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Smith TP, Clegg T, Ransome E, Martin-Lilley T, Rosindell J, Woodward G, Pawar S, Bell T. High-throughput characterization of bacterial responses to complex mixtures of chemical pollutants. Nat Microbiol 2024; 9:938-948. [PMID: 38499812 PMCID: PMC10994839 DOI: 10.1038/s41564-024-01626-9] [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: 02/22/2023] [Accepted: 01/30/2024] [Indexed: 03/20/2024]
Abstract
Our understanding of how microbes respond to micropollutants, such as pesticides, is almost wholly based on single-species responses to individual chemicals. However, in natural environments, microbes experience multiple pollutants simultaneously. Here we perform a matrix of multi-stressor experiments by assaying the growth of model and non-model strains of bacteria in all 255 combinations of 8 chemical stressors (antibiotics, herbicides, fungicides and pesticides). We found that bacterial strains responded in different ways to stressor mixtures, which could not be predicted simply from their phylogenetic relatedness. Increasingly complex chemical mixtures were both more likely to negatively impact bacterial growth in monoculture and more likely to reveal net interactive effects. A mixed co-culture of strains proved more resilient to increasingly complex mixtures and revealed fewer interactions in the growth response. These results show predictability in microbial population responses to chemical stressors and could increase the utility of next-generation eco-toxicological assays.
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Affiliation(s)
- Thomas P Smith
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK.
| | - Tom Clegg
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Emma Ransome
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Thomas Martin-Lilley
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - James Rosindell
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Guy Woodward
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Samraat Pawar
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Thomas Bell
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
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2
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Quilodrán CS, Currat M, Montoya-Burgos JI. Benchmarking the Mantel test and derived methods for testing association between distance matrices. Mol Ecol Resour 2023. [PMID: 38041538 DOI: 10.1111/1755-0998.13898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 12/03/2023]
Abstract
Testing the association between objects is central in ecology, evolution, and quantitative sciences in general. Two types of variables can describe the relationships between objects: point variables (measured on individual objects), and distance variables (measured between pairs of objects). The Mantel test and derived methods have been extensively used for distance variables. Yet, these methods have been criticized due to low statistical power and inflated type I error when spatial autocorrelation is present. Here, we assessed the statistical power between different types of tested variables and the type I error rate over a wider range of autocorrelation intensities than previously assessed, both on univariate and multivariate data. We also illustrated the performance of distance matrix statistics through computational simulations of genetic diversity. We show that the Mantel test and derived methods are not affected by inflated type I error when spatial autocorrelation affects only one variable when investigating correlations, or when either the response or the explanatory variable(s) is affected by spatial autocorrelation while investigating causal relationships. As previously noted, with autocorrelation affecting more variables, inflated type I error could be reduced by modifying the significance threshold. Additionally, the Mantel test has no problem of statistical power when the hypothesis is formulated in terms of distance variables. We highlight that transformation of variable types should be avoided because of the potential information loss and modification of the tested hypothesis. We propose a set of guidelines to help choose the appropriate method according to the type of variables and defined hypothesis.
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Affiliation(s)
- Claudio S Quilodrán
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Juan I Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
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3
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Rivera M, Edwards JA, Hauber ME, Woolley SMN. Machine learning and statistical classification of birdsong link vocal acoustic features with phylogeny. Sci Rep 2023; 13:7076. [PMID: 37127781 PMCID: PMC10151348 DOI: 10.1038/s41598-023-33825-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023] Open
Abstract
Birdsong is a longstanding model system for studying evolution and biodiversity. Here, we collected and analyzed high quality song recordings from seven species in the family Estrildidae. We measured the acoustic features of syllables and then used dimensionality reduction and machine learning classifiers to identify features that accurately assigned syllables to species. Species differences were captured by the first 3 principal components, corresponding to basic frequency, power distribution, and spectrotemporal features. We then identified the measured features underlying classification accuracy. We found that fundamental frequency, mean frequency, spectral flatness, and syllable duration were the most informative features for species identification. Next, we tested whether specific acoustic features of species' songs predicted phylogenetic distance. We found significant phylogenetic signal in syllable frequency features, but not in power distribution or spectrotemporal features. Results suggest that frequency features are more constrained by species' genetics than are other features, and are the best signal features for identifying species from song recordings. The absence of phylogenetic signal in power distribution and spectrotemporal features suggests that these song features are labile, reflecting learning processes and individual recognition.
