Effects of Sample Size in the Determination of the True Number of Haplogroups or ESUs Within a Species with Phylogeographic and Conservation Purposes: The Case of Cebus albifrons in Ecuador, and the Kinkajous and Coatis Throughout Latin America

Abstract

Geographical assignment of individuals, or tissues, seized from illegal traffic and hunting is relevant for the conservation of many species. For this, the real number of genetically differentiated groups within a species should be determined to know from where the specimens were illegally extracted or to know where the seized and rehabilitated specimens should be liberated. This determination is also crucial to study the evolutionary history of the species. In the current work, we show, by means of three examples, that sample size is more important than the number of genes or markers studied in determining the total number of well-differentiated genetic groups. The examples were related to the number of groups detected for the white-fronted capuchins (Cebus albifrons) in Ecuador, and for the number of well-differentiated groups throughout Latin America for the kinkajou (Potos flavus), and for the different species of coatis (Nasua and Nasuella). In all cases, larger sample sizes with fewer genes detected more genetically different groups than did smaller-sized with entire mitogenomes. Therefore, in regards to the geographical assignment of seized specimens from illegal traffic it is better to obtain larger sample sizes, which cover the most extensive geographical range possible even if they have just one or few mitochondrial genes rather than to rely on smaller sample sizes with entire mitogenome. Furthermore, we take into consideration that analyses of entire mitogenomes are more costly and require a higher DNA quality than a few mitochondrial genes.