Mitochondrial DNA D-loop Region Research Articles

Phylogenetic and population genetic analysis of Arunachali Yak (Bos grunniens) using mitochondrial DNA D-loop region.

The Arunachali yak (Bos grunniens) is an important breed native to the northeastern Himalayas of India. Understanding its genetic diversity and evolutionary relationships with other bovine species is crucial for effective conservation and breeding strategies. This study investigates the mitochondrial DNA (mtDNA) D-loop region of Arunachali yak and compares it with other bovines to elucidate these relationships. We collected blood samples from 18 Arunachali yak individuals and isolated genomic DNA. The partial mtDNA D-loop region was amplified using PCR and sequenced. Sequences were compared with those from Bos frontalis, Bos gaurus, Bos indicus, Bubalus bubalis, and Capra hircus available in GenBank. Phylogenetic relationships were assessed through Neighbor-Joining trees and median-joining networks. Genetic diversity indices and neutrality tests were applied to evaluate population genetic characteristics. Phylogenetic analysis identified three distinct clades, with Arunachali yak clustering closely with Bos indicus, and forming a separate branch from other bovine species. Median-joining networks revealed six haplogroups, with Arunachali yak uniquely representing Hap_3. Genetic diversity analysis showed no polymorphism within Arunachali yak, indicating very low genetic variation in the selected animal samples. AMOVA demonstrated significant genetic differentiation among populations (Fst = 0.30053, P < 0.001), with a substantial portion of variation occurring within populations. The Arunachali yak exhibits a close genetic relationship with Bos indicus, reflecting recent divergence. The study underscores the distinct genetic profile of Arunachali yak and highlights its limited genetic variability. These findings enhance our understanding of bovine evolutionary relationships and emphasize the need for targeted conservation measures to preserve the genetic integrity of Arunachali yak.

Identification of sequence polymorphism in the D-loop region of mitochondrial DNA as a risk factor for breast cancer.

Mitochondrial DNA (mtDNA) variations affect the efficiency of the electron transport chain and production of reactive oxygen species, contributing to carcinogenesis. The D-loop region of mtDNA has emerged as a variation hotspot region in human neoplasia; however, the potential contribution of these variations in breast cancer risk prediction remains unknown. We investigated the relationship between germline single nucleotide polymorphisms (SNPs) in the entire D-loop region and breast cancer risk in Chinese women. Peripheral blood-isolated mtDNA from 2329 patients with breast cancer and 2328 cancer-free controls was examined for SNPs. In the combined cohort, we used traditional risk factors, susceptibility germline polymorphisms, and logistic regression analysis to evaluate the predictive value of susceptibility variants for breast cancer risk. We calculated the area under the receiver operating characteristic curve (AUC) as a measure. We also measured the content of 8-hydroxy-2'-deoxyguanosine (8-OHdG). Individual polymorphisms SNP573 were significantly associated with breast cancer risk in both the discovery and validation cohorts. In the combined cohort, the AUC of the traditional risk factors was 64.3%; after adding susceptibility variants, the AUC was 64.9% (DeLong test, p = 0.007). 8-OHdG levels were significantly higher in patients with breast cancer than in controls and higher in individuals with SNP573 than in those negative for this variation. Overall, oxidative stress might be associated with the risk of breast cancer, and SNP573 might be associated with oxidative stress. Our results indicate the risk potential of polymorphisms in the D-loop region in breast cancer in Southern China.

Testing the applicability of environmental DNA metabarcoding to landscape genetics.

Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D-loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue-based approaches by the same D-loop region and genome-wide SNP data. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA- and tissue-based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when comparing both in the D-loop region. The removal of low-frequency reads or the conversion to semi-quantitative rankings of eDNA data did not alter the correlation of genetic diversity and differentiation statistics with tissue-based approaches much. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation-by-distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics.

