DOI: 10.6084/m9.figshare.30072211
title: Dataset: Genetic Polymorphism Data for MHC Class II Loci in Persian Fallow Deer (Dama mesopotamica) from Captive Breeding Programs in Iran

description: 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).