Origin and number of founders in an introduced insular primate: estimation from nuclear genetic data

Abstract

Cynomolgus macaques (Macaca fascicularis) were introduced on the island of Mauritius between 400 and 500 years ago and underwent a strong population expansion after a probable initial founding event. However, in practice, little is known of the geographical origin of the individuals that colonized the island, on how many individuals were introduced, and of whether the following demographic expansion erased any signal of this putative bottleneck. In this study, we asked whether the current nuclear genome of the Mauritius population retained a signature that would allow us to answer these questions. Altogether, 21 polymorphic autosomal and sex-linked microsatellites were surveyed from 81 unrelated Mauritius individuals and 173 individuals from putative geographical sources in Southeast Asia: Java, the Philippines islands and the Indochinese peninsula. We found that (i) the Mauritius population was closer to different populations depending on the markers we used, which suggests a possible mixed origin with Java playing most probably a major role; and (ii) the level of diversity was lower than the other populations but there was no clear and consistent bottleneck signal using either summary statistics or full-likelihood methods. However, summary statistics strongly suggest that Mauritius is not at mutation-drift equilibrium and favours an expansion rather than a bottleneck. This suggests that on a short time scale, population decline followed by growth can be difficult to deduce from genetic data based on mutation-drift theory. We then used a simple Bayesian rejection algorithm to estimate the number of founders under different demographic models (exponential, logistic and logistic with lag) and pure genetic drift. This new method uses current population size estimates and expected heterozygosity of Mauritius and source population(s). Our results indicate that a simple exponential growth is unlikely and that, under the logistic models, the population may have expanded from an initial effective number of individuals of 10-15. The data are also consistent with a logistic growth with different lag values, indicating that we cannot exclude past population fluctuation.

Hybridization and Stratification of Nuclear Genetic Variation in Macaca mulatta and M. fascicularis

“…The Mauritian animals, purportedly introduced from Java as recently as the seventeenth or eighteenth centuries Tattersall 1981, 1986), reflect strong founder effects by exhibiting approximately one fourth of all the alleles found in long-tailed macaques and in both macaque species, respectively. The low Mauritian diversity at STR (as observed in this study as well as that by Bonhomme et al 2008), MHC (Kawamoto et al 2008) and mtDNA ) loci and the absence of Y chromosomal variation Coke 2007, Kawamoto et al 2008) have been attributed to small founder representation and subsequent rapid population expansion , Kawamoto et al 2008, Bonhomme et al 2008. In contrast to the findings here that the Mauritian and Indonesian animals are indeed genetically distinct, Bonhomme et al (2008) and Kawamoto et al (2008) reported a higher degree of similarity between the Mauritian and Javan animals suggesting that the founders of the former population actually descend from Javanese ancestors.…”

“…The gradual loss of genetic diversity might have occurred as new areas on the mainland were colonized by the species. However, Tosi et al's data (2003), along with that of Street et al (2007) and Bonhomme et al (2008) imply that the long-tailed macaques in Indochina represent a very old population because of the large number of private alleles it retains, supporting the alternative hypothesis that the long-tailed macaques originated instead in Indochina. The fractured landscape of the Indonesian archipelago, rife with significant physical barriers that isolate wildlife populations, might then have caused the Indonesian macaques to diverge into new subspecies.…”

“…Therefore, results from this study suggest that there has been natural or human-assisted hybridization between long-tailed macaques and rhesus macaques. Studies of Y-chromosome haplotypes (Tosi et al, 2002) and STR loci (Bonhomme et al, 2008) provide evidence that inter-species gene flow was unidirectional, with introgression of rhesus macaque DNA into the long-tailed macaque genome. Thus, the high level of genetic heterogeneity in mainland long-tailed macaques might not reflect a mainland origin for the species.…”

The genome of the vervet (Chlorocebus aethiops sabaeus)

“…The macaque population of this isolated Indian Ocean island was characterized by only seven extended MHC haplotypes, together with recombinants between these ancestral haplotypes. As with the Caribbeanorigin vervets, this macaque population was founded in the 17th century by a small number of monkeys introduced by Europeans (Bonhomme et al 2008).…”

Approximate Bayesian Computation Without Summary Statistics: The Case of Admixture

“…The choice of d (and of the number of simulations) reflects to some extent a balance between computability and accuracy Marjoram et al 2003). In most ABC implementations the value of d is set as a quantile (the tolerance level P d ) from the empirical distance distribution found for a given observed data set, and typical values range from 10 À5 to 10 À2 (e.g., Estoup et al 2004;Becquet and Przeworski 2007;Fagundes et al 2007;Pascual et al 2007;Bonhomme et al 2008;Cox et al 2008). The quality of the ABC inference is expected to depend on the summary statistics, the distance metric, and the tolerance level P d used.…”