DOCSLIB.ORG

Community Ecology of Absent Species: Hidden and Dark Diversity Meelis Partel€

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Community Ecology of Absent Species: Hidden and Dark Diversity Meelis Partel€ Journal of Vegetation Science && (2014) SPECIAL FEATURE: VEGETATION PATTERNS AND THEIR UNDERLYING PROCESSES Community ecology of absent species: hidden and dark diversity Meelis Partel€ Keywords Abstract Absent species; Community composition; Dark diversity; DNA; Ecological community; Missing Community ecologists have so far focused mainly on species identified at a species; Species diversity; Species pool; site. I suggest that we can understand better patterns and their underlying Species richness processes in ecological communities if we also examine those species absent from the sampled community. However, there are various types of absences, Received 19 September 2013 which all harbour different information. Hidden diversity comprises species Accepted 22 January 2014 that are absent from our sight: dormant or locally very rare species over- Co-ordinating Editor: Rein Kalamees looked by traditional sampling. Fortunately, modern DNA-based techniques can help us to find hidden species when analysing environmental samples. Partel,€ M. ([email protected]): Institute of Depending on habitat type and sampling scale, a large number of co-existing Ecology and Earth Sciences, University of species might be hidden. Dark diversity comprises absent species that consti- Tartu, Lai 40, Tartu, 51005, Estonia tute the habitat-specific species pool. Dark diversity can be determined based on data on species distribution, dispersal potential and ecological require- ments. If we know both observed and dark diversity, we can estimate com- munity completeness and infer those processes that determine which species in the species pool actually co-exist locally. In addition, most species in the world do not actually belong to the habitat-specific species pool of the com- munity: their ecological requirements differ or their distribution area is else- where. Such other absent species are usually not directly relevant to a particular community. However, knowing ecologically suitable species from other regions can give early warning of possible future invasion of alien spe- cies (alien dark diversity). To conclude, species presences have meaning only if there are absences (and vice versa). Methods to detect absent species are rapidly developing and will soon form a standard toolbox for community ecology. allow community ecologists and conservation practitioners Introduction to better understand community patterns and their under- An ultimate goal of community ecology is to understand lying processes. why different sites host different species (Vellend 2010). Species absent from a particular community sample pro- Studies of ecological communities have concentrated pri- vide valuable information. Without absences, all samples marily on observations of species found in local sites. Spe- host the same species and the table can be represented as a cies identified in a set of ecological communities are simple species list. There is no reason why species absences typically listed in species 9 sample tables. If species compo- cannot be used instead of presences; it is simply a matter of sition varies among samples, these tables also feature tradition that we count presences in a species 9 sample absences. In fact, absences are usually more frequent than table. Ultimately the maximum number of absences in a presences in such tables. Scientists generally focus on spe- species 9 sample table is the total global flora or fauna. cies presences to examine variation in species diversity and For example, there are currently 283 556 accepted names community composition. Present species are also segre- of vascular plant species (www.theplantlist.org, accessed gated into groups of different functional types, alien or Dec 2013). An Estonian wooded meadow holds the world threatened species, etc. Here I outline the importance of record for the number of vascular plant species within a species absences and suggest how various types of absences 10 9 10 cm plot: 25 rooted species (Kull & Zobel 1991; Journal of Vegetation Science Doi: 10.1111/jvs.12169 © 2014 International Association for Vegetation Science 1 Community ecology of absent species M. P€artel Wilson et al. 2012). The very same plot also holds the Twenty years ago, Eddy van der Maarel and Martin world record for the lowest number of species absences at Sykes proposed the Carousel Model (van der Maarel & that scale, ‘just’ 283 531 (i.e. 283 556–25) absent species. Sykes 1993) after examining 10 9 10 cm permanent Why are these species absent? This question is by no plots in dry calcareous grasslands in Sweden. They noticed means as trivial as it might seem. Some absent species are high small-scale species mobility: each subsequent year found adjacent to the 10 9 10 cm plot. Several species revealed the appearance and disappearance of several spe- common to wooded meadows in the region are absent cies in all permanent plots. This was especially surprising both in the plot and its close