Dataset: Genetic Polymorphism Data for MHC Class II Loci in Persian Fallow Deer (Dama mesopotamica) from Captive Breeding Programs in Iran

This dataset provides raw genetic data supporting the manuscript titled "Genetic structure and MHC variability in Persian fallow deer after 50 years of captive breeding: evolutionary dynamics and conservation priorities" by Hossein Yazdandad et al. (submitted September 8, 2025). The study investigates polymorphism at two major histocompatibility complex (MHC) Class II loci—MHC-DRBIIA (Class IIA) and MHC-DOBIIB (Class IIB)—in 43 Persian fallow deer (Dama mesopotamica) individuals sampled from eight semi-captive breeding centers across Iran, plus historical founder samples from museum specimens. These loci are critical for immune function and disease resistance, and the data reveal high polymorphism at MHC-DRBIIA (nine haplotypes, 20% variable loci) contrasted with monomorphism at MHC-DOBIIB, highlighting adaptive potential despite inbreeding pressures in this endangered species.The data were generated using PCR amplification, single-strand conformation polymorphism (SSCP) analysis on polyacrylamide gels, and DNA sequencing of exon 2 regions (~300 bp fragments). Alleles/bands were scored as binary presence (1) or absence (0) based on banding patterns visualized via silver staining. Samples are coded by breeding center (e.g., ARS: Arsanjan; DEZ: Dez; ILM: Ilam; KRKH: Karkheh; MFARS: Mianketal; SARI: Dasht-e Naz/Sari; YAZD: Yazd/Bagh Shadi; UROM: Urmia/Ashk Island; GERM: German museum founders; ARAB/IRAN: Additional museum samples). This supports analyses of genetic diversity (e.g., heterozygosity Ho = 0.15, He = 0.23; inbreeding F ≈ 0.37), population structure via Discriminant Analysis of Principal Components (DAPC; four clusters identified), and selection signatures (balancing selection at DRBIIA, purifying at DOBIIB).The dataset consists of three files:Manuscript_Conserv_Gen_MS31.Sep8.docx (1.2 MB): The full manuscript draft, including methods, results, figures (e.g., Fig. 2: SSCP polymorphism images; Fig. 3: DAPC plot; Fig. 5: MHC polymorphism map; Fig. 6: Haplotype network; Figs. 4 & 7: Phylogenetic trees), and tables (e.g., Table 2: Genetic distances; Table 3: Nucleotide polymorphisms). This provides context for interpreting the data files.MHCIIb.xlsx (12 KB): Raw SSCP data for the MHC-DOBIIB locus (Class IIB). Sheet "MHCIIb" contains 7 rows × 40 columns:Row 1: Breeding center codes (e.g., ARS, DEZ).Row 2: Sample IDs (e.g., 1, 3, 4).Rows 3–7: Binary allele/band scores (0/1) across 5 bands/alleles, revealing monomorphism (no variation observed). This corresponds to Fig. 2 (bottom panel) and supports findings of purifying selection.MHCIIa.xlsx (18 KB): Raw SSCP data for the MHC-DRBIIA locus (Class IIA). Sheet "MHCIIa" contains 14 rows × 42 columns:Row 1: Breeding center codes (e.g., ARS, DEZ, including GERM, ARAB, IRAN).Row 2: Sample IDs (e.g., 1, 3, 4, up to 47).Rows 3–14: Binary allele/band scores (0/1) across 12 bands/alleles, showing high polymorphism (11 bands total, 16 alleles identified via sequencing). Sheet "Sheet1" (supplementary breakdown): 43 rows × 14 columns, listing individual samples by center and ID, with binary scores for 12 specific MHCIIa alleles (MHCIIa-1 to MHCIIa-12). This corresponds to Fig. 2 (top panel), Fig. 5 (polymorphism types by center: e.g., 8 types in Mianketal, 4 in Dez/GERM), and Table 3 (47 polymorphic positions, 9 haplotypes).