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    Biodiversity needs every tool in the box: use OECMs

    COMMENT
    26 July 2021

    Biodiversity needs every tool in the box: use OECMs

    To conserve global biodiversity, countries must forge equitable alliances that support sustainability in traditional pastoral lands, fisheries-management areas, Indigenous territories and more.

    Georgina G. Gurney

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    ,

    Emily S. Darling

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    ,

    Gabby N. Ahmadia

    2
    ,

    Vera N. Agostini

    3
    ,

    Natalie C. Ban

    4
    ,

    Jessica Blythe

    5
    ,

    Joachim Claudet

    6
    ,

    Graham Epstein

    7
    ,

    Estradivari

    8
    ,

    Amber Himes-Cornell

    9
    ,

    Harry D. Jonas

    10
    ,

    Derek Armitage

    11
    ,

    Stuart J. Campbell

    12
    ,

    Courtney Cox

    13
    ,

    Whitney. R. Friedman

    14
    ,

    David Gill

    15
    ,

    Peni Lestari

    16
    ,

    Sangeeta Mangubhai

    17
    ,

    Elizabeth McLeod

    18
    ,

    Nyawira A. Muthiga

    19
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    Josheena Naggea

    20
    ,

    Ravaka Ranaivoson

    21
    ,

    Amelia Wenger

    22
    ,

    Irfan Yulianto

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    &

    Stacy D. Jupiter

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    Georgina G. Gurney

    Georgina G. Gurney is a senior research fellow in environmental social science at the Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia.

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    Emily S. Darling

    Emily S. Darling is director, Coral Reef Conservation, Wildlife Conservation Society.

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    Gabby N. Ahmadia

    Gabby N. Ahmadia is director, Marine Conservation Science, Ocean Conservation, World Wildlife Fund.

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    Vera N. Agostini

    Vera N. Agostini is deputy director, Fisheries and Aquaculture Division, Food and Agriculture Organization of the United Nations.

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    Natalie C. Ban

    Natalie C. Ban is associate professor in environmental studies at the University of Victoria, Canada.

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    Jessica Blythe

    Jessica Blythe is assistant professor in environmental sustainability at Brock University, St Catharines, Canada.

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    Joachim Claudet

    Joachim Claudet is a senior researcher at the National Center for Scientific Research, CRIOBE, France.

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    Graham Epstein

    Graham Epstein is a postdoctoral research associate at the School of Politics, Security and International Affairs at the University of Central Florida, Orlando, USA.

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    Estradivari

    Estradivari is a researcher at the Leibniz Center for Tropical Marine Research (ZMT), Germany, and a conservation research manager, World Wildlife Fund Indonesia.

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    Amber Himes-Cornell

    Amber Himes-Cornell is a fisheries officer, Fisheries and Aquaculture Division, Food and Agricultural Organization of the United Nations.

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    Harry D. Jonas

    Harry D. Jonas is an international lawyer at Future Law, Kota Kinabalu, Malaysia, and co-chair of the IUCN WCPA Specialist Group on Other Effective Area-based Conservation Measures.

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    Derek Armitage

    Derek Armitage is a professor in the School of Environment, Resources and Sustainability, University of Waterloo, Canada.

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    Stuart J. Campbell

    Stuart J. Campbell is senior director, RARE Indonesia.

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    Courtney Cox

    Courtney Cox is senior director, Rare, Washington DC, USA.

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    Whitney. R. Friedman

    Whitney R. Friedman is a postdoctoral fellow at the University of California, Santa Barbara, USA.

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    David Gill

    David Gill is an assistant professor of marine science and conservation at Duke University, Durham, North Carolina, USA.

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    Peni Lestari

    Peni Lestari is a socioeconomic marine specialist, Wildlife Conservation Society.

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    Sangeeta Mangubhai

    Sangeeta Mangubhai is director, Fiji Program, Wildlife Conservation Society.

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    Elizabeth McLeod

    Elizabeth McLeod is global reef lead, The Nature Conservancy, Arlington, Virginia, USA.

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    Nyawira A. Muthiga

    Nyawira A. Muthiga is director, Marine Conservation Program, Kenya Program, Wildlife Conservation Society.

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    Josheena Naggea

    Josheena Naggea is a PhD candidate at Stanford University, California, USA, studying conservation in her home country of Mauritius.

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    Ravaka Ranaivoson

    Ravaka Ranaivoson is marine director, Madagascar Program, Wildlife Conservation Society.

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    Amelia Wenger

    Amelia Wenger is a research fellow in the School of Earth and environmental sciences at the University of Queensland, Brisbane, Australia, and a conservation scientist at the Wildlife Conservation Society.

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    Irfan Yulianto

    Irfan Yulianto is a researcher and lecturer at Institut Pertanian Bogor University, Indonesia, and a Senior Manager, Wildlife Conservation Society.

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    Stacy D. Jupiter

    Stacy D. Jupiter is Melanesia regional director at the Wildlife Conservation Society.

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    Customary fishing-rights holders from Totoya Island, Fiji, marking a sacred reef area as a no-fishing zone.Credit: Keith Ellenbogen

    Global support is growing for the 30 × 30 movement — a goal to conserve 30% of the planet by 2030. In May, the G7 group of wealthy nations endorsed the commitment to this target that had been made by more than 50 countries in January. It is likely to be the headline goal when parties to the Convention on Biological Diversity (CBD) meet to discuss the latest global conservation agreement in May 2022 in Kunming, China.So where do the sacred forests of Estonia or shipwrecks in North America’s Great Lakes come in? What do these share with managed fishing grounds in Fiji and bighorn-sheep hunting areas in Mexico? All have the potential to be recognized using a conservation policy tool called other effective area-based conservation measures, or OECMs. Together with protected areas — from Malaysia’s Taman Negara National Park to the Cerbère-Banyuls Marine Reserve in southern France — OECMs could help to achieve the 30% target.Devised in 2010 and defined in 2018, the OECM tool is little known outside specialist circles. Less than 1% of the world’s land and freshwater environments and less than 0.1% of marine areas are currently covered under this designation. Meanwhile, biodiversity is in free fall and protected areas alone can’t stem the loss. Both designations are among the international policy instruments being negotiated ahead of the CBD conference.We call on the CBD parties and the conservation community of policymakers, scientists, practitioners and donors to study and use OECMs more, alongside protected areas. This policy tool can advance equitable and effective conservation if CBD parties stay true to the convention’s intent to sustain biodiversity rather than ‘achieve’ area-based targets. But more groundwork must be laid to realize its potential.Improvements are needed in research, policy and practice. Local managers and CBD parties need better ways to assess whether potential OECMs contribute to sustaining biodiversity, so that areas are properly designated. The conservation community needs to develop processes to ensure that OECM recognition strengthens, rather than displaces, existing local governance. And researchers need to articulate the value of OECMs to encourage policymakers to use them.Bigger toolkit Protected areas have expanded rapidly in the past 10 years, and now cover 15.7% of the world’s land and fresh water, and 7.7% of the marine realm. Defined by the CBD as areas designated or regulated and managed for biodiversity conservation, they are an essential conservation approach. But some have failed to be equitable or effective: aligning biodiversity goals with local values, needs and governance can be difficult in some contexts1,2. This conflict can lead to inequities, non-compliance and poor biodiversity outcomes.
    Indigenous rights vital to survival
    OECMs can have an important and complementary role3. The tool recognizes managed areas that sustain biodiversity, irrespective of their objective. OECM recognition can support Indigenous and local communities in managing their lands and seas — be it for hunting, fishing or other cultural practices — while conserving nature. It opens up new conservation opportunities in landscapes where there is relatively light human usage, such as pastoralism with a low density of livestock. These regions make up nearly 56% of the world’s lands, and contain more Key Biodiversity Areas — sites of global important to biodiversity — than do remaining large wild areas4. So, management approaches that accommodate the ways people use landscapes and seascapes are crucial.Some managed areas do not safeguard biodiversity5. But there is a wealth of evidence suggesting that many do. For example, a study of the Peruvian Amazon found that Indigenous peoples’ territories were, on average, more effective than state-governed protected areas at preventing deforestation6. A review of 61 areas managed under territorial-use rights in fisheries in Chile found positive effects on biodiversity; some had levels of fish biomass and biodiversity that were comparable to those in a protected area that restricts all fishing7. And abandonment of agricultural management systems involving low-intensity farming methods in Europe — such as traditional haymaking in Romania — has been linked repeatedly to biodiversity loss8.Perhaps many of these could be recognized as OECMs (see ‘Conservation potential’). Doing so depends on the consent of the relevant governing bodies, and whether the managed area meets the CBD’s definition and criteria for OECMs, including demonstrated or expected biodiversity outcomes.

    EquityOECMs can help to ensure that international conservation targets are legitimate to the many and diverse actors required to turn the tide on biodiversity loss.Too often, the costs of conservation are felt locally while many of the benefits are shared globally — from carbon sequestration to preserving genetic resources. For instance, rainforest conservation, including a protected area, in the Ankeniheny-Zahamena Corridor in Madagascar meant that local farmers of vanilla, cloves and rice bore opportunity costs representing 27–84% of their average annual household income. The protection scheme is intended to cut 10 million tonnes of carbon dioxide emissions over 10 years9.Such inequities can occur when protected areas do not prioritize local values and needs. Although protected areas can have multiple objectives, the widely followed guidance from the International Union for Conservation of Nature (IUCN) advises that nature conservation should retain priority over all other objectives. This can alienate people who manage areas for other reasons. Even in the instance of Indigenous Protected Areas in Australia, which have resulted in an array of social and biodiversity benefits, the IUCN definition can undermine Indigenous Australians’ conceptualization of humans as part of nature, which underpins their governance systems2. This stands in contrast to the Western world view of humans as distinct from nature — a concept that is embedded in the IUCN definition and conservation more generally2,3.
    A spatial overview of the global importance of Indigenous lands for conservation
    However, OECMs need not have conservation as an objective. This means that they can be used to recognize the contributions of a myriad of actors who manage areas that sustain nature, regardless of why they do so. Indigenous peoples, for instance, manage 37% of the world’s natural lands10 for many reasons, such as maintaining rights, harvesting and cultural identity2,10,11. Recognition of Indigenous territories as OECMs could help to overcome current challenges of insecure rights, insufficient funding and exclusion of these communities from decision-making12. For example, Indonesia has initiated revisions to its conservation laws to accommodate coastal OECMs, which could provide opportunities for Indigenous and local communities to gain legal recognition of their rights to use and manage fisheries.OECMs can thus ensure a more equitable approach to conservation decision-making. They enable the participation of those who govern areas that sustain biodiversity but who are currently not involved in decision-making. For example, fisheries-management organizations have rebuilt some fish stocks, contributing to biodiversity and wider ecosystem health, yet the fisheries and conservation sectors are often divided13. OECMs can foster cooperation between sectors, and encourage the participation of fisheries-management organizations in conservation decision-making.EffectivenessCollectively, alongside protected areas, OECMs can increase the effectiveness of the global conservation system in four key ways.First, they support management that is tailored to its context14, and aligned with local values, governance and traditional knowledge systems. This fosters the local leadership, support and compliance that are key to biodiversity benefits14. For example, in Mo’orea, French Polynesia, protected areas that restricted all fishing did not meet fishers’ needs, leading to non-compliance and relatively little change in the density and biomass of coral-reef fish15. Conversely, a management area in Labrador, Canada, implemented at the behest of crab fishers, maintained the fishery and increased the biomass of fish species such as Atlantic cod (Gadus morhua) and other, non-target species16. This area seems likely to meet the OECM criteria.