Novel blood and tissue-based mitochondrial D-loop mutations detected in an Iranian NAFLD patient cohort

Non-alcoholic fatty liver disease (NAFLD) is an increasingly prevalent chronic liver disease characterized by an elusive etiology. In its advanced stages, this condition can pose life-threatening implications. Mitochondrial dysfunction due to its impact on hepatic lipid homeostasis, cytokine release, ROS production, and cell death, contributes to the pathogenesis of NAFLD. Previous research reveals a direct link between NAFLD genetic predictors and mitochondrial dysfunction. The emphasis on the D-loop stems from its association with impaired mtDNA replication, underscoring its crucial role in NAFLD progression. We included 38 Iranian NAFLD patients (comprising 16 patients with non-alcoholic fatty liver [NAFL] and 22 patients with non-alcoholic steatohepatitis [NASH]), with matched blood and liver tissue samples collected from each to compare variations in the mitochondrial D-loop sequence within samples. The mitochondrial DNA (mtDNA) D-loop region was amplified using PCR, and variations were identified through sequencing. The resultant sequences were compared with the reference sequence of human mtDNA available in the MITOMAP Database for comparative analysis. In this study, 97 somatic mutations in the mtDNA D-loop region were identified in NAFLD patients. Our study revealed significant difference between the NAFLD patients and control group in 13 detected mutations (P ≤ 0.05). Novel mutations were discovered in hepatic tissues, while mutation 16220-16221ins C was found in both tissues and blood. A significant difference was found in the distribution of D310 and mt514-mt523 (CA)n repeat variations between NAFLD patients and the control group (P < 0.001). C to T and T to C transitions were the prevalent substitution among patients. Identification of the 16220-16221ins C mutation in both blood and tissue samples from NAFLD patients holds substantial promise as a potential diagnostic marker. However, further research is imperative to corroborate these findings.

Identification of CRISPR/Cas12a (Cpf1) guideRNA Sequence Targeting the Mitochondrial DNA D-loop Region in Wild Pig (Sus scrofa) Through Homology Difference and Mismatch Analysis

Identification of CRISPR/Cas12a (Cpf1) guideRNA Sequence Targeting the Mitochondrial DNA D-loop Region in Wild Pig (Sus scrofa) Through Homology Difference and Mismatch Analysis

DNA variants and population structure of Magelang ducks across generation

Magelang ducks (MD) are Indonesian local ducks and are known as dual-purpose type ducks which have high egg production, duck day production (DDP), and body weight size. Nowadays, the MD is selected to establish the pure line to advance the egg production trait in the Breeding and Rearing Center of Non-Ruminant Animals Banyubiru, Central Java. The mitochondrial DNA (mtDNA) Dloop region, is highly polymorphic and could be used to analyze the population genetics. The present research aims to examine the impacts of continuous selection on population structure and genetic mutations on MD across two generations using the mtDNA D-loop region. Thirty-six blood samples from the second (G2) and third (G3) generations were examined using the sequencing method. The MEGA X and DnaSP software were applied to calculate the genetic diversity, genetic distance, and to generate a phylogenetic tree. The number of haplotypes (H), haplotype diversity (Hd), and Tajima's D are 26, 0.9746, and -1.46, respectively. The Fst value of MD is 0.156. The genetic distance among populations ranges from 0.0000 – 2.097. The UPGMA analysis constructs one clade in a phylogenetic tree between MD, Indonesian local Ducks, Indian Ducks, Vietnamese Ducks, and Chinese Ducks. The study found that the genetic variation and population structure did not significantly change between the second and third generations.

Genetic diversity and population structure of Turkish Aseel chickens

This study aimed to assess the genetic diversity, maternal origin, and population structure of Turkish Aseel chickens. The research was conducted on Aseel roosters and chicks older than one year. DNA was extracted from 96 Turkish Aseel feather samples collected from various regions of Türkiye for the study. Sample DNAs were amplified using specific primers for the D-loop region of the chicken mitochondrial DNA (mtDNA). The sequences were produced using the amplified DNA samples. The mtDNA D-loop regions were compared with the sequences of the same genetic area from other chicken breeds. Turkish Aseel chickens provided 34 haplotypes and 18 genuine polymorphisms across 41 distinct regions that were particular to the breed. According to the findings of the phylogenetic tree, Turkish Aseel chickens tend to establish clusters of haplogroups among themselves. Although most Turkish Aseel samples clustered individually into three clades, at least one sample has been discovered with five distinct clades. According to the phylogenetic tree and the Median Joining Network, it can be concluded that while many of the haplogroups of Turkish Aseel cluster among themselves, they have diverse maternal origins and lack breed-specific maternal lineages. This research is the first extensive study to examine genetic variability in Turkish Aseel chickens. Considering the lack of similar data on other Aseel varieties raised in different counties, the current work is a pioneering study with data on the genetic characterization of the Aseel breed.

The employment of real-time polymerase chain reaction for analysis of canine meat in meatball products for halal authentication analysis.

