51
|
Björk JR, Hui FKC, O’Hara RB, Montoya JM. Uncovering the drivers of host-associated microbiota with joint species distribution modelling. Mol Ecol 2018; 27:2714-2724. [PMID: 29761593 PMCID: PMC6025780 DOI: 10.1111/mec.14718] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 01/07/2023]
Abstract
In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model-based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host-specific factors are in structuring the microbiota; and (c) co-occurrence networks to visualize microbe-to-microbe associations.
Collapse
Affiliation(s)
- Johannes R. Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
- Theoretical and Experimental Ecology Station, CNRS-University Paul Sabatier, Moulis, France
| | - Francis K. C. Hui
- Mathematical Sciences Institute, The Australian National University, Canberra, Australia
| | - Robert B. O’Hara
- Department of Mathematical Sciences, NTNU, Trondheim, Norway
- Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Jose M. Montoya
- Theoretical and Experimental Ecology Station, CNRS-University Paul Sabatier, Moulis, France
| |
Collapse
|
52
|
Damgaard C. Spatio-Temporal Structural Equation Modeling in a Hierarchical Bayesian Framework: What Controls Wet Heathland Vegetation? Ecosystems 2018. [DOI: 10.1007/s10021-018-0259-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
53
|
Lany NK, Zarnetske PL, Schliep EM, Schaeffer RN, Orians CM, Orwig DA, Preisser EL. Asymmetric biotic interactions and abiotic niche differences revealed by a dynamic joint species distribution model. Ecology 2018; 99:1018-1023. [PMID: 29608784 DOI: 10.1002/ecy.2190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 11/12/2022]
Abstract
A species' distribution and abundance are determined by abiotic conditions and biotic interactions with other species in the community. Most species distribution models correlate the occurrence of a single species with environmental variables only, and leave out biotic interactions. To test the importance of biotic interactions on occurrence and abundance, we compared a multivariate spatiotemporal model of the joint abundance of two invasive insects that share a host plant, hemlock woolly adelgid (HWA; Adelges tsugae) and elongate hemlock scale (EHS; Fiorina externa), to independent models that do not account for dependence among co-occurring species. The joint model revealed that HWA responded more strongly to abiotic conditions than EHS. Additionally, HWA appeared to predispose stands to subsequent increase of EHS, but HWA abundance was not strongly dependent on EHS abundance. This study demonstrates how incorporating spatial and temporal dependence into a species distribution model can reveal the dependence of a species' abundance on other species in the community. Accounting for dependence among co-occurring species with a joint distribution model can also improve estimation of the abiotic niche for species affected by interspecific interactions.
Collapse
Affiliation(s)
- Nina K Lany
- Department of Forestry, Michigan State University, East Lansing, Michigan, 48824, USA.,Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Phoebe L Zarnetske
- Department of Forestry, Michigan State University, East Lansing, Michigan, 48824, USA.,Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Erin M Schliep
- Department of Statistics, University of Missouri, Columbia, Missouri, 65211, USA
| | - Robert N Schaeffer
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, USA
| | - Colin M Orians
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, USA
| | - David A Orwig
- Harvard Forest, Harvard University, Petersham, Massachusetts, 01366, USA
| | - Evan L Preisser
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA
| |
Collapse
|
54
|
Moral RA, Hinde J, Demétrio CGB, Reigada C, Godoy WAC. Models for Jointly Estimating Abundances of Two Unmarked Site-Associated Species Subject to Imperfect Detection. JOURNAL OF AGRICULTURAL, BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2018. [DOI: 10.1007/s13253-017-0316-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
55
|
Rocha R, Ovaskainen O, López-Baucells A, Farneda FZ, Sampaio EM, Bobrowiec PED, Cabeza M, Palmeirim JM, Meyer CFJ. Secondary forest regeneration benefits old-growth specialist bats in a fragmented tropical landscape. Sci Rep 2018; 8:3819. [PMID: 29491428 PMCID: PMC5830632 DOI: 10.1038/s41598-018-21999-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/06/2018] [Indexed: 11/30/2022] Open
Abstract
Tropical forest loss and fragmentation are due to increase in coming decades. Understanding how matrix dynamics, especially secondary forest regrowth, can lessen fragmentation impacts is key to understanding species persistence in modified landscapes. Here, we use a whole-ecosystem fragmentation experiment to investigate how bat assemblages are influenced by the regeneration of the secondary forest matrix. We surveyed bats in continuous forest, forest fragments and secondary forest matrix habitats, ~15 and ~30 years after forest clearance, to investigate temporal changes in the occupancy and abundance of old-growth specialist and habitat generalist species. The regeneration of the second growth matrix had overall positive effects on the occupancy and abundance of specialists across all sampled habitats. Conversely, effects on generalist species were negligible for forest fragments and negative for secondary forest. Our results show that the conservation potential of secondary forests for reverting faunal declines in fragmented tropical landscapes increases with secondary forest age and that old-growth specialists, which are often of most conservation concern, are the greatest beneficiaries of secondary forest maturation. Our findings emphasize that the transposition of patterns of biodiversity persistence in island ecosystems to fragmented terrestrial settings can be hampered by the dynamic nature of human-dominated landscapes.
