DOI: 10.5061/dryad.bvq83bkkk
title: Taita thrush genetic and demographic data

description: Predicting the fate of threatened populations remains a challenge in
 conservation biology. The study of genetic and demographic time series are
 crucial to unravel the role of population history, anthropogenic
 disturbance and conservation actions on current demographic and genetic
 patterns. However, such studies are still rare in threatened species. In
 this study, we integrate a quarter century of population demographic
 (capture-mark-recapture) and genetic (microsatellites) data for the
 globally endangered Taita Thrush Turdus helleri, a songbird endemic to the
 fragmented cloud forest of the Taita Hills, southeast Kenya. We found that
 the two largest remaining populations are prone to high demographic and
 genetic stochasticity. Furthermore, despite relatively high genetic
 diversity, the increase in inbreeding in recent years suggests
 vulnerability to extinction. Moreover, while the smallest population was
 close to extinction, assisted gene flow midway through the study led to a
 demographic rescue. We conclude that habitat protection, continued
 monitoring and conservation efforts are required for long-term survival of
 the endangered Taita Thrush, as the species may be prone to an extinction
 debt.
description: # Taita thrush genetic and demographic data
 [https://doi.org/10.5061/dryad.bvq83bkkk](https://doi.org/10.5061/dryad.bvq83bkkk) ## Description of the data and file structure **1. Microsatellite data**: "TT_genotypes.xlsx" This file contains 2 sheets: \- Sheet 'Translocated': genotypes of 8 Taita thrushes translocated from populations Mbololo to Chawia in 2008. SAMPLE: unique sample number RING: unique ring number (unique identifier of a specific individual) CU28 to PDO5: genotypes at 7 microsatellites (CU28_1: allele 1, CU28_2: allele 2 etc.) \- Sheet '3-pop genotypes': genotypes of Taita thrushes used in the study (population genetics analysis). RING: unique ring number CU28_1 to PDO5_2: microsatellites FRAG: population (MB: Mbololo, CH: Chawia, NG: Ngangao) PERIOD: time period (P1: 1997-1998, P2: 2005-2006, P3: 2015-2016, PRE: pre-translocaton i.e. before 2008 (Chawia only); POST: post-translocaton i.e. after2008 (Chawia only)) NEW: if 1, the individual was genotyped for the study; if 0, the individual was genotyped before the study in another lab. 0 in the genotypes means that the DNA could not be genotyped at that particular locus. **2. Sexing data**: "TT_sexing.txt" The sex of 310 individuals was molecularly determined using a set of sex-linked primers P2/P8 (Griffiths et al. 1998). RING: unique ring number SEX: sex of the individual (F: female, M: male) **3. Ringing data** "ch_CH.txt" / "ch_NG.txt" / "ch_MB.txt" capture histories of Taita thrushes in the different forest fragments (CH: Chawia, NG: Ngangao, MB: Mbololo). 0: not captured during the ringing session, 1: captured during the ringing session. Those are the input files for Mark software. "sessions_CH.xlsx" / "sessions_MB.xlsx" / "sessions_NG.xlsx" * trapping sessions with effort (net length and duration). - SESSION: unique identifier of the ringin session (format: year/month/day/population/unique_number_for the day) * DATE: date of the ringing session - FRAG: population * OPEN: time when msitnets were open - CLOSE: time when msitnets were closed * 18M: number of 18m nets used in the ringing session - 12M: number of 12m nets used in the ringing session * 10M: number of 10m nets used in the ringing session - 9M: number of 9m nets used in the ringing session * 7M: number of 7m nets used in the ringing session - YEAR: year of the ringing session * MONTH: month of the ringing session - PLOT: plot number (specific area in the population) * NET_LENGTH: total net length (number of 18m * 18 + number of 12m * 12 etc) - time.duration: CLOSE - OPEN * first_date: date of the start of a given capture occasion with a population - SAMPLING_EFFORT: NET_LENGTH * time.duration * SAMPLING_EFFORT_all: sum of all sampling effort accross different plots at over a specific capture occasion Missing data is noted as n/a