    Estonia’s sacred groves are protected for their spiritual significance.Credit: Toomas Tuul/FOCUS/Universal Images Group via Getty

    Second, OECMs, together with protected areas, can help to ensure a well-connected conservation network in which all elements of biodiversity are represented and in which ecological processes, such as species movements, are sustained. For instance, Kenya’s wildlife conservancies provide geographical bridges between protected areas for the movement of wildlife such as zebras, and have potential to be recognized as OECMs.Third, OECMs can increase the diversity of tools in the global conservation system. This bolsters the system’s resilience to social and biophysical shifts, including climate change14. Redundancy in governance arrangements can help to mitigate risks associated with the current reliance on government-led protected areas, which are vulnerable to shifts in national priorities. For example, in 2017, the Bears Ears National Monument, a protected area in Utah, was downsized by 85% to make way for oil and gas exploration under a former US presidential administration.Fourth, OECMs help to bring conservation outcomes into focus. A key criterion for official designation is demonstrated or expected biodiversity outcomes, such as the restoration of a crucial habitat. This is not the case for protected areas, where a focus on coverage has, in some cases, led to expansion with scant biodiversity gains4.Five steps Key concerns remain about the misuse of OECM recognition. CBD parties might use it to meet commitments without actually tackling biodiversity loss. For example, in 2017, Canada increased the marine area it planned to report almost sixfold, by reclassifying 51 fishery closures as OECMs17. This decision was criticized on the grounds of insufficient evidence that these areas sustain biodiversity. Another concern is that, despite the focus on equity, any attempts to influence local governance could be perceived as a ‘land grab’ or ‘sea grab’ by external actors such as national governments, foreigners or international organizations. For example, the establishment of some privately owned protected areas in southern Chile has been suggested to have involved coercion and intimidation of smallholder farmers.
    Area-based conservation in the twenty-first century
    The conservation community needs to take the following five steps to overcome these key challenges to using the OECM policy tool.Show that they work. The 2019 IUCN Guidelines for Recognizing and Reporting OECMs provide clear criteria for identifying managed areas that are suitable for a full assessment against the CBD’s definition. However, research is needed on how to meet the crucial criteria of demonstrated or expected in situ conservation of biodiversity. This is challenging and resource-intensive, especially because of the variety of actors involved. Ideas based in Western science might not align with the knowledge systems of all involved.Guidelines should build on existing approaches for evaluation, such as the IUCN Green List for Protected and Conserved Areas and the Indicators of Resilience in Socio-ecological Production Landscapes (SEPLs). They should include recent advances focused on outcomes18 and should be tailored to different types of managed area. To ensure that these are salient, credible and legitimate to those governing OECMs, they should be co-produced by groups such as rights holders, civil-society organizations, government and industry, as well as by academics from various disciplines. This transdisciplinary approach is growing rapidly, with examples ranging from management at the national level (such as New Zealand’s Sustainable Seas National Science Challenge) to the monitoring of coral reefs as social-ecological systems19.

    Pastoral lands in Africa are often governed to maintain sustainable grazing.Credit: Steve Pastor

    Strengthen existing local governance. Many rights holders have raised concerns that formal recognition of their managed areas for conservation might infringe their rights. For example, few communities in Fiji have had their fisheries-management areas recognized under national conservation laws, because that currently requires the communities to waive their customary rights20.Engaging with global conservation processes might also erode self-determination through the imposition of external world views2,3,12. Although OECMs open the door to recognizing diverse relations between humans and nature, it is crucial that the need for demonstrated or expected biodiversity outcomes does not diminish other priorities and values.OECM recognition must strengthen existing local governance, rather than displace or substantially alter it. This will require guidelines to be informed by principles of procedural equity and tailored to different types of managed area. Their development should draw on existing approaches such as the Australian Indigenous-led Healthy Country Planning and Our Knowledge, Our Way guidelines, which have underpinned engagement with the national carbon sequestration scheme11.Secure funding. Funding for recognizing and reporting OECMs should be made available to ensure costs are not a barrier or burden for under-resourced groups. A prominent role for OECMs in the next CBD agreement will help — this policy guides conservation investments from nations and donors.
    Sixty years of tracking conservation progress using the World Database on Protected Areas
    Importantly, the diversity of managed areas that OECMs encompass can provide funding opportunities beyond conventional conservation funders, whose resources for protected-area funding are already overstretched. Conservation practitioners should engage private sectors that manage areas that could be recognized as OECMs, and access funding earmarked for other priorities such as health and development. For example, the Watershed Interventions for Systems Health project in Fiji, which aims to reduce waterborne diseases using nature-based solutions, is supported by both conservation and public-health funding.Conservation donors and practitioners should co-design new funding strategies for OECMs with those governing these areas. This will help to ensure that local priorities are supported. For example, Coast Funds, a unique conservation trust fund, was developed by First Nations people in collaboration with conservation practitioners and the forestry industry to support stewardship of the Great Bear Rainforest and Haida Gwaii regions of British Columbia, Canada.Agree on metrics. The record of progress towards the CBD’s area-based target, the World Database on Protected Areas, assumes that all reported protected areas have biodiversity conservation as a main objective. But some CBD parties report areas that have other primary objectives, such as sustainable harvesting20. This leads to inaccurate accounting at the global level, and to misunderstanding of management actually occurring on the ground. Canada, among others, is developing legislation that demarcates protected areas and OECMs. But it is not clear whether all CBD parties will do the same.Policymakers need to agree on targets that are based on outcomes — not just coverage — for both OECMs and protected areas. These might include, for example, changes in the populations of multiple species relative to a reference point. In constructing these targets, the conservation community should be guided by the development and health sectors, which have long used outcome targets. For example, the United Nations Sustainable Development Goal 1.2 aims to reduce at least by half the proportion of people living in multidimensional, regionally-defined poverty by 2030. A common currency of outcomes could alleviate concerns that there is an uneven burden of proof for the OECM and protected-area tools. It could also prevent the misuse of either to meet targets based on area without actually sustaining biodiversity.Include OECMs in other environmental agreements. Addressing the interrelated global challenges of biodiversity loss, climate change and sustainability requires the coordination of policy across sectors. Right now, OECMs appear only in CBD policy. But they could contribute to the mandates of other intergovernmental initiatives. Policymakers should include OECMs alongside protected areas in international agreements such as the Sustainable Development Goals, new global climate agreements being negotiated under the UN convention on climate, and the emerging UN treaty on marine biodiversity in areas beyond national jurisdiction.New targets negotiated at the upcoming CBD meeting will set the global conservation agenda over the next decade. If the steps we outline here are implemented, OECMs could be central to the transformations needed for a sustainable future for the planet.

    Nature 595, 646-649 (2021)
    doi: https://doi.org/10.1038/d41586-021-02041-4

    References1.Oldekop, J. A., Holmes, G., Harris, W. E. & Evans, K. L. Conserv. Biol. 30, 133–141 (2016).PubMed 
    Article 

    Google Scholar 
    2.Lee, E. Antipode 48, 355–374 (2016).Article 

    Google Scholar 
    3.Jonas, H. D., Barbuto, V., Jonas, H. C., Kothari, A. & Nelson, F. PARKS 20, 111–128 (2014).Article 

    Google Scholar 
    4.Ellis, E. C. One Earth 1, 163–167 (2019).Article 

    Google Scholar 
    5.Donald, P. F. et al. Conserv. Lett. 12, e12659 (2019).Article 

    Google Scholar 
    6.Schleicher, J., Peres, C. A., Amano, T., Llactayo, W. & Leader-Williams, N. Sci. Rep. 7, 11318 (2017).PubMed 
    Article 

    Google Scholar 
    7.Gelcich, S., Martínez-Harms, M. J., Tapia-Lewin, S., Vasquez-Lavin, F. & Ruano-Chamorro, C. Conserv. Lett. 12, e12637 (2019).Article 

    Google Scholar 
    8.Lomba, A. et al. Front. Ecol. Environ. 18, 36–42 (2020).Article 

    Google Scholar 
    9.Poudyal, M. et al. PeerJ 6,e5106 (2018).PubMed 
    Article 

    Google Scholar 
    10.Garnett, S. T. et al. Nature Sustain. 1, 369–374 (2018).Article 

    Google Scholar 
    11.Ansell, J. et al. Int. J. Wildland Fire 29, 371–385 (2019).Article 

    Google Scholar 
    12.Corson, C. et al. Conserv. Soc. 12, 190–202 (2014).Article 

    Google Scholar 
    13.Hilborn, R. Nature 535, 224–226 (2016).PubMed 
    Article 

    Google Scholar 
    14.Carlisle, K. & Gruby, R. L. Policy Stud. J. 47, 927–952 (2019).Article 

    Google Scholar 
    15.Thiault, L. et al. Ecosphere 10, e02576 (2019).Article 

    Google Scholar 
    16.Kincaid, K. & Rose, G. Can. J. Fish. Aqua. Sci. 74, 1490–1502 (2017).Article 

    Google Scholar 
    17.Lemieux, C. J. & Gray, P. A. J. Environ. Stud. Sci. 10, 483–491 (2020).Article 

    Google Scholar 
    18.Geldmann, J. et al. Conserv. Lett. https://doi.org/10.1111/conl.12792 (2021).Article 

    Google Scholar 
    19.Gurney, G. G. et al. Biol. Conserv. 240, 108298 (2019).Article 

    Google Scholar 
    20.Govan, H. & Jupiter, S. PARKS 19, 73–80 (2013).Article 

    Google Scholar 
    Download references

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    Niche partitioning among dead wood-dependent beetles

    1.Polechová, J. & Storch, D. Ecological niche. Encycl. Ecol. 2, 1088–1097 (2008).
    Google Scholar 
    2.Vannette, R. L. & Fukami, T. Historical contingency in species interactions: Towards niche-based predictions. Ecol. Lett. 17, 115–124 (2014).PubMed 
    Article 

    Google Scholar 
    3.Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography (Princeton University Press, 2011).Book 

    Google Scholar 
    4.Clark, J. S. The coherence problem with the unified neutral theory of biodiversity. Trends Ecol. Evol. 27, 198–202 (2012).PubMed 
    Article 

    Google Scholar 
    5.McGill, B. J. A test of the unified neutral theory of biodiversity. Nature 422, 881–885 (2003).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    6.Bocci, A. et al. Sympatric snow leopards and Tibetan wolves: Coexistence of large carnivores with human-driven potential competition. Eur. J. Wildl. Res. 63, 92 (2017).Article 

    Google Scholar 
    7.Dueser, R. D. & Shuggart, H. H. Niche pattern in a forest-floor small-mammal fauna. Ecology 60, 108–118 (1979).Article 

    Google Scholar 
    8.Cloyed, C. S. & Eason, P. K. Niche partitioning and the role of intraspecific niche variation in structuring a guild of generalist anurans. R. Soc. Open Sci. 4, 170060 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Armstrong, R. A. & McGehee, R. Coexistence of species competing for shared resources. Theor. Popul. Biol. 9, 317–328 (1976).MathSciNet 
    CAS 
    PubMed 
    MATH 
    Article 

    Google Scholar 
    10.Paillet, Y. et al. The indicator side of tree microhabitats: A multi-taxon approach based on bats, birds and saproxylic beetles. J. Appl. Ecol. 55, 2147–2159 (2018).Article 

    Google Scholar 
    11.Kadowaki, K. Species coexistence patterns in a mycophagous insect community inhabiting the wood-decaying bracket fungus Cryptoporus volvatus (Polyporaceae: Basidiomycota). Eur. J. Entomol. 107, 89 (2010).Article 

    Google Scholar 
    12.Peter, A.-K. Survival in adults of the water frog Rana lessonae and its hybridogenetic associate Rana esculenta. Can. J. Zool. 79, 652–661 (2001).Article 

    Google Scholar 
    13.Borkowski, A. & Skrzecz, I. Ecological segregation of bark beetle (Coleoptera, Curculionidae, Scolytinae) infested Scots pine. Ecol. Res. 31, 135–144 (2016).Article 

    Google Scholar 
    14.Bobiec, A., Gutowski, J. M. & Laudenslayer, W. F. The Afterlife of a Tree (WWF Poland, 2005).
    Google Scholar 
    15.Alexander, K. N. Tree biology and saproxylic Coleoptera: issues of definitions and conservation language. Rev. Ecol. 10, 9–13 (2008).
    Google Scholar 
    16.Véle, A. & Horák, J. The importance of host characteristics and canopy openness for pest management in urban forests. Urban For. Urban Green. 36, 84–89 (2018).Article 

    Google Scholar 
    17.Přikryl, Z. B., Turčáni, M. & Horák, J. Sharing the same space: Foraging behaviour of saproxylic beetles in relation to dietary components of morphologically similar larvae. Ecol. Entomol. 37, 117–123 (2012).Article 

