The relationship between single nucleotide polymorphisms (SNPs) and phenotypes is noisy and cryptic due to the abundance of genetic factors and the influence of environmental factors on complex traits, which makes the idea of applying artificial neural networks (ANNs) as universal approximates of complex functions promising. In this study, we compared different ANN architectures and input parameters to predict the adult length of Pacific lampreys, which is the primary indicator of their total migratory distance. Feedforward and simple recurrent network architectures with a different range of input parameters and different sizes of hidden layers were compared. Results indicate that the highest performing ANN had an accuracy of 67.5% in discriminating between long and short specimens. Sensitivity and specificity were 62.16% and 70.73%, respectively. Our results imply that feedforward ANN architecture with a single hidden neuron is enough to solve the problem of specimen classification. Nonetheless, while ANNs are useful at approximating functions with unknown relationships in the case of SNP data, additional work needs to be performed to ensure that the chosen SNP markers are related to functional regions related to the examined trait, as the use of non-specific markers will result in the introduction of noise into the dataset.

abstract In a study of the Bosnian-Herzegovinian (B&H) population, Y-chromosome marker frequencies for 100 individuals, generated using the PowerPlex Y23 kit, were used to perform Y-chromosome haplogroup assignment via Whit Athey's Haplogroup Predictor. This algorithm determines Y-chromosome haplogroups from Y-chromosome short tandem repeat (Y-STR) data using a Bayesian probability-based approach. The most frequent haplogroup appeared to be I2a, with a prevalence of 49%, followed by R1a and E1b1b, each accounting for 17% of all haplogroups within the population. Remaining haplogroups were J2a (5%), I1 (4%), R1b (4%), J2b (2%), G2a (1%), and N (1%). These results confirm previously published preliminary B&H population data published over 10 years ago, especially the prediction about the B&H population being a part of the Western Balkan area, which served as the Last Glacial Maximum refuge for the Paleolithic human European population. Furthermore, the results corroborate the hypothesis that this area was a significant stopping point on the “Middle East—Europe highway” during the Neolithic farmer migrations. Finally, since these results are almost completely in accordance with previously published data on B&H and neighboring populations generated by Y-chromosome single nucleotide polymorphism analysis, it can be concluded that in silico analysis of Y-STRs is a reliable method for approximation of the Y-chromosome haplogroup diversity of an examined population.