DOI: 10.5061/dryad.tb2rbp047
title: Data from: Factors at multiple scales drive parasite community structure

description: 1. Understanding how ecological communities are assembled remains a key
 goal of ecosystem ecology. Because communities are hierarchical, factors
 acting at multiple scales can contribute to patterns of community
 structure. Parasites provide a natural system to explore this idea, as
 they exist as discrete communities within host individuals, which are
 themselves part of a community and metacommunity. 2. We aimed to
 understand the relative contribution of multi-scale drivers in parasite
 community assembly and assess how patterns at one level may mask those
 occurring at another. Specifically, we wanted to disentangle patterns
 caused by passive sampling from those determined by ecological drivers,
 and how these vary with scale. 3. We applied a Markov Random Fields model
 and assessed measures of β-diversity and nestedness for 420 replicate
 parasite infracommunities (parasite assemblages in host individuals)
 across two freshwater mussel host species, three sites and two time
 periods, comparing our results to simulations from four different
 ecologically relevant null models. 4. We showed that β-diversity between
 sites (explaining 25% of variation in parasite distribution) and host
 species (41%) is greater than expected, and β-diversity between individual
 hosts is smaller than expected, even after accounting for parasite
 prevalence and characteristics of host individuals. Further, parasite
 communities were significantly less nested than expected once parasite
 prevalence and host characteristics were both accounted for, but more
 nested than expected otherwise, suggesting a degree of modularity at the
 within-host level that is masked if underlying host and parasite
 characteristics are not taken into account. The Markov Random Fields model
 provided evidence for possible competitive within-host parasite
 interactions, providing a mechanism for the observed infracommunity
 modularity. 5. An integrative approach that examines factors at multiple
 scales is necessary to understand the composition of ecological
 communities. Further, patterns at one level can alter the interpretation
 of ecologically important drivers at another if variation at higher scales
 is not accounted for. 
description: We collected mussels from
 three sites in Cambridgeshire, UK: Brandon Creek (henceforth BC), King’s
 Dyke (KD) and the Old West River at Stretham (OW), all of which are part
 of the Great Ouse river system (Fig. 1). Sampling incorporated two
 species: the duck mussel Anodonta anatina (Linnaeus 1758) and the
 painter’s mussel Unio pictorum (Linnaeus 1758), both non-endangered
 unionid bivalves common throughout Europe (Lopes-Lima et al. 2017) that
 possess a broad range of parasites (Brian & Aldridge 2019). We
 sampled on two occasions: 7th May 2019 (“Visit 1”), and 7th November 2019
 (“Visit 2”).  At all sites, mussels were sampled by hand from
 the river margin. In total across both visits, we collected 420 mussels
 (240 A. anatina, 180 U. pictorum). Because extended storage of live
 mussels in the laboratory could cause parasites to leave the host, or move
 between hosts, we immediately placed mussels in 75% ethanol upon sampling
 before transporting them back to the laboratory. The two species were not
 mixed at any point once being removed from the river. Exploratory
 dissection on both ethanol-stored and live mussels showed that the storage
 of mussels in ethanol prior to analysis did not affect the detection of
 any parasites in the study, and it has previously been shown as an
 effective way of sampling mussel parasites (Conn et al. 2008). As we only
 sampled non-threatened non-cephalised invertebrates, no ethical approval
 was required. In the laboratory, we sliced the anterior and
 posterior adductor muscles to open the mussel. We inspected all parts of
 the mussel in systematic fashion, and identified all parasites to the
 finest possible taxonomic resolution using keys (we did not use molecular
 identification; see S1: Supplementary Methods). We inspected samples of
 mantle fluid (1 mL) under 40 magnification using a GXM-L3200
 compound microscope to identify the presence of ciliates and nematodes.
 The mantle, gills and pericardial cavity of the mussel were inspected
 under a GXMMZS0745-T stereomicroscope at 16 magnification to identify
 further ciliates, mites, chironomids, bitterling (Rhodeus amarus) embryos
 and aspidogastrean trematodes. Finally, we squashed samples of gonad
 tissue between two glass microscope slides and studied them at
 40 magnification (following Brian & Aldridge 2020) to identify
 digenean trematodes. For ciliates and digenean trematodes we only noted
 presence or absence, while for mites, chironomids, bitterling embryos,
 aspidogastrean trematodes, and nematodes we also counted the numbers of
 individuals. If the same parasite appeared in multiple life-history stages
 or in multiple host tissues, we treated them separately (following Brian
 & Aldridge 2021a). We measured the maximum length of all mussels
 (nearest 0.5 mm) with Vernier callipers, dried them to constant mass
 (nearest 0.001 g), and identified them as either male, non-gravid female
 or gravid female via inspection of their gill tissue (where gravidity
 refers to the phenomenon of female unionid mussels harbouring larval
 mussels in specialised water-tubes in their gills).
description: The files are provided as either .csv files (data files) or as .R
 files (accompaning code). Please see the 'README_file.docx' for
 full usage notes and a complete description of all files.