The use of multilayer network analysis in animal behaviour

Network analysis has driven key developments in research on animal behaviour by providing quantitative methods to study the social structures of animal groups and populations. A recent formalism, known as \emph{multilayer network analysis}, has advanced the study of multifaceted networked systems in many disciplines. It offers novel ways to study and quantify animal behaviour as connected 'layers' of interactions. In this article, we review common questions in animal behaviour that can be studied using a multilayer approach, and we link these questions to specific analyses. We outline the types of behavioural data and questions that may be suitable to study using multilayer network analysis. We detail several multilayer methods, which can provide new insights into questions about animal sociality at individual, group, population, and evolutionary levels of organisation. We give examples for how to implement multilayer methods to demonstrate how taking a multilayer approach can alter inferences about social structure and the positions of individuals within such a structure. Finally, we discuss caveats to undertaking multilayer network analysis in the study of animal social networks, and we call attention to methodological challenges for the application of these approaches. Our aim is to instigate the study of new questions about animal sociality using the new toolbox of multilayer network analysis.Comment: Thoroughly revised; title changed slightl

The assessment report of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services on pollinators, pollination and food production

The thematic assessment of pollinators, pollination and food production carried out under the auspices of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services aims to assess animal pollination as a regulating ecosystem service underpinning food production in the context of its contribution to nature’s gifts to people and supporting a good quality of life. To achieve this, it focuses on the role of native and managed pollinators, the status and trends of pollinators and pollinator-plant networks and pollination, drivers of change, impacts on human well-being, food production in response to pollination declines and deficits and the effectiveness of responses

Reconciling ecology and economics to conserve bumblebees

Many bumblebee species have experienced severe population declines in response to the use of intensive land management practices throughout the UK and western Europe during the latter half of the twentieth century. The loss of wildflower-rich unimproved lowland grasslands has been particularly detrimental and, as a result, in the UK two bumblebee species are now extinct, seven are listed on the UK Biodiversity Action Plan (BAP), and only six extant species remain common and ubiquitous. Populations of the rarer species are often fragmented and restricted to isolated areas, such as the crofting regions of northwest Scotland, in which the use of intensive farming practices has remained relatively limited. Consequently, in this study I primarily focus on the conservation of B. distinguendus and B. muscorum, two of the UK’s rarest species which have strongholds in the Outer Hebrides. In this region crofting is the dominant form of agriculture, and is traditionally typified by small-scale mixed livestock production accompanied by rotational cropping activities. With the use of very few artificial inputs, traditional crofting activities are environmentally sensitive and promote the diverse wildflower assemblages characteristic of the machair which provide suitable forage for bumblebees. However, the changing demographic structure of the islands, in conjunction with a range of other socio-economic factors, is resulting in the adoption of more intensive land management practices by crofters and changing the nature of the crofted landscape. These changes are likely to have a detrimental impact on the rare bumblebee populations that rely on crofting to provide suitable foraging habitats. Neglecting to examine the socio-economic issues behind the decline in crofting activities, and failure to develop a means of making the system economically viable and sustainable, is likely to reduce the effectiveness of any bumblebee conservation measures introduced in the region. Through my research I address this socio-ecological problem by taking an interdisciplinary approach, and combine the two disciplines of ecology and economics to find a way to ensure crofting is sustainable whilst promoting sympathetic land management practices to aid bumblebee conservation. The results of my research demonstrate that current croft land management practices do not support high abundances of foraging bumblebees in the Outer Hebrides, and that sheep grazing during the summer has a particularly negative impact on bumblebee abundance on croft land. My research also highlights the importance of non-agricultural habitats for foraging long-tongued bumblebee species in agricultural landscapes. Grazing management can promote bumblebee abundance, with cattle grazing providing a valuable foraging habitat for short-tongued bumblebees in southwest England. Therefore, to conserve bumblebees in agricultural landscapes the type of farming system needs to be taken into account in developing grazing management regimes, whilst non-agricultural habitats need to be integrated into local land management plans to ensure the provision of forage for bumblebees throughout the flight period. The outputs of the ecological-economic models show that compensation payments are not always required to encourage beneficial land management practices to enhance bumblebee populations in crofted areas. However, crofting is a marginal farming system that is heavily influenced by socio-economic factors, and this should be taken into consideration in the development of future agricultural policy for the region

