees and analyze its extremal properties. We also show that this index can be calculated in linear time. This new index turns out to be a generalization of a simple and well-known balance index, namely the cherry index, as well as a specialization of another, less established, balance index, namely Rogers' J index. Thus, it is the second objective of the present manuscript to compare the new symmetry nodes index to these two indices and to underline its advantages. In order to do so, we will derive some extremal properties of the cherry index and Rogers' J index along the way and thus complement existing studies on these indices. Moreover, we used the programming language R to implement all three indices in the software package symmeTree, which has been made publicly available.
Collapse
|
3
|
Wiens JJ. Patterns of Local Community Composition Are Linked to Large-Scale Diversification and Dispersal of Clades. Am Nat 2018; 191:184-196. [DOI: 10.1086/695495] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
4
|
Yang GD, Agapow PM, Yedid G. The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation. PLoS One 2017. [PMID: 28644846 PMCID: PMC5482465 DOI: 10.1371/journal.pone.0179553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors.
Collapse
Affiliation(s)
- Guan-Dong Yang
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Paul-Michael Agapow
- Data Science Institute, William Penney Laboratory, Imperial College, South Kensington, London, United Kingdom
| | - Gabriel Yedid
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- * E-mail:
| |
Collapse
|
5
|
Tucker CM, Cadotte MW, Carvalho SB, Davies TJ, Ferrier S, Fritz SA, Grenyer R, Helmus MR, Jin LS, Mooers AO, Pavoine S, Purschke O, Redding DW, Rosauer DF, Winter M, Mazel F. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol Rev Camb Philos Soc 2017; 92:698-715. [PMID: 26785932 PMCID: PMC5096690 DOI: 10.1111/brv.12252] [Citation(s) in RCA: 281] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 01/02/2023]
Abstract
The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.
Collapse
Affiliation(s)
- Caroline M. Tucker
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBox 334BoulderCO80309‐0334U.S.A.
| | - Marc W. Cadotte
- Biological SciencesUniversity of Toronto‐ScarboroughScarboroughM1C 1A4Canada
- Stake Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong, Higher Education Institutes, College of Ecology and EvolutionSun Yat‐sen UniversityGuangzhouPR China
| | - Silvia B. Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto4485‐661VairãoPortugal
| | - T. Jonathan Davies
- Department of BiologyMcGill UniversityMontréalH3A 1B1Canada
- African Centre for DNA BarcodingUniversity of JohannesburgPO Box 524Johannesburg2006South Africa
| | - Simon Ferrier
- CSIRO Ecosystem Sciences, Climate Adaptation FlagshipGPO BOX 1600Canberra2601Australia
| | - Susanne A. Fritz
- Biodiversity & Climate Research Centre (BiK‐F) and Senckenberg Gesellschaft für Naturforschung60325Frankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe University60438FrankfurtGermany
| | - Rich Grenyer
- School of Geography and the EnvironmentUniversity of OxfordOxfordOX1 3QYU.K.
| | - Matthew R. Helmus
- Department of Ecological Sciences ‐ Animal EcologyVrije UniversiteitAmsterdamNetherlands
- Center for Biodiversity, Department of BiologyTemple UniversitySuite 502PhiladelphiaPA19122U.S.A.
| | - Lanna S. Jin
- Ecology & Evolutionary BiologyUniversity of TorontoRoom 3055TorontoM5S 3B2Canada
| | - Arne O. Mooers
- Department of BiologySimon Fraser UniversityBurnabyV5A 1S6Canada
| | - Sandrine Pavoine
- Centre of Ecology and Conservation Sciences (UMR 7204 CESCO)Museum National d'Histoire NaturelleParisFrance
- Department of ZoologyUniversity of OxfordOxfordOX1 3QYUK
| | - Oliver Purschke
- German Centre of Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigDeutscher Platz 5eDE‐04103LeipzigGermany
- Geobotany and Botanical Garden, Institute of BiologyMartin Luther University, Halle‐WittenbergDE‐06108Halle (Saale)Germany
- Department of Computer ScienceMartin‐Luther‐University, Halle‐WittenbergDE‐06120Halle (Saale)Germany
| | - David W. Redding
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonWC1E 6BTU.K.
