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Kruger A, Shankar V, Jonathan Davies T. Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks. Syst Biol 2024; 73:546-561. [PMID: 38767123 PMCID: PMC11377182 DOI: 10.1093/sysbio/syae026] [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: 06/16/2022] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024] Open
Abstract
When communities are assembled through processes such as filtering or limiting similarity acting on phylogenetically conserved traits, the evolutionary signature of those traits may be reflected in patterns of community membership. We show how the model of trait evolution underlying community-structuring traits can be inferred from community membership data using both a variation of a traditional eco-phylogenetic metric-the mean pairwise phylogenetic distance (MPD) between taxa-and a recent machine learning tool, Convolutional Kitchen Sinks (CKS). Both methods perform well across a range of phylogenetically informative evolutionary models, but CKS outperforms MPD as tree size increases. We demonstrate CKS by inferring the evolutionary history of freeze tolerance in angiosperms. Our analysis is consistent with a late burst model, suggesting freeze tolerance evolved recently. We suggest that multiple data types that are ordered on phylogenies, such as trait values, species interactions, or community presence/absence, are good candidates for CKS modeling because the generative models produce structured differences between neighboring points that CKS is well-suited for. We introduce the R package kitchen to perform CKS for generic application of the technique.
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Affiliation(s)
- Avery Kruger
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Vaishaal Shankar
- Machine Learning Research, Apple Inc, Cupertino, CA 95014, USA
- Physical Stores, Amazon, San Francisco, CA 94105, USA
| | - T Jonathan Davies
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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2
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Oliveira EVDS, Landim MF, Gouveia SF. Assembly structures of coastal woody species of eastern South America: Patterns and drivers. PLANT DIVERSITY 2024; 46:611-620. [PMID: 39290883 PMCID: PMC11403147 DOI: 10.1016/j.pld.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 09/19/2024]
Abstract
Tropical regions have provided new insights into how ecological communities are assembled. In dry coastal communities, water stress has been hypothesized to determine plant assembly structure by favoring preadapted lineages from neighboring ecosystems, consistent with functional clustering. However, it is unclear whether this hypothesis is sufficient to explain how coastal communities in tropical ecosystems are assembled. Here, we test whether water stress or other factors drive community assembly in woody plant communities across the coastal zone of Brazil, a tropical ecosystem. We characterized functional and phylogenetic structures of these communities and determined the underlying environmental factors (e.g., water stress, historical climate stability, edaphic constraints, and habitat heterogeneity) that drive their community assembly. Assemblages of coastal woody species show geographically varied patterns, including stochastic arrangements, clustering, and overdispersion of species relative to their traits and phylogenetic relatedness. Topographic complexity, water vapor pressure, and soil nutrient availability best explained the gradient in the functional structure. Water deficit, water vapor pressure, and soil organic carbon were the best predictors of variation in phylogenetic structure. Our results support the water-stress conservatism hypothesis on functional and phylogenetic structure, as well as the effect of habitat heterogeneity on functional structure and edaphic constraints on functional and phylogenetic structure. These effects are associated with increased phenotypic and phylogenetic divergence of woody plant assemblages, which is likely mediated by abiotic filtering and niche opportunities, suggesting a complex pattern of ecological assembly.
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Affiliation(s)
- Eduardo Vinícius da Silva Oliveira
- Graduate Program in Ecology and Conservation, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- National Institute of Science and Technology Ecology, Evolution and Conservation of Biodiversity (INCT-EECBio), Goiânia, Goiás, Brazil
| | | | - Sidney F Gouveia
- National Institute of Science and Technology Ecology, Evolution and Conservation of Biodiversity (INCT-EECBio), Goiânia, Goiás, Brazil
- Department of Ecology, Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
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3
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Lemos-Costa P, Miller ZR, Allesina S. Phylogeny structures species' interactions in experimental ecological communities. Ecol Lett 2024; 27:e14490. [PMID: 39152685 DOI: 10.1111/ele.14490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 06/24/2024] [Accepted: 07/11/2024] [Indexed: 08/19/2024]
Abstract
Species' traits and interactions are products of evolutionary history. Despite the long-standing hypothesis that closely related species possess similar traits, and thus experience stronger competition, measuring the effect of evolutionary history on the ecology of natural communities remains challenging. We propose a novel framework to test whether phylogeny influences patterns of coexistence and abundance of species assemblages. In our approach, phylogenetic trees are used to parameterize species' interactions, which in turn determine the abundance of species in a given assemblage. We use likelihoods to score models parameterized with a given phylogeny, and contrast them with models built using random trees, allowing us to test whether phylogenetic information helps to predict species' abundances. Our statistical framework reveals that interactions are indeed structured by phylogeny in a large set of experimental plant communities. Our results confirm that evolutionary history can help predict, and potentially manage or conserve, the structure and function of complex ecological communities.