Meatballs are a popular meat-based food consumed widely in Indonesian society. However, the issue of unethical substitution of halal meatballs with non-halal meats, particularly pork and canine meat (CM), has emerged. The existence of non-halal meats, including CM, in food products is prohibited in Islam, necessitating the development of reliable analytical techniques for their identification. In this study, we designed species-specific primers (SSPs) targeting the D-loop region of mitochondrial DNA for CM meatball product identification. The study was commenced by creating specific primers for canine DNA using Integrated DNA Technologies software and subsequently performing DNA isolation. The designed primers were then subjected to comprehensive evaluation using RT-PCR, including specification, linearity, limit of detection, efficiency, and repeatability. The results indicated that the primer D-Loop 443 (forward: 5'-GGG ACA TCT CGA TGG ACTA ATG-3', reverse: 5'-GCG GTC ATA GAT GAG TGA TAG C-3') designed and validated in silico using primer-basic local alignment search tool nucleotide (BLAST) program from NCBI accurately identified canine DNA when the optimal annealing temperature was set at 57.5oC. The real-time PCR technique utilizing the D-loop 443 primer exhibited the ability to amplify canine DNA down to a minimum quantity of 100 pg, with an efficiency value of 91.8%, a correlation coefficient (R) of 0.990, and a precision value (RSD) of 0.30%. The SSP-based RT-PCR method developed is a versatile and efficient tool for detecting CM in meatballs. Its implementation helps maintain consumer trust and addresses concerns regarding the substitution of halal meats with non-halal alternatives.

Mitochondrial Diversity and Phylogenetic Relationship of Eight Native Bulgarian Sheep Breeds

The geographical, geomorphological, and climatic characteristics of Bulgaria are particularly favorable for animal breeding and, above all, for pastoral farming and sheep breeding. These conditions created prerequisites for the creation of about 30 unique local breeds of sheep. In this study we investigated the genetic diversity of eight of the most popular Bulgarian native breeds, based on the sequence analysis of a part of the mitochondrial D-loop region. An almost entire mitochondrial DNA (mtDNA) D-loop region (1180 bp) was amplified and sequenced. The obtained results showed the presence of a large number of haplotypes – 225, belonging to two main haplogroups. The majority of samples showed a high prevalence of the European haplogroup B (95.2%) while the remaining individuals were assigned to haplogroup A (4.8%). None of the other reported mitochondrial haplogroups were observed. The number of polymorphic sites, nucleotide and haplotype diversity was high (240, 0.01237, and 0.9968, respectively), which is evidence for multiple maternal origins in all populations. The Tajima D-test value in all the study populations was −1.905 (p &lt; 0.05), indicating that the abundance of rare alleles was most likely due to population expansion after a recent bottleneck. The Median joining network showed that almost all haplotypes belonging to haplogroup B formed a star-like network, which revealed a weak genetic differentiation and a large gene flow between the Bulgarian native breeds.

Dolphins from a prehistoric midden imply long-term philopatry of delphinids around Tokyo Bay

Abstract Cetaceans of the family Delphinidae are widely distributed throughout the global ocean, and it has been suggested that females exhibit philopatry. However, the duration of time that a maternal group of these highly mobile creatures spends inhabiting a particular region remains unknown. The objective of this study is to examine the genetic diversity of delphinids in the past and to shed light on the above question. In this study, we amplified and sequenced the mitochondrial DNA D-loop region from the skeletal remains of delphinids that were excavated from the Shomyoji Midden, a site situated on the western coast of Tokyo Bay and dating to 5000–3000 years before the present. We acquired prehistoric D-loop sequences of seven bottlenose dolphins, six Pacific white-sided dolphins, and a false killer whale. Notably, one or more haplotypes from the prehistoric individuals were detected in the geographically proximate modern conspecific populations across all three species. Whilst the genetic diversity of prehistoric and modern Pacific white-sided dolphin populations appears to be comparable, the modern bottlenose dolphin population demonstrates significantly lower genetic diversity when compared to its prehistoric counterpart in the vicinity of Tokyo Bay. The maternal groups of these species are speculated to have persisted in the same habitat for at least 4000 years.

