Additional file 1: of Evolution of contact and alarm calls in the Kenyan endemic Hinde’s babbler (Aves: Passeriformes)

Numbers of classification within each family of a k-means clustering of contact calls. Colors coincide with the colors given in the main text. Raw data (wav-files) of bird calls recorded and analyzed are available at figshare.com, https://figshare.com/s/ab27b9a4c1aca6897825 . (DOCX 144 kb

Maylandia_DLoop_dated_tree_Mol_Ecol

Dated phylogenetic tree for 317 individuals of Maylandia zebra and Maylandia benetos generated with BEAST v.1.7.4. We used the HKY + I model and a substitution rate of 0.0324. The simplest coalescent model (constant size) was used. The best clock model was estimated by running all four available clock models and using Tracer to determine the best model for our data set. All analyses were run for 100 million generations sampling every 10,000 generations for a total of 10,000 samples. Convergence of the run was confirmed with Tracer by checking the highest effective sample size (ESS). The exponential relaxed clock had the best likelihood scores (-1371.613, second best: lognormal relaxed clock -1381.808) and was therefore chosen as best clock model. The tree was summarized with TreeAnnotator v.1.7.4

Morphometric_Data

Landmark data from 16 morphometric landmarks for 315 specimen

CMR_data

This 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)

Phyllastrephus_cabanisi_microsatellites

Microsatellites 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

PG_genepop9loc

This 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)

F2 female behavior score

This is the dataset to evaluate time in association, male courting effort on female mate choic

Data for color pattern factor analysis

This is the dataset to calculate number of genetic factors for male color patter

Phylogenetic tree resulting from Bayesian analysis of the combined data set of three genes.

<p>Red color indicates the New World Trimerotropini, blue are the Old World Sphingonotini. Black circles represent posterior probabilities ≥ 0.95 in both analyses. Numbers are posterior probabilities below 0.95 for at least one of the analyses (upper value from BEAST analysis, lower value from MrBayes analysis). The numbers in parentheses represent the divergence time estimates derived from the BEAST analysis. Only the values for main branches of interest are shown and no intraspecific values are presented. Estimates of minimum and maximum emergence times of the studied islands in parentheses next to island names were taken from Geist and colleagues [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0118208#pone.0118208.ref005" target="_blank">5</a>].</p