Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites.

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.

In vivo fertilizing ability of stallion spermatozoa processed by single layer centrifugation with Androcoll-E™.

A colloid with a species specific silane-coated, silica-based formulation, optimized for stallion (Androcoll-E™), enables a better sub-population of spermatozoa to be selected from stallion ejaculates. However, such a practice has not been critically evaluated in stallions with fertility problems. In this study we evaluate whether single-layer centrifugation (SLC) through Androcoll-E™ could be used to enhance fertility rates in a subfertile stallion. Ejaculates were obtained from two different stallions, one Lusitano (fertile) and one Sorraia (subfertile), with distinct sperm characteristics and fertility. Motility, morphology, plasma membrane structural (eosin-nigrosin) and functional integrity (HOS test), mitochondrial functionality (Δψm; JC-1) and longevity (motility after 72 h cooling) after centrifugation in Androcoll-E™, as well as pregnancy rates obtained after artificial insemination (AI), with and without (control group) SLC-treated sperm were assessed. The effect of SLC on sperm characteristics, and fertility results were evaluated by ANOVA and Fisher procedures, respectively. Our results showed that SLC-selected sperm did not differ from the raw semen in terms of viability, morphology, response to hypo-osmotic conditions (HOS test) and mitochondrial membrane potential (↑ΔΨmit; JC-1). Sperm motility in cooled samples was not improved by SLC treatment. Our data show that SLC through Androcoll-E™ has no effect on pregnancy rates in the stallions used in this trial.

Differential effects of dietary protein on early life-history and morphological traits in natterjack toad (Epidalea calamita) tadpoles reared in captivity.

The production of high quality amphibian larvae through optimal diets is a critical component of amphibian conservation breeding programs. Larval period, survival, body weight and total length are frequently used as metrics of adequate nutrition. However, the effects of nutrition on tadpole and metamorph morphology are rarely tested in detail. In the present study, we analyzed the most common metrics and six other larval and post-metamorphic morphological traits in natterjack toads (Epidalea calamita) fed with three different commercial fish diets, varying in protein content (32.0%, 38.3%, and 46.2%). Our results suggest that early life-history (tadpole growth, development, and survival) and morphological traits of E. calamita tadpoles are differentially affected by the percentage of dietary protein. As protein content increased, tadpoles exhibited larger bodies along with shorter tail fins; however, with no significant differences in total length. Larval period was similar across treatments but mortality was lower in high-protein diet. At high-protein diets the metamorphs revealed significantly longer bodies, and wider heads and hind legs, but there was no significant difference in the average weight across all dietary treatments. Based on our results, feed containing 46.2% protein promotes growth, development and survival of E. calamita tadpoles better than either of the other two feeds tested. The use of other body measures beyond weight, tadpole total length, and snout-vent length in studies of amphibian nutrition in captivity may assist the selection of appropriate diets to optimize tadpole survival and metamorph fitness.

Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management.

The Sorraia horse is a closed breed with reduced effective population size and considered in critical maintained risk status. The breed exists in 2 main breeding populations, one in Portugal and one in Germany, with a smaller population size. A set of 22 microsatellite loci was used to examine genetic diversity and structure of the Sorraia horse breed and to compare individual inbreeding coefficient F, estimated from pedigree data, with individual heterozygosity and mean d(2). The Sorraia horse shows lower levels of microsatellite diversity when compared with other horse breeds. Due to management strategies, there are clear differences in the genetic structure of the 2 main Sorraia horse populations. Individual heterozygosity was shown to be a good estimator, used together with or as an alternative to inbreeding coefficient, in predicting fitness and evaluating the inbreeding level of the Sorraia horse. The information gathered in this study, combined with information available from previous studies, offers an important and wide information base for the future development of an effective breeding management of the Sorraia horse in order to preserve this endangered breed.

Iberian origins of New World horse breeds.

Fossil records, archaeological proofs, and historical documents report that horses persisted continuously in the Iberian Peninsula since the Pleistocene and were taken to the American continent (New World) in the 15th century. To investigate the variation within the mitochondrial DNA (mtDNA) control region of Iberian and New World horse breeds, to analyze their relationships, and to test the historical origin of New World horses, a total of 153 samples, representing 30 Iberian and New World breeds, were analyzed by sequencing mtDNA control region fragments. Fifty-four haplotypes were found and assigned to seven haplogroups. Reduced levels of variation found for the Menorquina, Sorraia, and Sulphur Mustang breeds are consistent with experienced bottlenecks or limited number of founders. For all diversity indices, Iberian breeds showed higher diversity values than South American and North American breeds. Although, the results show that the Iberian and New World breeds stem from multiple origins, we present a set of genetic data revealing a high frequency of Iberian haplotypes in New World breeds, which is consistent with historical documentation.