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Affiliation(s)
- Moises Rivera
- Department of Psychology, Hunter College and the Graduate Center, City University of New York, New York, NY, 10065, USA
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Jacob A Edwards
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
- Department of Psychology, Columbia University, New York, NY, 10027, USA
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Biological Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sarah M N Woolley
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA.
- Department of Psychology, Columbia University, New York, NY, 10027, USA.
- Zuckerman Institute at Columbia University, Jerome L. Greene Science Center, 3227 Broadway, L3.028, New York, NY, 10027, USA.
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4
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Using phylogenetic information to impute missing functional trait values in ecological databases. ECOL INFORM 2021. [DOI: 10.1016/j.ecoinf.2021.101315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Phylogenetic uncertainty and the inference of patterns in community ecology and comparative studies. Oecologia 2021; 196:633-647. [PMID: 34146131 DOI: 10.1007/s00442-021-04972-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/12/2021] [Indexed: 10/21/2022]
Abstract
Progress in phylogenetic community ecology is often limited by the availability of phylogenetic information and the lack of appropriate methods and solutions to deal with this problem. We estimate the effect of the lack of phylogenetic information on the relations among taxa measured by commonly used phylogenetic metrics in comparative studies and community ecology, namely: Blomberg's K phylogenetic signal, Faith's Phylogenetic Diversity (PD), Mean Phylogenetic Distance (MPD) and Mean Nearest Taxon Distance (MNTD). To overcome this problem, we tested two possible solutions: Polytomic trees and Operational trees. Our results show that the effects on K values strongly depended on the level of phylogenetic signal. In the case of the community metrics, the effects were insensitive to the patterns of species distribution in the communities. Community metrics tended to be overestimated with both Polytomic and Operational trees, but the overestimation was higher with Polytomic trees. PD and MPD metrics were less biased than MNTD metric. We show that the lack of phylogenetic resolution is not necessarily problematic for all analyses and that its effect will depend on the chosen metric and on the solutions used to deal with the problem. Based on our results, we suggest that ecologists should prefer the Operational tree solution to remove polytomies in the phylogenetic tree and take careful consideration while designing experiments, and analyzing and interpreting the results of phylogenetic metrics.
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Sun J, Wen Z, Feijó A, Cheng J, Wang Y, Li S, Ge D, Xia L, Yang Q. Elevation patterns and critical environmental drivers of the taxonomic, functional, and phylogenetic diversity of small mammals in a karst mountain area. Ecol Evol 2020; 10:10899-10911. [PMID: 33072304 PMCID: PMC7548175 DOI: 10.1002/ece3.6750] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/03/2022] Open
Abstract
Understanding how biodiversity components are related under different environmental factors is a fundamental challenge for ecology studies, yet there is little knowledge of this interplay among the biotas, especially small mammals, in karst mountain areas. Here, we examine the elevation patterns of the taxonomic diversity (TD), phylogenetic diversity (PD), and functional diversity (FD) of small mammals in a karst mountain area, the Wuling Mountains, Southwest China, and compare these patterns between taxa (Rodentia and Eulipotyphla) and scales (broad‐ and narrow‐range species). We also disentangle the impacts of the human influence index, net primary productivity (NPP), normalized difference vegetation index (NDVI), annual precipitation (AP), and annual mean temperature (AMT) on these three facets of biodiversity by using structural equation modeling. We recorded a total of 39 small mammal species, including 26 rodents and 13 species of the order Eulipotyphla. Our study shows that the facets of biodiversity are spatially incongruent. Net primary productivity has a positive effect on the three facets for most groups, while the effect of the NDVI is negative for TD and PD in most groups. AMT temperature and AP have negative effects on FD and PD, whereas TD is dependent on the species range scale. The human influence index effect on TD and PD also depends on the species range scale. These findings provide robust evidence that the ecological drivers of biodiversity differ among different biotas and different range scales, and future research should use multifacet approach to determine biodiversity conservation strategies.
