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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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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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3
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Gross CP, Stachowicz JJ. Extending trait dispersion across trophic levels: Predator assemblages act as top-down filters on prey communities. Ecology 2024; 105:e4320. [PMID: 38768562 DOI: 10.1002/ecy.4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/03/2024] [Accepted: 03/14/2024] [Indexed: 05/22/2024]
Abstract
Studies of community assembly typically focus on the effects of abiotic environmental filters and stabilizing competition on functional trait dispersion within single trophic levels. Predation is a well-known driver of community diversity and composition, yet the role of functionally diverse predator communities in filtering prey community traits has received less attention. We examined functionally diverse communities of predators (fishes) and prey (epifaunal crustaceans) in eelgrass (Zostera marina) beds in two northern California estuaries to evaluate the filtering effects of predator traits on community assembly and how filters acting on predators influence their ability to mediate prey community assembly. Fish traits related to bottom orientation were correlated with more clustered epifauna communities, and epifauna were generally overdispersed while fishes were clustered, suggesting prey may be pushed to disparate areas of trait space to avoid capture by benthic sit-and-wait predators. We also found correlations between the trait dispersions of predator and prey communities that strengthened after accounting for the effects of habitat filters on predator dispersion, suggesting that habitat filtering effects on predator species pools may hinder their ability to affect prey community assembly. Our results present compelling observational evidence that specific predator traits have measurable impacts on the community assembly of prey, inviting experimental tests of predator trait means on community assembly and explicit comparisons of how the relative effects of habitat filters and intraguild competition on predators impact their ability to affect prey community assembly. Integrating our understanding of traits at multiple trophic levels can help us better predict the impacts of community composition on food web dynamics as regional species pools shift with climate change and anthropogenic introductions.
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Affiliation(s)
- Collin P Gross
- Department of Evolution and Ecology, University of California, Davis, California, USA
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, California, USA
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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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5
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Brian JI, Catford JA. A mechanistic framework of enemy release. Ecol Lett 2023; 26:2147-2166. [PMID: 37921034 DOI: 10.1111/ele.14329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
The enemy release hypothesis (ERH) is the best-known hypothesis explaining high performance (e.g. rapid population growth) of exotic species. However, the current framing of the ERH does not explicitly link evidence of enemy release with exotic performance. This leads to uncertainty regarding the role of enemy release in biological invasions. Here, we demonstrate that the effect of enemy release on exotic performance is the product of three factors: enemy impact, enemy diversity, and host adaptation. These factors are modulated by seven contexts: time since introduction, resource availability, phylogenetic relatedness of exotic and native species, host-enemy asynchronicity, number of introduction events, type of enemy, and strength of growth-defence trade-offs. ERH-focused studies frequently test different factors under different contexts. This can lead to inconsistent findings, which typifies current evidence for the ERH. For example, over 80% of meta-analyses fail to consider ecological contexts which can alter study findings; we demonstrate this by re-analysing a recent ERH synthesis. Structuring the ERH around factors and contexts promotes generalisable predictions about when and where exotic species may benefit from enemy release, empowering effective management. Our mechanistic factor-context framework clearly lays out the evidence required to support the ERH, unifies many enemy-related invasion hypotheses, and enhances predictive capacity.
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Affiliation(s)
- Joshua I Brian
- Department of Geography, King's College London, London, UK
| | - Jane A Catford
- Department of Geography, King's College London, London, UK
- Fenner School of Environment & Society, The Australian National University, Canberra, Australia
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, Australia
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Smith AH, Bogar LM, Moeller HV. Fungal Fight Club: phylogeny and growth rate predict competitive outcomes among ectomycorrhizal fungi. FEMS Microbiol Ecol 2023; 99:fiad108. [PMID: 37697652 PMCID: PMC10516346 DOI: 10.1093/femsec/fiad108] [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: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023] Open
Abstract
Ectomycorrhizal fungi are among the most prevalent fungal partners of plants and can constitute up to one-third of forest microbial biomass. As mutualistic partners that supply nutrients, water, and pathogen defense, these fungi impact host plant health and biogeochemical cycling. Ectomycorrhizal fungi are also extremely diverse, and the community of fungal partners on a single plant host can consist of dozens of individuals. However, the factors that govern competition and coexistence within these communities are still poorly understood. In this study, we used in vitro competitive assays between five ectomycorrhizal fungal strains to examine how competition and pH affect fungal growth. We also tested the ability of evolutionary history to predict the outcomes of fungal competition. We found that the effects of pH and competition on fungal performance varied extensively, with changes in growth media pH sometimes reversing competitive outcomes. Furthermore, when comparing the use of phylogenetic distance and growth rate in predicting competitive outcomes, we found that both methods worked equally well. Our study further highlights the complexity of ectomycorrhizal fungal competition and the importance of considering phylogenetic distance, ecologically relevant traits, and environmental conditions in predicting the outcomes of these interactions.
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Affiliation(s)
- Alexander H Smith
- Department of Integrative Biology, University of Colorado, Denver Auraria Campus Science Building 1150 12th St, Denver CO 80204, USA
| | - Laura M Bogar
- Department of Plant Biology, University of California, Davis, 605 Hutchison Dr Green Hall rm 1002 Davis CA 95616-5720, USA
| | - Holly V Moeller
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara CA 93106-9620, USA
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Larkin DJ, Glasenhardt MC, Williams EW, Karimi N, Barak RS, Leavens E, Hipp AL. Evolutionary history shapes grassland productivity through opposing effects on complementarity and selection. Ecology 2023; 104:e4129. [PMID: 37342067 DOI: 10.1002/ecy.4129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/17/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
Phylogenetic diversity (PD), the evolutionary history of the organisms comprising a community, is increasingly recognized as an important driver of ecosystem function. However, biodiversity-ecosystem function experiments have rarely included PD as an a priori treatment. Thus, PD's effects in existing experiments are often confounded by covarying differences in species richness and functional trait diversity (FD). Here we report an experimental demonstration of strong PD effects on grassland primary productivity that are independent of FD, which was separately manipulated, and species richness, which was planted uniformly high to mimic diverse natural grasslands. Partitioning diversity effects demonstrated that higher PD increased complementarity (niche partitioning and/or facilitation) but lowered selection effects (probability of sampling highly productive species). Specifically, for every 5% increase in PD, complementarity increased by 26% on average (±8% SE), while selection effects decreased more modestly (8 ± 16%). PD also shaped productivity through clade-level effects on functional traits, that is, trait values associated with particular plant families. This clade effect was most pronounced in the Asteraceae (sunflower family), which, in tallgrass prairies, generally comprises tall, high-biomass species with low phylogenetic distinctiveness. FD also reduced selection effects but did not alter complementarity. Our results show that PD, independent of richness and FD, mediates ecosystem function through contrasting effects on complementarity and selection. This adds to growing evidence that consideration of phylogenetic dimensions of biodiversity can advance ecological understanding and inform conservation and restoration.
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Affiliation(s)
- Daniel J Larkin
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, Minnesota, USA
| | | | - Evelyn W Williams
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, Illinois, USA
| | - Nisa Karimi
- Herbarium and Center for Tree Science, The Morton Arboretum, Lisle, Illinois, USA
| | - Rebecca S Barak
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, Illinois, USA
| | - Emma Leavens
- Herbarium and Center for Tree Science, The Morton Arboretum, Lisle, Illinois, USA
| | - Andrew L Hipp
- Herbarium and Center for Tree Science, The Morton Arboretum, Lisle, Illinois, USA
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8
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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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Chai Y, Qiu S, Wang K, Xu J, Guo Y, Wang M, Yue M, Wang M, Zhu J. Partitioning and integrating of plant traits and phylogeny in assessing diversity along secondary forest succession in Loess Plateau of China. Ecol Evol 2023; 13:e10055. [PMID: 37181202 PMCID: PMC10170657 DOI: 10.1002/ece3.10055] [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: 09/22/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
Assessing plant diversity during community succession based on plant trait and phylogenetic features within a community (alpha scale) and among communities (beta scale) could improve our understanding of community succession mechanism. However, whether changes of community functional diversity at alpha and beta scale are structured by different traits and whether integrating plant traits and phylogeny can enhance the ability in detecting diversity pattern have not been studied in detail. Thirty plots representing different successional stages were established on the Loess Plateau of China and 15 functional traits were measured for all coexisting species. We first analyzed the functional alpha and beta diversity along succession by decomposing species trait into alpha and beta components and then integrated key traits with phylogenetic information to explore their roles in shaping species turnover during community succession. We found that functional alpha diversity increased along successional stages and was structured by morphological traits, while beta diversity decreased during succession and was more structured by stoichiometry traits. Phylogenetic alpha diversity showed congruent pattern with functional alpha diversity because of phylogenetic conservation of trait alpha components (variation within community), while beta diversity showed incongruent pattern due to phylogenetic randomness of trait beta components (variation among communities). Furthermore, only integrating relatively conserved traits (plant height and seed mass) and phylogenetic information can raise the detecting ability in assessing diversity change. Overall, our results reveal the increasing niche differentiation within community and functional convergence among communities with succession process, indicating the importance of matching traits with scale in studying community functional diversity and the asymmetry of traits and phylogeny in reflecting species ecological differences under long-term selection pressures.
