mtDNA Variation Research Articles

Chronic progressive external ophthalmoplegia (CPEO), a genetic syndrome characterized by slowly progressive paresis of extraocular muscles, is often due to single large-scale deletions of the mitochondrial genome (mtDNA). Owing to heteroplasmy, mtDNA variants are often not uniformly expressed across tissues. This genetic variability affects clinical presentation and diagnostic testing. We report a case of a 34-year-old woman who presented with symptoms suspicious for a genetic myopathy: chronic asymmetric ptosis, slowly progressive asymmetric weakness, and external ophthalmoplegia. After initial nondiagnostic peripheral genetic testing, whole-exome and mitochondrial genome sequencing of muscle revealed a single large-scale mtDNA deletion, consistent with a diagnosis of mtDNA deletion-associated CPEO. Of interest, electrophysiologic studies showed myotonia in select muscles, a rarely reported finding. We discuss the clinical presentation and diagnostic approach in suspected CPEO, with an emphasis on common pitfalls in genetic testing for mitochondrial myopathies and the need for appropriate tissue and genetic testing modality selection.

The Serrated Hinge-back Tortoise Kinixys erosa inhabits moist forests across Central and West Africa and is known to show phylogeographic structure. Based on extended geographic sampling, we re-examined its phylogeography using three mitochondrial genes and up to 17 nuclear loci. The observed mtDNA variation was considerable and corresponds to two major and well-supported clades from the western and the eastern part of the distribution range. Within the western clade, samples from Ghana represent a well-supported subclade. Nuclear loci support the genetic distinctness of these groups showing the Ghanian population as the most divergent. This suggests that K. erosa comprises hitherto unrecognized distinct taxa. Since no sufficient morphological data are available, and it is unclear to which clade the name K. erosa (Schweigger) refers, we abstain from taxonomic conclusions, but identify the genetic clusters as distinct Management Units for conservation.

Dysfunctional mitochondria are implicated in various diseases, however comprehensive characterization of mitochondrial DNA (mtDNA) in the Chinese population remains limited. Here, we conducted a systematic analysis of mtDNA from 7331 samples, comprising 4129 Chinese samples (NyuWa) and 3202 samples from the 1000 Genomes Project (1KGP). We identified 7216 distinct high-quality mtDNA variants, classified them into 22 macro-haplogroups, and detected 1466 distinct nuclear mitochondrial DNA segments (NUMTs). Among these, 88 mtDNA variants and 642 NUMTs were specific to NyuWa. Genome-wide association analyses revealed significant correlations between 12 mtDNA variants and 199 nuclear DNA (nDNA) variants. Our findings demonstrated that all individuals in both NyuWa and 1KGP harbored common NUMTs, while one-fifth possessed ultra-rare NUMTs that tended to insert into nuclear gene regions. Notably, rare NUMTs in the NyuWa cohort showed significant enrichment of nuclear breakpoints in long interspersed nuclear elements (LINEs) compared to 1KGP. Overall, this study provides the first comprehensive profile of NUMTs in the Chinese population and establishes the most extensive resource of Chinese mtDNA variants and NUMTs based on high-depth whole genome sequencing (WGS) to date, providing valuable reference resources for genetic research on mtDNA-related diseases.

In species where mitochondrial DNA (mtDNA) is maternally inherited such as vertebrates, mtDNA mutations harming males only are not subject to purifying selection and thus can spread in a population, especially when these mutations benefit females. Therefore, the mother's curse hypothesis (MCH) posits a greater mtDNA mutation load in males than in females. MCH is potentially important for human health, disease, and evolution, but a systematic test that considers the vast human mtDNA variation is lacking. Analyzing the genotypic and phenotypic data of approximately 0.5 million British participants in the UK Biobank, we estimate the reproductive fitness of mtDNA variants in each sex. Contradicting MCH, a positive intersexual correlation in the number of offspring exists across mitochondrial haplogroups. While a significant variation in the number of opposite-sex sexual partners-a proxy for reproductive fitness in premodern societies-is present among mitochondrial haplogroups, no significant intersexual correlation in this quantity is detected. The frequencies of a few mtDNA variants differ significantly between males and females, suggesting that these variants differentially affect the survival in the two sexes, but the number of such variants with lower male frequencies is not significantly different from that with lower female frequencies. Analysis of disease associations also finds no enrichment of male disease-associated mtDNA variants despite the discovery of multiple sex-biased disease associations. Together, these findings provide no genomic support to MCH in humans and suggest no difference in mtDNA mutation load between the two sexes that is detectable in the UK Biobank.