Genetic diversity and maternal origin of Vietnamese indigenous chicken breeds inferred from complete sequences of mitochondrial DNA D-loop region

Genetic diversity and maternal origin of Vietnamese indigenous chicken breeds inferred from complete sequences of mitochondrial DNA D-loop region

Mitochondrial displacement loop region single nucleotide polymorphisms and mitochondrial DNA copy number associated with risk of ankylosing spondylitis.

The pathogenesis of ankylosing spondylitis (AS) seems to be associated with genetics, the environment, heredity, and oxidative stress. Single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) region of mitochondrial DNA (mtDNA) and mtDNA copy number were investigated for their correlation with AS patients. This study included 83 AS patients and 100 healthy controls from the Second Hospital of Hebei Medical University. DNAs were extracted from blood samples for polymerase chain reaction analysis and quantitative real-time polymerase chain reaction analysis. Plasma reactive oxygen species (ROS) levels were measured by fluorescent probe technology. The distribution frequencies of the minor alleles of nucleotides 16304C (p = .037), 16311C (p = .027), and 152C (p = .034) were remarkably higher in AS patients than in healthy controls, which indicated that the16304C, 16311C, and 152C alleles were correlated with an increased risk of AS. Simultaneously, mtDNA copy number was statistically higher in patients with AS compared with controls (1.450 ± 0.876 versus 0.835 ± 0.626, p < .001). We also observed an increased ROS generation in AS patients compared with controls (27 066.169 ± 18 364.819 versus 14 758.330 ± 5854.946, p < .001) subsequently. In addition, the AS susceptible SNP 16311C is associated with high ROS levels (35 065.177 ± 26 999.934 vs. 25 005.818 ± 14 999.495, p = .043). Our study demonstrated that SNPs in the mtDNA D-loop could be AS risk biomarkers with the potential to promote oxidative stress levels; mtDNA copy number-induced mitochondrial dysfunction may also be involved in AS pathogenesis.

Bazı Anadolu Yerli Sığır Irklarının MtDNA D-loop Dizi Analizi: Genetik Çeşitlilik ve Popülasyon Geçmişinin Değerlendirilmesi

Mitochondrial DNA is the molecular indicator of maternal inheritance and is one of the frequently preferred markers in population genomics, phylogenetic and phylogeographic studies due to its features such as evolving faster than genomic DNA, lack of recombination and showing differences according to the geographical distribution of species. In this research, mitochondrial DNA D-Loop region sequence analyzes were performed in order to reveal the genetic diversity and phylogenetic relationships of some domestic cattle breeds bred in Anatolia. First of all, the sampling study of the cattle breeds that were the subject of the research, was completed. Mitochondrial DNA D-Loop region was amplified by Polymerase Chain Reaction from the DNA isolated samples using the Standard Phenol/Chloroform Method. After DNA sequencing, data of domestic cattle breeds were analyzed together with reference mitochondrial DNA sequences from GenBANK, and their haplotype and nucleotide diversity, and genetic and phylogenetic relationships within and between populations were evaluated. With the data obtained, it was determined that the nucleotide and haplotype diversity, haplotype numbers, intra and inter population variation were quite high in Anatolian native cattle breeds. It was also concluded that the native cattle breeds bred in Anatolia are phylogenetically between Asian and European cattle breeds.

Forensic Genetics and the Differentiation of Monozygotic Twins by Mitochondrial DNA Analysis

Forensic genetics uses STR markers as the gold standard for human identification. However, this technique does not allow the differentiation of monozygotic twins, since they originate from the fertilization of a single egg and a single sperm. Studies aiming to solve this problem have been developed and the complete sequencing of mitochondrial DNA has shown to be relevant. The present study aimed to verify the possibility of differentiating monozygotic twins through the analysis of the d-loop region of mitochondrial DNA, using the Sanger sequencing technique in blood and oral mucosa samples. Twelve pairs of volunteer monozygotic twins were selected, zygosity was confirmed by analyzing the genetic profile generated using STR markers. Regarding analyses of the d-loop region of mitochondrial DNA, a single pair of twins (gm46) showed a point heteroplasmy at position 16,290 (HV1). However, this finding was not able to differentiate between individuals of the same pair, since both showed the heteroplasmy in both biological samples (blood and oral mucosa). No other genetic variation was detected in the pairs of twins analyzed that could differentiate them. We suggest analyzing the mitochondrial DNA molecule as a whole in an attempt to identify a greater amount of potential variation by applying the Massive Parallel Sequencing technique.