vicinity. Moreover, most spe- since most species were perennial. Species moved around cies absent from the 10 9 10 cm plot inhabit other conti- like children on a merry-go-round. This high small-scale nents, other biogeographic regions or simply other mobility was originally attributed to the short life span of habitats, e.g. wetlands or seashores. Consequently, by dis- plant individuals and frequent regeneration from the seed tinguishing relevant types of absences, we can make the bank. However, community recruitment from seeds observed diversity – recorded presences – much more use- depends on favourable local conditions and can be highly ful. For simplicity, I shall neglect species abundances, but it stochastic (Eriksson & Froborg€ 1996). More recent is theoretically possible to account for this as well, e.g. research has stressed the importance of the below-ground when working with the effective number of species (Hill bud bank (Klimesova & Klimes 2007). Some plant species 1973). Here I present an overview of different types of can stay dormant below ground, sometimes for several absences representing hidden diversity and dark diversity, years (Reintal et al. 2010). In temperate grasslands, often as well as an overview of other absent species that might more than 75% of plant biomass is below ground in com- ‘stalk’ our study sites. plex symbiosis with other trophic levels (Jackson et al. 1997; Steinaker & Wilson 2005; Mokany et al. 2006). This means that a plant community might be more of a below- Hidden diversity ground phenomenon than often realized. How many We can expect that some species from our sampled area plant species actually co-exist in soil? Do above-ground (or volume) remain unobserved. I call this set of species plant community patterns reflect those below ground? hidden diversity, because these species are not in fact These aspects of vegetation science have been badly absent from the sample, but merely absent from observa- neglected because, until recently, plant roots and rhi- tion. At larger spatial scales, it is also likely that some rare zomes of different species were mostly indistinguishable. species remain overlooked (Gaston et al. 1997). Several Current DNA-based methods have started to shed light on methods, however, are available to estimate if sampling is this phenomenon (Partel€ et al. 2012). We have used the sufficient, e.g. species accumulation curves based on sam- next-generation sequencing to identify plant species in ples or individuals, rarefaction curves with resampling, temperate grasslands in 10 9 10 9 10 cm volume below Jackknife and Chao estimates which incorporate multiple the soil surface, the horizon where most roots in grass- subsamples (Gotelli & Colwell 2001; Cao et al. 2007). lands are located (Hiiesalu et al. 2012). We found that These methods can estimate how many species have been small-scale plant species richness below ground is up to overlooked but do not inform us of the identity of hidden twice that above ground. When we examined the whole diversity. Current developments in environmental DNA 2-ha grassland (cumulative data from several samples), metabarcoding have hinted that such methods might be there were still a number of species found only below sensitive enough to detect some rare species missed by tra- ground. All these species belonged to the local species pool ditional sampling (Taberlet et al. 2012; Ji et al. 2013; Zhan and were recorded in the study site in previous years. At et al. 2013). The potential and limitations of new DNA- the sampling time, however, they were present only in based methods await further testing. the soil. In addition, there are different species co-exis- When the sampling area is small, it is likely that all indi- tence patterns above and below the ground: more biotic viduals are counted and all species are observed above assembly rules were detected above ground, whereas the ground at any given time. At the same time, some species below ground part was largely determined abiotically in the community simply cannot be recorded by traditional (Price et al. 2012). Even relationships with other commu- visual inspection. This is readily apparent for mobile organ- nity properties such as productivity, heterogeneity or dis- isms; members of an ecological community might be turbance regime might differ between above- and below- absent temporarily (e.g. foraging for food). Sessile plants, ground realms (Partel€ et al. 2012). For example, if the however, can also be temporarily absent above ground. above-ground richness decreases with increasing soil fer- Species can be dormant, e.g. existing at the time of sam- tility, the number of species only found below ground pling as vegetative rhizomes or roots in the soil, or as part increases; hence, the total richness is independent of soil of the active seed bank. fertility (Hiiesalu et al. 2012). Journal of Vegetation Science 2 Doi: 10.1111/jvs.12169 © 2014 International Association for Vegetation Science M. P€artel Community ecology of absent species The recent knowledge of hidden diversity provides a ful- from astrophysics, where dark matter is the term for the ler picture of co-existing species.