Collapse
Affiliation(s)
- Ricardo Rocha
- Centre for Ecology, Evolution and Environmental Changes - cE3c, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal.
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research Institute, 69011-970, Manaus, Brazil.
- Metapopulation Research Centre, Faculty of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Otso Ovaskainen
- Metapopulation Research Centre, Faculty of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Adrià López-Baucells
- Centre for Ecology, Evolution and Environmental Changes - cE3c, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research Institute, 69011-970, Manaus, Brazil
- Granollers Museum of Natural Sciences, 08402, Catalunya, Spain
| | - Fábio Z Farneda
- Centre for Ecology, Evolution and Environmental Changes - cE3c, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research Institute, 69011-970, Manaus, Brazil
- Department of Ecology/PPGE, Federal University of Rio de Janeiro, 21941-901, Rio de Janeiro, Brazil
| | - Erica M Sampaio
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research Institute, 69011-970, Manaus, Brazil
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, 89069, Ulm, Germany
| | - Paulo E D Bobrowiec
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research Institute, 69011-970, Manaus, Brazil
| | - Mar Cabeza
- Metapopulation Research Centre, Faculty of Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Jorge M Palmeirim
- Centre for Ecology, Evolution and Environmental Changes - cE3c, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research Institute, 69011-970, Manaus, Brazil
| | - Christoph F J Meyer
- Centre for Ecology, Evolution and Environmental Changes - cE3c, Faculty of Sciences, University of Lisbon, 1749-016, Lisbon, Portugal
- Biological Dynamics of Forest Fragments Project, National Institute for Amazonian Research and Smithsonian Tropical Research Institute, 69011-970, Manaus, Brazil
- Ecosystems and Environment Research Centre (EERC), School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, United Kingdom
| |
Collapse
|
56
|
Nieto‐Lugilde D, Maguire KC, Blois JL, Williams JW, Fitzpatrick MC. Multiresponse algorithms for community‐level modelling: Review of theory, applications, and comparison to species distribution models. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12936] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diego Nieto‐Lugilde
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
- Departamento de Botánica Ecología y Fisiología Vegetal Universidad de Córdoba Córdoba Spain
| | | | - Jessica L. Blois
- School of Natural Sciences University of California Merced CA USA
| | - John W. Williams
- Center for Climatic Research University of Wisconsin Madison WI USA
- Department of Geography University of Wisconsin Madison WI USA
| | - Matthew C. Fitzpatrick
- Appalachian Laboratory University of Maryland Center for Environmental Science Frostburg MD USA
| |
Collapse
|
57
|
Schliep EM, Gelfand AE, Mitchell RM, Aiello‐Lammens ME, Silander JA. Assessing the joint behaviour of species traits as filtered by environment. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erin M. Schliep
- Department of Statistics University of Missouri Columbia MO USA
| | - Alan E. Gelfand
- Department of Statistical Science Duke University Durham NC USA
| | | | | | - John A. Silander
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
| |
Collapse
|
58
|
Brodie JF, Helmy OE, Mohd-Azlan J, Granados A, Bernard H, Giordano AJ, Zipkin E. Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment. Biotropica 2017. [DOI: 10.1111/btp.12500] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jedediah F. Brodie
- Division of Biological Sciences & Wildlife Biology Program; University of Montana; Missoula MT 59802 USA
| | - Olga E. Helmy
- Division of Biological Sciences & Wildlife Biology Program; University of Montana; Missoula MT 59802 USA
| | - Jayasilan Mohd-Azlan
- Department of Zoology; Faculty of Resource Science and Technology; Universiti Malaysia Sarawak; 94300 Kota Samarahan Sarawak Malaysia
| | - Alys Granados
- Department of Zoology; University of British Columbia; 2329 West Mall Vancouver BC V6T 1Z4 Canada
| | - Henry Bernard
- Institute for Tropical Biology and Conservation; Universiti Malaysia Sabah; 88999 Kota Kinabalu Sabah Malaysia
| | | | - Elise Zipkin
- Department of Integrative Biology; Michigan State University; East Lansing MI 48824 USA
| |
Collapse
|
59
|
Connecting Earth observation to high-throughput biodiversity data. Nat Ecol Evol 2017; 1:176. [PMID: 28812589 DOI: 10.1038/s41559-017-0176] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 04/26/2017] [Indexed: 01/26/2023]
Abstract
Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation, indicators based on Earth observation could be misleading and reduce the effectiveness of nature conservation and even unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, high-throughput DNA sequencing and modern ecological modelling to extract much more of the information available in Earth observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts on biodiversity and its functions and services.
