Chimpanzee why is it endangered

A new study provides insight into where chimpanzees Pan troglodytes avoided climate instability during glacial and interglacial periods in Africa over the past , years. An unexpected error has occurred. Please refresh the page. Challenges The main threats to chimpanzees are habitat loss, disease, and hunting, especially for bushmeat.

Our Goal With our partners, range state governments, and local communities, we strive to maximize our impact to protect chimps. Habituating Wild Chimps. Chimpanzees and Bushmeat. Chimpanzees in Entertainment. Chimps as pets: The Reality. Waterfall Displays. When conservation authorities confiscate illegally kept chimpanzees, they are placed at wildlife sanctuaries, often arbitrarily based on availability of space and proximity to the confiscation site. Whilst some of the rescued chimpanzees require specialised lifetime care, others may be successfully reintroduced into their natural habitats after extensive preparation Beck et al.

For chimpanzees destined to lifetime care, proper management planning requires knowledge about relatedness among sanctuary chimpanzees in order to set up family groups. In cases, were chimpanzees are suitable for reintroduction, knowledge of geographical origin is essential as several studies have shown lineage-specific adaptations in all four subspecies in their respective geographical ranges e.

Nye et al. In the first complete geo-referenced genomic map of the chimpanzee, de Manuel et al. Employing genetic testing at the site of confiscation e.

Alternatively, confiscated chimpanzees can be sent to a neighbouring sanctuary with housing capacity, where specialised care and rehabilitation can be provided, and if possible, future reintroduction can be planned.

Genetic testing at an early stage of confiscation also has the potential to understand and help break trafficking routes and enable CITES authorities to track and enforce law control in situations where chimpanzees are housed in disreputable zoos and entertainment facilities. However, to be a practical tool in conservation, the genetic test needs to maximise the inference accuracy, require very little investment, and pose as little risk to animal health as possible.

These requirements limit our choice of applicable data types. With a novel SNP array design where the level of genetic information is only surpassed by costly whole genome sequencing, we argue that our approach constitutes the most cost-efficient option for conservation management in situations where funding is often scarce and demands for rigorous solutions are high.

Using a selected panel of 59, targeted ancestry informative markers, we demonstrate the ability to infer robust estimates of ancestry in several generations of the EEP chimpanzee breeding population. We further show how this set of ancestry informative markers can be used to determine geographical origin of confiscated individuals and demonstrate how these methodologies can readily be applied to using non-invasive sampling.

In combination, these methods harbour great potential for future global management plans for the chimpanzee and provides an important exemplar for management of endangered species in general.

A total of chimpanzee samples were collected and analysed in the present study Supplementary File S1 SequencingStatistics. For the purpose of cross-validation between sequencing batches and to test our methodology on non-invasive hair sampling, a number of individuals were sequenced in duplicates and triplicates, which lead to unique individuals.

To form a reference panel, we complemented the genotypes of EEP and sanctuary chimpanzees with whole genome data from 58 geo-referenced wild-born chimpanzees, representing the four chimpanzee subspecies, and additionally, one known admixed individual Ptv-Donald and one known descendant of wild born individuals Ptv-Clint Prado-Martinez et al. DNA was extracted using a standard phenol-chloroform protocol.

Samples were quantified with a Qubit 2. DNA library preparation was carried out in three batches. The first batch of 24 libraries with 6 more samples not used in this study were prepared using 1.

For this third batch, we used inline barcoded short adaptors with the same seven nucleotide barcodes at the P5 and P7 adaptors. We performed a target capture enrichment experiment using baits synthesised by Agilent Technologies.

We targeted 59 autosomal sites that were ancestry informative markers and designed using the panTro4 genome. Marker selection was done using published chimpanzee genomes Prado-Martinez et al.

Variant sites were then weighted to identify the most informative markers for the first two principal components PCs and AIMs were extracted per segment. The genome was binned to have an unbiased and evenly distributed sampling of the genome and to have enough resolution to provide estimates of ancestry in highly admixed individuals. For target enrichment hybridisation, libraries were pooled equimolarly based on a library prep method to obtain a total of 19 pools see Supporting Information for a detailed description of the targeted enrichment hybridisation.

Each enriched sample was then quantified on a NanoDrop, BioAnalyzer and then sequenced. Libraries were sequenced on five lanes of a HiSeq ultra-high-throughput sequencing system, one lane for 24 chimpanzee samples, 2 lanes for 63 chimpanzee samples and 2 lanes for the remaining 92 samples.

