DOI: 10.5061/dryad.gqnk98snq
title: Amazonian epiphytic bryophytes: community matrix and tools to assess diversity across scales

description: Aim: Tropical forests are highly diverse at many spatial scales. In these
 forests, epiphytic bryophyte communities can be species-rich already
 within a few cm2, and their species numbers increase when expanding the
 sampling along the tree and the forest. Understanding how this diversity
 increase depends on scale and position within the tree is critical to
 evaluate the processes that maintain biodiversity. We, therefore, studied
 vertical zonation and alpha and beta diversity of epiphytic bryophytes
 across spatial scales ranging from 100-cm2 quadrats to 24 trees up to 10
 km apart. Location: Tropical lowland forest in Yasuní National Park
 (Amazonian Ecuador). Methods: We sampled epiphytic bryophytes in 100-cm2
 quadrats on 24 trees (15-22 sampling quadrats per tree), using a spatially
 hierarchical design. We applied ordination, indicator species analysis,
 linear mixed models, and beta partitioning to study alpha and beta
 diversity at different spatial grains and extents. Results: At the scale
 of quadrats, tree crowns held more bryophyte species than trunks.
 Contrastingly, all crown quadrats together held fewer species than all
 trunk quadrats together (77 vs. 93 species), as species turnover among
 trunk quadrats exceeded that among crown quadrats. Across spatial extents,
 species turnover consistently dominated beta diversity over nestedness.
 Beta diversity was higher between crowns and trunks within trees than
 among crowns of different trees at all studied scales, while beta
 diversity among trunks exceeded vertical diversity when considering all 24
 trees. Main conclusions: These bryophyte communities experience two
 distinct vertical zones, trunks and crowns, which differ more among them
 than trees up to 10 km apart. Still, high species turnover makes their
 species composition highly unpredictable, especially on trunks. Chance
 processes appear to play an important role in shaping these communities,
 although analyses at even finer spatial grains may identify the importance
 of fine-scale habitat filters and species interactions.
description: Community species matrix derived from 438 samples of non-vascular
 epiphytes, 240 collected in the medium canopy and 198 along the vertical
 gradient drawn between the ground level and the canopy of 12 valley trees
 and 12 ridge trees. These 24 trees were located in clusters of 6 trees (3
 valley trees and 3 ridge trees) at 4 distances (166, 500, 820, 5986 m)
 from the Tiputini river in the Yasuni National Park (Orellana, Ecuador),
 near the Yasuni Scientific Station of the Pontificia Universidad Catolica
 de Quito (PUCE). We sampled non-vascular epiphytic
 communities established in the middle canopy (<em>sensu</em>
 Johansson, 1974) and on the tree trunk along the vertical gradient from
 the ground level to the first living branch of the crown, by using adapted
 climbing techniques (Perry, 1978). The sampling protocol consisted of
 collecting the non-vascular epiphytes found in
 100-cm<sup>2</sup> quadrats randomly selected from a larger
 set of quadrats used to estimated epiphyte cover (ten out of 20 quadrats
 in the medium section of crown branches, and one out of four quadrats per
 distance from the tree base to the height of the first living canopy
 branch). Thus, our survey can be considered a representative sampling of
 the epiphytic bryophyte diversity of these tropical lowland forests
 (Gradstein et al., 2003). We sampled 24 trees, with 240 samples collected
 in the canopy layer (24 trees × 10 samples), and 204 samples collected in
 tree trunks (the number of samples collected per tree trunk varied between
 5 to 12 depending on the height of the first canopy branch, which averaged
 14 m). Collected samples were air-dried and transported
 to different herbaria.  Sample height (from the ground
 level), tree descriptors (DBH, total height, height of the first branch,
 average height of the canopy, taxonomic identity), and tree location
 (latitude, longitude, and elevation) are environmental descriptors.
 These were recorded at the tree and the quadrat level. Tree descriptors
 were valley/ridge position, distance from the Tiputini river (as a
 categorical variable identifying the 6-tree clusters), diameter at the
 breast height (DBH, cm), height (m) and average crown radius (m), a simple
 field measurement (Zhu, Kleinn, & Nölke, 2021) used as a proxy of
 crown size. The effect of tree species could not be analyzed, as most tree
 species were represented only once in our sample (Table S1). Quadrat
 descriptors were position on the trunk or in the crown and the height from
 the tree base (m). To estimate canopy cover, pictures were taken with a
 mobile phone and processed in Gap Light Analyzer (GLA Version 2.0; Frazer,
 Canham, & Lertzman, 1999) to estimate canopy openness, as an
 indicator of light availability.
 <strong>Analysis</strong>
 Ordination (NMDS), Indicator Species (ISA), Beta diversity
 partitioning, heatmaps based on Sörensen dissimilarity, and cluster
 analysis based on Euclidean distances.
description: R code compiled in an RMD script.