    Google Scholar 
    18.Brin, A. & Bouget, C. Biotic interactions between saproxylic insect species. In Saproxylic insects: Diversity, ecology and conservation (ed. Ulyshen, M. D.) 471–514 (Springer, 2018).Chapter 

    Google Scholar 
    19.Stokland, J. N., Siitonen, J. & Jonsson, B. G. Biodiversity in Dead Wood (Cambridge University Press, 2012).Book 

    Google Scholar 
    20.Radchuk, V., Turlure, C. & Schtickzelle, N. Each life stage matters: The importance of assessing the response to climate change over the complete life cycle in butterflies. J. Anim. Ecol. 82, 275–285 (2013).PubMed 
    Article 

    Google Scholar 
    21.Biedermann, P. H. & Taborsky, M. Larval helpers and age polyethism in ambrosia beetles. Proc. Natl. Acad. Sci. U.S.A. 108, 17064–17069 (2011).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Hanks, L. M. Influence of the larval host plant on reproductive strategies of cerambycid beetles. Annu. Rev. Entomol. 44, 483–505 (1999).CAS 
    PubMed 
    Article 

    Google Scholar 
    23.Horak, J. What is happening after an abiotic disturbance? Response of saproxylic beetles in the Primorsky Region woodlands (Far Eastern Russia). J. Insect Conserv. 19, 97–103 (2015).Article 

    Google Scholar 
    24.Hůrka, K. Beetles of the Czech and Slovak Republics (Kabourek, 2005).
    Google Scholar 
    25.Horák, J. & Chobot, K. Phenology and notes on the behaviour of Cucujus cinnaberinus: Points for understanding the conservation of the saproxylic beetle. North-West. J. Zool. 7, 352–355 (2011).
    Google Scholar 
    26.Finke, D. L. & Snyder, W. E. Niche partitioning increases resource exploitation by diverse communities. Science 321, 1488–1490 (2008).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    27.Crowson, R. Observations on Dendrophagus crenatus (Paykull)(Cucujidae) and some comparisons with piestine Staphylinidae (Coleoptera). Entomol. Mon. Mag. 104, 161–169 (1969).
    Google Scholar 
    28.Tarno, H. et al. The behavioral role of males of platypus quercivorus murayama in their subsocial colonies. Agrivita 38, 47–54 (2016).
    Google Scholar 
    29.Della Rocca, F. & Milanesi, P. Combining climate, land use change and dispersal to predict the distribution of endangered species with limited vagility. J. Biogeogr. 47, 1427–1438 (2020).Article 

    Google Scholar 
    30.Buse, J. “Ghosts of the past”: flightless saproxylic weevils (Coleoptera: Curculionidae) are relict species in ancient woodlands. J. Insect Conserv. 16, 93–102 (2012).Article 

    Google Scholar 
    31.Røed, K. H. et al. Isolation and characterization of ten microsatellite loci for the wood-living and threatened beetle Cucujus cinnaberinus (Coleoptera: Cucujidae). Conserv. Genet. Resour. 6, 641–643 (2014).Article 

    Google Scholar 
    32.Konvicka, M., Hula, V. & Fric, Z. Habitat of pre-hibernating larvae of the endangered butterfly Euphydryas aurinia (Lepidoptera: Nymphalidae): What can be learned from vegetation composition and architecture?. Eur. J. Entomol. 100, 313–322 (2003).Article 

    Google Scholar 
    33.Bonacci, T. et al. Artificial feeding and laboratory rearing of endangered saproxylic beetles as a tool for insect conservation. J. Insect Sci. 20, 20 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    34.Mazzei, A. et al. Rediscovering the ‘umbrella species’ candidate Cucujus cinnaberinus (Scopoli, 1763) in Southern Italy (Coleoptera Cucujidae), and notes on bionomy. Ital. J. Zool. 78, 264–270 (2011).Article 

    Google Scholar 
    35.Horák, J., Chumanová, E. & Chobot, K. Habitat preferences influencing populations, distribution and conservation of the endangered saproxylic beetle Cucujus cinnaberinus (Coleoptera: Cucujidae) at the landscape level. Eur. J. Entomol. 107, 81–88 (2010).Article 

    Google Scholar 
    36.Hardin, G. The competitive exclusion principle. Science 131, 1292–1297 (1960).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    37.Carmel, Y. et al. Using exclusion rate to unify niche and neutral perspectives on coexistence. Oikos 126, 1451–1458 (2017).Article 

    Google Scholar 
    38.Horák, J., Chumanová, E. & Hilszczański, J. Saproxylic beetle thrives on the openness in management: a case study on the ecological requirements of Cucujus cinnaberinus from Central Europe. Insect Conserv. Divers. 5, 403–413 (2012).Article 

    Google Scholar 
    39.Keddy, P. Competiton 2nd edn. (Springer, 2001).Book 

    Google Scholar 
    40.Bonacci, T. et al. Beetles “in red”: are the endangered flat bark beetles Cucujus cinnaberinus and C. haematodes chemically protected? (Coleoptera: Cucujidae). Eur. Zool. J. 85, 128–136 (2018).Article 
    CAS 

    Google Scholar 
    41.Chararas, C., Chipoulet, J. M. & Courtois, J. E. Purification partielle et caracterisation d’une beta-glucosidase des larves de Pyrochroa coccinea (Coleoptere, Pyrochroidae). C. R. Séances Soc. Biol. Fil. 1771, 22–27 (1983).
    Google Scholar 
    42.Dettner, K. Description of defensive glands from cardinal beetles (Coleoptera, Pyrochroidae)—their phylogenetic significance as compared with other heteromeran defensive glands. Entomol. Basil. 9, 204–215 (1984).
    Google Scholar 
    43.Nardi, G. & Bologna, M. Cantharidin attraction in Pyrochroa (Coleoptera: Pyrochroidae). Entomol. News 111, 74–75 (2000).
    Google Scholar 
    44.Hirzel, A. & Guisan, A. Which is the optimal sampling strategy for habitat suitability modelling. Ecol. Model. 157, 331–341 (2002).Article 

    Google Scholar 
    45.Jaworski, T. et al. Saproxylic moths reveal complex within-group and group-environment patterns. J. Insect Conserv. 20, 677–690 (2016).Article 

    Google Scholar 
    46.Gotelli, N. J., Hart, E. M. & Ellison, A. M. EcoSimR: Null Model Analysis for Ecologicaldata. R package version 0.1.0 (Zenodo, 2015).47.Heiberger, R. M. HH: Statistical Analysis and Data Display: Heiberger and Holland. https://CRAN.R-project.org/package=HH (2020).48.Walsh, C. & Mac Nally, R. M. Hier.Part: Hierarchical partitioning. https://cran.r-project.org/web/packages/hier.part/index.html (2020). More

  • in

    Quality assessment of Urochloa (syn. Brachiaria) seeds produced in Cameroon

    1.Renvoize, S., Clayton, W. D. & Kabuye C. H. S. In Brachiaria: Biology, Agronomy, and Improvement 1–15 (CIAT and Embrapa, 1996).2.Keller-Grein, G., Maass, B. L. & Hanson, J. In Brachiaria: Biology, Agronomy, and Improvement 16–42 (CIAT and Embrapa, 1996).3.Barnard, C. Herbage Plant Species 154 (Australian Herbage Plant Registration Authority, Canberra, Australia, 1969).4.Roberts, O. T. A review of pasture species in Fiji 1. Grasses. Trop. Grassl. 4, 129–137 (1970).
    Google Scholar 
    5.Serrão, E. A. S. & Simão Neto, M. Informaçõessobreduasespécies de gramíneasforrageiras do gênero Brachiaria na Amazônia: B. decumbens Stapf, B. ruziziensis Germain et Everard. Estudossobreforrageirasna Amazônia (IPEAN, 1971)6.Parsons, J. J. Spread of African pasture grasses to the American tropics. J. Range. Manag. 25, 12–17 (1972).Article 

    Google Scholar 
    7.Sendulsky, T. Brachiaria: Taxonomy of cultivated and native species in Brazil. Hoehnea 7, 99–139 (1978).
    Google Scholar 
    8.Oram, R. N. Register of Australian herbage plant cultivars. In Australian Herbage Plant Registration Authority, 304 (East Melbourne, Australia, 1990).9.Argel, P. J. & Keller-Grein, G. In Brachiaria: Biology, Agronomy, and Improvement 205–224 (CIAT and Embrapa, 1996).10.Pizarro, E. A., do Valle, C. B., Keller-Grein, G., Schultze-Kraft. R. & Zimmer, A. H. In Brachiaria: Biology, Agronomy, and Improvement 225–246 (CIAT and Embrapa, 1996).11.Jank, L., Barrios, S. C., Valle, C. B., Simeão, R. M. & Alves, G. F. The value of improved pastures to Brazilian beef production. Crop. Pasture Sci. 65, 1132–1137. https://doi.org/10.1071/CP13319 (2014).Article 

    Google Scholar 
    12.Rueda, Thaiana et al. Yield component responses of the Brachiaria brizantha forage grass to soil water availability in the Brazilian Cerrado. Agriculture 10(1), 13 (2020).Article 

    Google Scholar 
    13.Stür, W. W., Hopkinson, J. M. & Chen, C.P. In Brachiaria: Biology, Agronomy, and Improvement 258–271 (CIAT and Embrapa, 1996).14.Ndikumana, J. & de Leeuw, P. N. In Brachiaria: Biology, Agronomy, and Improvement 247–257(CIAT and Embrapa, 1996).15.Maass, B. L. et al. Home coming of Brachiaria: Improved hybrids prove useful for African animal agricultural. E. Afr. Agric. For. J. 81, 71–78 (2015).Article 

    Google Scholar 
    16.Mutimura, M. & Everson, T. M. On-farm evaluation of improved Brachiaria grasses in low rainfall and aluminum toxicity prone areas of Rwanda. Int. J. Biodivers. Conserv. 4, 137–154 (2012).Article 

    Google Scholar 
    17.Njarui, D. M. G., Gatheru, M. & Ghimire, S. R. In African Handbook of Climate Change Adaptation 1–21 https://doi.org/10.1007/978-3-030-42091-8_146-1 (2020).18.Ghimire, S. et al. In Proceedings of 23rd International Grassland Congress 361–370 (Range Management Society of India, 2015).19.Njarui, D. M. G., Gichangi, E. M., Ghimire, S. R. & Muinga, R. W. Climate smart Brachiaria Grass for Improving Livestock Production in East Africa—Kenya Experiences (KALRO, 2016).20.Mutimura, M., Ebong, C., Rao, I. M. & Nsahlai, I. V. Change in growth performance of crossbred (Ankole × Jersey) dairy heifers fed on forage grass diets supplemented with commercial concentrates. Trop. Anim. Health. Prod. 48, 741–746 (2016).Article 

    Google Scholar 
    21.Boonman, J. G. Experimental studies on seed production of tropical grasses in Kenya. 2. Tillering and heading in seed crops of eight grasses. Neth. J. Agric. Sci. 19, 237–249 (1971).
    Google Scholar 
    22.Pamo, E. T., Yonkeu, S. & Onana, J. Evaluation des plantesfourragèresintroduites dans l’AdamaouaCamerounais. Cahiers d’Agric. 6, 203–207 (1997).
    Google Scholar 
    23.Borget, M. Les recherchesfourragères à l’IRAT/Cameroun (Bilan à la mi-1968). L’AgronomieTropicale Série 2, Agronomie Générale. Etudes Techniques 23, 1231–1241 (1968).
    Google Scholar 
    24.Husson, O. et al. Brachiaria sp., B. ruziziensis, B. brizantha, B. decumbens, B. humidicola. Manuel pratique du semis direct à Madagascar (CIRAD, 2008).25.Ministry of Agriculture and Rural Development. The State of Biodiversity for Food and Agriculture in the Republic of Cameroon (MINADER, 2015), http://www.fao.org/3/CA3431EN/ca3431en.pdf26.Institute of Agricultural Research for Development. Annual report. Regional Agricultural Research Centre (Wakwa, Ngaoundéré, Cameroon, 2015).27.Addinsoft. XLSTAT Statistical and Data Analysis Solution. New York, USA. https://www.xlstat.com (2021).28.Botwright, T. L., Condon, A. G., Rebetzke, G. J. & Richards, R. A. Field evaluation of early vigour for genic improvement of grain yield in wheat. Aust. J. Agric. Res. 53, 1137–1145 (2002).Article 

