Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: Challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting, and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management, and no estimates of Ne have been obtained. In this study, we use the country’s range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss the strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient ..., Genomic data
Whole-genome sequences were produced from biological material collected from wild born chimpanzees: one road-killed (tissue sample T3-Chimp collected in 2011) and blood samples from four individuals (blood samples from Bo, Bella, Simão and Emilia chimpanzees, collected between 2018 and 2019) confiscated by the Institute for Biodiversity and Protected Areas (IBAP) from private premises. Blood was collected as part of the placement of the individuals in a sanctuary abroad (Sweetwaters Chimpanzee Sanctuary, Ol Pejeta, Kenya). The blood samples were drawn by a wildlife veterinarian (P. Melo, vet_natura, https://www.vetnatura.pt/) for health screening and as part of a parasites and virus detection procedure prior to translocation (Melo et al., 2018). Samples were collected in 5 mL collection tubes filled up with the anticoagulant ethylenediamine tetraacetic acid (EDTA) and preserved fresh until DNA extraction. The road-killed individual was found in the road next to CLNP and a s..., , ## **Whole genome sequencing data**

Whole genome sequencing data from 5 individuals analysed in the study entitled: Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management.

We deposited the BAM files of each sample aligned with the reference genome. Files are named according to name of the chimpanzee individuals - Bella, Bo, Emilia, Simão, and T3

Bella_PT_GB.Reference_genome.realigned.bam.zip

Bo_PT_GB.Reference_genome.realigned.bam.zip

Emi_PT_GB.Reference_genome.realigned.bam.zip

Simao_PT_GB.Reference_genome.realigned.bam.zip

T-3_Chimp.Reference_genome.realigned.bam.zip

## Unique genotypes (10 microsatellite loci) of the western chimpanzees in Guinea-Bissau, West Africa

## Description of the data and file structure

#### File: Database_10_loci_estimatingNechimps_less_accuracy.xlsx

The dataset consists of 143 unique genotypes for 10 microsatellite loc..., , **Changes after Oct 7, 2025:** A file was added. This file contain a dataset of unique genotypes from western chimpanzee in Guinea-Bissau (N=143 genotypes) for 10 autosomal loci.