Load more

Recommended publications
  • Does Pollen-Assemblage Richness Reflect Floristic Richness? a Review of 2 Recent Developments and Future Challenges 3
    1 1 Does pollen-assemblage richness reflect floristic richness? A review of 2 recent developments and future challenges 3 4 H. John B. Birksa,b,*, Vivian A. Feldea,c,*, Anne E. Bjunea,c, John-Arvid Grytnesd, Heikki Seppäe, Thomas 5 Gieseckef 6 a Department of Biology and Bjerknes Centre for Climate Research, University of Bergen, PO Box 7803, N-5020 7 Bergen, Norway 8 b Environmental Change Research Centre, University College London, Gower Street, London, WC1E 6BT, UK 9 c Uni Research Climate, Allégaten 55, N-5007 Bergen, Norway 10 d Department of Biology, University of Bergen, PO Box 7803, N-5020 Bergen, Norway 11 e Department of Geosciences and Geography, University of Helsinki, PO Box 64, FI-00014 Helsinki, Finland 12 f Department of Palynology and Climate Dynamics, Albrecht-von-Heller Institute for Plant Sciences, University of 13 Göttingen, Untere Karspüle 2, D-37073 Göttingen, Germany 14 * HJB Birks and VA Felde contributed equally 15 16 ABSTRACT 17 Current interest and debate on pollen-assemblage richness as a proxy for past plant richness have prompted us 18 to review recent developments in assessing whether modern pollen-assemblage richness reflects 19 contemporary floristic richness. We present basic definitions and outline key terminology. We outline four 20 basic needs in assessing pollen–plant richness relationships – modern pollen data, modern vegetation data, 21 pollen–plant translation tables, and quantification of the co-variation between modern pollen and vegetation 22 compositional data. We discuss three key estimates and one numerical tool – richness estimation, evenness 23 estimation, diversity estimation, and statistical modelling. We consider the inherent problems and biases in 24 assessing pollen–plant richness relationships – taxonomic precision, pollen-sample:pollen-population ratios, 25 pollen-representation bias, and underlying concepts of evenness and diversity.
    [Show full text]
  • A Simple Survey Protocol for Assessing Terrestrial Biodiversity in a Broad Range of Ecosystems
    RESEARCH ARTICLE A simple survey protocol for assessing terrestrial biodiversity in a broad range of ecosystems 1 2 1 Asko LõhmusID *, Piret Lõhmus , Kadri Runnel 1 Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise, Tartu, Estonia, 2 Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai, Tartu, Estonia a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 a1111111111 Abstract Finding standard cost-effective methods for monitoring biodiversity is challenging due to trade-offs between survey costs (including expertise), specificity, and range of applicability. These trade-offs cause a lack of comparability among datasets collected by ecologists and OPEN ACCESS conservationists, which is most regrettable in taxonomically demanding work on megadi- Citation: Lõhmus A, Lõhmus P, Runnel K (2018) A verse inconspicuous taxon groups. We have developed a site-scale survey method for simple survey protocol for assessing terrestrial diverse sessile land organisms, which can be analyzed over multiple scales and linked biodiversity in a broad range of ecosystems. PLoS with ecological insights and management. The core idea is that field experts can effectively ONE 13(12): e0208535. https://doi.org/10.1371/ journal.pone.0208535 allocate observation effort when the time, area, and priority sequence of tasks are fixed. We present the protocol, explain its specifications (taxon group; expert qualification; plot Editor: Maura (Gee) Geraldine Chapman, University of Sydney, AUSTRALIA size; effort) and applications based on >800 original surveys of four taxon groups; and we analyze its effectiveness using data on polypores in hemiboreal and tropical forests. We Received: July 12, 2018 demonstrate consistent effort-species richness curves and among-survey variation in con- Accepted: November 18, 2018 trasting ecosystems, and high effectiveness compared with casual observations both at Published: December 12, 2018 local and regional scales.
