Genetic Characterization of 12 X-STR Markers in an Autochthonous Population from Alicante, Southeastern Spain: Diversity and Interpopulation Comparisons

Background/Objectives: X-chromosomal short tandem repeats (X-STRs) complement autosomal and Y-chromosomal markers in forensic genetics, particularly for kinship testing and human identification. This study extends previous research on X-STR variation in Alicante (southeastern Spain), providing the largest regional X-STR reference database to date for a specific Spanish population, which includes and expands a previously reported pilot sample. Methods: A total of 316 unrelated, third-generation autochthonous individuals were genotyped for 12 X-STR loci using the Investigator Argus X-12 QS kit. Forensic parameters, haplotype distributions and linkage disequilibrium (LD) were analyzed, complemented by normalized entropy difference (NED) analysis of association between multiallelic loci. Interpopulation differentiation was assessed using pairwise FST values with European, Latin American and Mediterranean populations. Results: Genetic diversity was high across all markers (GD 0.676–0.927; PIC 0.623–0.922), and haplotype diversity ranged from 0.989 to 0.997 across the four linkage groups. Of the 66 pairwise locus comparisons, 16 showed nominal evidence of LD (p < 0.05), four of which remained significant after Bonferroni correction. Alicante showed low differentiation from other European populations, moderate differentiation from several Latin American populations, and low differentiation from several Mediterranean populations, particularly North African Berber and Iberian Mediterranean groups. These comparisons should be interpreted with caution, given the heterogeneity in sample size, sampling design and regional origin of the reference datasets. Conclusions: These findings support the forensic utility of the Investigator Argus X-12 QS panel in the Alicante population and provide a reference database for kinship testing, identification and future comparative population genetic studies.