Collapse
|
60
|
Tikhonov G, Abrego N, Dunson D, Ovaskainen O. Using joint species distribution models for evaluating how species‐to‐species associations depend on the environmental context. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12723] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gleb Tikhonov
- Metapopulation Research Centre Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
| | - Nerea Abrego
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology N‐7491 Trondheim Norway
| | - David Dunson
- Department of Statistical Science Duke University P.O. Box 90251 Durham NC USA
| | - Otso Ovaskainen
- Metapopulation Research Centre Department of Biosciences University of Helsinki P.O. Box 65 Helsinki FI‐00014 Finland
- Centre for Biodiversity Dynamics Department of Biology Norwegian University of Science and Technology N‐7491 Trondheim Norway
| |
Collapse
|
61
|
Ovaskainen O, Tikhonov G, Norberg A, Guillaume Blanchet F, Duan L, Dunson D, Roslin T, Abrego N. How to make more out of community data? A conceptual framework and its implementation as models and software. Ecol Lett 2017; 20:561-576. [PMID: 28317296 DOI: 10.1111/ele.12757] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/31/2017] [Accepted: 02/09/2017] [Indexed: 12/23/2022]
Abstract
Community ecology aims to understand what factors determine the assembly and dynamics of species assemblages at different spatiotemporal scales. To facilitate the integration between conceptual and statistical approaches in community ecology, we propose Hierarchical Modelling of Species Communities (HMSC) as a general, flexible framework for modern analysis of community data. While non-manipulative data allow for only correlative and not causal inference, this framework facilitates the formulation of data-driven hypotheses regarding the processes that structure communities. We model environmental filtering by variation and covariation in the responses of individual species to the characteristics of their environment, with potential contingencies on species traits and phylogenetic relationships. We capture biotic assembly rules by species-to-species association matrices, which may be estimated at multiple spatial or temporal scales. We operationalise the HMSC framework as a hierarchical Bayesian joint species distribution model, and implement it as R- and Matlab-packages which enable computationally efficient analyses of large data sets. Armed with this tool, community ecologists can make sense of many types of data, including spatially explicit data and time-series data. We illustrate the use of this framework through a series of diverse ecological examples.
Collapse
Affiliation(s)
- Otso Ovaskainen
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
| | - Gleb Tikhonov
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - Anna Norberg
- Department of Biosciences, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
| | - F Guillaume Blanchet
- Department of Mathematics and Statistics, McMaster University, 1280 Main Street West Hamilton, Ontario, L8S 4K1, Canada.,Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 Boulevard Université Sherbrooke, Québec, J1K 2R1, Canada
| | - Leo Duan
- Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA
| | - David Dunson
- Department of Statistical Science, Duke University, P.O. Box 90251, Durham, USA
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, Uppsala, 75651, Sweden
| | - Nerea Abrego
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.,Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, Helsinki, FI-00014, Finland
| |
Collapse
|
62
|
Foster SD, Hill NA, Lyons M. Ecological grouping of survey sites when sampling artefacts are present. J R Stat Soc Ser C Appl Stat 2017. [DOI: 10.1111/rssc.12211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Scott D. Foster
- Commonwealth Scientific and Industrial Research Organisation; Hobart Australia
| | | | | |
Collapse
|
63
|
Warton DI, Blanchet FG, O’Hara R, Ovaskainen O, Taskinen S, Walker SC, Hui FK. Extending Joint Models in Community Ecology: A Response to Beissinger et al . Trends Ecol Evol 2016; 31:737-738. [DOI: 10.1016/j.tree.2016.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 10/21/2022]
|