Background: The health and viability of captive elephants, which are central to off-site conservation efforts and health management in Thailand, is threatened by emerging infectious diseases. This is partly due to genetic differences in immune-related genes, especially in the major histocompatibility complex (MHC) and, among these, loci such as DQA play a crucial role in immune surveillance. Data pertaining to MHC polymorphisms in elephants are scarce, and thus this study investigated such polymorphisms and selection signatures in a partial fragment of exon 2 of the MHC Class II DQA gene. Methods: The approach we used targeted next-generation sequencing and diversity analyses of individuals from three captive elephant camps in Northern Thailand. Results: Eight alleles containing 11 SNPs were identified in the exon 2 fragment, encompassing both silent and missense mutations, some of which may influence immune function. Notably, the allele Elma-DQA*TH3, which is identical to Loaf-DQA*01 and Elma-DQA*01, previously reported as the most common alleles in Loxodonta and Elephas, was found at low frequencies. This shift may reflect local selective pressures that shape MHC allele distributions. Evidence of mixed selection (both positive and balancing) was detected in the partial fragment of DQA exon 2, suggesting a dynamic interplay between evolutionary forces. Positive selection likely reflects an adaptation to emerging or locally prevalent pathogens, whereas balancing selection maintains allelic diversity over time to enable a broad immunological response. Conclusions: Our findings reveal immunogenetic variations in captive Thai elephants, and provides insights into host–pathogen interactions that inform conservation and health strategies with the aim of improving disease resilience.

Background/Objectives: Clariid catfishes are a cornerstone of Southeast Asian aquaculture, where intensive breeding and interspecific hybridization have significantly decreased genetic diversity. To address the limited understanding of growth-governing molecular determinants, we characterized the genomic architecture and evolutionary dynamics of the myogenic factor 5 (Myf5) gene, a master regulator of myogenesis, in 511 individuals from 17 catfish populations in Thailand. Methods: A total of 511 individuals representing 17 catfish populations were analyzed. A 334-bp fragment of exon 1 of the Myf5 gene was sequenced using Illumina short-read technology. Genetic diversity indices were calculated to evaluate sequence variation, population structure, and selective constraints acting on the locus. Results: Sequence analysis of a 334-bp segment of exon 1 using Illumina short-read technology identified 17 haplotypes and 92 variable sites, which revealed moderate allelic richness despite low overall nucleotide diversity (π ≈ 0.008). Evolutionary analyses indicated that the Myf5 locus is governed by stringent purifying selection (ω = 0.063), wherein site-specific constraints preserve the stability of the α-helix folding architecture, which is essential for myogenic regulation. Population genetic analyses revealed substantial differentiation among taxa (56% among-population variation), while Bayesian clustering successfully resolved a hierarchical structure (K = 2) that distinguished Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus. These findings demonstrate that species-specific Myf5 haplotypes serve as diagnostic markers for identifying parental species and assisting in the identification of F₁ hybrid stocks. Conclusions: Overall, this study provides the molecular markers for species identification, broodstock authentication, hybrid detection, and sustainable genetic management of Thai Clariid resources, which are critical for balancing production efficiency with the conservation of native biodiversity in Southeast Asia.

Background/Objectives: Mahachai Betta (Betta mahachaiensis) is a bubble-nesting fighting fish endemic to brackish habitats in Bangkok, Samut Sakhon, and Samut Prakan, where rapid urbanization and industrial growth threaten persistence. We evaluated genetic structure and diversity across 10 populations (81 individuals) to inform conservation planning. Methods: This study combined microsatellite genotyping (13 loci) with ecological niche modeling to assess genetic variability, population connectivity, and landscape–environmental drivers of differentiation. Results: Habitat loss and fragmentation were associated with reduced gene flow and decreased genetic diversity. Mean allelic richness was 2.65 and expected heterozygosity ranged from 0.20 to 0.46, with F_ST values up to 0.400. Forward simulations predicted severe erosion of diversity within the next 12.5–37.5 years. Populations showed clear genetic subdivision, most pronounced in Samut Prakan and Samut Sakhon, with two Samut Sakhon populations (SKN3 and SKN7) reflecting strong environmental heterogeneity. Conclusions: Improving habitat connectivity and intensifying local community engagement are priority actions to enhance the resilience and long-term persistence of Mahachai Betta. This study provides the first integrated genetic and landscape-based assessment of the species, highlighting its rapid genetic erosion under urbanization and offering a foundation for targeted, evidence-based conservation strategies.

Background/Objectives: Understanding variabilities in the Major Histocompatibility Complex class I (MHC I) gene is essential for evaluating immunogenetic diversity in clariid catfish. MHC I plays a critical role in immune defense by presenting endogenous antigens to cytotoxic T cells. Therefore, we aimed to investigate the genetic diversity, selection patterns, and phylogenetic relationships of MHC I alleles in three important clariid catfish species (Clarias gariepinus, Clarias macrocephalus, and Clarias batrachus) across wild and hatchery populations in Thailand. Methods: Targeted next-generation sequencing of a 174 bp fragment partial exon 6 of MHC I-UAA gene was performed, along with phylogenetic analyses, neutrality tests and dN/dS analyses. Results: Overall, 91 novel alleles were identified in 674 individuals, all of which were novel (100% novelty), with none matching existing reference sequences, thereby revealing extensive variation in population-specific variants. Phylogenetic analyses revealed allele sharing among species, which was consistent with balanced selection. Neutrality tests and dN/dS analyses provided evidence of both purifying and diversifying selection, with episodic positive selection detected at multiple codon sites associated with the antigen-binding α1 domain. Distinct selection patterns among populations, influenced by local environmental conditions and human pressures, along with high allele richness, are reflected in the diversity of immunogenetic variations. Conclusions: These findings provide critical insights into immune adaptation and highlight the potential of MHC I as a functional marker for genetic monitoring. Although a causal relationship between MHC I polymorphism and disease resistance is debated, studies suggest associations with pathogen survival, indicating future implications for aquaculture breeding and conservation, particularly in marker-assisted selection for broodstock management in Thailand.