| | - Dan F. Rosauer
- Research School of BiologyAustralian National UniversityActon2601Australia
| | - Marten Winter
- German Centre of Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigDeutscher Platz 5eDE‐04103LeipzigGermany
| | - Florent Mazel
- Laboratoire d'Ecologie Alpine (LECA), CNRS ‐ Université Grenoble Alpes (UMR 5553)BP 5338041Grenoble Cedex 9France
| |
Collapse
|
6
|
Yguel B, Jactel H, Pearse IS, Moen D, Winter M, Hortal J, Helmus MR, Kühn I, Pavoine S, Purschke O, Weiher E, Violle C, Ozinga W, Brändle M, Bartish I, Prinzing A. The Evolutionary Legacy of Diversification Predicts Ecosystem Function. Am Nat 2016; 188:398-410. [PMID: 27622874 DOI: 10.1086/687964] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Theory suggests that the structure of evolutionary history represented in a species community may affect its functioning, but phylogenetic diversity metrics do not allow for the identification of major differences in this structure. Here we propose a new metric, ELDERness (for Evolutionary Legacy of DivERsity) to estimate evolutionary branching patterns within communities by fitting a polynomial function to lineage-through-time (LTT) plots. We illustrate how real and simulated community branching patterns can be more correctly described by ELDERness and can successfully predict ecosystem functioning. In particular, the evolutionary history of branching patterns can be encapsulated by the parameters of third-order polynomial functions and further measured through only two parameters, the "ELDERness surfaces." These parameters captured variation in productivity of a grassland community better than existing phylogenetic diversity or diversification metrics and independent of species richness or presence of nitrogen fixers. Specifically, communities with small ELDERness surfaces (constant accumulation of lineages through time in LTT plots) were more productive, consistent with increased productivity resulting from complementary lineages combined with niche filling within lineages. Overall, while existing phylogenetic diversity metrics remain useful in many contexts, we suggest that our ELDERness approach better enables testing hypotheses that relate complex patterns of macroevolutionary history represented in local communities to ecosystem functioning.
Collapse
|
7
|
Pearse WD, Jones FA, Purvis A. Barro Colorado Island's phylogenetic assemblage structure across fine spatial scales and among clades of different ages. Ecology 2013; 94:2861-72. [DOI: 10.1890/12-1676.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
8
|
Davies TJ, Cooper N, Diniz-Filho JAF, Thomas GH, Meiri S. Using phylogenetic trees to test for character displacement: a model and an example from a desert mammal community. Ecology 2012. [DOI: 10.1890/11-0400.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
9
|
González-Caro S, Parra JL, Graham CH, McGuire JA, Cadena CD. Sensitivity of metrics of phylogenetic structure to scale, source of data and species pool of hummingbird assemblages along elevational gradients. PLoS One 2012; 7:e35472. [PMID: 22558157 PMCID: PMC3338702 DOI: 10.1371/journal.pone.0035472] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 03/19/2012] [Indexed: 12/02/2022] Open
Abstract
Patterns of phylogenetic structure of assemblages are increasingly used to gain insight into the ecological and evolutionary processes involved in the assembly of co-occurring species. Metrics of phylogenetic structure can be sensitive to scaling issues and data availability. Here we empirically assess the sensitivity of four metrics of phylogenetic structure of assemblages to changes in (i) the source of data, (ii) the spatial grain at which assemblages are defined, and (iii) the definition of species pools using hummingbird (Trochilidae) assemblages along an elevational gradient in Colombia. We also discuss some of the implications in terms of the potential mechanisms driving these patterns. To explore how source of data influence phylogenetic structure we defined assemblages using three sources of data: field inventories, museum specimens, and range maps. Assemblages were defined at two spatial grains: coarse-grained (elevational bands of 800-m width) and fine-grained (1-km2 plots). We used three different species pools: all species contained in assemblages, all species within half-degree quadrats, and all species either above or below 2000 m elevation. Metrics considering phylogenetic relationships among all species within assemblages showed phylogenetic clustering at high elevations and phylogenetic evenness in the lowlands, whereas those metrics considering only the closest co-occurring relatives showed the opposite trend. This result suggests that using multiple metrics of phylogenetic structure should provide greater insight into the mechanisms shaping assemblage structure. The source and spatial grain of data had important influences on estimates of both richness and phylogenetic structure. Metrics considering the co-occurrence of close relatives were particularly sensitive to changes in the spatial grain. Assemblages based on range maps included more species and showed less phylogenetic structure than assemblages based on museum or field inventories. Coarse-grained assemblages included more distantly related species and thus showed a more even phylogenetic structure than fine-grained assemblages. Our results emphasize the importance of carefully selecting the scale, source of data and metric used in analysis of the phylogenetic structure of assemblages.