    [Show full text]
  • Observed and Dark Diversity
    ARGO RONK DISSERTATIONES BIOLOGICAE UNIVERSITATIS TARTUENSIS 300 Plant diversityPlant patterns observed and acrossdark Europe: diversity ARGO RONK Plant diversity patterns across Europe: observed and dark diversity Tartu 2016 1 ISSN 1024-6479 ISBN 978-9949-77-206-3 DISSERTATIONES BIOLOGICAE UNIVERSITATIS TARTUENSIS 300 DISSERTATIONES BIOLOGICAE UNIVERSITATIS TARTUENSIS 300 ARGO RONK Plant diversity patterns across Europe: observed and dark diversity Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Estonia Dissertation was accepted for the commencement of the degree of Doctor philo- sophiae in botany and mycology at the University of Tartu on May 16, 2016 by the Scientific Council of the Institute of Ecology and Earth Sciences University of Tartu. Supervisor: Prof Meelis Pärtel, University of Tartu, Estonia Opponent: Prof. Jens-Christian Svenning, University of Aarhus, Denmark Commencement: Council hall of the University of Tartu, 18 Ülikooli Street, Tartu, on September 15, 2016 at 10.15 a.m. Publication of this thesis is granted by the Institute of Ecology and Earth Sciences, University of Tartu ISSN 1024-6479 ISBN 978-9949-77-206-3 (print) ISBN 978-9949-77-207-0 (pdf) Copyright: Argo Ronk, 2016 University of Tartu Press www.tyk.ee CONTENTS LIST OF ORIGINAL PUBLICATIONS ...................................................... 6 INTRODUCTION ......................................................................................... 7 Objectives of the thesis ...........................................................................
    [Show full text]
  • Comparing Environmental DNA Metabarcoding and Underwater Visual Census to Monitor Tropical Reef Fishes
    Received: 4 April 2020 | Revised: 6 August 2020 | Accepted: 9 September 2020 DOI: 10.1002/edn3.140 SPECIAL ISSUE ORIGINAL ARTICLE Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes Andrea Polanco Fernández1 | Virginie Marques2,3 | Fabian Fopp4,5 | Jean-Baptiste Juhel2 | Giomar Helena Borrero-Pérez1 | Marie-Charlotte Cheutin2 | Tony Dejean6 | Juan David González Corredor1 | Andrés Acosta-Chaparro1 | Régis Hocdé2 | David Eme7 | Eva Maire2,8 | Manuel Spescha4,5 | Alice Valentini6 | Stéphanie Manel3 | David Mouillot2 | Camille Albouy7 | Loïc Pellissier4,5 1Programa de Biodiversidad y Ecosistemas Marinos, Museo de Historia Natural Abstract Marina de Colombia (MHNMC), Instituto Environmental DNA (eDNA) analysis is a revolutionary method to monitor marine de Investigaciones Marinas y Costeras- INVEMAR, Santa Marta, Colombia biodiversity from animal DNA traces. Examining the capacity of eDNA to provide 2MARBEC, CNRS, Ifremer, IRD, University of accurate biodiversity measures in species-rich ecosystems such as coral reefs is a Montpellier, Montpellier, France prerequisite for their application in long-term monitoring. Here, we surveyed two 3EPHE, CNRS, UM, UM3, IRD, UMR5175 CEFE, PSL Research University, Montpellier, Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near France Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected 4 Landscape Ecology, Institute of Terrestrial a large quantity of surface water (30 L per filter) above the reefs
    [Show full text]
  • The Biodiversity Offsetting Dilemma: Between Economic Rationales and Ecological Dynamics
    Sustainability 2015, 7, 7357-7378; doi:10.3390/su7067357 OPEN ACCESS sustainability ISSN 2071-1050 www.mdpi.com/journal/sustainability Article The Biodiversity Offsetting Dilemma: Between Economic Rationales and Ecological Dynamics Coralie Calvet 1,2,*, Claude Napoléone 2 and Jean-Michel Salles 3 1 Université d’Avignon et des Pays de Vaucluse, UMR CNRS IRD 7263/237 IMBE, Site Agroparc, BP 61207, 84911 Avignon, Cedex 09, France 2 INRA, UR0767 Ecodeveloppement, Site Agroparc, Domaine St Paul, CS 40509, 84914 Avignon, Cedex 09, France; E-Mail: [email protected] 3 CNRS, UMR5474 LAMETA, Campus SupAgro, 2 place Pierre Viala, 34060 Montpellier Cedex 2, France; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +33-687-035-497. Academic Editors: Géraldine Froger and Olivier Petit Received: 27 February 2015 / Accepted: 28 May 2015 / Published: 9 June 2015 Abstract: Although many countries have included biodiversity offsetting (BO) requirements in their environmental regulations over the past four decades, this mechanism has recently been the object of renewed political interest. Incorporated into the mitigation hierarchy in three steps aimed at avoiding, reducing and offsetting residual impacts on biodiversity arising from development projects, BO is promoted as the way to achieve the political goal of No Net Loss of biodiversity (NNL). The recent success of BO is mainly based on its ability to provide economic incentives for biodiversity conservation. However, the diversity of BO mechanisms (direct offsets, banking mechanism and offsetting funds) and the various institutional frameworks within which they are applied generate substantial confusion about their economic and ecological implications.