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Affiliation(s)
- Yongfu Chai
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaNorthwest UniversityXi'anChina
- School of Life SciencesNorthwest UniversityXi'anChina
| | - Shen Qiu
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaNorthwest UniversityXi'anChina
- School of Life SciencesNorthwest UniversityXi'anChina
| | - Kaiyue Wang
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaNorthwest UniversityXi'anChina
- School of Life SciencesNorthwest UniversityXi'anChina
| | - Jinshi Xu
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaNorthwest UniversityXi'anChina
- School of Life SciencesNorthwest UniversityXi'anChina
| | - Yaoxin Guo
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaNorthwest UniversityXi'anChina
- School of Life SciencesNorthwest UniversityXi'anChina
| | - Mao Wang
- College of Grassland and Environment SciencesXinjiang Agricultural UniversityUrumchiChina
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaNorthwest UniversityXi'anChina
- School of Life SciencesNorthwest UniversityXi'anChina
| | - Mingjie Wang
- Shuanglong State‐owned Ecological Experimental Forest Station of Qiaoshan State‐owned Forestry Administration of Yan'an CityYan'anChina
| | - Jiangang Zhu
- Shuanglong State‐owned Ecological Experimental Forest Station of Qiaoshan State‐owned Forestry Administration of Yan'an CityYan'anChina
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10
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Pauli B, Ajmera S, Kost C. Determinants of synergistic cell-cell interactions in bacteria. Biol Chem 2023; 404:521-534. [PMID: 36859766 DOI: 10.1515/hsz-2022-0303] [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: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
Bacteria are ubiquitous and colonize virtually every conceivable habitat on earth. To achieve this, bacteria require different metabolites and biochemical capabilities. Rather than trying to produce all of the needed materials by themselves, bacteria have evolved a range of synergistic interactions, in which they exchange different commodities with other members of their local community. While it is widely acknowledged that synergistic interactions are key to the ecology of both individual bacteria and entire microbial communities, the factors determining their establishment remain poorly understood. Here we provide a comprehensive overview over our current knowledge on the determinants of positive cell-cell interactions among bacteria. Taking a holistic approach, we review the literature on the molecular mechanisms bacteria use to transfer commodities between bacterial cells and discuss to which extent these mechanisms favour or constrain the successful establishment of synergistic cell-cell interactions. In addition, we analyse how these different processes affect the specificity among interaction partners. By drawing together evidence from different disciplines that study the focal question on different levels of organisation, this work not only summarizes the state of the art in this exciting field of research, but also identifies new avenues for future research.
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Affiliation(s)
- Benedikt Pauli
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany
| | - Shiksha Ajmera
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, Barbarastrasse 11, D-49076 Osnabrück, Germany
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11
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Song WY, Onditi KO, Li XY, Chen ZZ, He SW, Li Q, Jiang XL. Decomposing niche components reveals simultaneous effects of opposite deterministic processes structuring alpine small mammal assembly. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.999573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
IntroductionSpecies distribution in alpine areas is constrained by multiple abiotic and biotic stressors. This leads to discrepant assembly patterns between different locations and study objects as opposite niche-based processes—limiting similarity and habitat filtering—simultaneously structure communities, masking overall patterns. We aimed to address how these processes structure small mammal communities in the alpine tree line transition zone, one of the most distinct vegetation transitions between alpine and montane habitats.MethodsWe compiled a dataset of species checklist, phylogeny, and functional traits from field collection and published sources spanning 18 mountains in southwest China. We first examined hypothetical niche-based processes with frequently used phylogenetic and trait approaches using this dataset. The species traits were decomposed into different niche components to explore the respective effects of specific stressors. Indices representing evolutionary history, trait space, and pairwise species distance were estimated and compared with null model expectations. Linear mixed-effect models were used to assess the association patterns between diversity indices and elevation.ResultsThe results indicated that phylogenetic and functional richness were positively correlated with species richness. In contrast, distance-based indices were either negatively or weakly positively correlated with species richness. Null model analyses suggested no evidence of non-random phylogenetic or overall trait patterns. However, the resource acquisition niche tended to be more overdispersed (positive slopes), while the habitat affinity niche tended to be more clustered (negative slopes) beyond the high elevation tree line.DiscussionThese findings show that opposite niche-based processes simultaneously structure small mammal communities in alpine areas. Overall, the present study provides vital insights into the complexity of assembly processes in these habitats. It also highlights the importance of relating relevant traits to distinguish the influences of specific abiotic and biotic stressors.
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12
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Wang J, Xu B, Zhang C, Ji Y, Xue Y, Ren Y, Chen Y. Effect of sampling design on estimation of phylogenetic diversity metrics of fish community. Oecologia 2023; 201:129-141. [PMID: 36454330 DOI: 10.1007/s00442-022-05291-9] [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: 12/28/2021] [Accepted: 11/12/2022] [Indexed: 12/03/2022]
Abstract
Phylogenetic diversity has been widely used to explore diversity patterns and assess processes governing the species composition in community. The estimates of many metrics depend on high-quality data collected from well-designed sampling surveys. However, knowledge of impacts of sampling design on estimation of phylogenetic diversity metrics remains unclear. This study is aim to evaluate the influence of sampling design on phylogenetic diversity metrics estimation of fish community. Simple random sampling (SRS), systematic sampling (SS) and stratified random sampling (StRS) with different sampling intensities were chosen and mean pairwise distances (MPD), mean nearest taxon distance (MNTD), phylogenetic diversity (PD), phylogenetic species variability (PSV), phylogenetic species evenness (PSE) and phylogenetic species richness (PSR) were selected. SRS and StRS showed similar impact on phylogenetic diversity indices estimation and performed relatively well for collecting data to estimate phylogenetic diversity. The accuracy and precision of the estimation increased with sampling intensity under SRS and StRS except SS. MNTD was the only metric not underestimated in four seasons. Metrics strongly influenced by species richness were underestimated when sampling intensity was insufficient. MPD, PSV and PSE showed an obvious seasonal change, which was due to the seasonal differences in fish species composition. In cases where under-sampling is suspected or logistically unavoidable, phylogenetic diversity metrics that are relatively insensitive to sampling design (e.g., MPD and PSV) should be prioritized, especially for exploring the temporal variation in fish community. This study reveals it is indispensable to evaluate sampling design when estimating phylogenetic diversity metrics, especially those indices susceptible to species richness.
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Affiliation(s)
- Jiao Wang
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Binduo Xu
- College of Fisheries, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China.
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China.
| | - Chongliang Zhang
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Yupeng Ji
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Ying Xue
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Yiping Ren
- College of Fisheries, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266037, China
- Field Observation and Research Station of Haizhou Bay Fishery Ecosystem, Ministry of Education, Qingdao, 266003, China
| | - Yong Chen
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
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13
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Liu M, Xu L, Mu R, Zhang G, Yu R, Li L. Plant community assembly of alpine meadow at different altitudes in Northeast
Qinghai‐Tibet
Plateau. Ecosphere 2023. [DOI: 10.1002/ecs2.4354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Minxia Liu
- College of Geography and Environmental Science Northwest Normal University Lanzhou China
| | - Lu Xu
- College of Geography and Environmental Science Northwest Normal University Lanzhou China
| | - Ruolan Mu
- College of Geography and Environmental Science Northwest Normal University Lanzhou China
| | - Guojuan Zhang
- College of Geography and Environmental Science Northwest Normal University Lanzhou China
| | - Ruixin Yu
- College of Geography and Environmental Science Northwest Normal University Lanzhou China
| | - Liang Li
- College of Geography and Environmental Science Northwest Normal University Lanzhou China
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Silva KRDA, Gomes LG, Ferreira VL, Strüssmann C, Moreira LFB. Seasonal changes in taxonomic and functional diversity of lizard communities in southern Brazilian Pantanal. AN ACAD BRAS CIENC 2022; 94:e20201793. [PMID: 36477224 DOI: 10.1590/0001-3765202220201793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/17/2022] [Indexed: 11/29/2022] Open
Abstract
Seasonal changes play a key ecological role, structuring biotic processes and communities. Yet we generally lack an understanding of how seasonal flood regimes affect communities in floodplains. Herein, we investigated the effects of seasonal changes in taxonomic and functional diversity of lizard communities in southern Pantanal ecoregion. Lizards were sampled in seven sites encompassing seasonally flooded grasslands and dense arboreal savannas, across rainy and dry seasons (2005-2006). Functional diversity metrics were based on three morphological traits and included intraspecific variability. We collected a total of 810 lizards from 13 species. Species richness did not differ across seasons or months. Lizard abundance varied among sampling months, but did not differ between rainy and dry season. Low values of abundance were recorded at drawdown period. Community composition did not vary between seasons. Functional diversity metrics exhibited random distributions, and both functional richness and evenness were not influenced by seasons. Although communities seem to be resilient to seasonal variations, our findings highlighted that transition from rainy to dry season may represent an important constraint on lizard abundance. Including traits related to food acquisition and predator avoidance could provide new insights into the effects of seasonal floods on floodplains' lizard communities.
