DOI: 10.5061/dryad.pg4f4qrp3
title: Amphibian diversity in the Amazonian floating meadows: a Hanski core-satellite species system (scripts and codes)

description: The Amazon catchment is the largest river basin on earth, and up to 30% of
 its waters flow across floodplains. In its open waters, floating plants
 known as floating meadows abound. They can act as vectors of dispersal for
 their associated fauna and, therefore, can be important for the spatial
 structure of communities. Here, we focus on amphibian diversity in the
 Amazonian floating meadows over large spatial scales. We recorded 50
 amphibian species over 57 sites, covering around 7,000 km along river
 courses. Using multi-site generalised dissimilarity modelling of zeta
 diversity, we tested Hanski’s core-satellite (HCS) hypothesis and
 identified the existence of two functional groups of species operating
 under different ecological processes in the floating meadows. ‘Core’
 species are associated with floating meadows, while ‘satellite’ species
 are associated with adjacent environments, being only occasional or
 accidental occupants of the floating vegetation. At large scales,
 amphibian diversity in floating meadows is mostly determined by stochastic
 processes, whereas at regional scales, climate and deterministic processes
 are central drivers. Compared with the turnover of ‘core’ species, the
 turnover of ‘satellite’ species increases much faster with distances and
 is also controlled by a wider range of climatic features. Distance is not
 a limiting factor for ‘core’ species, suggesting that they have a stronger
 dispersal ability even over large distances. This is probably related to
 the existence of passive long-distance dispersal of individuals along
 rivers via vegetation rafts. In this sense, Amazonian rivers can serve as
 corridors, facilitating dispersal especially for species associated with
 riverine habitats such as floating meadows.
description: Zeta diversity, the number of species shared by multiple
 assemblages, is a novel concept and metric that unifies incidence-based
 diversity measures, patterns and relationships, turning into a propitious
 method for measuring biological diversity (Hui and McGeoch 2014, McGeoch
 et al. 2019). Integrating zeta diversity into Generalised Dissimilarity
 Modelling (Multi-Site Generalised Dissimilarity Modelling, MS-GDM) allows
 to understand the importance of environmental gradients and spatial
 distance in explaining the compositional turnover of the whole spectrum of
 species, from rare to common (Latombe et al. 2017, 2018a). In this sense,
 zeta diversity and MS-GDM become important tools to understand and
 describe the diversity patterns of amphibians in the Amazonian
 floodplains, allowing to shed light on the processes and drivers of these
 patterns. Moreover, given its very characteristics, MS-GDM provides a
 means to test whether common species (higher orders of zeta; largely
 ‘core’ species) operate under different rules/processes/mechanisms from
 rare species (lower orders of zeta; largely ‘satellite’ species), thus
 becoming an excellent tool to test the Hanski’s core-satellite (HCS)
 hypothesis (Hanski 1982, 1991; see also Hanski and Gyllenberg 1993). Zeta
 diversity and MS-GDM analyses were computed in R (R CoreTeam, 2018) using
 the <i>zetadiv</i> package v.1.1.1 (Latombe et al. 2018b, c).
 We provide here all scripts, codes and data used to run
 analyses. References: Hanski, I. 1982. Dynamics of regional distribution: the core and satellite species hypothesis. – Oikos 38: 210–221.  Hanski, I. 1991. Single–species metapopulation dynamics: concepts, models and observations. – Biol. J. Linn. Soc. Lond. 42: 17–38. Hanski, I. and Gyllenberg, M. 1993. Two general metapopulation models and the core–satellite species hypothesis. – Am. Nat. 142: 17–41. Hui, C. and McGeoch, A. 2014. Zeta diversity as a concept and metric that unifies incidence-based biodiversity patterns. – Am. Nat. 184: 684–694. Latombe, G., Hui, C. and McGeoch, M. A. 2017. Multi–Site Generalised Dissimilarity Modelling: using zeta diversity to differentiate drivers of turnover in rare and widespread species. – Methods Ecol. Evol. 8: 431–442.  Latombe, G., McGeoch, M. A., Nipperess, D. and Hui, C. 2018a. zetadiv: an R package for computing compositional change across multiple sites, assemblages or cases. – bioRxiv, 324897. Latombe, G., Richardson, D. M., Pyšek, P., Kučera, T. and Hui, C. 2018b. Drivers of species turnover vary with species commonness for native and alien plants with different residence times. – Ecology, 99(12), 2763–2775.  Latombe, G., McGeoch, M. A., Nipperess, D. A. and Hui, C. 2018c. zetadiv: Functions to compute compositional turnover using zeta diversity. R package version 1. 1. 1. https://cran. r–project. org/package=zetadiv McGeoch, M. A., Latombe, G., Andrew, N. R., Nakagawa, S., Nipperess, D. A., Roige, M., Marzinelli, E. M., Campbell, A. H., Verges, A., Thomas, T., Steinberg, P. D., Selwood, K. E. and Hui, C. 2019. Measuring continuous compositional change using decline and decay in zeta diversity. – Ecology 100: e02832. R Core Team. 2018. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www. R–project. org/