Population assignments for GenBank D-loop sequences used in a comparative analysis of ten indigenous African chicken populations
Description
This dataset provides the population assignments, country of origin, and ecotype labels for 277 mitochondrial D-loop (control region) sequences of indigenous chicken (Gallus gallus domesticus) used in the comparative population genetics study "Mitochondrial D-loop Diversity and Population Genetic Structure Among Ten Indigenous Chicken Populations Across Seven African Countries." All 277 sequences are pre-existing, publicly available records retrieved from NCBI GenBank; no new sequencing was performed for this study. This dataset does not duplicate those records but supplies the population context, country, ecotype, and analytical parameters applied to them in the associated study, which is not encoded in the GenBank records themselves. The ten populations span seven countries: Algeria (Adrar), Egypt, Kenya (Marsabit, Naivasha), Nigeria (Fulani, Yoruba ecotypes), South Africa (Jozini), Tanzania (Kuchi), and Uganda (Busoga, Ganda North), ranging from 14 to 48 sequences per population. Files included: population_mapping_final.csv — one row per sequence, with columns for GenBank accession number, country, population/ecotype, combined population label, organism, mitochondrial marker, length of the analysed alignment region (231 bp), and source database. Trimmed FASTA alignment (231 bp common region, 277 sequences) used as the direct input for all diversity, AMOVA, pairwise Phi-ST, haplotype network, Tajima's D, and neighbor-joining analyses reported in the associated manuscript. R analysis scripts covering diversity indices (haplotype and nucleotide diversity), analysis of molecular variance (AMOVA), pairwise Phi-ST and hierarchical clustering, median-joining haplotype network construction, Tajima's D neutrality testing, and neighbor-joining phylogenetic reconstruction. README file describing all columns, file contents, and reuse notes. This dataset is intended to make the exact accession-to-population assignments and analytical pipeline used in the associated study independently verifiable and reusable by other researchers working on African indigenous chicken genetic diversity, poultry conservation genetics, or comparative mitochondrial population structure. Researchers are encouraged to consult the original GenBank accessions for full sequence records and metadata from the originating studies. Distributed under a CC BY 4.0 license. Please cite both this dataset and the associated manuscript when reusing any part of this material.
Files
Steps to reproduce
Sequence retrieval. Mitochondrial D-loop sequences were retrieved from the NCBI GenBank database for ten indigenous chicken (Gallus gallus domesticus) populations across seven African countries: Algeria (Adrar, n = 22), Egypt (n = 18), Kenya (Marsabit, n = 15; Naivasha, n = 15), Nigeria (Fulani, n = 48; Yoruba, n = 48), South Africa (Jozini, n = 14), Tanzania (Kuchi, n = 21), and Uganda (Ganda North, n = 47; Busoga, n = 29), for a combined 277 sequences. Accession numbers and population assignments are listed in population_mapping_final.csv. Alignment and trimming. Sequences were imported into Geneious and aligned using MAFFT. Because source sequences differed in length and in which part of the D-loop they covered, the alignment was trimmed to a common 231 bp window (alignment positions 167–397) present without gaps across all 277 sequences. This trimmed alignment is provided as the accompanying FASTA file. Genetic diversity and neutrality statistics. Using R (package pegas), haplotype diversity (Hd) and nucleotide diversity (π) were calculated per population from the trimmed alignment, with pairwise deletion of gaps/ambiguous sites. Tajima's D was calculated per population from the number of segregating sites and mean pairwise differences. AMOVA. A two-level analysis of molecular variance (pegas::amova) partitioned molecular variance into among- and within-population components, based on a pairwise raw genetic distance matrix (ape::dist.dna, pairwise deletion). Significance of the overall Phi-ST was assessed via 1,000 permutations of population labels. Pairwise Phi-ST and clustering. Pairwise Phi-ST was computed for all 45 population pairs using the same distance-based AMOVA framework applied pairwise. The resulting matrix was used for hierarchical clustering (base R hclust) and visualized as a dendrogram and heatmap. Haplotype network. A median-joining haplotype network was built from the trimmed alignment using pegas::haploNet, identifying 36 distinct haplotypes across the 277 sequences. Phylogenetic reconstruction. A neighbor-joining tree of the ten populations was built with ape::nj from the pairwise genetic distance matrix. Software used: Geneious (sequence import/inspection); MAFFT (multiple sequence alignment); R (≥4.x) with packages pegas and ape (diversity statistics, AMOVA, Phi-ST, haplotype network, Tajima's D, neighbor-joining tree construction). To reproduce: Download the trimmed FASTA alignment and population_mapping_final.csv from this dataset, load both into R, and run the accompanying analysis scripts in the order listed above. No wet-lab materials, reagents, or physical samples were used; this is a fully in-silico re-analysis of public GenBank sequence data.