PHYLOGENETIC POSITION OF LONG-TAILED MACAQUE (Macaca fascicularis) IN PULAU TINGGI, JOHOR, MALAYSIA

Macaca fascicularis is one of the most common primates found in Malaysia; however, they are under-appreciated and under-studied, especially in the taxonomic field. The subspecies M. fascicularis laeta was previously hypothesized to be distributed in Pulau Tioman and Pulau Tinggi. Thus, in this study, we aim to verify the phylogenetic position of long-tailed macaque in Pulau Tinggi through a molecular approach based on the D-loop region of mitochondrial DNA using Neighbour-Joining (NJ), Maximum Parsimony (MP) and Bayesian Inference. Three samples were successfully analyzed with a 99% bootstrap value in NJ, 99% bootstrap value in MP and 1.00 posterior probability in Bayesian Inference for Pulau Tinggi’s clade. The phylogenetic analysis concluded that Pulau Tinggi’s population is similar to the mainland population, which is the subspecies M. f. fascicularis, with an estimated time of divergence at ~0.299 million years ago. Overall, this study generally provides baseline data to aid in the future translocation process and conservation management of M. fascicularis in Pulau Tinggi and Malaysia.

Variations in mitochondrial DNA coding and D-loop region are associated with early embryonic development defects in infertile women.

Mitochondrial DNA (mtDNA) plays a critical role in oocyte maturation, fertilization, and early embryonic development. Defects in mtDNA may determine the alteration of the mitochondrial function, affecting cellular oxidative phosphorylation and ATP supply, leading to impaired oocyte maturation, abnormal fertilization, and low embryonic developmental potential, ultimately leading to female infertility. This case-control study was established to investigate the correlation between mtDNA variations and early embryonic development defects. Peripheral blood was collected for next-generation sequencing from women who suffered the repeated failures of in vitro fertilization (IVF) and/or intracytoplasmic sperm injection (ICSI) cycles due to early embryonic development defects as well as in-house healthycontrols, and the sequencing results were statistically analyzed for all subjects. This study found that infertile women with early embryonic development defects carried more mtDNA variants, especially in the D-loop region, ATP6 gene, and CYTB gene. By univariate logistic regression analysis, 16 mtDNA variants were associated with an increased risk of early embryonic development defects (OR > 1, p < 0.05). Furthermore, we identified 16 potentially pathogenic mtDNA variants only in infertile cases. The data proved that mtDNA variations were associated with early embryonic development defects in infertile Chinese women.

HMGA2 mediates Cr (VI)-induced metabolic reprogramming through binding to mitochondrial D-Loop region.

Hexavalent chromium [Cr (VI)] exists environmentally and occupationally. It has been shown to pose a carcinogenic hazard in certain occupations. This study was to investigate the role of high mobility group A2 (HMGA2) in Cr (VI)-induced metabolism reprogramming from oxidative phosphorylation (OXPHOS) to glycolysis in A549 and HELF cells. First, knockdown of HMGA2 by siHMGA2 significantly attenuated Cr (VI)-reduced expression of OXPHOS-related proteins (COX IV and ND1) and mitochondrial mass, indicating that HMGA2 was involved in Cr (VI)-reduced OXPHOS. Overexpression of HMGA2 by transfection of HMGA2-DNA plasmids reduced the expression of COX IV, ND1 and mitochondrial mass, suggesting the negative role of HMGA2 in OXPHOS. Secondly, both CCCP, the inhibitor of mitochondrial function, and the ER stress inhibitor, 4-phenylbutyric acid (4-PBA), decreased the level of HMGA2, indicating that the interaction of mitochondrial dysfunction and ER stress resulted in Cr (VI)-induced HMGA2 expression. Further study demonstrated that ER stress/HMGA2 axis mediated the metabolism rewiring from OXPHOS to aerobic glycolysis. Notably, Cr (VI) induced the accumulation of HMGA2 proteins in mitochondria and ChIP assay demonstrated that HMGA2 proteins could bind to D-loop region of mitochondrial DNA (mtDNA), which provided the proof for HMGA2-modulating OXPHOS. Taken together, our results suggested that the interaction of mitochondria and ER stress-enhanced HMGA2 played an important role in Cr (VI)-induced metabolic reprogramming from OXPHOS to glycolysis by binding directly to D-loop region of mtDNA. This work informs on the potential mode of action for Cr (VI)-induced tumors and builds on growing evidence regarding the contribution of cellular metabolic disruption contributing to carcinogenicity.