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Affiliation(s)
- Jian Sun
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,University of Chinese Academy of Sciences Beijing China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Yanqun Wang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China.,University of Chinese Academy of Sciences Beijing China
| | - Song Li
- Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
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7
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Westeen EP, Durso AM, Grundler MC, Rabosky DL, Davis Rabosky AR. What makes a fang? Phylogenetic and ecological controls on tooth evolution in rear-fanged snakes. BMC Evol Biol 2020; 20:80. [PMID: 32646372 PMCID: PMC7346461 DOI: 10.1186/s12862-020-01645-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/22/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Fangs are a putative key innovation that revolutionized prey capture and feeding in snakes, and - along with their associated venom phenotypes - have made snakes perhaps the most medically-significant vertebrate animals. Three snake clades are known for their forward-positioned fangs, and these clades (Elapidae, Viperidae, and Atractaspidinae) contain the majority of snakes that are traditionally considered venomous. However, many other snakes are "rear-fanged": they possess potentially venom-delivering teeth situated at the rear end of the upper jaw. Quantification of fang phenotypes - and especially those of rear-fanged species - has proved challenging or impossible owing to the small size and relative rarity of many such snakes. Consequently, it has been difficult to understand the evolutionary history of both venom and prey-capture strategies across extant snakes. We quantified variation in the dentition of 145 colubriform ("advanced") snake species using microCT scanning and compared dental characters with ecological data on species' diet and prey capture method(s) to understand broader patterns in snake fang evolution. RESULTS Dental traits such as maxilla length, tooth number, and fang size show strong phylogenetic signal across Colubriformes. We find extreme heterogeneity and evolutionary lability in the rear-fanged phenotype in colubrid (colubrine, dipsadine, and natricine lineages) and lamprophiid snakes, in contrast to relative uniformity in the front fanged phenotypes of other groups (vipers and, to a lesser extent, elapids). Fang size and position are correlated with venom-use in vipers, elapids, and colubrid snakes, with the latter group shifting fangs anteriorly by shortening the entire maxillary bone. We find that maxilla length and tooth number may also be correlated with the evolution of dietary specialization. Finally, an ancestral state reconstruction suggests that fang loss is a recurring phenomenon in colubrid snakes, likely accompanied by shifts in diet and prey capture mode. CONCLUSIONS Our study provides a framework for quantifying the complex morphologies associated with venom use in snakes. Our results suggest that fang phenotypes, and particularly the rear-fanged phenotype, in snakes are both diverse and labile, facilitating a wide range of ecological strategies and contributing to spectacular radiations of these organisms in tropical and subtropical biomes worldwide.
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Affiliation(s)
- Erin P Westeen
- Department of Environmental Science, Policy, and Management & Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA.
| | - Andrew M Durso
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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8
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García-Girón J, Heino J, Baastrup-Spohr L, Bove CP, Clayton J, de Winton M, Feldmann T, Fernández-Aláez M, Ecke F, Grillas P, Hoyer MV, Kolada A, Kosten S, Lukács BA, Mjelde M, Mormul RP, Rhazi L, Rhazi M, Sass L, Xu J, Alahuhta J. Global patterns and determinants of lake macrophyte taxonomic, functional and phylogenetic beta diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 723:138021. [PMID: 32213415 DOI: 10.1016/j.scitotenv.2020.138021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
Documenting the patterns of biological diversity on Earth has always been a central challenge in macroecology and biogeography. However, for the diverse group of freshwater plants, such research program is still in its infancy. Here, we examined global variation in taxonomic, functional and phylogenetic beta diversity patterns of lake macrophytes using regional data from six continents. A data set of ca. 480 lake macrophyte community observations, together with climatic, geographical and environmental variables, was compiled across 16 regions worldwide. We (a) built the very first phylogeny comprising most freshwater plant lineages; (b) exploited a wide array of functional traits that are important to macrophyte autoecology or that relate to lake ecosystem functioning; (c) assessed if different large-scale beta diversity patterns show a clear latitudinal gradient from the equator to the poles using null models; and (d) employed evolutionary and regression models to first identify the degree to which the studied functional traits show a phylogenetic signal, and then to estimate community-environment relationships at multiple spatial scales. Our results supported the notion that ecological niches evolved independently of phylogeny in macrophyte lineages worldwide. We also showed that taxonomic and phylogenetic beta diversity followed the typical global trend with higher diversity in the tropics. In addition, we were able to confirm that species, multi-trait and lineage compositions were first and foremost structured by climatic conditions at relatively broad spatial scales. Perhaps more importantly, we showed that large-scale processes along latitudinal and elevational gradients have left a strong footprint in the current diversity patterns and community-environment relationships in lake macrophytes. Overall, our results stress the need for an integrative approach to macroecology, biogeography and conservation biology, combining multiple diversity facets at different spatial scales.