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Affiliation(s)
- Karoline R DA Silva
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal de Mato Grosso/UFMT, Instituto de Biociências, Av. Fernando Corrêa da Costa, 2367, 78060-900 Cuiabá, MT, Brazil
| | - Liara G Gomes
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal de Mato Grosso/UFMT, Instituto de Biociências, Av. Fernando Corrêa da Costa, 2367, 78060-900 Cuiabá, MT, Brazil
| | - Vanda L Ferreira
- Universidade Federal de Mato Grosso do Sul/UFMS, Instituto de Biociências, Av. Costa e Silva, s/n, 79070-900 Campo Grande, MS, Brazil
| | - Christine Strüssmann
- Universidade Federal de Mato Grosso/UFMT, Faculdade de Medicina Veterinária, Av. Fernando Corrêa da Costa, 2367, 78060-900 Cuiabá, MT, Brazil
| | - Leonardo F B Moreira
- Instituto Nacional de Pesquisa do Pantanal/INPP, Museu Paraense Emílio Goeldi, Av. Fernando Corrêa da Costa, 2367, 78060-900 Cuiabá, MS, Brazil
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Beck JJ, Li D, Johnson SE, Rogers D, Cameron KM, Sytsma KJ, Givnish TJ, Waller DM. Functional traits mediate individualistic species-environment distributions at broad spatial scales while fine-scale species associations remain unpredictable. AMERICAN JOURNAL OF BOTANY 2022; 109:1991-2005. [PMID: 36254552 PMCID: PMC10099973 DOI: 10.1002/ajb2.16085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 09/24/2022] [Accepted: 09/27/2022] [Indexed: 05/08/2023]
Abstract
PREMISE Numerous processes influence plant distributions and co-occurrence patterns, including ecological sorting, limiting similarity, and stochastic effects. To discriminate among these processes and determine the spatial scales at which they operate, we investigated how functional traits and phylogenetic relatedness influence the distribution of temperate forest herbs. METHODS We surveyed understory plant communities across 257 forest stands in Wisconsin and Michigan (USA) and applied Bayesian phylogenetic linear mixed-effects models (PGLMMs) to quantify how functional traits and phylogenetic relatedness influence the environmental distribution of 139 herbaceous plant species along broad edaphic, climatic, and light gradients. These models also allowed us to test how functional and phylogenetic similarity affect species co-occurrence within microsites. RESULTS Leaf height, specific leaf area, and seed mass all influenced individualistic plant distributions along landscape-scale gradients in soil texture, soil fertility, light availability, and climate. In contrast, phylogenetic relationships did not consistently predict species-environment relationships. Neither functionally similar nor phylogenetically related herbs segregated among microsites within forest stands. CONCLUSIONS Trait-mediated ecological sorting appears to drive temperate-forest community assembly, generating individualistic plant distributions along regional environmental gradients. This finding links classic studies in plant ecology and prior research in plant physiological ecology to current trait-based approaches in community ecology. However, our results fail to support the common assumption that limiting similarity governs local plant co-occurrences. Strong ecological sorting among forest stands coupled with stochastic fine-scale interactions among species appear to weaken deterministic, niche-based assembly processes at local scales.
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Affiliation(s)
- Jared J. Beck
- Negaunee Institute for Plant Conservation ScienceChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Daijiang Li
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana70808USA
- Center for Computation & TechnologyLouisiana State UniversityBaton RougeLouisiana70808USA
| | | | - David Rogers
- Department of Biological SciencesUniversity of Wisconsin‐ParksideKenoshaWisconsin53144USA
| | - Kenneth M. Cameron
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Kenneth J. Sytsma
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Thomas J. Givnish
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
| | - Donald M. Waller
- Department of BotanyUniversity of Wisconsin‐Madison430 Lincoln DriveMadisonWisconsin53706USA
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16
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Xu M, Li S, Dick JTA, Gu D, Fang M, Yang Y, Hu Y, Mu X. Exotic fishes that are phylogenetically close but functionally distant to native fishes are more likely to establish. GLOBAL CHANGE BIOLOGY 2022; 28:5683-5694. [PMID: 35904066 PMCID: PMC9543100 DOI: 10.1111/gcb.16360] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/04/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Since Darwin's time, degree of ecological similarity between exotic and native species has been assumed to affect the establishment success or failure of exotic species. However, a direct test of the effect of exotic-native similarity on establishment of exotics is scarce because of the difficulty in recognizing failures of species to establish in the field. Here, using a database on the establishment success and failure of exotic fish species introduced into 673 freshwater lakes, we evaluate the effect of similarity on the establishment of exotic fishes by combining phylogenetic and functional information. We illustrate that, relative to other biotic and abiotic factors, exotic-native phylogenetic and functional similarities were the most important correlates of exotic fish establishment. While phylogenetic similarity between exotic and resident fish species promoted successful establishment, functional similarity led to failure of exotics to become established. Those exotic species phylogenetically close to, but functionally distant from, native fishes were most likely to establish successfully. Our findings provide a perspective to reconcile Darwin's naturalization conundrum and suggest that, while phylogenetic relatedness allows exotic fish species to pre-adapt better to novel environments, they need to possess distinct functional traits to reduce competition with resident native fish species.
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Affiliation(s)
- Meng Xu
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien SpeciesMinistry of Agriculture and Rural AffairsGuangzhouChina
- Key Laboratory of Alien Species and Ecological Security (CAFS)Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangzhouChina
| | - Shao‐peng Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Jaimie T. A. Dick
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Dangen Gu
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien SpeciesMinistry of Agriculture and Rural AffairsGuangzhouChina
- Key Laboratory of Alien Species and Ecological Security (CAFS)Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangzhouChina
| | - Miao Fang
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien SpeciesMinistry of Agriculture and Rural AffairsGuangzhouChina
- Key Laboratory of Alien Species and Ecological Security (CAFS)Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangzhouChina
| | - Yexin Yang
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien SpeciesMinistry of Agriculture and Rural AffairsGuangzhouChina
- Key Laboratory of Alien Species and Ecological Security (CAFS)Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangzhouChina
| | - Yinchang Hu
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien SpeciesMinistry of Agriculture and Rural AffairsGuangzhouChina
- Key Laboratory of Alien Species and Ecological Security (CAFS)Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangzhouChina
| | - Xidong Mu
- Pearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouChina
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien SpeciesMinistry of Agriculture and Rural AffairsGuangzhouChina
- Key Laboratory of Alien Species and Ecological Security (CAFS)Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangzhouChina
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17
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Staples TL, Mayfield MM, England JR, Dwyer JM. Drivers of Acacia and Eucalyptus growth rate differ in strength and direction in restoration plantings across Australia. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2636. [PMID: 35404495 PMCID: PMC9539508 DOI: 10.1002/eap.2636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/24/2022] [Accepted: 02/18/2022] [Indexed: 05/31/2023]
Abstract
Functional traits are proxies for a species' ecology and physiology and are often correlated with plant vital rates. As such they have the potential to guide species selection for restoration projects. However, predictive trait-based models often only explain a small proportion of plant performance, suggesting that commonly measured traits do not capture all important ecological differences between species. Some residual variation in vital rates may be evolutionarily conserved and captured using taxonomic groupings alongside common functional traits. We tested this hypothesis using growth rate data for 17,299 trees and shrubs from 80 species of Eucalyptus and 43 species of Acacia, two hyper-diverse and co-occurring genera, collected from 497 neighborhood plots in 137 Australian mixed-species revegetation plantings. We modeled relative growth rates of individual plants as a function of environmental conditions, species-mean functional traits, and neighbor density and diversity, across a moisture availability gradient. We then assessed whether the strength and direction of these relationships differed between the two genera. We found that the inclusion of genus-specific relationships offered a significant but modest improvement to model fit (1.6%-1.7% greater R2 than simpler models). More importantly, almost all correlates of growth rate differed between Eucalyptus and Acacia in strength, direction, or how they changed along the moisture gradient. These differences mapped onto physiological differences between the genera that were not captured solely by measured functional traits. Our findings suggest taxonomic groupings can capture or mediate variation in plant performance missed by common functional traits. The inclusion of taxonomy can provide a more nuanced understanding of how functional traits interact with abiotic and biotic conditions to drive plant performance, which may be important for constructing trait-based frameworks to improve restoration outcomes.