Collapse
Affiliation(s)
- Sebastián González-Caro
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Juan L. Parra
- Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
| | - Catherine H. Graham
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Jimmy A. McGuire
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| |
Collapse
|
10
|
Soliveres S, Torices R, Maestre FT. Evolutionary relationships can be more important than abiotic conditions in predicting the outcome of plant-plant interactions. OIKOS 2011; 121:1638-1648. [PMID: 25914426 DOI: 10.1111/j.1600-0706.2011.20309.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Positive and negative plant-plant interactions are major processes shaping plant communities. They are affected by environmental conditions and evolutionary relationships among the interacting plants. However, the generality of these factors as drivers of pairwise plant interactions and their combined effects remain virtually unknown. We conducted an observational study to assess how environmental conditions (altitude, temperature, irradiance and rainfall), the dispersal mechanism of beneficiary species and evolutionary relationships affected the co-occurrence of pairwise interactions in 11 Stipa tenacissima steppes located along an environmental gradient in Spain. We studied 197 pairwise plant-plant interactions involving the two major nurse plants (the resprouting shrub Quercus coccifera and the tussock grass S. tenacissima) found in these communities. The relative importance of the studied factors varied with the nurse species considered. None of the factors studied were good predictors of the co-ocurrence between S. tenacissima and its neighbours. However, both the dispersal mechanism of the beneficiary species and the phylogenetic distance between interacting species were crucial factors affecting the co-occurrence between Q. coccifera and its neighbours, while climatic conditions (irradiance) played a secondary role. Values of phylogenetic distance between 207-272.8 Myr led to competition, while values outside this range or fleshy-fruitness in the beneficiary species led to positive interactions. The low importance of environmental conditions as a general driver of pairwise interactions was caused by the species-specific response to changes in either rainfall or radiation. This result suggests that factors other than climatic conditions must be included in theoretical models aimed to generally predict the outcome of plant-plant interactions. Our study helps to improve current theory on plant-plant interactions and to understand how these interactions can respond to expected modifications in species composition and climate associated to ongoing global environmental change.
