A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences.

Phylogenetic analyses can provide a wealth of information about the past demography of a population and the level of genetic diversity within and between species. By using special computer programs developed in recent years, large amounts of data have been produced in the molecular genetics area. To analyze these data, powerful new methods based on large computations have been applied in various software packages and programs. But these programs have their own specific input and output formats, and users need to create different input formats for almost every program. R is an open source software environment, and it supports open contribution and modification to its libraries. Furthermore, it is also possible to perform several analyses using a single input file format. In this article, by using the multiple sequences FASTA format file (.fas extension) we demonstrate and share a workflow of how to extract haplotypes and perform phylogenetic analyses and visualizations in R. As an example dataset, we used 120 Bombus terrestris dalmatinus mitochondrial cytochrome b gene (cyt b) sequences (373 bp) collected from eight different beehives in Antalya. This article presents a short guide on how to perform phylogenetic analyses using R and RStudio.

Determination of Genetic Diversity Using 15 Simple Sequence Repeats Markers in Long Term Selected Japanese Quail Lines.

Japanese quail is still used as a model for poultry research because of their usefulness as laying, meat, and laboratory animals. Microsatellite markers are the most widely used molecular markers, due to their relative ease of scoring and high levels of polymorphism. The objective of the research was to determine genetic diversity and population genetic structures of selected Japanese quail lines (high body weight 1 [HBW1], HBW2, low body weight [LBW], and layer [L]) throughout 15th generations and an unselected control (C). A total of 69 individuals from five quail lines were genotyped by fifteen microsatellite markers. When analyzed profiles of the markers the observed (Ho) and expected (He) heterozygosity ranged from 0.04 (GUJ0027) to 0.64 (GUJ0087) and 0.21 (GUJ0027) to 0.84 (GUJ0037), respectively. Also, Ho and He were separated from 0.30 (L and LBW) to 0.33 (C and HBW2) and from 0.52 (HBW2) to 0.58 (L and LBW), respectively. The mean polymorphic information content (PIC) ranged from 0.46 (HBW2) to 0.52 (L). Approximately half of the markers were informative (PIC≥0.50). Genetic distances were calculated from 0.09 (HBW1 and HBW2) to 0.33 (C and L). Phylogenetic dendrogram showed that the quail lines were clearly defined by the microsatellite markers used here. Bayesian model-based clustering supported the results from the phylogenetic tree. These results reflect that the set of studied markers can be used effectively to capture the magnitude of genetic variability in selected Japanese quail lines. Also, to identify markers and alleles which are specific to the divergence lines, further generations of selection are required.