pond_frog_populations — Pond frog population genetic differentiation (2014)
- Description
Weighted network of genetic differentiation among 27 populations of the black-spotted pond frog (Pelophylax nigromaculatus) from 24 islands of the Zhoushan Archipelago and three sites on the nearby mainland of China, from the study of S. Wang and collaborators on the loss of genetic diversity in insular populations (genotypes of 810 frogs deposited in the Dryad repository). 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 (file
mep_frogs_Rst.txt). Nodes are populations, and an undirected edge connects every pair of populations (the network is a complete graph), weighted by their pairwise genetic differentiation RST (Slatkin, 1995), computed from the variance of microsatellite allele sizes (nine neutral microsatellite loci). RST is 0 for genetically identical populations and grows with differentiation; small negative values arise from sampling error. Note that the documentation of the source describes the weights as the genetic similarity 1 - RST, but the file contains RST itself (with zeros on the diagonal). The populations are not identified in the source data.The edges have the property
weight, the pairwise RST.
- Tags
- Biological Genetic Weighted
- Citation
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- S. Wang, W. Zhu, X. Gao, X. Li, S. Yan, X. Liu, J. Yang, Z. Gao, Y. Li, "Population size and time since island isolation determine genetic diversity loss in insular frog populations." Molecular Ecology 23, 637-648 (2014) 10.1111/mec.12634 Sci-Hub
- S. Wang et al., "Data from: Population size and time since island isolation determine genetic diversity loss in insular frog populations." Dryad Digital Repository (2013) 10.5061/dryad.dq4g5 Sci-Hub
- M. Slatkin, "A measure of population subdivision based on microsatellite allele frequencies." Genetics 139(1), 457-462 (1995) 10.1093/genetics/139.1.457 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
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Tip: hover over a column header 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