    [Show full text]
  • Dark Diversity Reveals Importance of Biotic Resources and Competition for Plant Diversity Across Habitats
    Received: 22 August 2019 | Revised: 5 February 2020 | Accepted: 10 February 2020 DOI: 10.1002/ece3.6351 ORIGINAL RESEARCH Dark diversity reveals importance of biotic resources and competition for plant diversity across habitats Camilla Fløjgaard1 | Jose W. Valdez1 | Lars Dalby1 | Jesper Erenskjold Moeslund1 | Kevin K. Clausen1 | Rasmus Ejrnæs1 | Meelis Pärtel2 | Ane Kirstine Brunbjerg1 1Department of Bioscience – Kalø, Aarhus University, Rønde, Denmark Abstract 2Department of Botany, Institute of Ecology Species richness is the most commonly used metric to quantify biodiversity. However, and Earth Sciences, University of Tartu, examining dark diversity, the group of missing species which can potentially inhabit Tartu, Estonia a site, can provide a more thorough understanding of the processes influencing ob- Correspondence served biodiversity and help evaluate the restoration potential of local habitats. So Camilla Fløjgaard and Ane Kirstine Brunbjerg, Department of Bioscience – far, dark diversity has mainly been studied for specific habitats or large-scale land- Kalø, Aarhus University, Grenåvej 14, 8410 scapes, while less attention has been given to variation across broad environmental Rønde, Denmark. Emails: [email protected]; [email protected] gradients or as a result of local conditions and biotic interactions. In this study, we investigate the importance of local environmental conditions in determining dark Funding information Villum Fonden, Grant/Award Number: VKR- diversity and observed richness in plant communities across broad environmental 023343; Aage V Jensen Nature Fund gradients. Using the ecospace concept, we investigate how these biodiversity meas- ures relate to abiotic gradients (defined as position), availability of biotic resources (defined as expansion), spatiotemporal extent of habitats (defined as continuity), and species interactions through competition.
    [Show full text]
  • Environmental DNA Illuminates the Dark Diversity of Sharks Germain Boussarie, Judith Bakker, Owen S
    Environmental DNA illuminates the dark diversity of sharks Germain Boussarie, Judith Bakker, Owen S. Wangensteen, Stefano Mariani, Lucas Bonnin, Jean-Baptiste Juhel, Jeremy J. Kiszka, Michel Kulbicki, Stephanie Manel, William D. Robbins, et al. To cite this version: Germain Boussarie, Judith Bakker, Owen S. Wangensteen, Stefano Mariani, Lucas Bonnin, et al.. Environmental DNA illuminates the dark diversity of sharks. Science Advances , American Association for the Advancement of Science (AAAS), 2018, 4 (5), pp.1-8. 10.1126/sciadv.aap9661. hal-01826693 HAL Id: hal-01826693 https://hal.archives-ouvertes.fr/hal-01826693 Submitted on 16 Dec 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License SCIENCE ADVANCES | RESEARCH ARTICLE ECOLOGY Copyright © 2018 The Authors, some Environmental DNA illuminates the dark diversity rights reserved; exclusive licensee of sharks American Association for the Advancement 1,2 3 3,4 3 of Science. No claim to Germain Boussarie, * Judith Bakker, * Owen S. Wangensteen, Stefano Mariani, original U.S. Government 1,2 1,2 5 6 7 Lucas Bonnin, Jean-Baptiste Juhel, Jeremy J. Kiszka, Michel Kulbicki, Stephanie Manel, Works.