Inline barcoded libraries captured in the same pool 92 from Batch 3 were de-multiplexed using Sabre software v. Then, reads were mapped using BWA v. The total aligned reads were calculated by dividing the number of uniquely mapped reads the remaining reads after removing duplicates by the number of production reads.

The on-target aligned reads were calculated by dividing the target filtered reads by the production reads. Then, the total coverage was calculated by dividing aligned bases by the length of the assembly Hg19 and the target effective coverage dividing the on-target bases by the targeted genomic space. Finally, the enrichment factor of the capture performance was calculated by taking the ratio between the on-target reads by total mapped reads over the target size by genome size. We also included the genotype information of available whole genome data of aforementioned 58 wild-born geo-referenced chimpanzees and Ptv-Donald and Ptv-Clint Prado-Martinez et al.

We inferred proportions of shared ancestries in two approaches. Price et al. All samples were included without pruning of sites in linkage disequilibrium or MAF, in order to avoid exclusion of fixed sites between populations. To avoid any bias introduced from a joint analysis with related individuals, each of the unique individuals from the EEP and sanctuary populations were analysed separately one by one against a reference panel of all wild born individuals.

After applying a MAF filter --maf 0. To assess convergence, the iterations were evaluated to ensure that iterations did not differ by more than 1 log-likelihood value. In addition, we estimate where these immediate ancestors belong in the pedigree. For full documentation of the model, see Supplementary Information. We applied the FitOriGenModelFindUnknowns parameter to the highest ranked informative markers to assign individual geographical origin onto the allele frequency surface, inferred from the wild born reference panel.

To test our targeted capture approach on non-invasively collected hair samples, we sequenced three individuals where we had both blood samples, whole genome reference data and hair samples. Hair samples were capture sequenced using the same methodology as described above for blood samples, except we added a pre-treatment step in the DNA extraction of hair samples to enhance lysis of keratin.

Shared ancestry and geo-graphical origin was analysed as described above. First we quantified and assessed the performance of our capture methodology in the selected targeted space. We wanted to ensure sufficient representation of the targeted genomic regions to reliably call the selected variants. After removing PCR duplicates and considering only primary alignments with a mapping quality higher than 30, we obtained an average of 3.

The average effective target coverage on the 59, autosomal SNPs was In terms of capture performance, this last statistic is an underestimate since the full length of the capture bait is base pairs and in this analysis, we only considered the four base pairs around the targeted SNP.

Still, we considered it to be more accurate since it is the true space where the informative SNP falls. Lastly, to summarise the performance of the capture methodology, we computed the enrichment factor that relates the number of aligned reads on the target space divided by the production reads, with the size of the target space to the size of the whole genome.

The resulting enrichment factor of The maximum number of SNPs called in one individual was 51, and the minimum was 10, Fig. Among the variation found in western chimpanzees, only a third of these were polymorphic in the western chimpanzee Table S1 , yet, of the 46, polymorphic sites, 15, were private in the western chimpanzee Fig. For fixed sites, the western chimpanzee also had the highest number of private sites Fig.

Among the four subspecies, the eastern chimpanzee had the highest total number of polymorphic sites, followed by the central chimpanzee, Nigerian-Cameroon chimpanzee, and western chimpanzee, respectively Table S1.

The major axes of variance in EEP and sanctuary individuals were explored with a PC analysis with reference to the panel of geo-referenced individuals with known subspecies label from Prado-Martinez et al. The first PC PC1 explained With Individuals from the reference panel are labelled with a subspecies ancestry prefix and known sample name in previous literature Prado-Martinez et al. Inbreeding estimates were estimated within each cluster independently. Omnivorous — fruit, pith, leaves, shoots, flowers, honey and bark, insects and larvae, vertebrate prey such as red colobus, other species of monkey, duiker, young bushpig and bushbuck.

Primary and secondary forest, swamp forest, montane forest, dry forest, dry woodland savannah, and even farmland. Chimps range in a total area of about 2. Wild chimpanzees face a very high risk of extinction in the near future due to threats such as hunting, habitat loss and degradation due to industrial logging and agricultural expansion, and disease.

Chimpanzees are hunted for bushmeat. When adult females are killed, their infants may be taken and trafficked for the exotic pet trade, effectively removing two generations at once. Outbreaks of rapidly spreading infectious diseases, such as the Ebola virus and anthrax, have also led to declines in chimpanzee populations. Although vaccinating wild chimpanzees is a possibility, such a project would be extremely difficult and infectious disease is likely to remain an issue into the future.