BackgroundDoxorubicin induced cardiotoxicity in childhood cancer survivors is mediated by mitochondrial dysfunction. The aims of this research are to determine (i) the frequency of mitochondrial DNA (mtDNA) mutations in long-term survivors of childhood acute lymphoblastic leukemia (ALL), and (ii) to determine if co-administration of dexrazoxane reduces the occurrence of mutations.MethodsPatients previously treated on Dana-Farber Cancer Institute Childhood ALL protocols and at least 4 years from the date of ALL diagnosis were enrolled in this study. MtDNA was isolated from samples of peripheral blood lymphocytes. A vertical denaturing gradient gel electrophoresis method was used for detecting sequence variants in the 22 transfer RNA (tRNA) genes and flanking regions of the human mitochondrial genome. The patients were divided into two cohorts, those with mutations and those without, and compared. The patients and variants were also compared to healthy controls. Mutational status was compared with echocardiographic measurements.ResultsOf the patients who received chemotherapy, there were 51/167 (31%) children who were found to have 61 different sequence variants in mtDNA with 9 patients having more than one variant. There was no association between mutation status and cumulative doxorubicin dose, though patients receiving < 300 mg/m2 had fewer mutations of any kind. At a median time of 8.5 years after diagnosis, the number of ALL patients with mtDNA sequence variants was 2.4-fold higher than the number of control children with sequence variants (8 sequence variants in 7/55 or 12.7%). Among patients receiving doxorubicin-based therapies, with (n = 34) or without dexrazoxane (n = 132), there were no statistically significant differences in the patient characteristics or in the frequencies, locations, types, and distribution of mtDNA sequence variants. The mutational status was not associated with echocardiographic changes.ConclusionsThe results of this study indicate that doxorubicin chemotherapy is associated with increases in mtDNA sequence variants in lymphocytes. The role of mtDNA mutations in late-onset cardiomyopathy of doxorubicin, and the potential antimutagenic activity of dexrazoxane, were not established but warrant further investigation.

In Poland, the population of Western Pomerania stands out due to the near-total displacement of its inhabitants following World War II. The German population was displaced (1.6 million people), and these lands were subsequently resettled by Poles arriving from various regions of Poland and Europe. Currently, the population of the West Pomeranian Voivodeship is 1.63 million, with 298 unrelated individuals studied. The research aimed to assess the variability of the entire mitochondrial control region (16024..16569, 1..576 bp in rCRS) among the inhabitants of the West Pomeranian Voivodeship and to compare the data with those from European and Polish populations. The study revealed a high level of genetic diversity in mtDNA among the inhabitants of the West Pomeranian Voivodeship, making it one of the most diverse populations in Poland and Europe. A total of 243 haplotypes were identified, with the most common haplogroups being HV, U, T, J, and R0. Within this population, the probability of random matching was 1:145. The molecular parameters obtained indicate a high degree of heterogeneity in the population of the West Pomeranian Voivodeship compared to the neighbouring German population from Fore Pomerania.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-22219-4.

Burial practices and mtDNA variation in the Oaxacan Barrio of Teotihuacan, Mexico: On the genetic structure of the great Mesoamerican city and its external influences

ABSTRACTThe tumour microenvironment (TME) constitution is decisive for cancer outcome and is manifested in diffusion‐weighted (DW) magnetic resonance imaging (MRI). We hypothesized that the TME metabolic state is reflected by mitochondrial DNA (mtDNA) secreted in extracellular vesicles (EVs) and examined whether plasma EV‐mtDNA variants may divulge MRI‐assessed TME attributes of rectal cancer aggressiveness. On the diagnostic MRI scans from 60 rectal cancer patients, the apparent diffusion coefficient (ADC) was calculated on DW images (n = 29), and tumour volume (n = 57) and extramural vascular invasion (EMVI; all patients) were determined on anatomical images. Plasma EVs (all patients) were isolated by size exclusion chromatography and verified for EV features. The EV‐mtDNA was sequenced along with mtDNA in whole blood (WB; normal tissue) to calculate the EV/WB‐mtDNA total variant number (TVN) and heteroplasmic variant number (HVN)—as a proxy for TME intracellular mtDNA variants expelled in EVs. Low EV/WB‐mtDNA TVN and HVN, indicative of hampered clearance of mutated mtDNA via EVs, were associated with low ADC (high TME cell density; p = 0.018, p = 0.005) and a large tumour volume (p = 0.002, p = 0.003). Likewise, low EV/WB‐mtDNA TVN and HVN were associated with positive EMVI (tumour infiltration in blood vessels; p = 0.002, p = 0.003) and histologic ypN stage 1–2 (lymph nodes with tumour cells surviving radiotherapy; p = 0.002, p = 0.005), both indicators of high tumour aggressiveness. High cellular density may hamper the clearance of pathogenic tumour mtDNA variants by EVs and thus promote rectal cancer aggressiveness.Trial Registration: ClinicalTrials.gov: NCT01816607. Registered 22 March 2013, https://clinicaltrials.gov/ct2/show/NCT01816607