Responses to risks and opportunities associated with pollinators and pollination

The overall aim of the thematic assessment of Pollinators, Pollination and Food Production is to assess animal pollination as a regulating ecosystem service under pinning food production in the context of its contribution to nature'sgifts to people and supporting a good quality of life. Toachieve this, the focus is on the role of native and exoticpollinators, the status of, and trends in pollinators andpollinator-plant networks and pollination, drivers of change,impacts on human well-being, food production in responseto pollination declines and deficits and the effectiveness ofresponses from various governance systems to pollinationdeclines and deficits. The scope is global, covering allcontinents except Antarctica, where no pollinators areknown. The assessment brings together contributions notonly from natural, social and economic science perspectives but also from knowledge of indigenous and local community stake holders and practitioners.The assessment strives to critically review the broadest range of evidence and make its findings readily availableto support policy and management responses to declinesand deficits in pollination. The report represents the firstIPBES thematic assessment deliverable that aims toidentify policy-relevant findings for decision-making ingovernment, the private sector and civil society, as wellas helping to demonstrate how an essential ecosystem service could potentially contribute to the post-2015 development agendaFil: Dicks, Lynn. University of Cambridge; Reino UnidoFil: Viana, Blandina Felipe. Universidad federal de Bahia; BrasilFil: del Coro Arizmendi, Maria. Universidad Nacional Autónoma de México; MéxicoFil: Bommarco, Riccardo. Mid Sweden University.; SueciaFil: Brosi, Berry. University of Washington; Estados UnidosFil: Cunningham, Saul. Australian National University; AustraliaFil: Galetto, Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Lopes, Ariadna. Universidade Federal de Pernambuco; BrasilFil: Taki, Hisatomo. University of Florida; Estados Unido

The Benefits to People of Expanding Marine Protected Areas

This study focuses on how the economic value of marine ecosystem services to people and communities is expected to change with the expansion of marine protected areas (MPAs). It is recognised, however, that instrumental economic value derived from ecosystem services is only one component of the overall value of the marine environment and that the intrinsic value of nature also provides an argument for the conservation of the marine habitats and biodiversity

Patterns in Knowledge Production

abstract: This dissertation will look at large scale collaboration through the lens of online communities to answer questions about what makes a collaboration persist. Results address how collaborations attract contributions, behaviors that could give rise to patterns seen in the data, and the properties of collaborations that drive those behaviors. It is understood that collaborations, online and otherwise, must retain users to remain productive. However, before users can be retained they must be recruited. In the first project, a few necessary properties of the ``attraction'' function are identified by constraining the dynamics of an ODE (Ordinary Differential Equation) model. Additionally, more than 100 communities of the Stack Exchange networks are parameterized and their distributions reported. Collaborations do not exist in a vacuum, they compete with and share users with other collaborations. To address this, the second project focuses on an agent-based model (ABM) of a community of online collaborations using a mechanistic approach. The ABM is compared to data obtained from the Stack Exchange network and produces similar distributional patterns. The third project is a thorough sensitivity analysis of the model created in the second project. A variance based sensitivity analysis is performed to evaluate the relative importance of 21 parameters of the model. Results indicate that population parameters impact many outcome metrics, though even those parameters that tend towards a low impact can be crucial for some outcomes.Dissertation/ThesisDoctoral Dissertation Applied Mathematics for the Life and Social Sciences 201

Investigating Larval Spillover From Oyster Aquaculture Through Geospatial Habitat Suitability Index Modeling: A Damariscotta River Estuary Case Study

The eastern oyster (Crassostrea virginica) supports the ecological function of estuarine ecosystems by creating biogenic reef habitat (Purchon, 2013), and positively influencing coastal biogeochemistry in intertidal, and subtidal environments (Humphries et al., 2016; Ray and Fulweiler, 2020). As anthropogenic impacts continue to influence the health of marine environments globally (Halpern et al., 2008), oyster reef restoration is gaining increased attention as a means of maintaining the function of estuarine systems (Beck et al, 2011). Shellfish aquaculture has gained increased attention, contributing 21% of all aquaculture production globally (FAO 2020). Shellfish aquaculture provides a suite of social-ecological benefits while contributing to provisioning and supporting ecosystem services including nutrient removal, water clarification, coastal protection, and habitat creation (Gentry et al. 2020; Grizzle et al. 2008; Dame and Kenneth, 2011; Kellogg et al. 2014). In this way, shellfish aquaculture can exist in synergy with ecosystem processes, resulting in positive environmental outcomes while creating livelihoods through supply of seafood and commercial products (referred to as restorative aquaculture) (Blanchard et al., 2017). Despite the range of ecosystem services provided from bivalve aquaculture, the role of larval subsidy in population restoration has yet to be recognized (van der Schatte Olivier et al., 2020). However, evidence of green lipped mussel (P. canaliculus) restoration via larval subsidy has been documented (Norrie et al., 2020). Habitat suitability index (HSI) models have proven effective in facilitating population restoration of the American oyster in estuaries of the eastern United States by providing spatially explicit information regarding the quality of habitat over broad areas of interest (Soniat and Brody, 1988; Barnes et al., 2007; Starke et al., 2011; Pollack et al., 2012; Linhoss et al., 2016; Theuerkauf and Lipcius, 2016; Puckett et al., 2018). This study employs a geospatial HSI model for the eastern oyster to investigate a recent population resurgence in an estuary where oysters were once extirpated, the Damariscotta River estuary (DRE), Maine, USA. As a means of internal validation, we combine HSI model predictions with local ecological knowledge gained through participatory interviews and surveys of local shellfish harvesters targeting eastern oysters, oyster aquaculture producers operating within the estuary, and researchers familiar with the system. By assessing the viability of incidental restoration resulting from larval subsidy from oyster aquaculture, this study explores the implications of low-cost restoration strategies which integrate fisheries, aquaculture, and conservation interests within a reciprocal conservation paradigm