Collapse
Affiliation(s)
- Santiago Soliveres
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Rubén Torices
- Área de Botánica, Departamento de Ciencias Agroforestales, E.U.I. Agrarias de Soria, Universidad de Valladolid, Campus de los Pajaritos, 42004 Soria, Spain
| | - Fernando T Maestre
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| |
Collapse
|
11
|
Carnicer J, Brotons L, Stefanescu C, Peñuelas J. Biogeography of species richness gradients: linking adaptive traits, demography and diversification. Biol Rev Camb Philos Soc 2011; 87:457-79. [PMID: 22129434 DOI: 10.1111/j.1469-185x.2011.00210.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here we review how adaptive traits contribute to the emergence and maintenance of species richness gradients through their influence on demographic and diversification processes. We start by reviewing how demographic dynamics change along species richness gradients. Empirical studies show that geographical clines in population parameters and measures of demographic variability are frequent along latitudinal and altitudinal gradients. Demographic variability often increases at the extremes of regional species richness gradients and contributes to shape these gradients. Available studies suggest that adaptive traits significantly influence demographic dynamics, and set the limits of species distributions. Traits related to thermal tolerance, resource use, phenology and dispersal seem to play a significant role. For many traits affecting demography and/or diversification processes, complex mechanistic approaches linking genotype, phenotype and fitness are becoming progressively available. In several taxa, species can be distributed along adaptive trait continuums, i.e. a main axis accounting for the bulk of inter-specific variation in some correlated adaptive traits. It is shown that adaptive trait continuums can provide useful mechanistic frameworks to explain demographic dynamics and diversification in species richness gradients. Finally, we review the existence of sequences of adaptive traits in phylogenies, the interactions of adaptive traits and community context, the clinal variation of traits across geographical gradients, and the role of adaptive traits in determining the history of dispersal and diversification of clades. Overall, we show that the study of demographic and evolutionary mechanisms that shape species richness gradients clearly requires the explicit consideration of adaptive traits. To conclude, future research lines and trends in the field are briefly outlined.
Collapse
Affiliation(s)
- Jofre Carnicer
- Community and Conservation Ecology Group, Centre for Life Sciences, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | | | | | | |
Collapse
|
12
|
Purvis A, Fritz SA, Rodríguez J, Harvey PH, Grenyer R. The shape of mammalian phylogeny: patterns, processes and scales. Philos Trans R Soc Lond B Biol Sci 2011; 366:2462-77. [PMID: 21807729 DOI: 10.1098/rstb.2011.0025] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'-points at which net diversification rate has changed-identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of 'rules'. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space.
Collapse
Affiliation(s)
- Andy Purvis
- Department of Life Sciences, Imperial College London, Silwood Park, UK.
| | | | | | | | | |
Collapse
|
13
|
Davies TJ, Buckley LB. Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals. Philos Trans R Soc Lond B Biol Sci 2011; 366:2414-25. [PMID: 21768156 PMCID: PMC3130431 DOI: 10.1098/rstb.2011.0058] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.
Collapse
Affiliation(s)
- T Jonathan Davies
- Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1.
| | | |
Collapse
|
14
|
Detection of selection utilizing molecular phylogenetics: a possible approach. Genetica 2011; 139:639-48. [DOI: 10.1007/s10709-011-9560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 02/28/2011] [Indexed: 11/25/2022]
|
15
|
HUGALL ANDREWFORREST, STANISIC JOHN. Beyond the prolegomenon: a molecular phylogeny of the Australian camaenid land snail radiation. Zool J Linn Soc 2011. [DOI: 10.1111/j.1096-3642.2010.00644.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
16
|
Morlon H, Schwilk DW, Bryant JA, Marquet PA, Rebelo AG, Tauss C, Bohannan BJM, Green JL. Spatial patterns of phylogenetic diversity. Ecol Lett 2010; 14:141-9. [PMID: 21166972 PMCID: PMC3047708 DOI: 10.1111/j.1461-0248.2010.01563.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ecologists and conservation biologists have historically used species-area and distance-decay relationships as tools to predict the spatial distribution of biodiversity and the impact of habitat loss on biodiversity. These tools treat each species as evolutionarily equivalent, yet the importance of species' evolutionary history in their ecology and conservation is becoming increasingly evident. Here, we provide theoretical predictions for phylogenetic analogues of the species-area and distance-decay relationships. We use a random model of community assembly and a spatially explicit flora dataset collected in four Mediterranean-type regions to provide theoretical predictions for the increase in phylogenetic diversity - the total phylogenetic branch-length separating a set of species - with increasing area and the decay in phylogenetic similarity with geographic separation. These developments may ultimately provide insights into the evolution and assembly of biological communities, and guide the selection of protected areas.