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Affiliation(s)
- Jorge García-Girón
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
| | - Jani Heino
- Finnish Environment Institute, Freshwater Centre, P.O. Box 413, 90014 Oulu, Finland.
| | - Lars Baastrup-Spohr
- Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, 2100 København Ø, Denmark.
| | - Claudia P Bove
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro, RJ 20940-040, Brazil
| | - John Clayton
- National Institute of Water and Atmospheric Research Limited, P.O. Box 11115, Hamilton, New Zealand.
| | - Mary de Winton
- National Institute of Water and Atmospheric Research Limited, P.O. Box 11115, Hamilton, New Zealand.
| | - Tõnu Feldmann
- Centre for Limnology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 61117 Rannu, Tartumaa, Estonia.
| | | | - Frauke Ecke
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), P.O. Box 7050, 750 07 Uppsala, Sweden; Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences (SLU), 901 83 Umeå, Sweden.
| | - Patrick Grillas
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, Le Sambuc, 13200 Arles, France.
| | - Mark V Hoyer
- Fisheries and Aquatic Sciences, School of Forest Resources and Conservation, Institute of Food and Agricultural Services, University of Florida, 7922 NW 71st Street, Gainesville, FL 32609, USA.
| | - Agnieszka Kolada
- Department of Freshwater Protection, Institute of Environmental Protection-National Research Institute, Krucza 5/11D, 00-548 Warsaw, Poland.
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, the Netherlands.
| | - Balázs A Lukács
- Department of Tisza River Research, MTA Centre for Ecological Research, DRI, Bem tér 18/C, Debrecen 4026, Hungary.
| | - Marit Mjelde
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, 0349 Oslo, Norway.
| | - Roger P Mormul
- Department of Biology, Research Group in Limnology, Ichthyology and Aquaculture-Nupélia, State University of Maringá, Av. Colombo 5790, Bloco H90, CEP-87020-900 Mringá, PR, Brazil
| | - Laila Rhazi
- Research Center of Plant and Microbial Biotechnologies, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, 4 avenue Ibn Battouta, B.P. 1014 RP, Rabat, Morocco
| | - Mouhssine Rhazi
- Faculty of Science and Technology, Department of Biology, Moulay Ismail University, PB 509, Boutalamine, Errachidia, Morocco
| | - Laura Sass
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA.
| | - Jun Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430070, China.
| | - Janne Alahuhta
- Finnish Environment Institute, Freshwater Centre, P.O. Box 413, 90014 Oulu, Finland; Geography Research Unit, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland.
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9
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García-Girón J, Fernández-Aláez C, Fernández-Aláez M, Alahuhta J. Untangling the assembly of macrophyte metacommunities by means of taxonomic, functional and phylogenetic beta diversity patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133616. [PMID: 31377370 DOI: 10.1016/j.scitotenv.2019.133616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Metacommunity ecology has broadened considerably with the recognition that measuring beta diversity beyond the purely taxonomic viewpoint may improve our understanding of the dispersal- and niche-based mechanisms across biological communities. In that perspective, we applied a novel multidimensional approach including taxonomic, functional and phylogenetic data to enhance our basic understanding of macrophyte metacommunity dynamics. For each beta diversity metric, we calculated the mean overall value and tested whether the mean value was different from that expected by chance using null models. We also employed evolutionary and spatially constrained models to first identify the degree to which the studied functional traits showed a phylogenetic signal, and then to estimate the relative importance of spatial and environmental effects on metacommunity structure. We first found that most individual ponds were inhabited by species that were merely random draws from the taxonomic and phylogenetic species pool available in the study region. Contrary to our expectations, not all measured traits were conserved along the phylogeny. We also showed that trait and phylogenetic dimensions strongly increased the amount of variation in beta diversity that can be explained by degree of environmental filtering and dispersal limitation. This suggests that accounting for functional traits and phylogeny in metacommunity ecology helps to explain idiosyncratic patterns of variation in macrophyte species distribution. Importantly, phylogenetic and functional analyses identified the influence of underlying mechanisms that would otherwise be missed in an analysis of taxonomic turnover. Together, these results let us conclude that macrophyte species have labile functional traits adapted to dispersal-based processes and some evolutionary trade-offs that drive community assembly via species sorting. Overall, our exploration of different facets of beta diversity showed how functional and phylogenetic information may be used with species-level data to test community assembly hypotheses that are more ecologically meaningful than assessments of environmental patterns based on the purely taxonomic viewpoint.