    Google Scholar 
    29.Dholakia, B. B. et al. Molecular marker analysis of kernel size and shape in bread wheat. Plant Breed. 122, 392–395 (2003).CAS 
    Article 

    Google Scholar 
    30.Wu, W. et al. A measurement system of thousand kernel weight based on the Android Platform. Agronomy 8(9), 178 (2018).Article 

    Google Scholar 
    31.Heimbach, U. Variability of thousand grain weights of seed batches of important arable and some horticultural crops. J. für Kulturpflanzen 70, 250–254 (2018).
    Google Scholar 
    32.Parihar, S. S. & Pathak, P. S. Flowering phenology and seed biology of selected tropical perennial grasses. Trop. Ecol. 47, 81–87 (2006).
    Google Scholar 
    33.Hare, M., Tatsapong, P. P. & Phengphet, S. Effect of storage duration, storage room and bag type on seed germination of Brachiaria hybrid cv.. Mulato. Trop. Grassl. 42, 224–228 (2008).
    Google Scholar 
    34.de Andrade, R. P., Thomas, D. & Ferguson, J. E. Seed production of pasture species in a tropical savanna region of Brazil. II Grasses. Trop. Grassl. 17, 59–64 (1983).
    Google Scholar 
    35.Nakamanee, G. & Phaikaew, C. In Proceedings of the third regional meeting of the Forages for Smallholders Project 155–162 (CIAT, 1998).36.Song, L. & Kalms, I. Improving germination of tropical grasses with new seed-coating technologies. Trop. Grassl. 41, 242 (2007).
    Google Scholar 
    37.Adkins, S. W., Bellairs, S. M. & Loch, D. S. Seed dormancy mechanisms in warm season grass species. Euphytica 126, 13–20 (2002).CAS 
    Article 

    Google Scholar 
    38.Simpson, G. M. Seed Dormancy in Grasses (Cambridge University Press, Cambridge, 1990).Book 

    Google Scholar 
    39.Hopkinson, J. M., de Souza, F. H. D., Diulgheroff, S., Ortiz, A. & Sanchez, M. In Brachiaria: Biology, Agronomy, and Improvement 124–140 (CIAT, 1996)40.Food and Agriculture Organization. Genebank Standards for Plant Genetic Resources for Food and Agriculture (FAO, 2013).41.Hare, M. D., Sutin, N., Phengphet, S. & Songsiri, T. Germination of tropical forage seeds stored for six years in ambient and controlled temperature and humidity conditions in Thailand. Trop. Grassl. Forrajes Trop. 6, 26–33 (2018).Article 

    Google Scholar 
    42.Mobli, A., Mollaee, M., Manalil, S. & Chauhan, B. S. Germination ecology of Brachiaria eruciformis in Australia and its implications for weed management. Agronomy 10, 30. https://doi.org/10.3390/agronomy10010030 (2020).CAS 
    Article 

    Google Scholar 
    43.Romani, F., Inacio, R. & de Carvalho, R. I. N. Break dormancy, germination and vigour of Brachiaria brizantha cv. Brs Piatã seeds. R. Eletr. Cient Uergs. Porto Alegre 2, 235–239 (2016).Article 

    Google Scholar 
    44.Pizarro, E. A., Hare, M. D., Mutimura, M. & Changjun, B. Brachiaria hybrids: potential, forage use and seed yield. Trop. Grassl. Forrajes. Trop. 1, 31–35 (2013).Article 

    Google Scholar 
    45.Herrera, J. Efecto de alguns tratamentos para interromper o resto em sementes de grama. II. Urochloa decumbens. Agron. Costarric 18, 75–85 (1994).
    Google Scholar 
    46.Whiteman, P. C. & Mendra, K. Effects of storage and seed treatments on germination of Brachiaria decumbens. Seed Sci. Technol. 10, 233–242 (1982).
    Google Scholar 
    47.Bakhtavar, M. A. & Afzal, I. Preserving wheat grain quality and preventing aflatoxin accumulation during storage without pesticides using dry chain technology. Environ. Sci. Pollut. Res. Int. 27, 42064–42071 (2020).CAS 
    Article 

    Google Scholar 
    48.Batista, T. B., da Silva Binotti, F. F., Cardoso, E. D., Costa, E. & do Nascimento, D. M. Appropriate hydration period and chemical agent improve priming in Brachiaria seeds. Pesqui. Agropecu. Trop. 46, 350–356 (2016).Article 

    Google Scholar 
    49.Pereira, S. R., da Lima, A. E. S., Contreiras-Rodrigues, A. P. D., de Oliveira, D. R. & Laura, V. A. Priming of Urochloa brizantha cv. Xaraes seeds. Afr. J. Agric. Res. 13, 2804–2807 (2018).CAS 
    Article 

    Google Scholar 
    50.Ferguson, J. E., Thomas, D., de Andrade, R. P., Costa, N. S. & Jutzi, S. In Proceedings of XIV International Grassland Congress 275–278 (Westview Press, 1983)51.Boonman, J. G. East Africa’s Grasses and Fodders: Their Ecology and Husbandry (Kluwer Academic Publishers, The Netherlands, 1993).Book 

    Google Scholar  More

  • in

    Response of deep soil moisture to different vegetation types in the Loess Plateau of northern Shannxi, China

    1.Feng, Q., Zhao, W. W., Zhao, M. Y. & Zhong, L. N. Spatial heterogeneity of soil moisture and the scale variability of its influencing factors: A case study in the Loess Plateau of China. Water 5, 1228 (2013).ADS 
    Article 

    Google Scholar 
    2.Hu, W., Shao, M. A., Wang, Q. J. & Reichardt, K. Time stability of soil water storage measured by neutron probe and the effects of calibration procedures in a small watershed. CATENA 79(1), 72–82 (2009).CAS 
    Article 

    Google Scholar 
    3.Legates, D. R. et al. Soil moisture: A central and unifying theme in physical geography. Prog. Phys. Geogr. 35(1), 65–86 (2010).Article 

    Google Scholar 
    4.Hou, G. R. et al. Response of soil moisture to single-rainfall events under three vegetation types in the gully region of the Loess Plateau. Sustainability 10, 3793 (2018).CAS 
    Article 

    Google Scholar 
    5.Chen, L. D., Huang, Z. L., Gong, J., Fu, B. J. & Huang, Y. L. The effect of land cover/vegetation on soil water dynamic in the hilly area of the loess plateau, China. CATENA 70(2), 200–208 (2007).Article 

    Google Scholar 
    6.Li, Y. S. The properties of water cycle in soil and their effect on water cycle for land in the Loess Region. Acta Ecol Sin 3(2), 91–101 (1983) (in Chinese).7.Li, Y. Y. & Shao, M. A. Climatic change, vegetation evolution and low moisture layer of soil on the Loess Plateau. J. Arid Land Resour. Environ. 15(1), 72–77 (2001) (in Chinese).8.Mu, X. M., Xu, X. X., Wang, W. L., Wen, Z. M. & Du, F. Impact of artificial forest on soil moisture of the deep soil layer on Loess Platea. Acta Pedo. Sin. 2, 210–217 (2003) ((in Chinese)).
    Google Scholar 
    9.Yang, L., Wei, W., Chen, L. D. & Mo, B. R. Response of deep soil moisture to land use and afforestation in the semi-arid Loess Plateau, China. J. Hydrol. 475, 111–122 (2012).ADS 
    Article 

    Google Scholar 
    10.Zhao, X. K., Li, Z. Y., Zhu, D. H., Zhu, Q. K. & Robeson, M. Revegetation using the deep planting of container seedings to overcome the limitations associated with topsoil desiccation on exposed steep earthy road slopes in the semiarid loess region of China. Land Degrad. Dev. 2018(29), 2797–2807 (2018).Article 

    Google Scholar 
    11.Jia, Y. H. & Shao, M. A. Dynamics of deep soil moisture in response to vegetational restoration on the Loess Plateau of China. J. Hydrol. 519, 523–531 (2014).ADS 
    Article 

    Google Scholar 
    12.Deng, L., Shangguan, Z. P. & Li, R. Effects of the grain-for-green program on soil erosion in China. Int. J. Sediment. Res. 27(1), 120–127 (2012).Article 

    Google Scholar 
    13.Zhou, P., Wen, A. B., Zhang, X. B. & He, X. B. Soil conservation and sustainable eco-environment in the Loess Plateau of China. Environ. Earth Sci. 2013(68), 633–639 (2013).
    Google Scholar 
    14.Chen, Y. P. et al. Balancing green and grain trade. Nat. Geosci. 10(8), 739–741 (2015).ADS 
    Article 
    CAS 

    Google Scholar 
    15.Liu, Y. X., Lu, Y. H., Fu, B. J., Harris, P. & Wu, L. H. Quantifying the spatio-temporal drivers of planned vegetation restoration on ecosystem services at a regional scale. Sci. Total Environ. 650, 1029–1040 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    16.Wang, K. B. et al. Dynamics of ecosystem carbon stocks during vegetation restoration on the Loess Plateau of China. J. Arid Land 8(2), 207–220 (2016).Article 

    Google Scholar 
    17.Su, B. Q. & Shangguan, Z. P. Decline in soil moisture due to vegetation restoration on the Loess Plateau of China. Land Degrad. Dev. 30, 290–299 (2019).Article 

    Google Scholar 
    18.Wang, Y. Q., Shao, M. A., Zhu, Y. J. & Liu, Z. P. Impacts of land use and plant characteristics on dried soil layers in different climatic regions on the Loess Plateau of China. Agric. Forest Meteorol. 151(4), 437–448 (2011).ADS 
    Article 

    Google Scholar 
    19.Wang, Y. Q., Shao, M. A., Liu, Z. P. & Warrington, D. N. Regional spatial pattern of deep soil water content and its influencing factors. Hydrol. Sci. J. 57(2), 265–281 (2012).Article 

    Google Scholar 
    20.Wang, Y. Q., Shao, M. A. & Liu, Z. P. Vertical distribution and influencing factors of soil water content within 21-m profile on the Chinese Loess Plateau. Geoderma 193, 300–310 (2013).ADS 
    Article 
    CAS 

    Google Scholar 
    21.Nosetto, M. D., Jobbagy, E. G., Toth, T. & Di Bella, C. M. The effects of tree establishment on water and salt dynamics in naturally salt-affected grasslands. Oecologia 152(4), 695–705 (2007).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    22.Deng, X. Z., Shi, Q. L., Zhang, Q., Shi, C. C. & Yin, F. Impacts of land use and land cover changes on surface energy and water balance in the Heihe River Basin of China, 2000–2010. Phys. Chem. 79–82, 2–10 (2015).ADS 

    Google Scholar 
    23.Sun, Z. X., Wu, F., Shi, C. C. & Zhan, J. Y. The impact of land use change on water balance in Zhangye city, China. Phys. Chem. Earth 96, 64–73 (2016).Article 

    Google Scholar 
    24.Porporato, A., D’Odorico, P., Laio, F. & Rodriguez-Iturbe, I. Ecohydrology of water-controlled ecosystems. Adv. Water Resour. 25(8–12), 1335–1348 (2002).ADS 
    Article 

    Google Scholar 
    25.Chen, H. S., Shao, M. A. & Li, Y. S. Soil desiccation in the Loess Plateau of China. Geoderma 143, 91–100 (2008).ADS 
    Article 

    Google Scholar 
    26.Shen, M. S. et al. Seasonal variations in the influence of vegetation cover on soil water on the loess hillslope. J. Mt. Sci. 17(9), 2148–2160 (2020).Article 

    Google Scholar 
    27.Wang, S., Fu, B. J., Gao, G. Y., Liu, Y. & Zhou, J. Responses of soil moisture in different land cover types to rainfall events in a re-vegetation catchment area of the Loess Plateau, China. CATENA 101(2), 122–128 (2013).Article 

    Google Scholar 
    28.Fu, B. J., Wang, J., Chen, L. D. & Qiu, Y. The effects of land use on soil moisture variation in the Danangou catchment of the Loess Plateau, China. CATENA 54, 197–213 (2003).Article 