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Affiliation(s)
- Timothy L. Staples
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
- CSIRO Land and Water, EcoSciences PrecinctDutton ParkQueenslandAustralia
| | - Margaret M. Mayfield
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - John M. Dwyer
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
- CSIRO Land and Water, EcoSciences PrecinctDutton ParkQueenslandAustralia
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18
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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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Liu H, Ye Q, Simpson KJ, Cui E, Xia J. Can evolutionary history predict plant plastic responses to climate change? THE NEW PHYTOLOGIST 2022; 235:1260-1271. [PMID: 35488493 DOI: 10.1111/nph.18194] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Plant plastic responses are critical to the adaptation and survival of species under climate change, but whether they are constrained by evolutionary history (phylogeny) is largely unclear. Plant leaf traits are key in determining plants' performance in different environments, and if these traits and their variation are phylogenetically dependent, predictions could be made to identify species vulnerable to climate change. We compiled data on three leaf traits (photosynthetic rate, specific leaf area, and leaf nitrogen content) and their variation under four environmental change scenarios (warming, drought, elevated CO2 , or nitrogen addition) for 434 species, from 210 manipulation experiments. We found phylogenetic signal in the three traits but not in their variation under the four scenarios. This indicates that closely related species show similar traits but that their plastic responses could not be predicted from species relatedness under environmental change. Meanwhile, phylogeny weakened the slopes but did not change the directions of conventional pairwise trait relationships, suggesting that co-evolved leaf trait pairs have consistent responses under contrasting environmental conditions. Phylogeny can identify lineages rich in species showing similar traits and predict their relationships under climate change, but the degree of plant phenotypic variation does not vary consistently across evolutionary clades.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou, 510650, China
| | - Qing Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Guangzhou, 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou, 341000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), no. 1119, Haibin Road, Nansha District, Guangzhou, 511458, China
| | - Kimberley J Simpson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Erqian Cui
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Research Center for Global Change and Ecological Forecasting, East China Normal University, Shanghai, 200241, China
| | - Jianyang Xia
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Research Center for Global Change and Ecological Forecasting, East China Normal University, Shanghai, 200241, China
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20
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Changes in plant biodiversity facets of rocky outcrops and their surrounding rangelands across precipitation and soil gradients. Sci Rep 2022; 12:9022. [PMID: 35637253 PMCID: PMC9151709 DOI: 10.1038/s41598-022-13123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Climate and soil factors induce substantial controls over plant biodiversity in stressful ecosystems. Despite of some studies on plant biodiversity in extreme ecosystems including rocky outcrops, simultaneous effects of climate and soil factors have rarely been studied on different facets of biodiversity including taxonomic and functional diversity in these ecosystems. In addition, we know little about plant biodiversity variations in such extreme ecosystems compared to natural environments. It seems that environmental factors acting in different spatial scales specifically influence some facets of plant biodiversity. Therefore, we studied changes in taxonomic and functional diversity along precipitation and soil gradients in both landscapes (i) rocky outcrops and (ii) their nearby rangeland sites in northeast of Iran. In this regard, we considered six sites across precipitation and soil gradients in each landscape, and established 90 1m2 quadrates in them (i.e. 15 quadrats in each site; 15 × 6 = 90 in each landscape). Then, taxonomic and functional diversity were measured using RaoQ index, FDis and CWM indices. Finally, we assessed impacts of precipitation and soil factors on biodiversity indices in both landscapes by performing regression models and variation partitioning procedure. The patterns of taxonomic diversity similarly showed nonlinear changes along the precipitation and soil factors in both landscapes (i.e. outcrop and rangeland). However, we found a more negative and significant trends of variation in functional diversity indices (except for CWMSLA) across precipitation and soil factors in outcrops than their surrounding rangelands. Variations of plant biodiversity were more explained by precipitation factors in surrounding rangelands, whereas soil factors including organic carbon had more consistent and significant effects on plant biodiversity in outcrops. Therefore, our results represent important impacts of soil factors in structuring plant biodiversity facets in stressful ecosystems. While, environmental factors acting in regional and broad scales such as precipitation generally shape vegetation and plant biodiversity patterns in natural ecosystems. We can conclude that rocky outcrops provide suitable microenvironments to present plant species with similar yields that are less able to be present in rangeland ecosystems.
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21
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Anderegg LDL, Griffith DM, Cavender-Bares J, Riley WJ, Berry JA, Dawson TE, Still CJ. Representing plant diversity in land models: An evolutionary approach to make "Functional Types" more functional. GLOBAL CHANGE BIOLOGY 2022; 28:2541-2554. [PMID: 34964527 DOI: 10.1111/gcb.16040] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Plants are critical mediators of terrestrial mass and energy fluxes, and their structural and functional traits have profound impacts on local and global climate, biogeochemistry, biodiversity, and hydrology. Yet, Earth System Models (ESMs), our most powerful tools for predicting the effects of humans on the coupled biosphere-atmosphere system, simplify the incredible diversity of land plants into a handful of coarse categories of "Plant Functional Types" (PFTs) that often fail to capture ecological dynamics such as biome distributions. The inclusion of more realistic functional diversity is a recognized goal for ESMs, yet there is currently no consistent, widely accepted way to add diversity to models, that is, to determine what new PFTs to add and with what data to constrain their parameters. We review approaches to representing plant diversity in ESMs and draw on recent ecological and evolutionary findings to present an evolution-based functional type approach for further disaggregating functional diversity. Specifically, the prevalence of niche conservatism, or the tendency of closely related taxa to retain similar ecological and functional attributes through evolutionary time, reveals that evolutionary relatedness is a powerful framework for summarizing functional similarities and differences among plant types. We advocate that Plant Functional Types based on dominant evolutionary lineages ("Lineage Functional Types") will provide an ecologically defensible, tractable, and scalable framework for representing plant diversity in next-generation ESMs, with the potential to improve parameterization, process representation, and model benchmarking. We highlight how the importance of evolutionary history for plant function can unify the work of disparate fields to improve predictive modeling of the Earth system.
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Affiliation(s)
- Leander D L Anderegg
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
| | - Daniel M Griffith
- US Geological Survey Western Geographic Science Center, Moffett Field, California, USA
- NASA Ames Research Center, Moffett Field, California, USA
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, Oregon, USA
| | - Jeannine Cavender-Bares
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - William J Riley
- Climate & Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Joseph A Berry
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
| | - Todd E Dawson
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Christopher J Still
- Department of Forest Ecosystems & Society, Oregon State University, Corvallis, Oregon, USA
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22
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Tree functional traits, forest biomass, and tree species diversity interact with site properties to drive forest soil carbon. Nat Commun 2022; 13:1097. [PMID: 35233020 PMCID: PMC8888738 DOI: 10.1038/s41467-022-28748-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 02/02/2022] [Indexed: 01/04/2023] Open
Abstract
Forests constitute important ecosystems in the global carbon cycle. However, how trees and environmental conditions interact to determine the amount of organic carbon stored in forest soils is a hotly debated subject. In particular, how tree species influence soil organic carbon (SOC) remains unclear. Based on a global compilation of data, we show that functional traits of trees and forest standing biomass explain half of the local variability in forest SOC. The effects of functional traits on SOC depended on the climatic and soil conditions with the strongest effect observed under boreal climate and on acidic, poor, coarse-textured soils. Mixing tree species in forests also favours the storage of SOC, provided that a biomass over-yielding occurs in mixed forests. We propose that the forest carbon sink can be optimised by (i) increasing standing biomass, (ii) increasing forest species richness, and (iii) choosing forest composition based on tree functional traits according to the local conditions. Forests constitute important ecosystems in the global carbon cycle. This study investigates how tree species influence soil organic carbon using a global dataset, showing the importance of tree functional traits and forest standing biomass to optimise forest carbon sink.
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23
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Jiang L, Hu D, Wang H, Lv G. Discriminating ecological processes affecting different dimensions of α- and β-diversity in desert plant communities. Ecol Evol 2022; 12:e8710. [PMID: 35342610 PMCID: PMC8933320 DOI: 10.1002/ece3.8710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 02/11/2022] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
Understanding the spatial distribution of plant diversity and its drivers are major challenges in biogeography and conservation biology. Integrating multiple facets of biodiversity (e.g., taxonomic, phylogenetic, and functional biodiversity) may advance our understanding on how community assembly processes drive the distribution of biodiversity. In this study, plant communities in 60 sampling plots in desert ecosystems were investigated. The effects of local environment and spatial factors on the species, functional, and phylogenetic α- and β-diversity (including turnover and nestedness components) of desert plant communities were investigated. The results showed that functional and phylogenetic α-diversity were negatively correlated with species richness, and were significantly positively correlated with each other. Environmental filtering mainly influenced species richness and Rao quadratic entropy; phylogenetic α-diversity was mainly influenced by dispersal limitation. Species and phylogenetic β-diversity were mainly consisted of turnover component. The functional β-diversity and its turnover component were mainly influenced by environmental factors, while dispersal limitation dominantly effected species and phylogenetic β-diversity and their turnover component of species and phylogenetic β-diversity. Soil organic carbon and soil pH significantly influenced different dimensions of α-diversity, and soil moisture, salinity, organic carbon, and total nitrogen significantly influenced different dimensions of α- and β-diversity and their components. Overall, it appeared that the relative influence of environmental and spatial factors on taxonomic, functional, and phylogenetic diversity differed at the α and β scales. Quantifying α- and β-diversity at different biodiversity dimensions can help researchers to more accurately assess patterns of diversity and community assembly.