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Affiliation(s)
- Jorge García-Girón
- Group for Limnology and Environmental Biotechnology, Area of Ecology, Universidad de León, Campus de Vegazana, León, Spain.
| | - Camino Fernández-Aláez
- Group for Limnology and Environmental Biotechnology, Area of Ecology, Universidad de León, Campus de Vegazana, León, Spain.
| | - Margarita Fernández-Aláez
- Group for Limnology and Environmental Biotechnology, Area of Ecology, Universidad de León, Campus de Vegazana, León, Spain.
| | - Janne Alahuhta
- Geography Research Unit, University of Oulu, P.O. Box 3000, FI-90140 University of Oulu, Finland.
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10
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Fang YT, Tuanmu MN, Hung CM. Asynchronous evolution of interdependent nest characters across the avian phylogeny. Nat Commun 2018; 9:1863. [PMID: 29760391 PMCID: PMC5951845 DOI: 10.1038/s41467-018-04265-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 04/13/2018] [Indexed: 12/01/2022] Open
Abstract
Nest building is a widespread behavior among birds that reflects their adaptation to the environment and evolutionary history. However, it remains unclear how nests evolve and how their evolution relates to the bird phylogeny. Here, by examining the evolution of three nest characters—structure, site, and attachment—across all bird families, we reveal that nest characters did not change synchronically across the avian phylogeny but had disparate evolutionary trajectories. Nest structure shows stronger phylogenetic signal than nest site, while nest attachment has little variation. Nevertheless, the three characters evolved interdependently. For example, the ability of birds to explore new nest sites might depend on the emergence of novel nest structure and/or attachment. Our results also reveal labile nest characters in passerines compared with other birds. This study provides important insights into avian nest evolution and suggests potential associations between nest diversification and the adaptive radiations that generated modern bird lineages. Nearly all bird species build nests; however, there is extensive variation in both how and where their nests are built. Here, Fang and colleagues reconstruct the evolution of nest structure, nest site and nest attachment across all extant bird families.
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Affiliation(s)
- Yi-Ting Fang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mao-Ning Tuanmu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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11
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Duarte LDS, Debastiani VJ, Carlucci MB, Diniz-Filho JAF. Analyzing community-weighted trait means across environmental gradients: should phylogeny stay or should it go? Ecology 2017; 99:385-398. [PMID: 29121389 DOI: 10.1002/ecy.2081] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 09/19/2017] [Accepted: 10/24/2017] [Indexed: 11/05/2022]
Abstract
Functional traits mediate ecological responses of organisms to the environment, determining community structure. Community-weighted trait means (CWM) are often used to characterize communities by combining information on species traits and distribution. Relating CWM variation to environmental gradients allows for evaluating species sorting across the metacommunity, either based on correlation tests or ordinary least squares (OLS) models. Yet, it is not clear if phylogenetic signal in both traits and species distribution affect those analyses. On one hand, phylogenetic signal might indicate niche conservatism along clade evolution, reinforcing the environmental signal in trait assembly patterns. On the other hand, it might introduce phylogenetic autocorrelation to mean trait variation among communities. Under this latter scenario, phylogenetic signal might inflate type I error in analysis relating CWM variation to environmental gradients. We explore multiple ways phylogenetic history may influence analysis relating CWM to environmental gradients. We propose the concept of neutral trait diffusion, which predicts that for a functional trait x, CWM variation among local communities does not deviate from the expectation that x evolved according to a neutral evolutionary process. Based on this framework we introduce a graphical tool called neutral trait diffusion representation (NTDR) that allows for the evaluation of whether it is necessary to carry out phylogenetic correction in the trait prior to analyzing the association between CWM and environmental gradients. We illustrate the NTDR approach using simulated traits, phylogenies and metacommunities. We show that even under moderate phylogenetic signal in both the trait used to define CWM and species distribution across communities, OLS models relating CWM variation to environmental gradients lead to inflated type I error when testing the null hypothesis of no association between CWM and environmental gradient. To overcome this issue, we propose a phylogenetic correction for OLS models and evaluate its statistical performance (type I error and power). Phylogeny-corrected OLS models successfully control for type I error in analysis relating CWM variation to environmental gradients but may show decreased power. Combining the exploratory tool of NTDR and phylogenetic correction in traits, when necessary, guarantees more precise inferences about the environmental forces driving trait-mediated species sorting across metacommunities.