    Google Scholar 
    29.Gao, X. D. et al. Soil moisture variability along transects over a well-developed gully in the Loess Plateau, China. CATENA 87(3), 357–367 (2011).Article 

    Google Scholar 
    30.Mei, X. M. et al. The spatial variability of soil water storage and its controlling factors during dry and wet periods on loess hillslopes. CATENA 162, 333–344 (2018).Article 

    Google Scholar 
    31.Liu, B. X. & Shao, M. A. Response of soil water dynamics to precipitation years under different vegetation types on the northern Loess Plateau, China. J. Arid Land 8(1), 47–59 (2016).Article 

    Google Scholar 
    32.Longobardi, A. Observing soil moisture temporal variability under fluctuating climatic conditions. Hydrol. Earth Syst. Sci. 5, 935–969 (2008).
    Google Scholar 
    33.Shao, M. A., Wang, Y. Q., Xia, Y. Q. & Jia, X. X. Soil drought and water carrying capacity for vegetation in the critical zone of the Loess Plateau: A review. Vadose Zone J. 17(1), 170017 (2018).34.Vörösmarty, C. J., Green, P. J., Salisbury, J. & Lammers, R. B. Global water resources: Vulnerability from climate change and population growth. Science 289(5477), 284–288 (2000).ADS 
    PubMed 
    Article 

    Google Scholar 
    35.Wang, L., Wang, Q. J., Wei, S. P., Shao, M. A. & Yi, L. Soil desiccation for Loess soils on natural and regrown areas. Forest Ecol. Manag. 255(7), 2467–2477 (2008).Article 

    Google Scholar 
    36.Yang, L., Wei, W., Mo, B. R. & Chen, L. D. Soil water deficit under different artificial vegetation restoration in the semi-arid hilly region of the Loess Plateau. Acta Ecol. Sin. 31(11), 3060–3068 (2011) ((in Chinese)).
    Google Scholar 
    37.Cao, R. X. et al. Deep soil water storage varies with vegetation type and rainfall amount in the Loess Plateau of China. Sci. Rep. 8(1), 12346 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    38.Fang, X. N. et al. Variations of deep soil moisture under different vegetation types and influencing factors in a watershed of the Loess Plateau, China. Hydrol. Earth Syst. Sci. 20(8), 3309–3323 (2016).ADS 
    Article 

    Google Scholar 
    39.Yang, L., Chen, L. D., Wei, W., Yu, Yang. & Zhang, H. D. Comparison of deep soil moisture in two re-vegetation watersheds in semi-arid regions. J. Hydrol. 513, 314–321 (2014).40.Xiao, L., Xue, S., Liu, G. B. & Zhang, C. Soil moisture variability under different land uses in the Zhifanggou catchment of the Loess Plateau, China. Arid Land Res. Manag. 28(3), 274–290 (2014).Article 

    Google Scholar 
    41.Mei, X. M. et al. The variability in soil water storage on the loess hillslopes in China and its estimation. CATENA 172, 807–818 (2019).Article 

    Google Scholar 
    42.Guo, Z. S. Estimating method of maximum infiltration depth and soil water supply. Sci. Rep. 10(1), 9726 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    43.Guo, Z. S. & Shao, M. A. Dynamics of soil water supply and consumption inartificial caragana shrub land. J. Soil Water Conserv. 2007(02), 119–123 (2007) ((in Chinese)).
    Google Scholar 
    44.Wang, Z. Q., Liu, B. Y. & Zhang, Y. Soil moisture of different vegetation types on the Loess Plateau. J. Geogr. Sci. 19(6), 707–718 (2009).Article 

    Google Scholar 
    45.Cheng, L. P. & Liu, W. Z. Long term effects of farming system on soil water content and dry soil layer in deep loess profile of Loess Tableland in China. J. Integr. Agric. 13(6), 1382–1392 (2014).Article 

    Google Scholar 
    46.Sun, C. F. & Ma, Y. Y. Effects of non-linear temperature and precipitation trends on Loess Plateau droughts. Quatern. Int. 372, 175–179 (2015).Article 

    Google Scholar 
    47.Mei, X. M. et al. Responses of soil moisture to vegetation restoration type and slope length on the loess hillslope. J. Mt. Sci. 15(3), 548–562 (2018).Article 

    Google Scholar  More

  • in

    Cascading effects of moth outbreaks on subarctic soil food webs

    1.Pickett, S. T. A. & White, P. S. The Ecology of Natural Disturbance and Patch Dynamics (Academic Press, 1985).
    Google Scholar 
    2.IPBES. Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES Secretariat, 2019).
    Google Scholar 
    3.Brun, P. et al. Large-scale early-wilting response of Central European forests to the 2018 extreme drought. Glob. Change Biol. 00, 1–15 (2020).CAS 

    Google Scholar 
    4.Cardinale, B. J., Gonzalez, A., Allington, G. R. H. & Loreau, M. Is local biodiversity declining or not? A summary of the debate over analysis of species richness time trends. Biol. Conserv. 219, 175–183 (2018).Article 

    Google Scholar 
    5.Vellend, M. et al. Global meta-analysis reveals no net change in local-scale plant biodiversity over time. Proc. Natl. Acad. Sci. U.S.A. 110, 19456–19459 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    6.Bardgett, R. D. & Wardle, D. A. Aboveground-Belowground Linkages: Biotic Interactions, Ecosystem Processes, and Global Change (Oxford University Press, 2010).
    Google Scholar 
    7.Bardgett, R. D. & van der Putten, W. H. Belowground biodiversity and ecosystem functioning. Nature 515, 505–511 (2014).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    8.Bardgett, R. D. & Caruso, T. Soil microbial community responses to climate extremes: Resistance, resilience and transitions to alternative states. Philos. Trans. R. Soc. Lond. B Biol. Sci. 375, 20190112 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    9.Thom, D. & Seidl, R. Natural disturbance impacts on ecosystem services and biodiversity in temperate and boreal forests: Disturbance impacts on biodiversity and services. Biol. Rev. 91, 760–781 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    10.van der Putten, W. H. et al. Trophic interactions in a changing world. Basic Appl. Ecol. 5, 487–494 (2004).Article 

    Google Scholar 
    11.Lafferty, K. D. & Suchanek, T. H. Revisiting Paine’s 1966 sea star removal experiment, the most-cited empirical article in the American Naturalist. Am. Nat. 188, 365–378 (2016).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    12.Scherber, C. et al. Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment. Nature 468, 553–556 (2010).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    13.Barnes, A. D. et al. Direct and cascading impacts of tropical land-use change on multi-trophic biodiversity. Nat. Ecol. Evol. 1, 1511–1519 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    14.Barbier, M. & Loreau, M. Pyramids and cascades: A synthesis of food chain functioning and stability. Ecol. Lett. 22, 405–419 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    15.Mancinelli, G. & Mulder, C. Chapter three—detrital dynamics and cascading effects on supporting ecosystem services. In Advances in ecological research Vol. 53 (eds Woodward, G. & Bohan, D. A.) 97–160 (Academic Press, 2015).
    Google Scholar 
    16.Mulder, C., Vonk, J. A., Hollander, H. A. D., Hendriks, A. J. & Breure, A. M. How allometric scaling relates to soil abiotics. Oikos 120, 529–536 (2011).Article 

    Google Scholar 
    17.Allen, A. P. & Gillooly, J. F. Towards an integration of ecological stoichiometry and the metabolic theory of ecology to better understand nutrient cycling. Ecol. Lett. 12, 369–384 (2009).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    18.de Ruiter, P. C., Neutel, A.-M. & Moore, J. C. Energetics, patterns of interaction strengths, and stability in real ecosystems. Science 269, 1257–1260 (1995).ADS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    19.Estes, J. A. et al. Trophic downgrading of planet earth. Science 333, 301–306 (2011).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    20.Taberlet, P., Bonin, A., Zinger, L. & Coissac, E. Environmental DNA: For Biodiversity Research and Monitoring (Oxford University Press, 2018).Book 

    Google Scholar 
    21.Gravel, D., Albouy, C. & Thuiller, W. The meaning of functional trait composition of food webs for ecosystem functioning. Philos. Trans. R. Soc. Lond. B Biol. Sci. 371, 20150268 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    22.Barnes, A. D. et al. Energy flux: The link between multitrophic biodiversity and ecosystem functioning. Trends Ecol. Evol. 33, 186–197 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    23.Elton, C. S. Animal Ecology 1–256 (Macmillan Co., 1927). https://doi.org/10.5962/bhl.title.7435.Book 

    Google Scholar 
    24.Bohan, D. A. et al. Next-generation global biomonitoring: Large-scale, automated reconstruction of ecological networks. Trends Ecol. Evol. 32, 477–487 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    25.Roslin, T. & Majaneva, S. The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!. Genome 59, 603–628 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    26.Cohen, J. E. et al. Improving food webs. Ecology 74, 252–258 (1993).Article 

    Google Scholar 
    27.Buzhdygan, O. Y. et al. Biodiversity increases multitrophic energy use efficiency, flow and storage in grasslands. Nat. Ecol. Evol. 4, 393–405 (2020).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    28.Martinez, N. D. Effects of resolution on food web structure. Oikos 66, 403 (1993).Article 

    Google Scholar 
    29.Thompson, R. M. et al. Food webs: Reconciling the structure and function of biodiversity. Trends Ecol. Evol. 27, 689–697 (2012).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    30.Kardol, P., Throop, H. L., Adkins, J. & de Graaff, M.-A. A hierarchical framework for studying the role of biodiversity in soil food web processes and ecosystem services. Soil Biol. Biochem. 102, 33–36 (2016).CAS 
    Article 

    Google Scholar 
    31.Ohlmann, M. et al. Diversity indices for ecological networks: A unifying framework using Hill numbers. Ecol. Lett. 22, 737–747 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    32.Pellissier, L. et al. Comparing species interaction networks along environmental gradients. Biol. Rev. 93, 785–800 (2017).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    33.Jepsen, J. U. et al. Ecosystem impacts of a range expanding forest defoliator at the forest-tundra ecotone. Ecosystems 16, 561–575 (2013).Article 

    Google Scholar 
    34.Karlsen, S. R., Jepsen, J. U., Odland, A., Ims, R. A. & Elvebakk, A. Outbreaks by canopy-feeding geometrid moth cause state-dependent shifts in understorey plant communities. Oecologia 173, 859–870 (2013).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    35.Jepsen, J. U., Hagen, S. B., Ims, R. A. & Yoccoz, N. G. Climate change and outbreaks of the geometrids Operophtera brumata and Epirrita autumnata in subarctic birch forest: Evidence of a recent outbreak range expansion. J. Anim. Ecol. 77, 257–264 (2008).PubMed 
    Article 

    Google Scholar 
    36.Vindstad, O. P. L., Jepsen, J. U., Ek, M., Pepi, A. & Ims, R. A. Can novel pest outbreaks drive ecosystem transitions in northern-boreal birch forest?. J. Ecol. 107, 1141–1153 (2019).Article 

    Google Scholar 
    37.Sandén, H. et al. Moth outbreaks reduce decomposition in subarctic forest soils. Ecosystems 23, 151–163 (2019).Article 
    CAS 

    Google Scholar 
    38.Vindstad, O. P. L. et al. Numerical responses of saproxylic beetles to rapid increases in dead wood availability following geometrid moth outbreaks in sub-arctic mountain birch forest. PLoS ONE 9, e99624 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    39.Nilsson, M.-C. & Wardle, D. A. Understory vegetation as a forest ecosystem driver: Evidence from the northern Swedish boreal forest. Front. Ecol. Environ. 3, 421–428 (2005).Article 

    Google Scholar 
    40.Bråthen, K. A. & Ravolainen, V. T. Niche construction by growth forms is as strong a predictor of species diversity as environmental gradients. J. Ecol. 103, 701–713 (2015).Article 

    Google Scholar 
    41.Bråthen, K. A., Gonzalez, V. T. & Yoccoz, N. G. Gatekeepers to the effects of climate warming? Niche construction restricts plant community changes along a temperature gradient. Perspect. Plant Ecol. Evol. Syst. 30, 71–81 (2018).Article 