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Affiliation(s)
- Paula Lemos-Costa
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Zachary R Miller
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
| | - Stefano Allesina
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, USA
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4
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Rosindell J, Manson K, Gumbs R, Pearse WD, Steel M. Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage. Syst Biol 2024; 73:158-182. [PMID: 38102727 PMCID: PMC11129585 DOI: 10.1093/sysbio/syad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce "EvoHeritage", a generalization of PD that is founded on the joint processes of accumulation and attrition of features. We argue that while PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.
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Affiliation(s)
- James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Kerry Manson
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Rikki Gumbs
- EDGE of Existence Programme, Zoological Society of London, Regent’s Park, London NW1 4RY, UK
| | - William D Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
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5
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Zhigila DA, Elliott TL, Schmiedel U, Muasya AM. Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands? ANNALS OF BOTANY 2024; 133:833-850. [PMID: 38401154 PMCID: PMC11082514 DOI: 10.1093/aob/mcae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/23/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND AND AIMS The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields. METHODS We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments. KEY RESULTS We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even. CONCLUSIONS Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.
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Affiliation(s)
- Daniel A Zhigila
- Department of Botany, Gombe State University, PMB 127, Tudun Wada, Gombe, Gombe State, Nigeria
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Tammy L Elliott
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Ute Schmiedel
- Organismic Botany and Mycology, Institute of Plant Science and Microbiology, University of Hamburg, Germany
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
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6
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Li Z, Linard B, Vogler AP, Yu DW, Wang Z. Phylogenetic diversity only weakly mitigates climate-change-driven biodiversity loss in insect communities. Mol Ecol 2023; 32:6147-6160. [PMID: 36271787 DOI: 10.1111/mec.16747] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/30/2022]
Abstract
To help address the underrepresentation of arthropods and Asian biodiversity from climate-change assessments, we carried out year-long, weekly sampling campaigns with Malaise traps at different elevations and latitudes in Gaoligongshan National Park in southwestern China. From these 623 samples, we barcoded 10,524 beetles and compared scenarios of climate-change-induced biodiversity loss, by designating seasonal, elevational, and latitudinal subsets of beetles as communities that plausibly could go extinct as a group, which we call "loss sets". The availability of a published mitochondrial-genome-based phylogeny of the Coleoptera allowed us to compare the loss of species diversity with and without accounting for phylogenetic relatedness. We hypothesised that phylogenetic relatedness would mitigate extinction, since the extinction of any loss set would result in the disappearance of all its species but only part of its evolutionary history, which is still extant in the remaining loss sets. We found different patterns of community clustering by season and latitude, depending on whether phylogenetic information was incorporated. However, accounting for phylogeny only slightly mitigated the amount of biodiversity loss under climate change scenarios, against our expectations: there is no phylogenetic "escape clause" for biodiversity conservation. We achieve the same results whether phylogenetic information was derived from the mitogenome phylogeny or from a de novo barcode-gene tree. We encourage interested researchers to use this data set to study lineage-specific community assembly patterns in conjunction with life-history traits and environmental covariates.