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Affiliation(s)
- Leandro D S Duarte
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500 CP 15007, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
| | - Vanderlei J Debastiani
- Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500 CP 15007, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
| | - Marcos B Carlucci
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, CP 19031, Curitiba, Paraná, 81531-980, Brazil
| | - José Alexandre F Diniz-Filho
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, CP 131, Goiânia, Goiás, 74690-900, Brazil
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Verde Arregoitia LD, Fisher DO, Schweizer M. Morphology captures diet and locomotor types in rodents. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160957. [PMID: 28280593 PMCID: PMC5319359 DOI: 10.1098/rsos.160957] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 12/15/2016] [Indexed: 05/10/2023]
Abstract
To understand the functional meaning of morphological features, we need to relate what we know about morphology and ecology in a meaningful, quantitative framework. Closely related species usually share more phenotypic features than distant ones, but close relatives do not necessarily have the same ecologies. Rodents are the most diverse group of living mammals, with impressive ecomorphological diversification. We used museum collections and ecological literature to gather data on morphology, diet and locomotion for 208 species of rodents from different bioregions to investigate how morphological similarity and phylogenetic relatedness are associated with ecology. After considering differences in body size and shared evolutionary history, we find that unrelated species with similar ecologies can be characterized by a well-defined suite of morphological features. Our results validate the hypothesized ecological relevance of the chosen traits. These cranial, dental and external (e.g. ears) characters predicted diet and locomotion and showed consistent differences among species with different feeding and substrate use strategies. We conclude that when ecological characters do not show strong phylogenetic patterns, we cannot simply assume that close relatives are ecologically similar. Museum specimens are valuable records of species' phenotypes and with the characters proposed here, morphology can reflect functional similarity, an important component of community ecology and macroevolution.
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Affiliation(s)
| | - Diana O. Fisher
- School of Biological Sciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Manuel Schweizer
- Naturhistorisches Museum Bern, Bernastrasse 15, Bern 3005, Switzerland
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Verde Arregoitia LD, Fisher DO, Schweizer M. Morphology captures diet and locomotor types in rodents. ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 28280593 DOI: 10.5281/zenodo.201147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
To understand the functional meaning of morphological features, we need to relate what we know about morphology and ecology in a meaningful, quantitative framework. Closely related species usually share more phenotypic features than distant ones, but close relatives do not necessarily have the same ecologies. Rodents are the most diverse group of living mammals, with impressive ecomorphological diversification. We used museum collections and ecological literature to gather data on morphology, diet and locomotion for 208 species of rodents from different bioregions to investigate how morphological similarity and phylogenetic relatedness are associated with ecology. After considering differences in body size and shared evolutionary history, we find that unrelated species with similar ecologies can be characterized by a well-defined suite of morphological features. Our results validate the hypothesized ecological relevance of the chosen traits. These cranial, dental and external (e.g. ears) characters predicted diet and locomotion and showed consistent differences among species with different feeding and substrate use strategies. We conclude that when ecological characters do not show strong phylogenetic patterns, we cannot simply assume that close relatives are ecologically similar. Museum specimens are valuable records of species' phenotypes and with the characters proposed here, morphology can reflect functional similarity, an important component of community ecology and macroevolution.
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Affiliation(s)
| | - Diana O Fisher
- School of Biological Sciences , University of Queensland , St Lucia, Queensland 4072 , Australia
| | - Manuel Schweizer
- Naturhistorisches Museum Bern, Bernastrasse 15, Bern 3005 , Switzerland
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