    Google Scholar 
    42.Vindstad, O. P. L., Jepsen, J. U. & Ims, R. A. Resistance of a sub-arctic bird community to severe forest damage caused by geometrid moth outbreaks. Eur. J. For. Res. 134, 725–736 (2015).Article 

    Google Scholar 
    43.Parker, T. C. et al. Slowed biogeochemical cycling in sub-arctic birch forest linked to reduced mycorrhizal growth and community change after a defoliation event. Ecosystems 20, 316–330 (2017).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    44.Saravesi, K. et al. Moth outbreaks alter root-associated fungal communities in subarctic mountain birch forests. Microb. Ecol. 69, 788–797 (2015).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    45.Dunne, J. A. The network structure of food webs. In Ecological Networks: Linking Structure to Dynamics in Food Webs (eds Pascual, M. & Dunne, J. A.) 27–86 (Oxford University Press, 2006).
    Google Scholar 
    46.Rodriguez-Ramos, J. C. et al. Changes in soil fungal community composition depend on functional group and forest disturbance type. New Phytol. 00, 1–13 (2020).
    Google Scholar 
    47.Decaëns, T. Macroecological patterns in soil communities. Glob. Ecol. Biogeogr. 19, 287–302 (2010).Article 

    Google Scholar 
    48.Bardgett, R. D., Yeates, G. W. & Anderson, J. M. Patterns and determinants of soil biological diversity. In Biological Diversity and Function in Soils (eds Hopkins, D. et al.) 100–118 (Cambridge University Press, 2005).Chapter 

    Google Scholar 
    49.Worm, B. & Duffy, J. E. Biodiversity, productivity and stability in real food webs. Trends Ecol. Evol. 18, 628–632 (2003).Article 

    Google Scholar 
    50.Ponsard, S., Arditi, R. & Jost, C. Assessing top-down and bottom-up control in a litter-based soil macroinvertebrate food chain. Oikos 89, 524–540 (2000).Article 

    Google Scholar 
    51.Kristensen, J. Å., Rousk, J. & Metcalfe, D. B. Below-ground responses to insect herbivory in ecosystems with woody plant canopies: A meta-analysis. J. Ecol. 108, 917–930 (2020).Article 

    Google Scholar 
    52.González, V. T. et al. Batatasin-III and the allelopathic capacity of Empetrum nigrum. Nord. J. Bot. 33, 225–231 (2015).ADS 
    Article 

    Google Scholar 
    53.Veen, G. F. et al. The role of plant litter in driving plant-soil feedbacks. Front. Environ. Sci. 7, 168 (2019).Article 

    Google Scholar 
    54.Calizza, E., Rossi, L., Careddu, G., Sporta Caputi, S. & Costantini, M. L. Species richness and vulnerability to disturbance propagation in real food webs. Sci. Rep. 9, 19331 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    55.Antiqueira, P. A. P., Petchey, O. L., dos Santos, V. P., de Oliveira, V. M. & Romero, G. Q. Environmental change and predator diversity drive alpha and beta diversity in freshwater macro and microorganisms. Glob. Change Biol. 24, 3715–3728 (2018).ADS 
    Article 

    Google Scholar 
    56.Hedlund, K. et al. Trophic interactions in changing landscapes: Responses of soil food webs. Basic Appl. Ecol. 5, 495–503 (2004).Article 

    Google Scholar 
    57.Ettema, C. H. & Wardle, D. A. Spatial soil ecology. Trends Ecol. Evol. 17, 177–183 (2002).Article 

    Google Scholar 
    58.O’Brien, S. L. et al. Spatial scale drives patterns in soil bacterial diversity. Environ. Microbiol. 18, 2039–2051 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    59.Jiménez, J. J., Decaëns, T., Lavelle, P. & Rossi, J.-P. Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability. BMC Ecol. 14, 26 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    60.Taberlet, P. et al. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol. Ecol. 21, 1816–1820 (2012).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    61.Zinger, L. et al. Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA. Soil Biol. Biochem. 96, 16–19 (2016).CAS 
    Article 

    Google Scholar 
    62.Binladen, J. et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2, e197 (2007).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    63.Valentini, A. et al. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: The trnL approach. Mol. Ecol. Resour. 9, 51–60 (2009).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    64.Boyer, F. et al. obitools: A unix-inspired software package for DNA metabarcoding. Mol. Ecol. Resour. 16, 176–182 (2016).CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    65.Mercier, C., Boyer, F., Bonin, A. & Coissac, E. SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. in Programs and Abstracts of the SeqBio 2013 workshop. Abstract 27–29 (Citeseer, 2013).66.Zinger, L. et al. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Mol. Ecol. 28, 1857–1862 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    67.Zinger, L. et al. metabaR : an R package for the evaluation and improvement of DNA metabarcoding data quality. https://doi.org/10.1101/2020.08.28.271817 (2020).68.R Core Team. A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2019).69.Nguyen, N. H. et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 20, 241–248 (2016).Article 

    Google Scholar 
    70.Louca, S., Parfrey, L. W. & Doebeli, M. Decoupling function and taxonomy in the global ocean microbiome. Science 353, 1272–1277 (2016).ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    71.Adl, S. M. et al. Revisions to the classification, nomenclature, and diversity of eukaryotes. J. Eukaryot. Microbiol. 66, 4–119 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    72.Fiore-Donno, A. M. et al. Functional traits and spatio-temporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland. Front. Microbiol. 10, 1332 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    73.Ho, A., Lonardo, D. P. D. & Bodelier, P. L. E. Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol. Ecol. 93, 6 (2017).
    Google Scholar 
    74.Calderón-Sanou, I., Münkemüller, T., Boyer, F., Zinger, L. & Thuiller, W. From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices?. J. Biogeogr. 47, 193–206 (2020).Article 

    Google Scholar 
    75.Antunes, P. M. & Koyama, A. Chapter 9 – Mycorrhizas as Nutrient and Energy Pumps of Soil Food Webs: Multitrophic Interactions and Feedbacks. in Mycorrhizal Mediation of Soil Fertility, Structure, and Carbon Storage (eds. Johnson, N. C., Gehring, C. & Jansa, J.) 149–173 (Elsevier, 2017).76.Goodrich, B., Gabry, J., Ali, I. & Brilleman, S. rstanarm: Bayesian applied regression modeling via Stan. (R package version 2.21.1, 2020).77.McArtor, D. B., Lubke, G. H. & Bergeman, C. S. Extending multivariate distance matrix regression with an effect size measure and the asymptotic null distribution of the test statistic. Psychometrika 82, 1052–1077 (2017).MathSciNet 
    PubMed 
    MATH 
    Article 
    PubMed Central 

    Google Scholar  More

  • in

    Kinship networks of seed exchange shape spatial patterns of plant virus diversity

    1.Chakraborty, S. & Newton, A. C. Climate change, plant diseases and food security: an overview. Plant Pathol. 60, 2–14 (2011).Article 

    Google Scholar 
    2.Savary, S. et al. The global burden of pathogens and pests on major food crops. Nat. Ecol. Evol. 3, 430–439 (2019).PubMed 
    Article 
    PubMed Central 

    Google Scholar 
    3.McGuire, S. & Sperling, L. Seed systems smallholder farmers use. Food Secur. 8, 179–195 (2016).Article 

    Google Scholar 
    4.Almekinders, C. J., Louwaars, N. P. & De Bruijn, G. H. Local seed systems and their importance for an improved seed supply in developing countries. Euphytica 78, 207–216 (1994).Article 

    Google Scholar 
    5.McGuire, S. & Sperling, L. Making seed systems more resilient to stress. Global Environ. Chang. 23, 644–653 (2013).Article 

    Google Scholar 
    6.Legg, J. et al. Community phytosanitation to manage Cassava Brown Streak Disease. Virus Res. 241, 236–253 (2017).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    7.McQuaid, C. F. et al. Spatial dynamics and control of a crop pathogen with mixed-mode transmission. PLoS Comput. Biol. 13, e1005654 (2017a).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    8.Chernela, J. M. Os cultivares de mandioca na área do Uaupés (Tukâno). In Suma Etnológica Brasileira (ed Ribeiro, D.) 151–158 (Finep, Petrópolis, 1986).9.Emperaire, L., Pinton, F. & Second, G. Gestion dynamique de la diversité variétale du manioc en Amazonie du Nord-Ouest. Nat. Sci. Soc. 6, 27–42 (1998).Article 

    Google Scholar 
    10.Sirbanchongkran, A., Yimyam, N., Boonma, W. & Rerkasem, K. Varietal turnover and seed exchange: implications for conservation of rice genetic diversity on farm. Int. Rice Res. Notes 29, 12–14 (2004).
    Google Scholar 
    11.Delêtre, M., McKey, D. B. & Hodkinson, T. R. Marriage exchanges, seed exchanges, and the dynamics of manioc diversity. Proc. Natl Acad. Sci. USA 108, 18249–18254 (2011).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    12.Labeyrie, V., Thomas, M., Muthamia, Z. K. & Leclerc, C. Seed exchange networks, ethnicity, and sorghum diversity. Proc. Natl Acad. Sci. USA 113, 98–103 (2016).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    13.Brown, J. K. et al. Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Arch. Virol. 160, 1593–1619 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    14.Legg, J. P. et al. Comparing the regional epidemiology of the cassava mosaic and cassava brown streak pandemics in Africa. Virus Res. 159, 161–170 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    15.Patil, B. L. & Fauquet, C. M. Cassava mosaic geminiviruses: actual knowledge and perspectives. Mol. Plant Pathol. 10, 685–701 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    16.Harrison, B. D., Zhou, X., Otim‐Nape, G. W., Liu, Y. & Robinson, D. J. Role of a novel type of double infection in the geminivirus‐induced epidemic of severe cassava mosaic in Uganda. Ann. Appl. Biol. 131, 437–448 (1997).Article 

    Google Scholar 
    17.Consultative Group for International Agricultural Research. CGIAR Research Program 3.4: Roots, tubers, and bananas for food security and income. Final revised proposal. September 2011. https://hdl.handle.net/10947/5314.18.Duffy, S. & Holmes, E. C. Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J. Gen. Virol. 90, 1539–1547 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    19.Grenfell, B. T. et al. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303, 327–332 (2004).ADS 
    CAS 
    Article 

    Google Scholar 
    20.Pybus, O. G. & Rambaut, A. Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 10, 540–550 (2009).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    21.Fauquet, C. & Fargette, D. African cassava mosaic virus: etiology, epidemiology and control. Plant Dis. 74, 404–411 (1990).Article 

    Google Scholar 
    22.Zhou, X. et al. Evidence that DNA A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. J. Gen. Virol. 78, 2101–2111 (1997).CAS 
    PubMed 
    Article 

    Google Scholar 
    23.Pita, J. S. et al. Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. J. Gen. Virol. 82, 655–665 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    24.Lefeuvre, P. & Moriones, E. Recombination as a motor of host switches and virus emergences: geminiviruses as case studies. Curr. Opin. Virol. 10, 14–19 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    25.Tiendrébéogo, F. et al. Evolution of African cassava mosaic virus by recombination between bipartite and monopartite begomoviruses. Virol. J. 9, 67 (2012).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    26.Syrjala, S. E. A statistical test for a difference between the spatial distributions of two populations. Ecology 77, 75–80 (1996).Article 

    Google Scholar 
    27.Chevenet, F., Jung, M., Peeters, M., de Oliveira, T. & Gascuel, O. Searching for virus phylotypes. Bioinformatics 29, 561–570 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    28.Jost, L. Entropy and diversity. Oikos 113, 363–375 (2006).Article 

    Google Scholar 
    29.Pallmann, P. et al. Assessing group differences in biodiversity by simultaneously testing a user‐defined selection of diversity indices. Mol. Ecol. Resour. 12, 1068–1078 (2012).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    30.Volz, E. M., Koelle, K. & Bedford, T. Viral phylodynamics. PLoS Comput. Biol. 9, e1002947 (2013).ADS 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    31.Legg, J. P. & Fauquet, C. M. Cassava mosaic geminiviruses in Africa. Plant Mol. Biol. 56, 585–599 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    32.Legg, J. P., Ndjelassili, F. & Okao-Okuja, G. First report of cassava mosaic disease and cassava mosaic geminiviruses in Gabon. Plant Pathol. 53, 232 (2004).Article 