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Affiliation(s)
- Lamei Jiang
- College of Resources and Environmental ScienceXinjiang UniversityUrumqiChina
| | - Dong Hu
- College of Resources and Environmental ScienceXinjiang UniversityUrumqiChina
| | - Hengfang Wang
- College of Resources and Environmental ScienceXinjiang UniversityUrumqiChina
| | - Guanghui Lv
- College of Resources and Environmental ScienceXinjiang UniversityUrumqiChina
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Arnillas CA, Borer ET, Seabloom EW, Alberti J, Baez S, Bakker JD, Boughton EH, Buckley YM, Bugalho MN, Donohue I, Dwyer J, Firn J, Gridzak R, Hagenah N, Hautier Y, Helm A, Jentsch A, Knops JMH, Komatsu KJ, Laanisto L, Laungani R, McCulley R, Moore JL, Morgan JW, Peri PL, Power SA, Price J, Sankaran M, Schamp B, Speziale K, Standish R, Virtanen R, Cadotte MW. Opposing community assembly patterns for dominant and nondominant plant species in herbaceous ecosystems globally. Ecol Evol 2021; 11:17744-17761. [PMID: 35003636 PMCID: PMC8717298 DOI: 10.1002/ece3.8266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/14/2021] [Accepted: 09/18/2021] [Indexed: 11/30/2022] Open
Abstract
Biotic and abiotic factors interact with dominant plants-the locally most frequent or with the largest coverage-and nondominant plants differently, partially because dominant plants modify the environment where nondominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing nondominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually limit nondominants. Hence, the nature of interactions among nondominant species could be modified by dominant species. Furthermore, these differences could translate into a disparity in the phylogenetic relatedness among dominants compared to the relatedness among nondominants. By estimating phylogenetic dispersion in 78 grasslands across five continents, we found that dominant species were clustered (e.g., co-dominant grasses), suggesting dominant species are likely organized by environmental filtering, and that nondominant species were either randomly assembled or overdispersed. Traits showed similar trends for those sites (<50%) with sufficient trait data. Furthermore, several lineages scattered in the phylogeny had more nondominant species than expected at random, suggesting that traits common in nondominants are phylogenetically conserved and have evolved multiple times. We also explored environmental drivers of the dominant/nondominant disparity. We found different assembly patterns for dominants and nondominants, consistent with asymmetries in assembly mechanisms. Among the different postulated mechanisms, our results suggest two complementary hypotheses seldom explored: (1) Nondominant species include lineages adapted to thrive in the environment generated by dominant species. (2) Even when dominant species reduce resources to nondominant ones, dominant species could have a stronger positive effect on some nondominants by ameliorating environmental stressors affecting them, than by depleting resources and increasing the environmental stress to those nondominants. These results show that the dominant/nondominant asymmetry has ecological and evolutionary consequences fundamental to understand plant communities.
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Affiliation(s)
- Carlos Alberto Arnillas
- Department of Physical and Environmental SciencesUniversity of Toronto ScarboroughTorontoONCanada
| | | | | | - Juan Alberti
- Instituto de Investigaciones Marinas y Costeras (IIMyC, UNMdP, CONICET)Mar del PlataArgentina
| | - Selene Baez
- Department of BiologyEscuela Politécnica NacionalQuitoEcuador
| | - Jonathan D. Bakker
- School of Environmental and Forest SciencesUniversity of WashingtonSeattleWashingtonUSA
| | | | - Yvonne M. Buckley
- School of Natural Sciences, ZoologyTrinity College DublinDublinIreland
| | - Miguel Nuno Bugalho
- Centre for Applied Ecology Prof. Baeta Neves (CEABN‐InBIO)School of AgricultureUniversity of LisbonLisbonPortugal
| | - Ian Donohue
- School of Natural Sciences, ZoologyTrinity College DublinDublinIreland
| | - John Dwyer
- University of Queensland, School of Biological SciencesST‐LuciaQldAustralia
| | - Jennifer Firn
- Queensland University of Technology (QUT) BrisbaneQldAustralia
| | | | - Nicole Hagenah
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Yann Hautier
- Ecology and Biodiversity GroupDepartment of BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Aveliina Helm
- Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Anke Jentsch
- Department of Disturbance EcologyBayCEERUniversity of BayreuthBayreuthGermany
| | - Johannes M. H. Knops
- Department of Health and Environmental SciencesXi'an Jiaotong Liverpool UniversitySuzhouChina
- School of Biological SciencesUniversity of NebraskaLincolnNebraskaUSA
| | | | - Lauri Laanisto
- Department of Agricutural and Environmental SciencesEstonian University of Life SciencesTartuEstonia
| | | | - Rebecca McCulley
- Department of Plant and Soil SciencesUniversity of KentuckyLexingtonKentuckyUSA
| | - Joslin L. Moore
- School of Biological SciencesMonash UniversityClaytonVicAustralia
| | | | | | - Sally A. Power
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithAustralia
| | - Jodi Price
- Institute for Land, Water and SocietyCharles Sturt UniversityAlburyNSWAustralia
| | - Mahesh Sankaran
- National Centre for Biological SciencesTIFRBengaluruIndia
- School of BiologyUniversity of LeedsLeedsUK
| | | | - Karina Speziale
- Grupo de Investigaciones en Biología de la Conservación, Laboratorio EcotonoINIBIOMA (CONICET‐UNCOMA)San Carlos de BarilocheRío NegroArgentina
| | - Rachel Standish
- Environmental and Conservation Sciences, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | | | - Marc W. Cadotte
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoONCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
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25
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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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26
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Qiao X, Zhang N, Zhang C, Zhang Z, Zhao X, Gadow K. Unravelling biodiversity–productivity relationships across a large temperate forest region. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13922] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xuetao Qiao
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration Beijing Forestry University Beijing China
| | - Naili Zhang
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration Beijing Forestry University Beijing China
| | - Chunyu Zhang
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration Beijing Forestry University Beijing China
| | - Zhonghui Zhang
- Jilin Provincial Academy of Forestry Sciences Changchun China
| | - Xiuhai Zhao
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration Beijing Forestry University Beijing China
| | - Klaus Gadow
- Faculty of Forestry and Forest Ecology Georg‐August‐University Göttingen Göttingen Germany
- Department of Forest and Wood Science University of Stellenbosch Stellenbosch South Africa
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27
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Williams EW, Zeldin J, Semski WR, Hipp AL, Larkin DJ. Phylogenetic distance and resource availability mediate direction and strength of plant interactions in a competition experiment. Oecologia 2021; 197:459-469. [PMID: 34476548 DOI: 10.1007/s00442-021-05024-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 08/22/2021] [Indexed: 11/30/2022]
Abstract
Phylogenetic ecology uses evolutionary history to improve understanding of plant interactions. Phylogenetic distance can mediate plant interactions such as competition (e.g., via limiting similarity) and facilitation (e.g., via niche complementarity), influencing community assembly patterns. Previous research has found evidence both for and against a relationship between phylogenetic distance and the strength of plant interactions, and has found that other factors, such as trait differences, may be more influential. In addition to phylogenetic distance and species' traits, environmental conditions can also influence competition, with facilitative interactions-particularly among distantly related species-potentially becoming more pronounced under stressful, resource-limited conditions. We tested the prediction that greater phylogenetic distance is associated with decreased competition in a greenhouse experiment using plant species of the North American tallgrass prairie. We calculated the Relative Interaction Index for 81 species pairs using plant height, leaf length, and biomass as indicators of performance. We found that phylogenetic distance alone did not significantly affect competition. However, the interaction between phylogenetic distance and stressful conditions (sandier soils with low nutrient availability and water retention vs. resource-rich potting soil) altered plant traits and competition. Under stressful conditions, more distantly related species competed more strongly, leading to smaller plants. Conversely, under benign conditions more distantly related species pairs competed less and were larger. These results were contrary to our expectations that distant relatives would compete less under stressful conditions. Our experiment provides evidence that, while relatedness alone may not drive competition, phylogenetic distance can nonetheless be influential through interactions with environmental conditions.
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Affiliation(s)
- Evelyn W Williams
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, IL, USA. .,Adaptive Restoration LLC., 8864 Offerdahl Road, Mount Horeb, WI, 53572, USA.
| | - Jacob Zeldin
- Plant Science and Conservation, Chicago Botanic Garden, Glencoe, IL, USA
| | - Wendy R Semski
- Department of Biological Sciences, University of WI-Milwaukee, Milwaukee, WI, USA
| | - Andrew L Hipp
- Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | - Daniel J Larkin
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, Saint Paul, MN, USA
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28
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Lee RH, Morgan B, Liu C, Fellowes JR, Guénard B. Secondary forest succession buffers extreme temperature impacts on subtropical Asian ants. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Roger Ho Lee
- School of Biological Sciences The University of Hong Kong Pokfulam Hong Kong
| | - Brett Morgan
- School of Biological Sciences The University of Hong Kong Pokfulam Hong Kong
| | - Cong Liu
- Department of Organismic and Evolutional Biology, Museum of Comparative Zoology Harvard University 26 Oxford Street Cambridge Massachusetts 02138 USA
| | | | - Benoit Guénard
- School of Biological Sciences The University of Hong Kong Pokfulam Hong Kong
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29
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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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30
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Wiegand T, Wang X, Anderson-Teixeira KJ, Bourg NA, Cao M, Ci X, Davies SJ, Hao Z, Howe RW, Kress WJ, Lian J, Li J, Lin L, Lin Y, Ma K, McShea W, Mi X, Su SH, Sun IF, Wolf A, Ye W, Huth A. Consequences of spatial patterns for coexistence in species-rich plant communities. Nat Ecol Evol 2021; 5:965-973. [PMID: 33941904 PMCID: PMC8257505 DOI: 10.1038/s41559-021-01440-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023]
Abstract
Ecology cannot yet fully explain why so many tree species coexist in natural communities such as tropical forests. A major difficulty is linking individual-level processes to community dynamics. We propose a combination of tree spatial data, spatial statistics and dynamical theory to reveal the relationship between spatial patterns and population-level interaction coefficients and their consequences for multispecies dynamics and coexistence. Here we show that the emerging population-level interaction coefficients have, for a broad range of circumstances, a simpler structure than their individual-level counterparts, which allows for an analytical treatment of equilibrium and stability conditions. Mechanisms such as animal seed dispersal, which result in clustering of recruits that is decoupled from parent locations, lead to a rare-species advantage and coexistence of otherwise neutral competitors. Linking spatial statistics with theories of community dynamics offers new avenues for explaining species coexistence and calls for rethinking community ecology through a spatial lens.