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Affiliation(s)
- Zongxu Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Benjamin Linard
- LIRMM, University of Montpellier, CNRS, Montpellier, France
- SPYGEN, Le Bourget-du-Lac, France
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Zhengyang Wang
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
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7
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Ward D, Kirkman K, Morris C. Long-term subtropical grassland plots take a long time to change: Replacement is more important than richness differences for beta diversity. Ecol Evol 2023; 13:ECE310195. [PMID: 37325718 PMCID: PMC10266706 DOI: 10.1002/ece3.10195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 04/07/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
We studied β diversity of grasses in a subtropical grassland over 60 years in South Africa. We examined the effects of burning and mowing on 132 large plots. We sought to determine the effects of burning and mowing, and mowing frequency, on the replacement of species and the species richness. We conducted the study at Ukulinga, research farm of the University of KwaZulu-Natal, Pietermaritzburg, South Africa (29°24'E, 30°24'S) from 1950-2010. Plots were burned annually, biennially, triennially, and a control (unburned). Plots were mowed in spring, late summer, spring plus late summer, and a control (unmowed). We calculated β diversity, with a focus on replacement and richness differences. We also used distance-based redundancy analyses to examine the relative effects of replacement and richness differences on mowing and burning. We used beta regressions to test for the effect of soil depth and its interactions with mowing and burning. There was no significant change in grass beta diversity until 1995. Thereafter, there were changes in β diversity that demonstrated the primary effects of summer mowing frequency. There was no significant effect of richness differences but a strong effect of replacement post-1995. There was a significant interaction between mowing frequency and soil depth in one of the analyses. Changes in grassland composition took a long time to manifest themselves and were unapparent prior to 1988. However, there was a change in sampling strategy prior to 1988, from point hits to nearest plants, that may also have influenced the rates of changes in replacement and richness differences. Using β-diversity indices, we found that mowing was more important than burning that burning frequency was unimportant, and there was a significant interaction effect between mowing and soil depth in one of the analyses.
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Affiliation(s)
- David Ward
- Department of Biological SciencesKent State UniversityKentOhioUSA
| | - Kevin Kirkman
- School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
| | - Craig Morris
- School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
- Agricultural Research Council – Animal Productionc/o University of KwaZulu‐NatalPietermaritzburgSouth Africa
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8
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Martinez ND. Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology. Ecol Evol 2023; 13:e9872. [PMID: 36911308 PMCID: PMC9994474 DOI: 10.1002/ece3.9872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 03/11/2023] Open
Abstract
Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.
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Affiliation(s)
- Neo D. Martinez
- Center for Complex Networks and Systems, School of Informatics, Computing, and EngineeringIndiana University, BloomingtonIndianaBloomingtonUSA
- Pacific Ecoinformatics and Computational Ecology LabCABerkeleyUSA
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9
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Maestri R, Luza AL, Hartz SM, de Freitas TRO, Patterson BD. Bridging macroecology and macroevolution in the radiation of sigmodontine rodents. Evolution 2022; 76:1790-1805. [PMID: 35794070 DOI: 10.1111/evo.14561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 01/22/2023]
Abstract
Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily oriented null model, whereas the opposite may indicate constraints on phenotypic evolution. We gathered phylogenies, biogeographic distributions, and data on the skull morphology of sigmodontine rodents to discover which regions of the Neotropics were more influenced by divergent, neutral, or constrained phenotypic evolution. We found that regions with higher disparity than expected by the evolutionary-oriented null model, in terms of both size and shape, were concentrated in the Atlantic Forest, suggesting a larger role for divergent natural selection there. Phenotypic disparity in the rest of South America, mainly the Amazon basin, northeastern Brazil, and Southern Andes, was constrained-lower than predicted by the evolutionary model. We also demonstrated equivalence between the disparity produced by randomization-based null models and constrained-evolution null models. Therefore, including evolutionary simulations into the null modeling framework used in ecophylogenetics can strengthen inferences on the processes underlying phenotypic evolution.
