The aim of the present paper was to evaluate genetic diversity within and among Ecuadorian bovine breeds using microsatellite markers. The genetic identity and the exotic influences from taurine or zebuine cosmopolitan breeds on Macabea, Loja, Santa Elena, Manabí and Isla de Puná breeds were evaluated. Twenty-eight microsatellite markers were tested across 254 individuals belonging to the five Ecuadorian populations to investigate intra and inter population genetic diversity levels. Nineteen markers in common with a set of 1595 samples of 35 previously typed breeds were used to determine the potential origin of Ecuadorian bovine breeds and to identify and quantify their genetic relationships. The findings of FIS > FST (0.0814 > 0.0499), even in the context of low but significant FST values, may be indicative of the intrapopulation origin of the variability of allelic frequencies across populations. Conclusively, the study of genetic distances and population structure suggested the origin of Ecuadorian populations may likely stem from Southern Spanish breeds, with no significant recent influence from cosmopolitan Taurine or Zebuine breeds. These findings may provide a solid basis for the demonstration of an Ecuadorian breeds identity in the framework of the genetic conservation of the American creole populations.

In this study, we aimed to evaluate the genetic diversity within and among chicken breeds from the northeast region of Brazil (states of Bahia and Piauí) using microsatellite markers. In addition, we assessed the identity and genetic relationships of chickens from Europe, Africa, and South America, as well as their influence on the formation of the Brazilian breeds. A total of 25 microsatellite markers and a panel containing 886 samples from 20 breeds (including the Brazilian chickens) were used in this study. Different statistical parameters were used to estimate the genetic diversity and relationship among the genetic groups studied. Our study indicates that the Brazilian Creole chickens have high genetic variability. The results show that chickens reared in the states of Bahia and Piauí could have originated from different ancestors. The Brazilian breeds studied have an evolutionary relationship with chickens from Portugal, Nigeria, Chile, and Spain. Our results will contribute directly to the conservation and recognition of Brazilian Creole chicken breeds and provide a solid basis for the demonstration of their genetic identity and genetic conservation of American Creole chicken populations.

Domestic pig breeds reached America on the second Columbus trip; from this date, Iberian pig genetic resources were disseminated throughout the continent, forming diverse creole breeds. These Ecuadorian Creole pigs are important for food production but have been genetically eroded since the introduction of transboundary breeds. In this study, we sought to characterize this erosion more thoroughly through mitochondrial DNA D-Loop analysis of Ecuadorian Pillareño Creole pigs from seven regions of Ecuador. To allow comparison, we also included in our analysis sequences from wild species, commercial lines, and domestic pigs, which were obtained from the NCBI GenBank database. Creole pigs' population showed overall moderate Hd values and low π values, and a negative value of Tajima's D was observed. The greatest differentiation from the Ecuadorian Pillareño Creole pigs was observed between Asian wild and Asian domestic pigs. The haplotype analysis revealed three different phylogenetic clades (A, E I, and E II) and 65 haplotypes. Ecuadorian Creole populations were grouped into nine haplotypes for Clade E I and E II, which have not previously been reported for Creole Pillareño populations. Our analysis indicates that in the establishment of Creole Pillareño pigs, individuals most likely separated from the Asian pig population and appear to be genetically influenced by European and Iberian populations raised in Spain.

STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters K opt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (dapc, flock, PCoA, and structure with different run scenarios) all revealed general, broad-scale breed relationships that largely reflect known breed histories but diverged how they characterized small-scale patterns. structure failed to consistently identify K opt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a K opt, was consistent with known breed histories. The over-reliance on K opt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.