DOI: 10.5061/dryad.8n5d7
title: Data from: Post-fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source-sink population network

description: The impact of demographic parameters on the genetic population structure
 and viability of organisms is a long-standing issue in the study of
 fragmented populations. Demographic and genetic tools are now readily
 available to estimate census and effective population sizes and migration
 and gene flow rates with increasing precision. Here we analysed the
 demography and genetic population structure over a recent 15-year time
 span in five remnant populations of Cabanis's greenbul
 (Phyllastrephus cabanisi), a cooperative breeding bird in a severely
 fragmented cloud forest habitat. Contrary to our expectation, genetic
 admixture and effective population sizes slightly increased, rather than
 decreased between our two sampling periods. In spite of small effective
 population sizes in tiny forest remnants, none of the populations showed
 evidence of a recent population bottleneck. Approximate Bayesian
 modelling, however, suggested that differentiation of the populations
 coincided at least partially with an episode of habitat fragmentation. The
 ratio of meta-Ne to meta-Nc was relatively low for birds, which is
 expected for cooperative breeding species, while Ne/Nc ratios strongly
 varied among local populations. While the overall trend of increasing
 population sizes and genetic admixture may suggest that Cabanis's
 greenbuls increasingly cope with fragmentation, the time period over which
 these trends were documented is rather short relative to the average
 longevity of tropical species. Furthermore, the critically low Nc in the
 small forest remnants keep the species prone to demographic and
 environmental stochasticity, and it remains open if, and to what extent,
 its cooperative breeding behaviour helps to buffer such effects.
description: Phyllastrephus_cabanisi_microsatellitesMicrosatellites data: 10 loci; RING = individual ID; FRAG: Forest fragment; PERIOD: 1 (1996-2000) and 2 (2006-2010); followed by 10 loci (one column per allele): Ase18, Indigo41, Ls1, Ls2, Mcyu4, Pca3, Pca4, Pfi04, Pfl54, WBSW2.CMR_dataThis folder contains all minimally necessary information to run the Jolly-Seber models with program MARK (White, Gary C., and Kenneth P. Burnham. Program MARK: survival estimation from populations of marked animals. Bird study 46.S1 (1999): S120-S139) as mentioned in the main paper. There are 10 input files for program MARK, two for each of the five fragments (MB:Mbololo,NG:Ngangao,FU:Fururu,ND:Ndiwenyi,CH:Chawia) that represent periods 1 & 2 respectively. Additionally, another 10 auxiliary datasets are provided to adjust for unequal interval lengths between sampling occasions within each fragment (see program MARK documentation). Each input data file is a tab-separated text file (.txt) in which the first column represents an encounter history of an individual, for a given fragment and time period (columns 2 and 3). Each auxiliary data file is a tab-separated text file (.txt) with interval id, starting date of interval, interval length (in days) and interval length (in fraction of a year).PG_genepop9locThis genepop file contains the genetic data (9 microsatellites) used in most genetic analyses: Effective sizes, STRUCTURE, DiyABC, Bottleneck, BIMr (adults). The file is divided by forest fragments (MB:Mbololo,NG:Ngangao,FU:Fururu,ND:Ndiwenyi,CH:Chawia) and period (1 and 2).PG_BIMr_nestlings_fledglingsDataset used to estimate recent migration rates (BIMr software: Faubet & Gaggiotti 2008) from nestlings and recent fledglings (second period only).