Collapse
Affiliation(s)
- Hélène Morlon
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR, USA.
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Pavoine S, Bonsall MB. Measuring biodiversity to explain community assembly: a unified approach. Biol Rev Camb Philos Soc 2010; 86:792-812. [DOI: 10.1111/j.1469-185x.2010.00171.x] [Citation(s) in RCA: 402] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
18
|
Parra J, McGuire J, Graham C. Incorporating Clade Identity in Analyses of Phylogenetic Community Structure: An Example with Hummingbirds. Am Nat 2010; 176:573-87. [DOI: 10.1086/656619] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
19
|
Gotelli NJ, Anderson MJ, Arita HT, Chao A, Colwell RK, Connolly SR, Currie DJ, Dunn RR, Graves GR, Green JL, Grytnes JA, Jiang YH, Jetz W, Kathleen Lyons S, McCain CM, Magurran AE, Rahbek C, Rangel TFLVB, Soberón J, Webb CO, Willig MR. Patterns and causes of species richness: a general simulation model for macroecology. Ecol Lett 2009; 12:873-86. [PMID: 19702748 DOI: 10.1111/j.1461-0248.2009.01353.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas J Gotelli
- Department of Biology, University of Vermont, Burlington, VT 05405, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Cavender-Bares J, Kozak KH, Fine PVA, Kembel SW. The merging of community ecology and phylogenetic biology. Ecol Lett 2009; 12:693-715. [PMID: 19473217 DOI: 10.1111/j.1461-0248.2009.01314.x] [Citation(s) in RCA: 1021] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.
Collapse
Affiliation(s)
- Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA.
| | | | | | | |
Collapse
|
21
|
Jabot F, Chave J. Inferring the parameters of the neutral theory of biodiversity using phylogenetic information and implications for tropical forests. Ecol Lett 2009; 12:239-48. [DOI: 10.1111/j.1461-0248.2008.01280.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
22
|
Vamosi SM, Heard SB, Vamosi JC, Webb CO. Emerging patterns in the comparative analysis of phylogenetic community structure. Mol Ecol 2008; 18:572-92. [PMID: 19037898 DOI: 10.1111/j.1365-294x.2008.04001.x] [Citation(s) in RCA: 312] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The analysis of the phylogenetic structure of communities can help reveal contemporary ecological interactions, as well as link community ecology with biogeography and the study of character evolution. The number of studies employing this broad approach has increased to the point where comparison of their results can now be used to highlight successes and deficiencies in the approach, and to detect emerging patterns in community organization. We review studies of the phylogenetic structure of communities of different major taxa and trophic levels, across different spatial and phylogenetic scales, and using different metrics and null models. Twenty-three of 39 studies (59%) find evidence for phylogenetic clustering in contemporary communities, but terrestrial and/or plant systems are heavily over-represented among published studies. Experimental investigations, although uncommon at present, hold promise for unravelling mechanisms underlying the phylogenetic community structure patterns observed in community surveys. We discuss the relationship between metrics of phylogenetic clustering and tree balance and explore the various emerging biases in taxonomy and pitfalls of scale. Finally, we look beyond one-dimensional metrics of phylogenetic structure towards multivariate descriptors that better capture the variety of ecological behaviours likely to be exhibited in communities of species with hundreds of millions of years of independent evolution.
Collapse
Affiliation(s)
- S M Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4.
| | | | | | | |
Collapse
|
23
|
KRASNOV BORISR, KHOKHLOVA IRINAS, SHENBROT GEORGYI, POULIN ROBERT. Geographic patterns of diversification: an example with ectoparasitic insects. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01107.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
24
|
How are the host spectra of hematophagous parasites shaped over evolutionary time? Random choice vs selection of a phylogenetic lineage. Parasitol Res 2008; 102:1157-64. [DOI: 10.1007/s00436-008-0884-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2007] [Accepted: 01/11/2008] [Indexed: 11/25/2022]
|