    Google Scholar 
    33.Legg, J. P. Bemisia tabaci: the whitefly vector of cassava mosaic geminiviruses in Africa: an ecological perspective. Afr. Crop Sci. J. 2, 437–448 (1994).
    Google Scholar 
    34.Fargette, D. & Thresh, J. M. The ecology of African cassava mosaic geminivirus. In Ecology of Plant Pathogens (eds Blakeman, J. P. & Williamson, B.) 269–282 (CAB International, Oxford, 1994).35.Anderson, P. K. & Morales, F. Whitefly and whitefly borne viruses in the tropics: building a knowledge base for global action (International Center for Tropical Agriculture, Cali, 2005).36.Zinga, I. et al. Epidemiological assessment of cassava mosaic disease in Central African Republic reveals the importance of mixed viral infection and poor health of plant cuttings. Crop Prot. 44, 6–12 (2013).Article 

    Google Scholar 
    37.Delêtre, M. The ins and outs of manioc diversity in Gabon, Central Africa: a pluridisciplinary approach to the dynamics of genetic diversity of Manihot esculenta Crantz (Euphorbiaceae) (Trinity College Dublin, 2010).38.Messe Mbega, C. Y. Les régions transfrontalières: un exemple d’intégration sociospatiale de la population en Afrique centrale? Éthique publique 17, http://ethiquepublique.revues.org/1724 (2015).39.Akinbade, S. A. et al. First report of the East African cassava mosaic virus-Uganda (EACMV-UG) infecting cassava (Manihot esculenta) in Cameroon. N. Dis. Rep. 22, 2044–0588 (2010).
    Google Scholar 
    40.Valam-Zango, A. et al. First report of cassava mosaic geminiviruses and the Uganda strain of East African cassava mosaic virus (EACMV-UG) associated with cassava mosaic disease in Equatorial Guinea. N. Dis. Rep. 32, 29 (2015).Article 

    Google Scholar 
    41.Trovão, N. S. et al. Host ecology determines the dispersal patterns of a plant virus. Virus Evol. 1, vev016 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    42.Sallinen, S. et al. Intraspecific host variation plays a key role in virus community assembly. Nat. Commun. 11, 5610 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    43.Patil, B. L., Legg, J. P., Kanju, E. & Fauquet, C. M. Cassava brown streak disease: a threat to food security in Africa. J. Gen. Virol. 96, 956–968 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    44.Maruthi, M. N., Jeremiah, S. C., Mohammed, I. U. & Legg, J. P. The role of the whitefly, Bemisia tabaci (Gennadius), and farmer practices in the spread of cassava brown streak ipomoviruses. J. Phytopathol. 165, 707–717 (2017).CAS 
    Article 

    Google Scholar 
    45.McQuaid, C. F., Gilligan, C. A. & van den Bosch, F. Considering behaviour to ensure the success of a disease control strategy. R. Soc. Open Sci. 4, 170721 (2017b).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    46.Almekinders, C. J. et al. Understanding the relations between farmers’ seed demand and research methods: the challenge to do better. Outlook Agric. 48, 16–21 (2019a).Article 

    Google Scholar 
    47.Almekinders, C. J. et al. Why interventions in the seed systems of roots, tubers and bananas crops do not reach their full potential. Food Secur. 11, 23–42 (2019b).Article 

    Google Scholar 
    48.R Foundation for Statistical Computing. R: a language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, 2018).49.Zeileis, A. ineq: Measuring inequality, concentration, and poverty. R package version 0.2-13. https://CRAN.R-project.org/package=ineq (2014).50.Alabi, O. J., Kumar, P. L. & Naidu, R. A. Multiplex PCR method for the detection of African cassava mosaic virus and East African cassava mosaic Cameroon virus in cassava. J. Virol. Methods 154, 111–120 (2008).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    51.Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    52.Martin, D. P., Murrell, B., Golden, M., Khoosal, A. & Muhire, B. RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol. 1, vev003 (2015).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    53.Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    54.Anisimova, M. & Gascuel, O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 55, 539–552 (2006).PubMed 
    Article 

    Google Scholar 
    55.Rambaut, A., Lam, T. T., de Carvalho, L. M. & Pybus, O. G. Exploring the temporal structure of heterochronous sequences using TempEst. Virus Evol. 2, vew007 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    56.Ragonnet-Cronin, M. et al. Automated analysis of phylogenetic clusters. BMC Bioinforma. 14, 317 (2013).Article 

    Google Scholar 
    57.Chao, A. et al. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecol. Monogr. 84, 45–67 (2014).Article 

    Google Scholar 
    58.Hsieh, T. C., Ma, K. H. & Chao, A. iNEXT: an R package for interpolation and extrapolation of species diversity (Hill numbers). Methods Ecol. Evol. 7, 1451–1456 (2016).Article 

    Google Scholar 
    59.Scherer, R. & Pallmann, P. Simboot: simultaneous inference for diversity indices. R package version 0.2-6. https://CRAN.R-project.org/package=simboot (2017).60.Oksanen J. et al. vegan: Community Ecology Package. R package version 2.4-1. https://CRAN.R-project.org/package=vegan (2016).61.Prost, S. & Anderson, C. N. K. TempNet: a method to display statistical parsimony networks for heterochronous DNA sequence data. Methods Ecol. Evol. 2, 663–667 (2011).Article 

    Google Scholar 
    62.Posada, D. & Crandall, K. A. Intraspecific gene genealogies: trees grafting into networks. TRENDS Ecol. Evol. 16, 37–45 (2001).CAS 
    PubMed 
    Article 

    Google Scholar 
    63.Corander, J., Marttinen, P., Sirén, J. & Tang, J. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinforma. 9, 539 (2008).Article 
    CAS 

    Google Scholar 
    64.Cheng, L., Connor, T. R., Sirén, J., Aanensen, D. M. & Corander, J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol. Biol. Evol. 30, 1224–1228 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    65.De la Cruz, M. Métodos para analizar datos puntuales. In Introducción al Análisis Espacial de Datos en Ecología y Ciencias Ambientales: Métodos y Aplicaciones (eds Maestre, F. T., Escudero, A. & Bonet, A.) 76–127. (Asociación Española de Ecología Terrestre, Universidad Rey Juan Carlos y Caja de Ahorros del Mediterráneo, Madrid, 2008).66.Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

    Google Scholar 
    67.Mayaux, P., Bartholomé, E., Fritz, S. & Belward, A. A new land‐cover map of Africa for the year 2000. J. Biogeogr. 31, 861–877 (2004).Article 

    Google Scholar 
    68.Guthrie, M. The Classification of the Bantu Languages (Oxford Univ. Press for the International African Institute, London, 1948).69.Nei, M., Tajima, F. & Tateno, Y. Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. J. Mol. Evol. 19, 153–170 (1983).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    70.Rogers, J. S. Deriving phylogenetic trees from allele frequencies: a comparison of nine genetic distances. Syst. Biol. 35, 297–310 (1986).Article 

    Google Scholar  More

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    Seasonality and landscape characteristics impact species community structure and temporal dynamics of East African butterflies

    Study sitesOur study sites are located on the Yatta Plateau in south-eastern Kenya. This region is characterized by dry savannahs. Annual rainfall (average: 810 mm) occurs during two periods, from March to May (average: 330 mm) and from October to January (average 480 mm) (c.f. Jaetzold et al.37). The commonest soil types are ferralsols and luvisols, which are of low fertility37. 97.1% of the human population in our study region depend on subsistence crop farming38, and the population has almost doubled in number from 1999 to 200938. Consequently, fallow periods for fields are omitted, which further decreases soil fertility, and increases pressure on pristine habitats.The dry savannah landscape is traversed by temporary (seasonal) rivers. These rivers are bordered by riparian vegetation, consisting of a diverse and unique plant community. However, this vegetation is frequently exploited for timber, charcoal and brick production39,40. The region is further affected by climate change, with an increase in rainfall variability and mean temperature37. These factors lower the reliability of agricultural production and food security, hence leading to severe destruction of pristine habitats.We selected two study sites, affected by different anthropogenic pressures, but which are subject to identical biotic and abiotic preconditions (including seasonality): Firstly, a highly degraded anthropogenic landscape along Nzeeu River, south of Kitui city. Secondly, a largely intact dryland environment along Kainaini River located near the university campus of the South Eastern Kenya University, north of Kitui city (Fig. 1). The landscape along Nzeeu River is densely populated by subsistence farmers. Thus, the original riparian and savannah vegetation has been mostly transformed into arable fields for the cultivation of maize, sorghum, peas, and mangos. Furthermore, the riparian vegetation, where it still exists, has largely been replaced by invasive exotic plant species (e.g. Lantana camara)12. The landscape of our second study site along Kainaini River represents a still largely intact riparian forest with adjoining dry savannahs. It remains mostly undisturbed, except for some moderate live-stock pasturing by nearby subsistence settlers.Butterfly assessmentsWe counted butterflies in both habitat types along line-transects, each 150 m long. We set 24 transects along each of the two rivers, with eight transects along the river bank, eight 250 m distant to the river, and another eight 500 m distant to the river (in total: 2 × 24 transects = 48 transects). The minimum distance between transects was at least 200 m, to minimize spatial autocorrelation. Exact GPS coordinates of each transect are given in Appendix S2.We recorded all butterflies encountered during transect counts (species, number of individuals of each species). Each transect was visited eight times during the dry season (August/September 2019) and eight times during the rainy season (January/February 2020). Data collection was performed between 9 a.m. and 4 p.m. Each butterfly individual within 5 m of the transect line (horizontally to vertically) was recorded by visual observation and, if needed, a butterfly net (see Pollard15, with modifications). While recording butterflies, the observers walked very slowly and spent about 15 min per transect. Species were identified either immediately while the butterfly was on the wing, or individuals were netted and then determined in the field. Individuals of species for which ad hoc identification was critical (e.g. many blues and skippers) were caught with the net, photographed (upper and under wing side) and released again. The photograph-based identification of these individuals was performed later using literature25. Apart from species and number of individuals per species, we recorded cloud cover during each transect walk (classified as: clear, slightly cloudy, mostly cloudy, overcast), exact time, and date. Field teams comprised two observers and one person making notes of all observations. Transects are displayed in Fig. 1. All butterfly data collected are compiled in Appendix S3.TraitsThe occurrence of a species in a specific environment strongly depends on its ecology, behaviour, and life-history41. Therefore, we considered these characteristics for each butterfly species recorded in the field. These trait data were compiled from Larsen25 and web-sites (e.g. www.gbif.org, www.lepiforum.de/non-eu.pl). We considered the following characteristics: wing span (mm), ratio length/width of the forewing (relative), ratio forewing length/thorax width (relative), geographic distribution (4 categories), savannah index (5 categories), forest index (5 categories), tree index (3 categories), wetness index (3 categories), habitat specialisation (3 categories), larval foodplant specialisation (3 categories), larval food plant type (dicotyledonous, monocotyledonous), and hemeroby index (4 categories). Detailed classifications are provided in Appendix S4.Habitat parametersHabitat structures impact species´ occurrence, abundances and community structures42. In our study, we considered habitat structures for each transect. Habitat parameters were recorded (counted and estimated) every 20 m along each transect. We estimated the following habitat parameters: Canopy cover (percentage of leaf cover vs. sky measured with the CanopeoApp); herb, shrub and tree cover (percentage coverage of each layer within a radius of 3 m); flowers on herbs, shrubs and trees (estimated within a radius of 3 m, and subsequently allocated to the classes 0, 1–10, 11–50, 51–100 and  > 100 flowers); occurrence of Lantana camara shrub, and exotic trees (estimated coverage within a radius of 3 m, and subsequently allocated to the classes 0 (no), 1 (rare), 2 (present) and 3 (dominant), respectively); and water availability (presence/absence) within a radius of 3 m. All raw data of habitat parameters are provided in Appendix S5.StatisticsWe first arranged the raw data in three matrices: a 71 × 14 species × trait matrix T, a 71 × 96 species × transect matrix M, and a 6 × 96 habitat characteristics × transect matrix H. Matrix multiplication of E = T−1MA−1, where A is the vector of total abundances in the transects, returned a matrix E of average trait expression in each transect.To answer the first research question, we compared species richness, abundances, and trait expression between the transects and used general linear modelling (glm) to detect differences in richness and trait expression with respect to the study sites (i.e. the two river systems with their different land-use patterns), season, distance from the rivers, as well as to environmental variables. Some of the habitat variables and trait expressions were highly positively correlated (Appendix S1). Consequently, the glm included only variables correlated by less than r = 0.7 (i.e. shrub cover, tree cover, habitat specialisation, savannah index, larval foodplant specialisation, and hemeroby).To infer differences in community structure between transects (second research question), we first calculated the two most dominant eigenvectors, which explained 91.5% and 3.5% of variance, of a principal components analysis of the M matrix. These eigenvectors cover differences in species composition between and within transects. We used glm and two-way Permanova to relate these differences to season, distance to river, and study sites (i.e. different land-use types in the two river systems). Additionally, we assessed the degree of β-diversity among sets of transects with the proportional turnover metric of Tuomisto43: (beta =1-frac{alpha }{gamma }); where α denotes the average species richness per transect and γ the corresponding total richness.To infer species spill-over effects from the riparian forests into the adjoining savannah (third research question), we calculated the Bray–Curtis similarities for three groups of transects within each season and study site. First, we compared average pairwise Bray–Curtis values between transects of intermediate and greater distance with the near-river transects within each study site. Second, we calculated the average Bray–Curtis similarities between all transects within each study site (2)—season (2)—distance class to river (3) combination. Third, we calculated the average within-transect Bray–Curtis similarity for the rainy season, to infer small scale compositional variability. The latter calculations were impossible for the dry season, due to the overall low number of recorded species. Calculations were done with Statistica 12. More