Examination of D-loop region and DBY gene as tools for identifying hybridisation in alpacas (Vicugna pacos) based on Polish populations

Hybridisation between alpacas (Vicugna pacos) and llamas (Lama glama) is a well-known phenomenon among alpaca breeders worldwide. Hybridisation causes poor fibre quality, which leads to economic losses. In the present study, we aimed to evaluate the d-loop region of mitochondrial DNA and the DBY gene located on chromosome Y to identify alpaca × llama hybrids. Moreover, based on these tools, the genetic diversity of alpacas in Poland was presented. We analysed the d-loop region in 235 individuals and investigated 90 pure males for the DBY gene. We generated 34 haplotypes with 446 segregation sites for the d-loop region and two haplotypes with four segregation sites for the DBY gene. Phylogenetic analysis based on the Bayesian clustering approach and a principal coordinate test showed a high level of mitochondrial DNA introgression between alpacas and llamas with a high gene flow value based on the sequence and on the haplotype data information. We found evidence of maternal line hybridisation in the d-loop region between alpacas and llamas, while this evidence was not found within the DBY gene. Moreover, the d-loop region investigation showed high levels of genetic diversity in the alpacas maintained in Poland.

Identification of sequence polymorphisms in the D-loop region of mitochondrial DNA as valuable biomarkers for salivary gland tumors: an observational study

BackgroundSalivary gland tumor frequency in the head and neck region is quite less and mostly benign. However, pathogenesis is associated with oxidative stress in the mitochondria. Hence, we are aiming to identify single nucleotide polymorphisms (SNP)/single nucleotide variants (SNV) in the mitochondrial DNA D-loop region of salivary gland tumors (SGT). We analyzed 19 biopsied tissue (formalin-fixed paraffin-embedded) tumors, i.e., pleomorphic adenoma-5, mucoepidermoid carcinoma-6, adenoid cystic carcinoma-5, and polymorphous low-grade adenocarcinoma-3. This extracted DNA was amplified to visualize the entire D-loop region of the mitochondrial genome of SGT.ResultsThe three hotspot mutation were noticed at 16,519 (thymine-cytosine) (number = 10), 73 (adenine-guanine) (number = 8), and 195 (thymine-adenine) (number = 4) in the D-loop in salivary gland tumors. We observed novel synonymous mutation in the 195 region of mitochondrial D-loop, which is a novel as per Mitomap (a human mitochondrial genomic database).ConclusionsWe hypothesized that the biological behavior of SGT is majorly dependent upon the stress level at mitochondria in the D-loop region. SNPs noted in mt-DNA should be noted as a pivotal biomarker for the progression or metastasis of SGT in individuals at risk.

Origin and Demographic History of Philippine Pigs Inferred from Mitochondrial DNA.

The Philippines is a mega-diverse country that lies at the crossroads of past human migrations in the Asia-Pacific region and is believed to have never been connected to the Asian continent, even during the major sea-level subsidence of the Quaternary. As a result, the history of pig dispersal in the Philippines remains controversial, due to limited molecular studies and absence of archaeological evidence of pig domestication. This study provides the first comprehensive analysis of 184 complete mitochondrial DNA D-loop region from Philippine pigs to elucidate their early dispersal history by performing a phylogenetic comparison with wild boars and domestic pigs worldwide. The results showed a demographic signal of the ancestry of Philippine pigs that had a close genetic relationship with those from the mainland Southeast Asia and Northeast Asia, suggesting gene flow that may have resulted from human migration and trade. Here we have suggested two possible dispersal routes. One parallels the Neolithic expansion in Island Southeast Asia and Oceania via Northeast Asia, the other from the mainland Southeast Asia, into Palawan and Sulu Archipelago as early as prehistoric times via the Sundaic Region. Despite geographic barriers to migration, numerous genetic lineages have persisted across the Philippine islands, even justifying the recognition of a Philippine Lanyu subclade. The prehistoric population history suggests a demographic expansion that coincided with the interglacial periods of the Pleistocene and may have spread from the southern regions into the eastern and central regions of the Philippines. The intriguing signal of discrepancy discovered between the ancestral pattern and distribution range of the numerous endemic Philippine wild pigs opens a challenging new approach to illuminate complexity among these animals. Our study has contributed significantly towards completing the sparse molecular studies on Philippine pigs, an essential for creating win-win conservation measures.