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Affiliation(s)
- Thorsten Wiegand
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Xugao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, .
| | - Kristina J Anderson-Teixeira
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Forest Global Earth Observatory (ForestGEO), Smithsonian Tropical Research Institute, Washington, DC, USA
| | - Norman A Bourg
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Min Cao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
| | - Xiuqin Ci
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
| | - Stuart J Davies
- Forest Global Earth Observatory (ForestGEO), Smithsonian Tropical Research Institute, Washington, DC, USA
| | - Zhanqing Hao
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences
- School of Ecology and Environment, Northwestern Polytechnical University
| | - Robert W Howe
- Department of Natural and Applied Sciences, University of Wisconsin-Green Bay, Green Bay, WI, USA
| | - W John Kress
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Juyu Lian
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences
| | - Jie Li
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
| | - Luxiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences
| | - Yiching Lin
- Department of Life Science, Tunghai University
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences
| | - William McShea
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences
| | | | - I-Fang Sun
- Center for Interdisciplinary Research on Ecology and Sustainability, National Dong Hwa University
| | - Amy Wolf
- Department of Natural and Applied Sciences, University of Wisconsin-Green Bay, Green Bay, WI, USA
| | - Wanhui Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences
| | - Andreas Huth
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Environmental Systems Research, University of Osnabrück, Osnabrück, Germany
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31
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Skeels A, Dinnage R, Medina I, Cardillo M. Ecological interactions shape the evolution of flower color in communities across a temperate biodiversity hotspot. Evol Lett 2021; 5:277-289. [PMID: 34136275 PMCID: PMC8190448 DOI: 10.1002/evl3.225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/17/2021] [Accepted: 03/09/2021] [Indexed: 01/11/2023] Open
Abstract
Processes driving the divergence of floral traits may be integral to the extraordinary richness of flowering plants and the assembly of diverse plant communities. Several models of pollinator-mediated floral evolution have been proposed; floral divergence may (i) be directly involved in driving speciation or may occur after speciation driven by (ii) drift or local adaptation in allopatry or (iii) negative interactions between species in sympatry. Here, we generate predictions for patterns of trait divergence and community assembly expected under these three models, and test these predictions in Hakea (Proteaceae), a diverse genus in the Southwest Australian biodiversity hotspot. We quantified functional richness for two key floral traits (pistil length and flower color), as well as phylogenetic distances between species, across ecological communities, and compared these to patterns generated from null models of community assembly. We also estimated the statistical relationship between rates of trait evolution and lineage diversification across the phylogeny. Patterns of community assembly suggest that flower color, but not floral phenology or morphology, or phylogenetic relatedness, is more divergent in communities than expected. Rates of lineage diversification and flower color evolution were negatively correlated across the phylogeny and rates of flower colour evolution were positively related to branching times. These results support a role for diversity-dependent species interactions driving floral divergence during the Hakea radiation, contributing to the development of the extraordinary species richness of southwest Australia.
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Affiliation(s)
- Alexander Skeels
- Division of Ecology and Evolution, Research School of BiologyAustralian National UniversityCanberraACT 0200Australia
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichCH‐8092Switzerland
- Unit of Land Change Science, Swiss Federal Research Institute for ForestSnow and Landscape WSLBirmensdorfCH‐8903Switzerland
| | - Russell Dinnage
- Institute for Applied EcologyUniversity of CanberraCanberraACT 2617Australia
| | - Iliana Medina
- Division of Ecology and Evolution, Research School of BiologyAustralian National UniversityCanberraACT 0200Australia
- School of BioSciencesUniversity of MelbourneMelbourneVIC 3010Australia
| | - Marcel Cardillo
- Division of Ecology and Evolution, Research School of BiologyAustralian National UniversityCanberraACT 0200Australia
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32
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Yin D, Liu Y, Ye Q, Cadotte MW, He F. Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest. Ecol Evol 2021; 11:7366-7377. [PMID: 34188819 PMCID: PMC8216963 DOI: 10.1002/ece3.7567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 11/11/2022] Open
Abstract
The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or due to competitive exclusion of inferior competitors (hereafter hierarchical competition).We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering, and hierarchical competition on species co-occurrence.We found that trait dissimilarity was generally negatively related to interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages.This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.
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Affiliation(s)
- Deyi Yin
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical Garden, Chinese Academy of SciencesGuangzhouChina
- Center for Plant Ecology, Core Botanical GardenChinese Academy of SciencesGuangzhouChina
- Department of Biological SciencesUniversity of Toronto‐ScarboroughTorontoOntarioCanada
| | - Yu Liu
- ECNU‐Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Qing Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied BotanySouth China Botanical Garden, Chinese Academy of SciencesGuangzhouChina
- Center for Plant Ecology, Core Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Marc W. Cadotte
- Department of Biological SciencesUniversity of Toronto‐ScarboroughTorontoOntarioCanada
- Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Fangliang He
- ECNU‐Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental SciencesEast China Normal UniversityShanghaiChina
- Department of Renewable ResourcesUniversity of AlbertaEdmontonAlbertaCanada
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33
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Zhong L, Didham RK, Liu J, Jin Y, Yu M. Community re‐assembly and divergence of woody plant traits in an island–mainland system after more than 50 years of regeneration. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Lei Zhong
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Raphael K. Didham
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
- CSIRO Land and WaterCenter for Environment and Life Science Floreat Western Australia Australia
| | - Jinliang Liu
- College of Life and Environmental Science Wenzhou University Wenzhou China
- National & Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution Wenzhou University Wenzhou China
| | - Yi Jin
- State Key Laboratory of Plant Physiology and Development in Guizhou Province School of Life Sciences Guizhou Normal University Guiyang China
| | - Mingjian Yu
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
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34
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Davies TJ. Ecophylogenetics redux. Ecol Lett 2021; 24:1073-1088. [PMID: 33565697 DOI: 10.1111/ele.13682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/20/2020] [Indexed: 12/24/2022]
Abstract
Species' evolutionary histories shape their present-day ecologies, but the integration of phylogenetic approaches in ecology has had a contentious history. The field of ecophylogenetics promised to reveal the process of community assembly from simple indices of phylogenetic pairwise distances - communities shaped by environmental filtering were composed of closely related species, whereas communities shaped by competition were composed of less closely related species. However, the mapping of ecology onto phylogeny proved to be not so straightforward, and the field remains mired in controversy. Nonetheless, ecophylogenetic methods provided important advances across ecology. For example the phylogenetic distances between species is a strong predictor of pest and pathogen sharing, and can thus inform models of species invasion, coexistence and the disease dilution/amplification effect of biodiversity. The phylogenetic structure of communities may also provide information on niche space occupancy, helping interpret patterns of facilitation, succession and ecosystem functioning - with relevance for conservation and restoration - and the dynamics among species within foodwebs and metacommunities. I suggest leveraging advances in our understanding of the process of evolution on phylogenetic trees would allow the field to progress further, while maintaining the essence of the original vision that proved so seductive.
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Affiliation(s)
- T Jonathan Davies
- Departments of Botany, Forest & Conservation Sciences, Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada.,African Centre for DNA Barcoding, University of Johannesburg, Johannesburg, 2092, South Africa
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Moroti MDT, Soares PT, Pedrozo M, Provete DB, Santana DJ. The effects of morphology, phylogeny and prey availability on trophic resource partitioning in an anuran community. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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36
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Oliveira AGD, Peláez O, Agostinho AA. The effectiveness of protected areas in the Paraná-Paraguay basin in preserving multiple facets of freshwater fish diversity under climate change. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2021-0034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Our objective was to evaluate the effectiveness of protected areas (PAs) in the Paraná-Paraguay basin on multiple facets of ichthyofauna, both currently and in future climate change scenarios, based on reaching the 17% of conserved terrestrial and inland water defined by Aichi Target 11. Analyses were carried out vis-à-vis a distribution of 496 native species, modeling for the present and for the future, and in moderate and pessimistic scenarios of greenhouse gases. We calculated species richness, functional richness, and phylogenetic diversity, overlapping the combination of these facets with the PAs. The results indicate that the current PAs of the Paraná-Paraguay basin are not efficient in protecting the richest areas of ichthyofauna in their multiple facets. While there is a larger overlap between PAs and the richest areas in phylogenetic diversity, the values are too low (2.37%). Currently, the overlap between PAs and areas with larger species richness, functional richness, and phylogenetic diversity is only 1.48%. Although this value can increase for future projections, the values of the indices decrease substantially. The relevant aquatic environments, biological communities, and climate change should be considered as part of the systematic planning of PAs that take into consideration the terrestrial environments and their threats.