    [Show full text]
  • Throwing Light on Dark Diversity of Vascular Plants in China: Predicting the Distribution of Dark and Threatened Species Under Global Climate Change
    Throwing light on dark diversity of vascular plants in China: predicting the distribution of dark and threatened species under global climate change Lili Tang1, Runxi Wang1, Kate S. He2, Cong Shi3, Tong Yang1, Yaping Huang1, Pufan Zheng1 and Fuchen Shi1 1 College of Life Sciences, NanKai University, Tianjin, China 2 Department of Biological Sciences, Murray State University, Murray, KY, USA 3 School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China ABSTRACT Background: As global climate change accelerates, ecologists and conservationists are increasingly investigating changes in biodiversity and predicting species distribution based on species observed at sites, but rarely consider those plant species that could potentially inhabit but are absent from these areas (i.e., the dark diversity and its distribution). Here, we estimated the dark diversity of vascular plants in China and picked up threatened dark species from the result, and applied maximum entropy (MaxEnt) model to project current and future distributions of those dark species in their potential regions (those regions that have these dark species). Methods: We used the Beals probability index to estimate dark diversity in China based on available species distribution information and explored which environmental variables had significant impacts on dark diversity by incorporating bioclimatic data into the random forest (RF) model. We collected occurrence data of threatened dark species (Eucommia ulmoides, Liriodendron chinense, Phoebe bournei, Fagus longipetiolata, Amentotaxus argotaenia, and Cathaya argyrophylla) Submitted 28 August 2018 and related bioclimatic information that can be used to predict their distributions. In Accepted 6 March 2019 addition, we used MaxEnt modeling to project their distributions in suitable areas Published 9 April 2019 under future (2050 and 2070) climate change scenarios.
    [Show full text]
  • Relationships Between Macro-Fungal Dark Diversity and Habitat
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.02.185553; this version posted January 10, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 1 Relationships between macro-fungal dark diversity and 2 habitat parameters using LiDAR 3 Jose W. Valdez1, Ane Kirstine Brunbjerg1, Camilla Fløjgaard1, Lars Dalby1, Kevin K. 4 Clausen1, Meelis Pärtel2, Norbert Pfeifer3, Markus Hollaus3, Michael H. Wimmer3, Rasmus 5 Ejrnæs1, Jesper Erenskjold Moeslund1* 6 1Department of Bioscience, Aarhus University, Grenåvej 14, 8410, Rønde, Denmark 7 2 Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, 8 Tartu, 51005, Estonia 9 3 Department of Geodesy and Geoinformation, Technische Universität Wien, Wiedner 10 Hauptstraße 8/E120, 1040 Vienna, Austria 11 *Corresponding author. Email: [email protected] 12 Abstract 13 Despite the important role of fungi for ecosystems, relatively little is known about the factors 14 underlying the dynamics of their diversity. Moreover, studies do not typically consider their 15 dark diversity: the species absent from an otherwise suitable site. Here, we examined 16 potential drivers of local fungal dark diversity in temperate woodland and open habitats using 17 LiDAR and in-situ field measurements, combined with a systematically collected and 18 geographically comprehensive macro-fungi and plant data set. For the first time, we also 19 estimated species pools of fungi by considering both plant and fungi co-occurrences.
    [Show full text]
  • Community Completeness As a Measure of Restoration Success: Multiple-Study Comparisons Across Ecosystems and Ecological Groups
    Biodiversity and Conservation (2020) 29:3807–3827 https://doi.org/10.1007/s10531-020-02050-1(0123456789().,-volV)(0123456789().,-volV) ORIGINAL PAPER Community completeness as a measure of restoration success: multiple-study comparisons across ecosystems and ecological groups Norbertas Noreika1,2 • Meelis Pa¨rtel3 • Erik O¨ ckinger1 Received: 21 May 2020 / Revised: 18 August 2020 / Accepted: 9 September 2020 / Published online: 17 September 2020 Ó The Author(s) 2020 Abstract When restoring habitat for biodiversity, the most effective outcome will be achieved by restoration projects which target several organism groups or ecosystem types. Such inte- grated approaches require direct comparisons among different ecological communities while evaluating success of restoration. The Community Completeness Index (CCI) is a recently developed metric that allows such comparisons by accounting for both present and absent but otherwise suitable taxa. We empirically evaluated the applicability of CCI for assessing the outcome of ecological restoration. We analyzed how species richness and the completeness of ecological communities recover after restoration, for different ecological groups and ecosystem types, and how it develops over time after restoration. Analyses were performed on 18 datasets with per site presence-absence data from Northern Europe. Each dataset represented one of the three habitat types (mire, forest, grassland) and dif- ferent ecological groups (plants, flying insects, epigeic invertebrates). Datasets contained pristine, degraded and restored sites. We calculated the dark diversity and subsequently CCI based on species co-occurrences. Our multiple-study analyses revealed that CCI of grassland plant communities increased faster after restoration than invertebrate commu- nities or plant communities in forests and mires.