The use of multilayer network analysis in animal behaviour

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.We gratefully acknowledge the 806 supporters of MX16: the UC Davis Institute for Social Sciences, the U.S. Army Research Office 807 under Multidisciplinary University Research Initiative Award No. W911NF-13-1-0340, the UC 808 Davis Complexity Sciences Center, the UC Davis Anthropology Department, the UC Davis 809 Graduate Student Association, the UC Davis Department of Engineering, and the UC Davis 810 Office of Research.Network analysis has driven key developments in research on animal behaviour by providing quantitative methods to study the social structures of animal groups and populations. A recent formalism, known as multilayer network analysis, has advanced the study of multifaceted networked systems in many disciplines. It offers novel ways to study and quantify animal behaviour through connected ‘layers’ of interactions. In this article, we review common questions in animal behaviour that can be studied using a multilayer approach, and we link these questions to specific analyses. We outline the types of behavioural data and questions that may be suitable to study using multilayer network analysis. We detail several multilayer methods, which can provide new insights into questions about animal sociality at individual, group, population and evolutionary levels of organization. We give examples for how to implement multilayer methods to demonstrate how taking a multilayer approach can alter inferences about social structure and the positions of individuals within such a structure. Finally, we discuss caveats to undertaking multilayer network analysis in the study of animal social networks, and we call attention to methodological challenges for the application of these approaches. Our aim is to instigate the study of new questions about animal sociality using the new toolbox of multilayer network analysis.Natural Environment Research Council (NERC)National Science Foundation (NSF) Graduate Research FellowshipNFS IOS grantNIH R01NERC standard gran

Why are Some Plant Species Missing from Restorations? A Diagnostic Tool for Temperate Grassland Ecosystems

The U.N. Decade on Ecosystem Restoration aims to accelerate actions to prevent, halt, and reverse the degradation of ecosystems, and re-establish ecosystem functioning and species diversity. The practice of ecological restoration has made great progress in recent decades, as has recognition of the importance of species diversity to maintaining the long-term stability and functioning of restored ecosystems. Restorations may also focus on specific species to fulfill needed functions, such as supporting dependent wildlife or mitigating extinction risk. Yet even in the most carefully planned and managed restoration, target species may fail to germinate, establish, or persist. To support the successful reintroduction of ecologically and culturally important plant species with an emphasis on temperate grasslands, we developed a tool to diagnose common causes of missing species, focusing on four major categories of filters, or factors: genetic, biotic, abiotic, and planning & land management. Through a review of the scientific literature, we propose a series of diagnostic tests to identify potential causes of failure to restore target species, and treatments that could improve future outcomes. This practical diagnostic tool is meant to strengthen collaboration between restoration practitioners and researchers on diagnosing and treating causes of missing species in order to effectively restore them

Foraging resource use by grey-headed flying-foxes in urban and non-urban Australia

Urbanisation is a major threat to ecosystems globally, resulting in habitat loss and habitat fragmentation, reduced biodiversity, and/or species extinction. However, urban habitats also create opportunities for exploitation by adaptable species, and this often leads to unbalanced management actions that have little regard for species conservation. Better understanding of the underlying drivers of wildlife species urbanisation will assist wildlife managers in developing effective and balanced conservation-management strategies. The grey-headed flying-fox (Pteropus poliocephalus), is a large, highly mobile species, that is becoming increasingly dependent on urban areas. Flying-fox urbanisation has been hypothesised to be a result of loss of natural foraging habitat, an attraction to increased spatiotemporal stability of food resources in urban areas, and/or both. Yet, little is known about how P. poliocephalus utilise urban areas for foraging. This study aims to investigate foraging resource availability as a driver of the documented P. poliocephalus urbanisation. Foraging habitat use was assessed using a large satellite tracking dataset from 98 individuals between 2012-2017. These data were combined with vegetation type data, and published indices of P. poliocephalus habitat quality to assess foraging habitat preferences. Tracked individuals were overwhelmingly dependent on human-modified landscapes for foraging, particularly where they roosted in major-urban areas. To identify the specific food plant species that support P. poliocephalus in urban areas, paired GPS and accelerometer data were used to identify trees visited by foraging individuals roosting in Adelaide. Tracked individuals preferentially visited residential areas and road-side habitats. Individuals visited a relatively high diversity of food plant species in these habitats, and flowering/fruiting phenology records indicated collective year-round availability of food resources for P. poliocephalus. This study suggests that P. poliocephalus urbanisation is, at least in part, driven by spatiotemporal availability and stability of food resources