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Affiliation(s)
- Renan Maestri
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605
| | - André L Luza
- Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Sandra M Hartz
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Thales R O de Freitas
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970, Brazil
| | - Bruce D Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605
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10
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Si X, Cadotte MW, Davies TJ, Antonelli A, Ding P, Svenning JC, Faurby S. Phylogenetic and functional clustering illustrate the roles of adaptive radiation and dispersal filtering in jointly shaping late-Quaternary mammal assemblages on oceanic islands. Ecol Lett 2022; 25:1250-1262. [PMID: 35275608 DOI: 10.1111/ele.13997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/29/2021] [Accepted: 02/11/2022] [Indexed: 12/15/2022]
Abstract
Islands frequently harbour unique assemblages of species, yet their ecological roles and differences are largely ignored in island biogeography studies. Here, we examine eco-evolutionary processes structuring mammal assemblages on oceanic islands worldwide, including all extant and extinct late-Quaternary mammal species. We find island mammal assemblages tend to be phylogenetically clustered (share more recent evolutionary histories), with clustering increasing with island area and isolation. We also observe that mammal assemblages often tend to be functionally clustered (share similar traits), but the strength of clustering is weak and generally independent from island area or isolation. These findings indicate the important roles of in situ speciation and dispersal filtering in shaping island mammal assemblages under pre-anthropogenic conditions, notably through adaptive radiation of a few clades (e.g. bats, with generally high dispersal abilities). Our study demonstrates that considering the functional and phylogenetic axes of diversity can better reveal the eco-evolutionary processes of island community assembly.
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Affiliation(s)
- Xingfeng Si
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming (IEC), Shanghai, China
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandre Antonelli
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.,Royal Botanic Gardens, Richmond, Surrey, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ping Ding
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark.,Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Søren Faurby
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
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11
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Gougherty AV, Davies TJ. Towards a phylogenetic ecology of plant pests and pathogens. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200359. [PMID: 34538142 PMCID: PMC8450633 DOI: 10.1098/rstb.2020.0359] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2021] [Indexed: 01/17/2023] Open
Abstract
Plant-pathogens and insect pests, hereafter pests, play an important role in structuring ecological communities, yet both native and introduced pests impose significant pressure on wild and managed systems, and pose a threat to food security. Global changes in climate and land use, and transportation of plants and pests around the globe are likely to further increase the range, frequency and severity of pest outbreaks in the future. Thus, there is a critical need to expand on current ecological theory to address these challenges. Here, we outline a phylogenetic framework for the study of plant and pest interactions. In plants, a growing body of work has suggested that evolutionary relatedness, phylogeny, strongly structures plant-pest associations-from pest host breadths and impacts, to their establishment and spread in new regions. Understanding the phylogenetic dimensions of plant-pest associations will help to inform models of invasive species spread, disease and pest risk in crops, and emerging pest outbreaks in native plant communities-which will have important implications for protecting food security and biodiversity into the future. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Andrew V. Gougherty
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - T. Jonathan Davies
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2092, South Africa
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12
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Strydom T, Catchen MD, Banville F, Caron D, Dansereau G, Desjardins-Proulx P, Forero-Muñoz NR, Higino G, Mercier B, Gonzalez A, Gravel D, Pollock L, Poisot T. A roadmap towards predicting species interaction networks (across space and time). Philos Trans R Soc Lond B Biol Sci 2021; 376:20210063. [PMID: 34538135 PMCID: PMC8450634 DOI: 10.1098/rstb.2021.0063] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 11/12/2022] Open
Abstract
Networks of species interactions underpin numerous ecosystem processes, but comprehensively sampling these interactions is difficult. Interactions intrinsically vary across space and time, and given the number of species that compose ecological communities, it can be tough to distinguish between a true negative (where two species never interact) from a false negative (where two species have not been observed interacting even though they actually do). Assessing the likelihood of interactions between species is an imperative for several fields of ecology. This means that to predict interactions between species-and to describe the structure, variation, and change of the ecological networks they form-we need to rely on modelling tools. Here, we provide a proof-of-concept, where we show how a simple neural network model makes accurate predictions about species interactions given limited data. We then assess the challenges and opportunities associated with improving interaction predictions, and provide a conceptual roadmap forward towards predictive models of ecological networks that is explicitly spatial and temporal. We conclude with a brief primer on the relevant methods and tools needed to start building these models, which we hope will guide this research programme forward. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Tanya Strydom
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | - Michael D. Catchen
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Francis Banville
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- Université de Sherbrooke, Sherbrooke, Canada
| | - Dominique Caron
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Gabriel Dansereau
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | - Philippe Desjardins-Proulx
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | - Norma R. Forero-Muñoz
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
| | | | - Benjamin Mercier
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- Université de Sherbrooke, Sherbrooke, Canada
| | - Andrew Gonzalez
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Dominique Gravel
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- Université de Sherbrooke, Sherbrooke, Canada
| | - Laura Pollock
- Québec Centre for Biodiversity Sciences, Montréal, Canada
- McGill University, Montréal, Canada
| | - Timothée Poisot
- Sciences Biologiques, Université de Montréal, Montréal, Canada H2V 0B3
- Québec Centre for Biodiversity Sciences, Montréal, Canada
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13
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Jin L, Liu JJ, Xiao TW, Li QM, Lin LX, Shao XN, Ma CX, Li BH, Mi XC, Ren HB, Qiao XJ, Lian JY, Hao G, Ge XJ. Plastome-based phylogeny improves community phylogenetics of subtropical forests in China. Mol Ecol Resour 2021; 22:319-333. [PMID: 34233085 DOI: 10.1111/1755-0998.13462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.
