reef_fish_atlantic — Western Atlantic reef fish communities (2014)

Description

Weighted bipartite networks of the occurrence of reef fish groups in 24 reef communities along the Western Atlantic (2 in the North-western Atlantic, 5 in the Caribbean and 17 in the South-western Atlantic, mostly along the Brazilian coast and oceanic islands), from the reef-fish community database of S. R. Floeter, D. R. Barneche and collaborators. Fishes were surveyed by underwater visual census in strip transects (20 m x 2 m) on shallow reefs (depth < 20 m), where all individuals (536,378 in total) were counted, their total length estimated in 10-cm bins, and identified to species. The data were compiled by M. Cantor and collaborators for a study of nestedness across levels of biological organization, and are distributed in the repository of that study (files met_gen_scmass.txt, met_sd_scmass.txt and met_sdms_scmass.txt). The species are grouped either taxonomically or into functional groups (combinations of traits, following D. Mouillot and collaborators):

genera: 161 genera.
diet_size: 40 functional groups combining diet and body size class.
diet_size_mobility_school: 122 functional groups combining diet, body size class, mobility and school size.

A node is either a site (community) or a group of fishes, and an edge connects a group to a site where it was recorded, weighted by its abundance in the site measured by size-corrected body mass (following A. P. Allen and collaborators, as in the study of Barneche et al.), which accounts for the biological turnover among individuals of different mass and for differences in size structure among communities. The units are not stated in the source. (Cantor et al. projected these matrices onto the fish groups using the Bray-Curtis similarity of their abundances across sites.)

The networks have the following properties:

Nodes: is_site, whether the node is a site (otherwise it is a group of fishes); name, the name of the site (e.g. "abrolhos", "florida_keys") or of the group: the genus name in genera, or the functional group code of the source in the other networks (traits separated by underscores, e.g. "1_c2" or "1_c2_1_3", with codes not explained in the source).
Edges: weight, the size-corrected biomass of the group in the site.

Tags

Biological Weighted Metadata

Citation

S. R. Floeter, W. Krohling, J. L. Gasparini, C. E. L. Ferreira, I. R. Zalmon, "Reef fish community structure on coastal islands of the southeastern Brazil: the influence of exposure and benthic cover." Environmental Biology of Fishes 78, 147-160 (2007) 10.1007/s10641-006-9084-6 Sci-Hub
D. R. Barneche, M. Kulbicki, S. R. Floeter, A. M. Friedlander, J. Maina, A. P. Allen, "Scaling metabolism from individuals to reef-fish communities at broad spatial scales." Ecology Letters 17, 1067-1076 (2014) 10.1111/ele.12309 Sci-Hub
D. Mouillot et al., "Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs." Proceedings of the National Academy of Sciences 111, 13757-13762 (2014) 10.1073/pnas.1317625111 Sci-Hub
A. P. Allen, J. F. Gillooly, J. H. Brown, "Linking the global carbon cycle to individual metabolism." Functional Ecology 19, 202-213 (2005) 10.1111/j.1365-2435.2005.00952.x Sci-Hub
M. Cantor, M. M. Pires, F. M. D. Marquitti, R. L. G. Raimundo, E. Sebastián-González, P. P. Coltri, S. I. Perez, D. R. Barneche, D. Y. C. Brandt, K. Nunes, F. G. Daura-Jorge, S. R. Floeter, P. R. Guimarães Jr., "Nestedness across biological scales." PLoS ONE 12(2), e0171691 (2017) 10.1371/journal.pone.0171691 Sci-Hub

Upstream URL OK

https://bitbucket.org/maucantor/unodf_analyses

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
genera	185	1,239	13.39	17.10	26.16	1.44	-0.78	4	1.00	Undirected	Bipartite	is_site name	weight	13 KiB	15 KiB	15 KiB	14 KiB
diet_size	64	589	18.41	8.44	20.86	0.88	-0.40	4	1.00	Undirected	Bipartite	is_site name	weight	6 KiB	8 KiB	8 KiB	7 KiB
diet_size_mobility_school	146	1,173	16.07	16.87	26.51	1.21	-0.79	4	1.00	Undirected	Bipartite	is_site name	weight	11 KiB	14 KiB	14 KiB	13 KiB