Dataset Information

Effective population size dynamics and the demographic collapse of Bornean orang-utans.

ABSTRACT: Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200-2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions.

SUBMITTER: Sharma R

PROVIDER: S-EPMC3499548 | biostudies-other | 2012

REPOSITORIES: biostudies-other

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Effective population size dynamics and the demographic collapse of Bornean orang-utans.

Sharma Reeta R Arora Natasha N Goossens Benoit B Nater Alexander A Morf Nadja N Salmona Jordi J Bruford Michael W MW Van Schaik Carel P CP Krützen Michael M Chikhi Lounès L

PloS one 20121115 11

Bornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recen ...[more]

PMID: 23166666

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Project description:BackgroundThe calculation of demographic measures is a useful tool for evaluating the genomic architecture of dog breeds and enables ranking dog breeds in terms of genetic diversity. To achieve this for the German Dalmatian dog population, 307 purebred animals of this breed were genotyped on the Illumina Canine high density BeadChip. The analysis of pedigree-based inbreeding was performed based on a pedigree with 25,761 dogs including the genotyped dogs.ResultsThe effective population size derived from squared correlation coefficients between SNP alleles (r 2) was 69. The maximum value of r 2 was 0.56, resulting in a 50% decay value of 0.28 at a marker distance of 37.5 kb. The effective population size calculated from pedigree data using individual increase in inbreeding over equivalent generations was 116. The pedigree inbreeding coefficient was 0.026. The genomic inbreeding coefficient based on the length of runs of homozygosity (ROH) was calculated for seven length categories of ROHs, and ranged from 0.08 to 0.28. The fixation coefficients FIS_PED and FIS_GENO were at 0.017 and 0.004. PANTHER statistical overrepresentation analysis of genes located in consensus ROHs revealed highly underrepresented biological processes in 50% of the investigated dogs. One of those is the 0.28 fold enriched "immune response", which might be associated to the high prevalence of allergic dermatitis in the breed. Candidate genes for congenital sensorineural deafness (CCSD, a highly prevalent disease in the Dalmatian) were discovered in consensus ROHs.ConclusionsThe fast decay of r 2 and the moderate inbreeding coefficients indicate that the German Dalmatian dog population is rather diverse. Pedigree- and genomic-based inbreeding measures were highly correlated and therefore prove good reliability for the given population. Analyses of consensus ROHs with genes coding for deafness and other breed-defining traits, such as hyperuricosuria, indicate that those ROH became fixed in the Dalmatian population about 500 years ago. In case of the Dalmatian dog, a ROH of 40 SNPs length is enough to investigate signatures of selection (e.g. the ROH with the fixed hyperuricosuria mutation) as far back as the breed formation point approximately 500 years ago.

Project description:Simple Summary Wildlife conservation effectiveness relies on the accuracy of population data used to build management plans. Estimating population size and dynamics of large vertebrates living on wide areas is a challenging task and results can vary depending on the methods adopted. In the present study, the size of a wolf population was estimated both by field monitoring and statistical modeling on demographic data. Results showed discrepancies with respect to previous bibliographic estimates which resulted significantly lower. Moreover, statistical techniques on demographic data allowed a deeper knowledge of population’s trend, pointing out the importance of mortality rates in driving population growth. We suggest combining statistical modeling and field monitoring to achieve a satisfactory knowledge of population size and dynamics useful to foster reliable management and conservation plans. Abstract We estimated the current size and dynamics of the wolf population in Tuscany and investigated the trends and demographic drivers of population changes. Estimates were obtained by two different approaches: (i) mixed-technique field monitoring (from 2014 to 2016) that found the minimum observed pack number and estimated population size, and (ii) an individual-based model (run by Vortex software v. 10.3.8.0) with demographic inputs derived from a local intensive study area and historic data on population size. Field monitoring showed a minimum population size of 558 wolves (SE = 12.005) in 2016, with a density of 2.74 individuals/100 km2. The population model described an increasing trend with an average annual rate of increase λ = 1.075 (SE = 0.014), an estimated population size of about 882 individuals (SE = 9.397) in 2016, and a density of 4.29 wolves/100 km2. Previously published estimates of wolf population were as low as 56.2% compared to our field monitoring estimation and 34.6% in comparison to our model estimation. We conducted sensitivity tests to analyze the key parameters driving population changes based on juvenile and adult mortality rates, female breeding success, and litter size. Mortality rates played a major role in determining intrinsic growth rate changes, with adult mortality accounting for 62.5% of the total variance explained by the four parameters. Juvenile mortality was responsible for 35.8% of the variance, while female breeding success and litter size had weak or negligible effects. We concluded that reliable estimates of population abundance and a deeper understanding of the role of different demographic parameters in determining population dynamics are crucial to define and carry out appropriate conservation and management strategies to address human–wildlife conflicts.

Dataset Information

Effective population size dynamics and the demographic collapse of Bornean orang-utans.

Publications

Effective population size dynamics and the demographic collapse of Bornean orang-utans.

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