It has been proposed that mitochondrial DNA variations can affect mitochondrial function, increasing the risk of drug-induced liver injury. This study aims to explore the association between mitochondrial DNA (mtDNA) variants and anti-tuberculosis drug-induced liver injury (ATT_DILI) in Korean tuberculosis patients. Whole mitochondrial genomes from 185 patients (61 with ATT_DILI and 124 without liver injury) were sequenced. Comparative analyses examined mtDNA variants, variant counts, and haplogroups between the two groups, adjusted with Bonferroni correction. The m.16189 T > C variant, associated with reduced mtDNA copy number, was more frequent in ATT_DILI cases (39.3%) than in controls (29.0%). Logistic regression suggested a potential association (odds ratio 4.92, 95% confidence interval 1.14-21.23, p = 0.033), though this significance was lost after correction. No significant differences in mtDNA variant counts or haplogroups were observed between groups. While mtDNA variants and haplogroups appear to have a limited role in predicting ATT_DILI risk, the m.16189 T > C variant warrants further investigation.

The evolving landscape of mitochondrial base editing: advances in precision, modeling, and therapeutic potential.

Investigating the interplay between mitochondrial DNA (mtDNA) variations and epigenetic aging metrics may elucidate biological mechanisms associated with age-related diseases. We estimated epigenetic age acceleration (EAA) metrics from DNA methylation data and derived mtDNA metrics, including heteroplasmic variants and mtDNA copy number (mtDNA CN) from whole genome sequencing. Linear regressions and meta-analyses were conducted to assess associations between EAA and mtDNA metrics, adjusting for chronological age, self-identified sex, and other covariates in 6,316 participants (58% female, 41% non-White Americans). Mediation analysis was conducted to examine whether EAA mediated the relationship between mtDNA CN and metabolic traits. A higher burden of rare heteroplasmic variants was associated with accelerations of first-generation EAA metrics, while a lower level mtDNA CN was associated with accelerations of second- and third-generation EAA metrics. For example, one standard deviation (SD) higher MSS, a score based on the predicted functions of rare heteroplasmic variants, was associated with a 0.22-year higher EAA by the Hannum method (p = 1.3E-6) among all participants, while one SD lower mtDNA CN was associated with higher DunedinPACE (β = -0.005, p = 6.0E-4). No significant association was observed between the heteroplasmy burden of common variants and EAAs. Furthermore, we observed DunedinPACE mediated 11.1% and 10.8% of the associations of mtDNA CN with obesity and T2DM in older FHS participants, respectively. Our analysis indicated that higher levels of heteroplasmy burden of rare variants and lower mtDNA CN were associated with accelerated epigenetic aging, and these associations showed stronger magnitudes among older participants.