    [Show full text]
  • Mechanisms of Community Assembly Explaining Beta‐Diversity Patterns
    Received: 12 March 2018 | Revised: 22 February 2021 | Accepted: 3 March 2021 DOI: 10.1111/jvs.13032 RESEARCH ARTICLE Journal of Vegetation Science Mechanisms of community assembly explaining beta- diversity patterns across biogeographic regions Miguel Muñoz Mazón1 | J. Sebastián Tello2 | Manuel J. Macía3,4 | Jonathan A. Myers5,6 | Peter M. Jørgensen7 | Victoria Cala8 | Alfredo F. Fuentes7,9 | Vania Torrez9 | Gabriel Arellano10 1Department of Ecology and Natural Resource Management, Norwegian Abstract University of Life Sciences (NMBU), Ås, Aim: We examined tree beta diversity in four biogeographical regions with contrast- Norway ing environmental conditions, latitude, and diversity. We tested: (a) the influence of 2Center for Conservation and Sustainable Development, Missouri Botanical Garden, the species pool on beta diversity; (b) the relative contribution of niche- based and St. Louis, Missouri, USA dispersal- based assembly to beta diversity; and (c) differences in the importance of 3Departamento de Biología, Área de Botánica, Universidad Autónoma de Madrid, these two assembly mechanisms in regions with differing productivity and species Madrid, Spain richness. 4 Centro de Investigación en Biodiversidad Location: Lowland and montane tropical forests in the Madidi region (Bolivia), low- y Cambio Global (CIBC- UAM), Universidad Autónoma de Madrid, Madrid, Spain land temperate forests in the Ozarks (USA), and montane temperate forests in the 5Department of Biology, Washington Cantabrian Mountains (Spain). University in St. Louis, St. Louis, Missouri, Methods: We surveyed woody plants with a diameter ≥2.5 cm following a standard- USA 6Tyson Research Center, Washington ized protocol in 236 0.1- ha forest plots in four different biogeographical regions. We University in St. Louis, St.
    [Show full text]
  • Environmental DNA Illuminates the Dark Diversity of Sharks
    SCIENCE ADVANCES | RESEARCH ARTICLE ECOLOGY Copyright © 2018 The Authors, some Environmental DNA illuminates the dark diversity rights reserved; exclusive licensee of sharks American Association for the Advancement 1,2 3 3,4 3 of Science. No claim to Germain Boussarie, * Judith Bakker, * Owen S. Wangensteen, Stefano Mariani, original U.S. Government 1,2 1,2 5 6 7 Lucas Bonnin, Jean-Baptiste Juhel, Jeremy J. Kiszka, Michel Kulbicki, Stephanie Manel, Works. Distributed 8,9,10 1† 2,11†‡ William D. Robbins, Laurent Vigliola, David Mouillot under a Creative Commons Attribution In the era of “Anthropocene defaunation,” large species are often no longer detected in habitats where they NonCommercial formerly occurred. However, it is unclear whether this apparent missing, or “dark,” diversity of megafauna License 4.0 (CC BY-NC). results from local species extirpations or from failure to detect elusive remaining individuals. We find that despite two orders of magnitude less sampling effort, environmental DNA (eDNA) detects 44% more shark species than traditional underwater visual censuses and baited videos across the New Caledonian archipelago (south-western Pacific). Furthermore, eDNA analysis reveals the presence of previously unobserved shark species in human- impacted areas. Overall, our results highlight a greater prevalence of sharks than described by traditional survey methods in both impacted and wilderness areas. This indicates an urgent need for large-scale eDNA assessments to improve monitoring of threatened and elusive megafauna. Finally, our findings emphasize the need for conservation efforts specifically geared toward the protection of elusive, residual populations. INTRODUCTION whereas the confirmed absence of species requires different manage- Human activities are largely responsible for the ongoing defaunation of ment considerations (6).
    [Show full text]