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    Effects of eliminating interactions in multi-layer culture on survival, food utilization and growth of small sea urchins Strongylocentrotus intermedius at high temperatures

    Sea urchins and experimental designSeven hundred small S. intermedius (31.9 ± 0.4 mm of test diameter, mean ± SD) were chosen from an aquaculture farm in Changhai County, Dalian (122° 63′ N, 39° 25′ E) on 23 July 2020. They were subsequently transported to the Key Laboratory of Mariculture and Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs at Dalian Ocean University (121° 56′ N, 38° 87′ E) and maintained in a fiberglass tank (a closed culture system, length × width × height: 150 × 100 × 60 cm) with aeration for 7 days to acclimatize to laboratory conditions. The kelp Saccharina japonica, which is the most common food used for S. intermedius culture58, was fed ad libitum under the neutral photoperiod (12 h light:12 h dark). One-half of the seawater was changed daily. Water temperature, pH and salinity were 22.6 ± 0.2 °C, 7.7 ± 0.3 and 30.7 ± 0.1 ‰ (Mean ± SD) according to the daily measurement using a portable water quality monitor (YSI Incorporated, OH, USA), respectively.The rearing space was defined as the ratio of culture volume to the number of sea urchins (cm3 ind−1). Rearing assemblage is the main factor being tested in this study. To simulate the currently used rearing assemblage in longline culture, 24 individuals were placed at plastic devices without layer divisions (length × width × height: 24.5 × 16.8 × 6 cm for culture volume; 25 holes of 0.5 cm diameter/100 cm2) as group A (the control group, 102.9 cm3 ind−1 of initial rearing space, Fig. 7a). To investigate whether multi-layer rearing assemblage improves the survival, food utilization and growth, 24 sea urchins were equally put into the cages where were evenly divided into three layers (8 sea urchins in each layer and length × width × height: 24.5 × 16.8 × 6 cm for each layer, 308.7 cm3 ind−1 of initial rearing space; 25 holes of 0.5 cm diameter/100 cm2; group B; Fig. 7b). Further, to evaluate whether eliminating interaction further contributes to the improvement of these commercially important traits of sea urchins in multi-layer rearing assemblage, 8 sea urchins were divided into eight divisions for each layer in the cages as group C (length × width × height: 8.3 × 5.9 × 6 cm for each division, 297.36 cm3 ind−1 of initial rearing space; 25 holes of 0.5 cm diameter/100 cm2; Fig. 7c). Each treatment had 8 replicates. All devices were placed in a fiberglass tank (length × width × height: 150 × 100 × 60 cm) and immersed in water for ~ 30 cm with aeration. They were easily disassembled for the experimental management.Figure 7Diagrams of the experimental cages used for the groups A (a), B (b) and C (c), the sea urchin with the spotting disease (d) and without the disease (e) and the devices used for measuring the Aristotle’s lantern reflex (f).Full size imageThe experimental period was about ~ 7 weeks (from 31 July 2020 to 20 September 2020) under the neutral photoperiod (12 h light: 12 h dark). The kelp, which was regularly collected in the intertidal waters at Heishijiao, Dalian (121° 58′ E, 38° 87′ N), was daily provided to sea urchins in abundance for all the groups. The remained kelp, feces and dead sea urchins were removed daily. One-half of the seawater was replaced daily by the fresh and filtered seawater which was pumped from the coast of Heishijiao, Dalian. Water temperature was not controlled, ranging from 22.2 to 24.5 °C (the natural seasonal cycle of increasing temperature during summer in the region). Water quality parameters were measured weekly as salinity 29.3 ± 0.6 ‰, pH 7.8 ± 0.2 (mean ± SD) using a portable water quality monitor (YSI Incorporated, OH, USA).To ensure the random sampling, sea urchins were taken out from the experimental device and placed in 24 plastic boxes (labeled from number 1 to number 24, length × width × height: 6 × 6 × 4 cm for each box). Individuals were chosen corresponding to the number (within 24) generated by the “sample” function in R studio (1.1.463). Sampling was re-conducted if the number corresponds to empty, dead or diseased sea urchins.Mortality and morbiditySpotting disease, which appears as spotting lesions with red, purple or blackish color on the test (Fig. 7d), is the most common lethal disease in S. intermedius aquaculture12. Sea urchin without disease is shown in Fig. 7e. Dead sea urchins were removed daily and the number of survivor and diseased sea urchins was recorded weekly for each cage during the experiment (N = 8).Food consumptionThe measurement of food consumption (g dry weight) was conducted once a week (24 h from Tuesday to Wednesday) (N = 8). The total supplied and remained diets were weighted wet by an electric balance (G & G Co., San Diego, USA) after the removal of the surface moisture. The dried weights of feces and samples of supplied and uneaten kelp were determined after 4 days at 80 °C in a convection oven (Yiheng Co., Shanghai, China).Food consumption was calculated as follows (revised from Hu et al.9 for being more concise):$${text{F}} = frac{{{text{A}}_{0} times frac{{{text{A}}_{1} }}{{{text{A}}_{2} }} – {text{B}}_{0} times frac{{{text{B}}_{1} }}{{{text{B}}_{2} }}}}{{text{N}}}$$F = dry food intake per sea urchin (g ind−1 day−1), A0 = wet weight of total supplied diets (g), B0 = wet weight of total uneaten diets (g), A1 = dried weight of sample supplied diets (g), A2 = wet weight of sample supplied diets (g), B1 = dry weight of sample uneaten diets (g), B2 = wet weight of sample uneaten diets (g), N = the number of sea urchins.GrowthTest diameter and lantern length were measured using a digital vernier caliper (Mahr Co., Ruhr, Germany). Body, lantern and gut were weighted wet using an electric balance (G & G Co., San Diego, USA). Test diameter and body weight were evaluated every Wednesday. The average value of the three individuals was considered as the trait value for each replicate (N = 8). Lantern length, wet lantern weight and wet gut weight were recorded in week 4 (29 August 2020) and week 7 (20 September 2020) (N = 8).Aristotle’s lantern reflexAristotle’s lantern reflex, which refers to one cycle from the opening to the closing of the teeth59, was measured using a simple device according to the method of Ding et al.38. There were small compartments (length × width × height: 4.8 × 5.6 × 4.5 cm) with a film (made by 3 g agar and 2 g kelp powder) on the bottom of the device38 (Fig. 7f). The frequency of Aristotle’s lantern reflex was counted within 5 min using a digital camera (Canon Co., Shenzhen, China) under the device in week 4 (29 August 2020) and week 7 (20 September 2020). The average value of all the 5 individuals was considered as Aristotle’s lantern reflex for each replicate (N = 8).5-HT concentrationThe 5-HT is a signaling molecule, playing an important role in regulating feeding behavior52. To evaluate whether 5-HT is involved in Aristotle’s lantern reflex, 5-HT concentration of muscle in lantern was measured for each treatment in week 4 and week 7. 5-HT concentration was considered as the average value of all the 3 healthy individuals for each replicate (N = 8).The concentration of 5-HT was measured using ELISA kits (Nanjing Jiancheng Bio-engineering Institute, Nanjing, China) according to the instructions of the manufacturer. After adding the enzyme-labeled antibody, the substrate became a colored product that was directly related to the amount of the substance tested. The concentrations of 5-HT were calculated by comparing the optical density (O.D.) value of the samples to the standard curve and calculated according to the following formula (according to the kit’s instructions):$${text{Y}} = frac{1}{{({text{a }} + {text{bx}}^{{text{c}}} )}}$$Y = the concentration of 5-HT (ng mL−1), x = the O.D. value of the samples, a = 0.00027, b = 0.12086, c = 1.36806.Pepsin activityPepsin is important for sea urchins to digest protein-rich algae40,60. Pepsin activity was analyzed using the pepsin kits (Nanjing Jiancheng Bio-engineering Institute, Nanjing, China) in week 4 and week 7, following the instructions of the manufacturer. The average value of all the 3 individuals was considered as the pepsin activity for each replicate (N = 8). The procedures include enzyme reaction and color development reaction39. The temperature of reaction was 37 °C and pepsin activities were counted as U mg protein−1. The formula of pepsin activity is shown as follows (according to the kit’s instructions):$${text{P}} = frac{{{text{M}}_{0} – {text{M}}_{1} }}{{{text{M}}_{2} – {text{M}}_{3} }} times frac{{{text{S}}_{0} }}{{{text{S}}_{1} }} times frac{{{text{V}}_{1} times {text{V}}_{2} }}{{{text{V}}_{3} }}$$P = pepsin activity (U/mg prot), M0 = the O.D. value of the sample, M1 = the O.D. value of comparison, M2 = the standard O.D. value, M3 = blank O.D. value, S0 = the standard concentration (50 μg mL−1), S1 = reaction time (10 min), V1 = total volume of reaction solution (0.64 mL), V2 = sample protein concentration (0.04 mL), V3 = sampling volume (mg prot/mL).Gut morphological examinationAfter sea urchins were dissected on week 4 and week 7, all gut tissue samples (~ 1 g for each sample) were fixed in Bouin’s solution (glacial acetic acid: formaldehyde: saturated picric acid solution = 1:5:15) according to the method of Wu et al.61. They were subsequently transferred for gradient dehydration, embedding, cutting, staining and observation62 (N = 24).Statistical analysisKolmogorov–Smirnov test and Levene test were used to analyze the normal distribution and homogeneity of the data, respectively. Rearing assemblage was set as the main factor in the one-way ANOVA with three levels: the control system without layer divisions (group A), a second system with divisions in the cages to simulate the three layers cages (group B) and a third system with individual divisions for each sea urchin (group C). One-way ANOVA was used to analyze the mortality (in weeks 3, 4, 5, 6, 7), morbidity (in weeks 3, 6, 7), food consumption (in weeks 2, 5, 7), test diameter (in weeks 1, 2, 3, 4, 5, 6), body weight (in weeks 1, 4, 5, 7), 5-HT, pepsin activity, lantern length, lantern weight and gut weight. Duncan multiple comparison analysis was performed when significant differences were found in the one-way ANOVA. Kruskal–Wallis test was carried out to compare the differences of mortality (weeks 1, 2), morbidity (weeks 1, 2, 4, 5), food consumption (weeks 1, 3, 4, 6), test diameter (week 7), body weight (weeks 2, 3, 6) and Aristotle’s lantern reflex, because of non-normal distribution and/or heterogeneity of variance. A non-parametric post-hoc test was carried out when significant differences were found in the Kruskal–Wallis test. All data analyses were performed using SPSS 19.0 statistical software. A probability level of P  More