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37
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Phylogenetic structure of alpine steppe plant communities along a precipitation and temperature gradient on the Tibetan Plateau. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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A test of the lateral semicircular canal correlation to head posture, diet and other biological traits in "ungulate" mammals. Sci Rep 2020; 10:19602. [PMID: 33177568 PMCID: PMC7658238 DOI: 10.1038/s41598-020-76757-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/02/2020] [Indexed: 02/08/2023] Open
Abstract
For over a century, researchers have assumed that the plane of the lateral semicircular canal of the inner ear lies parallel to the horizon when the head is at rest, and used this assumption to reconstruct head posture in extinct species. Although this hypothesis has been repeatedly questioned, it has never been tested on a large sample size and at a broad taxonomic scale in mammals. This study presents a comprehensive test of this hypothesis in over one hundred "ungulate" species. Using CT scanning and manual segmentation, the orientation of the skull was reconstructed as if the lateral semicircular canal of the bony labyrinth was aligned horizontally. This reconstructed cranial orientation was statistically compared to the actual head posture of the corresponding species using a dataset of 10,000 photographs and phylogenetic regression analysis. A statistically significant correlation between the reconstructed cranial orientation and head posture is found, although the plane of the lateral semicircular canal departs significantly from horizontal. We thus caution against the use of the lateral semicircular canal as a proxy to infer precisely the horizontal plane on dry skulls and in extinct species. Diet (browsing or grazing) and head-butting behaviour are significantly correlated to the orientation of the lateral semicircular canal, but not to the actual head posture. Head posture and the orientation of the lateral semicircular canal are both strongly correlated with phylogenetic history.
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Scher CL, Karimi N, Glasenhardt M, Tuffin A, Cannon CH, Scharenbroch BC, Hipp AL. Application of remote sensing technology to estimate productivity and assess phylogenetic heritability. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11401. [PMID: 33304664 PMCID: PMC7705335 DOI: 10.1002/aps3.11401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/17/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Measuring plant productivity is critical to understanding complex community interactions. Many traditional methods for estimating productivity, such as direct measurements of biomass and cover, are resource intensive, and remote sensing techniques are emerging as viable alternatives. METHODS We explore drone-based remote sensing tools to estimate productivity in a tallgrass prairie restoration experiment and evaluate their ability to predict direct measures of productivity. We apply these various productivity measures to trace the evolution of plant productivity and the traits underlying it. RESULTS The correlation between remote sensing data and direct measurements of productivity varies depending on vegetation diversity, but the volume of vegetation estimated from drone-based photogrammetry is among the best predictors of biomass and cover regardless of community composition. The commonly used normalized difference vegetation index (NDVI) is a less accurate predictor of biomass and cover than other equally accessible vegetation indices. We found that the traits most strongly correlated with productivity have lower phylogenetic signal, reflecting the fact that high productivity is convergent across the phylogeny of prairie species. This history of trait convergence connects phylogenetic diversity to plant community assembly and succession. DISCUSSION Our study demonstrates (1) the importance of considering phylogenetic diversity when setting management goals in a threatened North American grassland ecosystem and (2) the utility of remote sensing as a complement to ground measurements of grassland productivity for both applied and fundamental questions.
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Affiliation(s)
- C. Lane Scher
- Nicholas School of the EnvironmentDuke UniversityDurhamNorth Carolina27708USA
- Center for Tree ScienceThe Morton ArboretumLisleIllinois60532USA
| | - Nisa Karimi
- Center for Tree ScienceThe Morton ArboretumLisleIllinois60532USA
| | | | - Ashley Tuffin
- Center for Tree ScienceThe Morton ArboretumLisleIllinois60532USA
- Edge Hill UniversityOrmskirkL39 4QPUnited Kingdom
| | | | - Bryant C. Scharenbroch
- Center for Tree ScienceThe Morton ArboretumLisleIllinois60532USA
- College of Natural ResourcesUniversity of Wisconsin–Stevens PointStevens PointWisconsin54481USA
| | - Andrew L. Hipp
- Center for Tree ScienceThe Morton ArboretumLisleIllinois60532USA
- The Field MuseumChicagoIllinois60605USA
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40
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Zheng Y, Huang F, Liang M, Liu X, Yu S. The effects of density dependence and habitat preference on species coexistence and relative abundance. Oecologia 2020; 194:673-684. [PMID: 33094381 DOI: 10.1007/s00442-020-04788-5] [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: 11/27/2019] [Accepted: 10/10/2020] [Indexed: 11/24/2022]
Abstract
In plant communities, some mechanisms maintain differences in species' abundances, while other mechanisms promote coexistence. Asymmetry in conspecific negative density dependence (CNDD) and/or habitat preference is hypothesized to shape relative species abundance, whereas community compensatory trends (CCTs) induced by community-level CNDD and heterospecific facilitation are hypothesized to promote coexistence. We use survey data from three 1-ha permanent dynamic plots in a subtropical forest over the course of a decade to find out which of these processes are important and at which life-history stages (the seedling, sapling, and juvenile stages) they exert their effects. CNDD was not related to abundance in any of the life-history stages. Suitable habitats positively influenced plant abundance at all tested life stages, but especially so for juveniles. Community-level CNDD of seedling neighbors was detected at the seedling stage, while heterospecific facilitation was detected across all tested life-history stages. A CCT in seedling survival was detected, but there was no evidence for such trends across the other life-history stages. Altogether, our results suggest that habitat specificity increases the rarity of species, whereas a CCT at the seedling stage, which is likely to be induced by CNDD and heterospecific facilitation, enables such species to maintain their populations.
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Affiliation(s)
- Yi Zheng
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Fengmin Huang
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Minxia Liang
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xubing Liu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shixiao Yu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China.
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41
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Ritchie AM, Hua X, Cardillo M, Yaxley KJ, Dinnage R, Bromham L. Phylogenetic diversity metrics from molecular phylogenies: modelling expected degree of error under realistic rate variation. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Andrew M. Ritchie
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Xia Hua
- Research School of Biological Sciences Australian National University Canberra ACT Australia
- Mathematical Sciences Institute Australian National University Canberra ACT Australia
| | - Marcel Cardillo
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Keaghan J. Yaxley
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Russell Dinnage
- Research School of Biological Sciences Australian National University Canberra ACT Australia
| | - Lindell Bromham
- Research School of Biological Sciences Australian National University Canberra ACT Australia
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42
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Zhang Z, Liu Y, Yuan L, Weber E, van Kleunen M. Effect of allelopathy on plant performance: a meta‐analysis. Ecol Lett 2020; 24:348-362. [DOI: 10.1111/ele.13627] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/19/2020] [Accepted: 09/27/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Zhijie Zhang
- Ecology Department of Biology University of Konstanz Konstanz78464Germany
| | - Yanjie Liu
- Key Laboratory of Wetland Ecology and Environment Northeast Institute of Geography and AgroecologyChinese Academy Sciences Changchun130102China
| | - Ling Yuan
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation Taizhou University Taizhou318000China
| | - Ewald Weber
- Department of Biodiversity Research Institute of Biochemistry and BiologyUniversity of Potsdam Potsdam14469Germany
| | - Mark van Kleunen
- Ecology Department of Biology University of Konstanz Konstanz78464Germany
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation Taizhou University Taizhou318000China
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43
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Baulechner D, Jauker F, Neubauer TA, Wolters V. Convergent evolution of specialized generalists: Implications for phylogenetic and functional diversity of carabid feeding groups. Ecol Evol 2020; 10:11100-11110. [PMID: 33144951 PMCID: PMC7593144 DOI: 10.1002/ece3.6746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 01/19/2023] Open
Abstract
Closely related species are often assumed to be functionally similar. Phylogenetic information is thus widely used to infer functional diversity and assembly of communities. In contrast, evolutionary processes generating functional similarity of phylogenetically distinct taxa are rarely addressed in this context.To investigate the impact of convergent evolution on functional diversity (FD) and phylogenetic diversity (PD), we reconstructed the phylogenetic structure of carabid trophic groups. We then analyzed the mandible shapes using geometric morphometrics to link specialization in functional morphology with feeding specialization among herbivores, generalist carnivores, and specialized consumers of Collembola.Our results show that carabid feeding groups are paraphyletic. Herbivory evolved at least twice and specialization to Collembola predation at least three times. Species within feeding groups share a remarkably similar mandible morphology, which evolved convergently. While specialized mandibles of herbivores and collembolan specialists represent an adaptation to their main food source, the particular mandible morphologies do not necessarily reflect the degree of food specialization within feeding groups. Only a few species with a specialized herbivorous mandible may occasionally feed on animals, but the range of specific food resources in generalist carnivore species is large, despite an almost identical mandible shape.Thus, convergent evolution in specialized feeding groups reverses the relationship between PD and functional similarity compared with generalist carnivores. We conclude that phylogenetic relationship is a poor proxy of FD in carabids. Moreover, the inconsistencies between relatedness, morphological adaptation, and ecological function require caution in the characterization of functional groups. Rather than assuming general relationships between PD and FD, we suggest integrating the analysis of evolutionary processes into functional community analyses.