Abstract Background and Aims Polycystic kidney disease (PKD) is characterized by cyst development and kidney enlargement, inducing progressive kidney failure. Cystic cells appear to shift towards a metabolic state resembling tumours, but the mechanism is unclear. Mitochondrial DNA (mtDNA) variants can be pathogenic, causing multi-system disorders that often involve the kidney; these are largely heteroplasmic, or occur in only some mitochondria in the body. mtDNA variants and mitochondrial abnormalities have been identified in cysts from PKD patients. Additionally, mtDNA haplogroups have been associated with clinical outcomes in other kidney diseases. Collectively, this evidence suggests a role of mitochondria in PKD phenotypes. Here, we present the initial investigation of the mitochondrial genome in an Irish PKD cohort. Methods Exome sequencing with a mtDNA spike-in was conducted on 303 PKD patients from the Irish Kidney Gene Project. After filtering for &amp;gt;80× mtDNA coverage, 281 samples remained for analysis. GATK Mutect2 on mitochondrial mode was used for mitochondrial variant calling, and all variants with PASS filter were kept. Variants within homopolymeric tracts were excluded. Remaining variants were annotated with MseqDR, VEP, and MitImpact. Homoplasmic variants were identified with variant allele frequency &amp;gt;0.95 and used for determining haplogroups with Haplogrep3. Genotyping data was available for 264/281 patients. These 264 PKD patients were projected onto an Irish ancestry reference dataset of &amp;gt;2000 individuals using PCA to generate principal components of ancestry. Initial regression analyses were conducted using a Cox proportional hazards model in R to test for associations between mitochondrial haplogroup and age at kidney failure, correcting for sex, diagnostic variant, and ancestry. Statistical significance was determined from Bonferroni-corrected p-value &amp;lt;0.05 (0.05/10 = 0.005). Results 687 mtDNA variants were found across the 281 PKD patients, with 163 found as heteroplasmic and 639 found as homoplasmic. 99 individuals had at least one heteroplasmic variant. ACMG classification is underway for determining pathogenicity of the heteroplasmic variants. Mitochondrial haplogroups were assigned to 276/281 individuals, with 10 distinct haplogroups occurring in the cohort. The haplogroup distribution aligns with a prior Irish population study, confirming our cohort represents what is expected of an Irish population. 92 individuals had all data required to run the regression analysis. Initial regression analyses suggest that mitochondrial haplogroups I and T decrease kidney survival 15 years (adjusted-P = 0.009) and 19 years (adjusted-P = 0.006), respectively. However, further testing is required to confirm this signal. Conclusions Mitochondrial variation even within a small Irish PKD cohort is quite diverse. Heteroplasmic variants commonly occurred in our cohort, but these must be fully investigated for pathogenicity. We have built upon previous mitochondrial haplogroup association studies by incorporating an ancestry covariate to clarify the contributions of mitochondrial haplogroups to PKD clinical phenotypes.

Sequence variation in mitochondrial DNA was once considered neutral, but growing evidence indicates it can influence metabolic, physiological and life-history traits. Two hypotheses offer explanations for this non-neutral mtDNA variation: the mitochondrial climatic adaptation hypothesis, which posits that natural selection shapes mtDNA variation to match local environments, and the mother's curse hypothesis, which predicts the accumulation of male-harming variants due to maternal inheritance. We explored these hypotheses using genetic strains of Drosophila melanogaster bearing eight mtDNA haplotypes-nested within two distinct haplogroups (A1 and B1) that segregate along an Australian latitudinal cline. We measured the longevity of flies under cool (18 °C) and warm (28 °C) conditions, predicting that the A1 haplogroup-which has been reported to predominate at subtropical latitudes-would confer higher longevity in warm but reduced longevity in cool temperatures relative to the B1 counterpart. We also tested whether effects of mtDNA haplotype on longevity were larger in males, as predicted under the mother's curse hypothesis. We found mtDNA haplogroup and haplotype is associated with longevity, with the magnitude of effects varying with temperature, but not in a pattern consistent with either hypothesis. Haplogroup-by-environment interactions did not align with reported spatial distributions of the haplogroups, and haplotype effects on longevity were similar across sexes. Our findings add to the growing evidence that mtDNA variation contributes to thermal plasticity in longevity, but do not provide clear insight into whether this variation is adaptive or maladaptive.

Abstract The Siberian roe deer (Capreolus pygargus) is distributed throughout continental Asia. In Eastern Europe, individuals of the European roe deer species (Capreolus capreolus) displaying mitochondrial DNA (mtDNA) of C. pygargus have been recorded. However, it is not clear if the origin of this introgression is an effect of natural processes or a consequence of human-mediated translocation of the Siberian roe deer. Only a large-scale phylogeographic analysis, spanning both the natural range of C. pygargus and the introgression zone, can answer this question. To reveal the cause of the introgression and to provide the most comprehensive picture of Siberian roe deer phylogeography, we analysed the mtDNA control region fragment (610 bp) of 352 individuals combined with 132 sequences available in GenBank, covering a vast region extending from Eastern Europe to Eastern Asia. We detected 101 mtDNA haplotypes and 6 haplogroups. The proportion of different haplogroups, varying along longitudinal gradients, showed a notable shift in the central parts of Siberia. Haplogroups B and D were the most frequent in the introgression zone. Seven genetic clusters of Siberian roe deer, including two in the introgression zone, were detected. MtDNA diversity of Siberian roe deer proved to be greater than previously documented. Two genetically and evolutionarily distinct haplogroups, occurring predominantly in Europe, appear to be remnants of natural interbreeding between the two roe deer species that could have occurred during one hundred thousand years ago in at least two different time periods. Additionally, past human-mediated translocations of the Siberian roe deer contributed to the observed introgression.