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Affiliation(s)
- Lu Jin
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jia-Jia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Na Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen-Xin Ma
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bu-Hang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hai-Bao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Juan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ju-Yu Lian
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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14
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Phylogenetic uncertainty and the inference of patterns in community ecology and comparative studies. Oecologia 2021; 196:633-647. [PMID: 34146131 DOI: 10.1007/s00442-021-04972-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/12/2021] [Indexed: 10/21/2022]
Abstract
Progress in phylogenetic community ecology is often limited by the availability of phylogenetic information and the lack of appropriate methods and solutions to deal with this problem. We estimate the effect of the lack of phylogenetic information on the relations among taxa measured by commonly used phylogenetic metrics in comparative studies and community ecology, namely: Blomberg's K phylogenetic signal, Faith's Phylogenetic Diversity (PD), Mean Phylogenetic Distance (MPD) and Mean Nearest Taxon Distance (MNTD). To overcome this problem, we tested two possible solutions: Polytomic trees and Operational trees. Our results show that the effects on K values strongly depended on the level of phylogenetic signal. In the case of the community metrics, the effects were insensitive to the patterns of species distribution in the communities. Community metrics tended to be overestimated with both Polytomic and Operational trees, but the overestimation was higher with Polytomic trees. PD and MPD metrics were less biased than MNTD metric. We show that the lack of phylogenetic resolution is not necessarily problematic for all analyses and that its effect will depend on the chosen metric and on the solutions used to deal with the problem. Based on our results, we suggest that ecologists should prefer the Operational tree solution to remove polytomies in the phylogenetic tree and take careful consideration while designing experiments, and analyzing and interpreting the results of phylogenetic metrics.
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15
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Sreekar R, Si X, Sam K, Liu J, Dayananda S, Goodale U, Kotagama S, Goodale E. Land use and elevation interact to shape bird functional and phylogenetic diversity and structure: Implications for designing optimal agriculture landscapes. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Rachakonda Sreekar
- Institute of Entomology Biology Centre of the Czech Academy of Sciences Ceske Budejovice Czech Republic
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Xingfeng Si
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station School of Ecological and Environmental Sciences East China Normal University Shanghai China
| | - Katerina Sam
- Institute of Entomology Biology Centre of the Czech Academy of Sciences Ceske Budejovice Czech Republic
- Faculty of Science University of South Bohemia Ceske Budejovice Czech Republic
| | - Jiajia Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering School of Life Sciences Fudan University Shanghai China
| | - Salindra Dayananda
- Guangxi Key Laboratory of Forest Ecology and Conservation College of Forestry Guangxi University Nanning China
- Field Ornithology Group of Sri Lanka Department of Zoology University of Colombo Colombo Sri Lanka
| | - Uromi Goodale
- Guangxi Key Laboratory of Forest Ecology and Conservation College of Forestry Guangxi University Nanning China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro‐Bioresources College of Forestry Guangxi University Nanning China
- Seed Conservation Specialist Group Species Survival CommissionInternational Union for Conservation of Nature Gland Switzerland
| | - Sarath Kotagama
- Field Ornithology Group of Sri Lanka Department of Zoology University of Colombo Colombo Sri Lanka
| | - Eben Goodale
- Guangxi Key Laboratory of Forest Ecology and Conservation College of Forestry Guangxi University Nanning China
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