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Affiliation(s)
- Dennis Baulechner
- Department of Animal Ecology and SystematicsJustus Liebig University GiessenGiessenGermany
| | - Frank Jauker
- Department of Animal Ecology and SystematicsJustus Liebig University GiessenGiessenGermany
| | - Thomas A. Neubauer
- Department of Animal Ecology and SystematicsJustus Liebig University GiessenGiessenGermany
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Volkmar Wolters
- Department of Animal Ecology and SystematicsJustus Liebig University GiessenGiessenGermany
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44
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Griffith DM, Osborne CP, Edwards EJ, Bachle S, Beerling DJ, Bond WJ, Gallaher TJ, Helliker BR, Lehmann CER, Leatherman L, Nippert JB, Pau S, Qiu F, Riley WJ, Smith MD, Strömberg CAE, Taylor L, Ungerer M, Still CJ. Lineage-based functional types: characterising functional diversity to enhance the representation of ecological behaviour in Land Surface Models. THE NEW PHYTOLOGIST 2020; 228:15-23. [PMID: 33448428 DOI: 10.1111/nph.16773] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/28/2020] [Indexed: 06/12/2023]
Abstract
Process-based vegetation models attempt to represent the wide range of trait variation in biomes by grouping ecologically similar species into plant functional types (PFTs). This approach has been successful in representing many aspects of plant physiology and biophysics but struggles to capture biogeographic history and ecological dynamics that determine biome boundaries and plant distributions. Grass-dominated ecosystems are broadly distributed across all vegetated continents and harbour large functional diversity, yet most Land Surface Models (LSMs) summarise grasses into two generic PFTs based primarily on differences between temperate C3 grasses and (sub)tropical C4 grasses. Incorporation of species-level trait variation is an active area of research to enhance the ecological realism of PFTs, which form the basis for vegetation processes and dynamics in LSMs. Using reported measurements, we developed grass functional trait values (physiological, structural, biochemical, anatomical, phenological, and disturbance-related) of dominant lineages to improve LSM representations. Our method is fundamentally different from previous efforts, as it uses phylogenetic relatedness to create lineage-based functional types (LFTs), situated between species-level trait data and PFT-level abstractions, thus providing a realistic representation of functional diversity and opening the door to the development of new vegetation models.
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Affiliation(s)
- Daniel M Griffith
- Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA
- US Geological Survey Western Geographic Science Center, Moffett Field, CA, 94035, USA
- NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Seton Bachle
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - William J Bond
- South African Environmental Observation Network, National Research Foundation, Claremont, 7735, South Africa
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Timothy J Gallaher
- Department of Biology and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98915, USA
- Bishop Museum, Honolulu, HI, 96817, USA
| | - Brent R Helliker
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19401, USA
| | | | - Lila Leatherman
- Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA
| | - Jesse B Nippert
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Stephanie Pau
- Department of Geography, Florida State University, Tallahassee, FL, 32303, USA
| | - Fan Qiu
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - William J Riley
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Melinda D Smith
- Department of Biology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Caroline A E Strömberg
- Department of Biology and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98915, USA
| | - Lyla Taylor
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark Ungerer
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Christopher J Still
- Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331, USA
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45
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Eagar AC, Cosgrove CR, Kershner MW, Blackwood CB. Dominant community mycorrhizal types influence local spatial structure between adult and juvenile temperate forest tree communities. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew C. Eagar
- Department of Biological Sciences Kent State University Kent OH USA
| | | | - Mark W. Kershner
- Department of Biological Sciences Kent State University Kent OH USA
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46
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Moreira LFB, Castilhos HZ, Castroviejo‐Fisher S. Something is not quite right: Effects of two land uses on anuran diversity in subtropical grasslands. Biotropica 2020. [DOI: 10.1111/btp.12836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leonardo Felipe Bairos Moreira
- Programa de Pós‐Graduação em Ecologia e Conservação da Biodiversidade Instituto de Biociências UFMT—Universidade Federal de Mato Grosso Cuiabá Brazil
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47
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Jin LS, Yin D, Fortin MJ, Cadotte MW. The mechanisms generating community phylogenetic patterns change with spatial scale. Oecologia 2020; 193:655-664. [PMID: 32621030 DOI: 10.1007/s00442-020-04695-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 06/16/2020] [Indexed: 10/23/2022]
Abstract
Studies that test community assembly hypotheses in observational communities frequently evaluate patterns for plots or entire communities, yet studies that examine assembly patterns across spatial scales show that they are greatly influenced by scale. Here, we test the spatial dependency of patterns of relatedness and plant height for all individual herbaceous plants along five 40-m old-field transects (Southern Ontario, Canada). We identified each individual plant and measured its distance along the transect and its height, and we constructed a molecular phylogeny for all observed species. To uncover the scale at which community phylogenetic and trait similarities shift, we used partial Mantel correlograms and distance-based Moran Eigenvector Maps (dbMEMs). We found that communities shift from significantly overdispersed at relatively smaller scales (i.e., < 15 m) to spatially clustered at larger scales, showing that assembly mechanism influence depends on scale of observation. This pattern was observed for both phylogeny and height, but was the strongest when considering phylogeny only. These results reveal the importance of spatial scale when examining community phylogenetic or trait patterns, where finding support for one assembly mechanism at a single scale does not necessarily mean that other mechanisms are also not important for structuring community composition and diversity.
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Affiliation(s)
- Lanna S Jin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Deyi Yin
- Department of Biological Sciences, University of Toronto at Scarborough, Scarborough, 416-208-5105, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Marc W Cadotte
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada. .,Department of Biological Sciences, University of Toronto at Scarborough, Scarborough, 416-208-5105, Canada.
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48
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Keppeler FW, Winemiller KO. Can ancestry and morphology be used as surrogates for species niche relationships? Ecol Evol 2020; 10:6562-6578. [PMID: 32724533 PMCID: PMC7381567 DOI: 10.1002/ece3.6390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/23/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023] Open
Abstract
Species interactions are difficult to quantify, and, consequently, many studies have used species traits and phylogeny as proxies under an assumption of niche conservatism (i.e., closely related and morphologically similar species should have similar niches). However, few studies have investigated whether niches actually are conserved within and across diverse communities. Here, we tested the degree to which phylogenetic relatedness and morphological similarity predict diets and stable isotopic ratios (δ 15N and δ 13C), two common descriptors of the trophic niche, in fish assemblages of two small streams in the Neotropics. We also tested the strength of the association between isotopic ratios and diet composition and found significant correlations implying that isotopic signals reveal trophic structure despite error associated with estimates of trophic enrichment and variation associated with tissue preservation, metabolism, and other factors affecting isotopic ratios. Morphological traits yielded a significant phylogenetic signal, and both morphological traits and phylogeny were correlated with diet composition, with morphological traits being a stronger predictor. We infer that functionally relevant morphological traits of fish can be used to infer trophic niches for certain kinds of questions and analyses when trophic data are lacking. However, we highlight that using phylogenetic and morphological data in combination with dietary and/or isotopic data can improve resolution of assemblage trophic structure and niche diversification.
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Affiliation(s)
- Friedrich W. Keppeler
- Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTXUSA
| | - Kirk O. Winemiller
- Department of Ecology and Conservation BiologyTexas A&M UniversityCollege StationTXUSA
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49
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Menezes BS, Martins FR, Dantas Carvalho EC, Souza BC, Silveira AP, Loiola MIB, Araújo FS. Assembly rules in a resource gradient: Competition and abiotic filtering determine the structuring of plant communities in stressful environments. PLoS One 2020; 15:e0230097. [PMID: 32168330 PMCID: PMC7069682 DOI: 10.1371/journal.pone.0230097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 02/21/2020] [Indexed: 12/02/2022] Open
Abstract
The relative importance of different community assembly mechanisms varies depending on the environment. According to the stress-dominance hypothesis (SDH), assembly mechanisms range from strong abiotic filtering to competition as the environment becomes more favourable. Most evidence for the SDH comes from studies in gradients of conditions (i.e. abiotic environmental factors that influence the functioning of organisms but are not consumed by them). However, we hypothesized that in resource gradients, competition increases as abiotic filtering becomes stronger. To test our hypothesis, we set up eight plots at different sites along an abiotic severity gradient in the Brazilian semi-arid region (BSAR). In each plot, we identified and measured each woody plant species found, and we recorded 11 functional traits of the main species, dividing the traits into alpha (competition effects) and beta (abiotic filtering effects). We investigated the presence of phylogenetic signal in the traits, the community phylogenetic and phenotypic patterns, and associated the variation in these patterns with the availability of water and soil nutrients. We found phylogenetic signal for most (91%) of the traits analysed. The phylogenetic patterns varied from clustered in stressful sites to random or overdispersed in favourable sites, and we concluded that these phylogenetic patterns were the result of historical processes influencing community assembly in different environments in the BSAR. In general, the phenotypic patterns varied from clustered at the most stressful end to random at less stressful sites. Our results show that in resource gradients, any restriction of the resource (hydric or edaphic) intensifies abiotic filtering and, at the same time, increases the competitive hierarchy among species. On the other hand, stochastic processes seem to have a stronger influence under more favourable abiotic conditions, where abiotic filtering and competition are weaker. Thus, we conclude that the SDH is not supported in resource gradients.
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Affiliation(s)
- Bruno Sousa Menezes
- Department of Biology, Science Centre, Federal University of Ceará—UFC, Fortaleza, CE, Brazil
| | - Fernando Roberto Martins
- Department of Plant Biology, Institute of Biology, University of Campinas—UNICAMP, Campinas, SP, Brazil
| | | | - Bruno Cruz Souza
- Department of Biology, Science Centre, Federal University of Ceará—UFC, Fortaleza, CE, Brazil
| | | | | | - Francisca Soares Araújo
- Department of Biology, Science Centre, Federal University of Ceará—UFC, Fortaleza, CE, Brazil
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50
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Martín-Regalado CN, Briones-Salas M, Manríquez-Morán N, Sánchez-Rojas G, Cornejo-Latorre C, Lavariega MC, Moreno CE. Assembly mechanisms and environmental predictors of the phylogenetic diversity of cricetid rodents in southern Mexico. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10034-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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