Abstract Mitochondria regulate energy metabolism by converting nutrients into ATP through the process of oxidative phosphorylation. A series of protein complexes in the inner mitochondrial membrane facilitate ATP production via electron transfer, with respiratory complex I (i.e., NADH dehydrogenase) transferring electrons from NADH to build the proton gradient that facilitates ATP synthesis. Efficient complex I activity supports ATP production in muscle tissue, sustaining mitochondrial function and metabolic processes essential for muscle efficiency and overall animal performance. Despite mitochondria’s key role in energy production, mitochondrial DNA (mtDNA) variation has been largely overlooked in livestock breeding, with its impact on economically relevant traits remaining largely unexplored due to the focus on paternal genetics and nuclear DNA. Therefore, the objective of this study was to investigate the relationship between mitochondrial haplotype and complex I activity in skeletal muscle to determine if genetic variation in mtDNA influences complex I function. Haplotype was determined by performing low-pass sequencing (average 55X mitochondrial coverage) on DNA of 84 beef steers from the composite University of Nebraska-Lincoln herd. Sequencing data were trimmed and aligned to the ARS-UCD2.0 genome using BWA-MEM and variants called using GATK. Mitochondrial haplotypes were defined by considering only nonsynonymous variants. Nine haplotypes were considered with 4-25 (average = 9) cattle represented per group. Calorimetric assays were used to quantify citrate synthase and complex I activities of sternomandibularis muscle homogenates collected at harvest. Complex I activity was normalized to citrate synthase activity to account for differences in mitochondrial content. Citrate synthase activity averaged 176.40 ± 83.60 nmol/min/mg of protein. Complex I activity normalized to citrate synthase activity averaged 0.99 ± 0.67. A linear mixed model was implemented with complex I activity normalized to citrate synthase as the dependent variable to assess the effect of mitochondrial haplotype on complex I activity. Fixed effects included mitochondrial haplotype, contemporary group (birth and harvest cohort), and age at sampling. A random animal effect, modeled using a genomic relationship matrix based on ~90,000 nuclear genomic markers, accounted for polygenic influences. Mitochondrial haplotype was not associated with complex I activity for these steers. Age and contemporary group also had no effect on complex I activity, suggesting that variation in these animals was driven by factors other than mitochondrial haplotype. Given that mitochondrial respiratory complexes are derived from both mitochondrial and nuclear-encoded genes, nuclear genetic variation or the interaction of nuclear and mitochondrial genes may have been more influential than complex I haplotype alone in determining the complex’s efficiency. Future analysis of data from more animals and consideration of complex I activity’s relationship to growth traits (e.g., average daily gain, dry matter intake, and feed-to-gain ratio) will further characterize its role in beef cattle production traits.

Abstract Background Type 2 Diabetes Mellitus (T2DM) is a multifactorial metabolic disorder influenced by genetic and environmental factors. Emerging evidence suggests that mitochondrial DNA (mtDNA) variations contribute to the pathogenesis of T2DM, particularly in cases of Maternally Inherited Diabetes and Deafness (MIDD). Understanding these mtDNA variations could provide insights into mitochondrial dysfunction, insulin resistance, and ß-cell failure, paving the way for precision medicine approaches. Methods This study employed MassARRAY technology to analyze mtDNA variations in a cohort of 20 participants, including 15 T2DM patients and 5 non-diabetic controls. DNA was extracted from EDTA blood samples, and specific mtDNA loci, including A12026G and C12258A, were targeted for mutation analysis. Genotype frequencies were compared between T2DM and control groups. Statistical analysis was performed using chi-square tests and logistic regression to evaluate the association between mtDNA variations and T2DM risk. Results Most individuals exhibited wild-type (WT) mtDNA genotypes across the analyzed loci. However, two significant mutations were identified in the T2DM group. The A12026G mutation was observed in one patient and was associated with MIDD, suggesting a potential link to mitochondrial dysfunction. Another patient exhibited heteroplasmy at the C12258A locus, indicating mitochondrial instability. No mutations were detected in the control group. Statistical analysis revealed a significant association between the A12026G mutation and increased risk of T2DM (p &amp;lt; 0.05). Conclusion This study suggests that specific mtDNA variations, particularly A12026G and C12258A, may contribute to the pathogenesis of T2DM through mitochondrial dysfunction, leading to insulin resistance and ß-cell failure. The association of A12026G with MIDD reinforces the role of mitochondrial inheritance in diabetes susceptibility. These findings highlight the potential of mtDNA mutations as biomarkers for early detection and risk assessment in T2DM. Future research with larger cohorts is needed to validate these associations and explore mitochondrial-targeted therapies for diabetes management.

