DOI: 10.5061/dryad.3tx95x6ms
title: Fish sampling and physicochemical data for aquatic habitats in the Santarem region of the Lower Amazon, Brazil

description: Explaining the mechanisms underlying spatial and temporal variation in
 community composition is a major challenge. Nevertheless, the processes
 controlling temporal variation at a site (i.e., temporal β-diversity,
 including its turnover and nestedness components) are less understood than
 those affecting variation among sites (i.e., spatial β-diversity).
 Short-term temporal turnover (e.g., throughout an annual cycle) is
 expected to correlate positively with seasonal environmental variability
 and landscape connectivity, but also species pool size (γ-diversity). We
 use the megadiverse Amazonian freshwater ichthyofauna as a model to ask
 whether seasonality and landscape connectivity drive variation in temporal
 species turnover among geomorphological habitat types, while accounting
 for between-habitat variation in γ-diversity. 11,397 fish
 representing 260 species were collected during a year-long sampling
 program from an area containing the lowland Amazon’s four major
 geomorphological habitat types: rivers, floodplains, terra firme streams,
 and shield streams. River-floodplain systems exhibit strong but
 predictable seasonality (via a high-amplitude annual flood pulse), high
 connectivity, and high species richness with many rare species. Terra
 firme and shield streams exhibit low seasonality, low connectivity, and
 low species richness with proportionally fewer rare species. Based on
 these parameters we predicted that river-floodplain systems should have
 higher temporal turnover than stream systems. Using a null model approach
 combined with β-deviation calculations, we confirmed that rivers and
 floodplains do exhibit higher turnover (but not nestedness) than terra
 firme and shield streams, even when controlling for the potentially
 confounding effect of higher species richness in river-floodplain systems.
 All habitats exhibit low temporal nestedness, indicating that short-term
 changes in community composition result primarily from temporal species
 turnover. Our results provide a timely reminder that efforts to conserve
 the Amazon’s threatened aquatic biodiversity should account for the
 distinct temporal dynamics of habitat types and variation in hydrological
 seasonality.
description: We studied one of the few Amazonian regions where all four
 geomorphological habitats occur in close proximity (near Santarém, Brazil,
 Fig. 1d). This lower Amazon region also includes river-floodplain systems
 belonging to the three distinct biogeochemical water types of the Amazon
 basin: nutrient-poor, humic-stained ‘blackwaters’  (BW); nutrient-poor
 ‘clearwaters’ (CW); and nutrient rich, sediment-laden ‘whitewaters’  (WW)
 (Sioli 1984, Bogotá-Gregory et al., 2020). We estimated temporal
 β-diversity for rivers-floodplain systems in all three water types,
 allowing us to evaluate whether water type, as well as geomorphological
 habitat type, influence rates of temporal turnover and
 nestedness. We sampled 16 sites (Fig. 1d) every two
 months through a complete annual hydrological cycle, beginning October
 2014: Rivers: two river-margin sites in the BW River (R.) Arapiuns (BR1,
 BR2), two in the CW R. Tapajós (CR1, CR2), and two in the WW R. Amazonas
 (WR1, WR2); Floodplains: two floodplain lake sites in the BW R. Arapiuns
 (BF1, BF2), two in the CW R. Tapajós (CF1, CF2), and two in the WW R.
 Amazonas (WF1, WF2); Terra firme streams: two sites in the lowland terra
 firme peneplain (Cretaceous Alter do Chão formation) (TS1, TS2); Shield
 streams: two sites in the upland Paleozoic shield (Devonian Ererê
 formation) (SS1, SS2). Hence our sampling design comprised eight
 geomorphological habitat/water type combinations, each replicated at two
 sites, and sampled six times through the year for a planned total of 96
 sampling events. TS1 and TS2 were sampled only five times due to
 logistical challenges during the first sampling event, and BF2 and WR2
 were sampled only five times due to severe weather at the first event for
 BF2 and fifth for WR2. Thus, the actual number of sampling events was
 92.<br>The river-floodplain habitats exhibited a flood cycle of ca.
 5 m amplitude, with an April-July high-water period and October-December
 low-water period. Year-long variation in water levels in the shield and
 terra firme streams is &lt; 0.5 m (except briefly after heavy rain) in
 response to local rainfall – with a December-June wet season followed by a
 dry season. We selected permanent floodplain lakes of similar size (BF1,
 0.17 km2; BF2, 0.25 km2; CF1, 0.18 km2; CF2, 0.21 km2; WF1, 0.18 km2, WF2,
 0.26 km2; Fig. 1d) and permanent terra firme and shield streams of similar
 sizes (3-6 m wide, to 1 m deep). All 16 sites were surrounded by
 relatively well-protected natural forest. Due to
 habitat heterogeneity, it was impossible to use the same gear and sample
 technique in all habitat types. Therefore, for each habitat we used the
 gear considered to obtain a representative sampling and then standardized
 for effort within a given habitat type across all sampling events in the
 annual cycle. To maximize sampled species diversity in river and
 floodplain sites, we sampled with gill nets deployed ca. 30 m from the
 shoreline in batteries of four (25 x 3 m, 15, 30, 45, 60 mm mesh) from 6
 am to 9 am and from 6 pm to 9 pm. In the much smaller habitat volumes of
 terra firme and shield streams, we used three gear types, each with a
 timed effort of 2 hours/sampling event during daylight hours: a 1.5 x 6 m
 seine net (5 mm mesh) in deeper pools; a 2.0 x 1.1 m bag-seine (2 mm mesh)
 in riffles and margins; a dipnet (Expedition Hex-Trapnet, Duraframe
 Dipnet, Viola WI, with 3 mm mesh and 30 cm bag depth), used with the aid
 of an electric fish finder (Haag et al. 2019), in leaf litter and marginal
 root mats; the dipnet-electric fish finder combination sampled gymnotiform
 electric fish and other nocturnally active fish hiding in the substrate.
 For each stream, all gear types were used along a 100 m stretch in a
 downstream-upstream direction with the ends of the section blocked with
 net panels to minimize escape. Fish were euthanized with 600 mg L-1
 eugenol, preserved, and deposited at the biodiversity collections listed
 in Supporting Information Appendix S1. We identified specimens using
 species descriptions and keys from the taxonomic literature. 
 Measuremens of physicochemical water parameters
 follow: <br>Bogotá-Gregory, J.D., Lima, F.C.T., Correa, S.B.,
 Silva-Oliveira, C., Jenkins, D., Ribeiro, F.R., Lovejoy, N.R., Reis, R.E.
 & Crampton, W.G.R. (2020) Biogeochemical water type influences
 community composition, species richness, and biomass in megadiverse
 Amazonian fish assemblages. Scientific Reports, 10, 15349.