The rising incidence of human–crocodile conflict involving the endangered Sunda gharial, Tomistoma schlegelii, has led to a growing number of wild-caught individuals being placed in conservation centres and zoos. But the genetic diversity and coancestry of the captive individuals is unknown which could result in an increased inbreeding or outbreeding, defeating the purpose of ex situ conservation efforts. Therefore, this study analysed the genetic diversity, population structure and identification of important clusters for future breeding programs. Blood samples from 38 individuals were analysed using 14 species-specific microsatellite loci and the partial mitochondrial DNA sequences of ND6–tRNAGlu–cyt b region and control region. The STRUCTURE results revealed six clusters displaying low nuclear gene diversity, with mtDNA diversity noted in only one cluster. Two important clusters were identified to facilitate future breeding programs of this species.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-17481-5.

INTRODUCTIONMitochondrial DNA (mtDNA) variation may influence cognitive performance, but prior findings are inconsistent.METHODSWe analyzed data from 2308 participants in the Coronary Artery Risk Development in Young Adults (CARDIA) study, assessing heteroplasmy (mtHz) burden and haplogroups (mtHg) from blood‐derived mtDNA at three timepoints and cognitive function across multiple domains. Multivariate linear regression models and multivariate linear mixed models adjusted for age, sex, education, and race.RESULTSMtDNA heteroplasmy burden and count were not associated with cognitive performance. However, mtHgs in macro‐mtHg L were linked to poorer cognitive outcomes, particularly in processing speed and global cognition in cross‐sectional and longitudinal analyses. Associations remained significant after adjusting for social determinants of health (SDOH) or APOE ε4, comorbidities, and lifestyle variables.DISCUSSIONThe mtDNA variation, especially mtHgs, may play a role in influencing cognitive trajectories, warranting further research on its role in cognitive aging.HighlightsHeteroplasmy burden was not associated with cognitive performance at midlife.Haplogroups were associated with cognitive outcomes at midlife.Longitudinal analysis revealed that haplogroups are associated with cognitive trajectories.

Mitochondrial replacement techniques: The perspectives of mitochondrial disease specialists in Germany.

ABSTRACTThree Stenella species, S. attenuata, S. coeruleoalba, and S. longirostris, are widely distributed throughout the Indo‐Pacific region, but genetic information on each population remains scarce. This gap is particularly notable in Thai waters, where these species co‐occur in overlapping oceanic habitats. In contrast, previous studies in the Atlantic have revealed moderate to high mitochondrial genetic diversity and signs of ongoing hybridization among Stenella species. These findings raise the question of whether similar genetic patterns exist in other regions. To address this, we investigated genetic diversity, population structure, potential hybridization, and historical demographic change among three Stenella dolphin species in Thai waters. We analyzed 113 stranded specimens using 20 microsatellite loci and partial mitochondrial DNA (mtDNA) control region sequences. Results revealed high genetic diversity across all species, with expected heterozygosity highest in S. attenuata (He = 0.689), followed by S. longirostris (He = 0.651), and then S. coeruleoalba (He = 0.607). By contrast, S. longirostris exhibits the highest mtDNA diversity (haplotype diversity (H) = 0.988, nucleotide diversity (π) = 0.0194), followed by S. coeruleoalba (H = 0.986, π = 0.0173), and S. attenuata (H = 0.768, π = 0.0125). No population structure was detected within individual species by Bayesian clustering methods. However, analysis of the combined dataset for all three species suggests the presence of three genetic clusters (K = 3), with evidence of admixture across species but no shared mtDNA haplotypes, indicative of male‐mediated gene flow. Unique haplotypes were also found in all three species inhabiting Thai waters. Differing demographic histories likely reflect species‐specific responses to past environmental changes and recent anthropogenic impacts. These findings provide critical genetic insights for monitoring and informing conservation strategies in Thailand and surrounding regions.