Mitochondrial DNA D-loop Research Articles

Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus

Introduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.

Reduced genetic diversity in greater one-horned rhinoceros in Chitwan National Park A new challenge and opportunity for rhino conservation in Nepal

Understanding the genetic diversity of a species is vital to improve the effectiveness of conservation management interventions. The greater one-horned rhinoceros (Rhinoceros unicornis) is one of the most iconic megaherbivores in South Asia but is classified as Vulnerable by the IUCN. The species is now broadly confined to two isolated populations in Chitwan National Park (CNP), Nepal and Northeast India, which are both constrained by poaching, and the loss or degradation of habitat. Since 2016, rhino mortalities have increased in CNP for unknown reasons. To assess the impact of any current or previous mortality events, we investigated the genetic diversity in the current CNP rhino population. We collected skin samples from 67 dead rhinos found in CNP and its buffer zone between 2012 and 2019. Fragments 428 bp of mitochondrial DNA D-loop were amplified from extracted DNA using PCR and sequenced to compare with complementary sequences derived from a previous study of CNP rhinos conducted during 1986-1987. A total of six haplotypes were detected in the older sample set with a haplotype diversity (Hd) of 0.38012 compared to only four haplotypes and a Hd of 0.3374 in our cohort. This decline in haplotype diversity was unexpected as the CNP rhino population has increased by 69% over the previous 27 years. In addition, we found the haplotypes were not equally distributed across CNP, with a greater variation detected in the eastern sector (4 haplotypes) compared to the west (1 haplotype). We recommend that CNP management authorities consider translocations within the park boundaries to promote breeding between the eastern and western subpopulations to disseminate and maintain haplotype diversity throughout the population.

Phylogenetic Study of Philippine Pigs (Sus scrofa L.) from Ifugao and Kalinga Based on Mitochondrial DNA D-loop Analysis

Conservation genetic studies for Philippine pigs are essential to sustain global biodiversity. To study the phylogenetic relationship of Philippine pigs, 79 samples were collected from Ifugao (n = 41) and Kalinga (n = 38) provinces located in the Cordillera Administrative Region, northern Philippines. Mitochondrial DNA control region analysis was undertaken to investigate the phylogenetic relationship between the pig populations from the two provinces and other Asian and European pig breeds. Fourteen (14) haplotypes (H1–H14) were detected in the Ifugao and Kalinga samples. Several haplotypes – specifically, H1, H4, H9, H12, and H14 – formed an independent clade with the Type I Lanyu haplotypes, which are known to be unique in Taiwan pigs. The remaining haplotypes (H2, H3, H5–H8, H10, H11, and H13) clustered with the haplotypes of other Asian pig breeds within the major Asian clade. These results suggest the close relationship between Kalinga and Ifugao pigs and Type I Lanyu pigs. The existence of duplicate motifs also revealed that the native pigs from Ifugao and Kalinga belong to a distinct genetic lineage that clustered with other Philippine pig samples and separate from other Asian pigs, whereas the other samples may represent a recent introgression of modern lineages.

Mitochondrial D-loop sequences and haplotypes diversity in Egyptian rabbit breeds

Rabbit breeds in Egypt are local and adapted foreign breeds that have been imported since the middle of the last century. Stressful environmental conditions including climatic changes, exposure to diseases and breeding selection have an influence on how gene flow has shaped the genetic diversity of the breeds. Mitochondrial DNA D-loop is a genetic marker used to trace the geographic distribution of genetic variation for the investigation of expansions, migrations and other gene flow patterns. The study aimed to determine the genetic diversity of the mitochondrial DNA D-loop (mtDNA D-loop) in Black Baladi, Red Baladi, Gabali, APRI line and New Zealand breeds to gather the scientific data required to create a proper conservation and sustainable management plan. Blood samples were taken from animals unrelated to each other. A 332-bp of mtDNA D-loop was successfully amplified and alignment sequences were deposited in the GenBank database. The results detected six haplotypes in the five breeds. Haplotype diversity within individual breeds varied from 0 (Red Baladi) to 0.551±0.114 (Gabali). The nucleotide diversity (π) value was relatively low (0.001-0.006), with greater values in APRI and New Zealand. Pairwise distances between breeds yielded varying values ranging from 0 to 0.254, and the values between the Red Baladi and other breeds were comparatively high, with pairwise distances from 0.172 to 0.254. The phylogenetic analysis involved 74 nucleotide sequences of the Egyptian rabbit and thirty-one sequences retrieved from GenBank of the reference samples of different haplogroups. The results of the phylogenetic analysis correlated to the reference mtDNA GenBank database showed that the five Egyptian rabbit breeds were grouped into haplotypes A, B and K. The results of the genetic diversity using mtDNA shed light on the importance of the local breed’s genetic diversity information and revealed unique mtDNA haplotypes, which is an important finding for breeding strategies designed to conserve genetic variants and provide sustainable management.

Genetic Structure of a Native Neotropical Fish Species: New Insights about a South American Bioindicator.

The biodiversity of Neotropical region is affected by anthropogenic disturbance. Throughout Brazil, Argentina and Uruguay, the native fish, Cnesterodon decemmaculatus, is well distributed and widely used as an excellent bioindicator of environmental quality. We investigated the diversity and genetic structure of its populations along a water pollution gradient to answer the following questions: 1- Does the genetic diversity decrease under the stressful conditions of a severe water quality gradient? and 2- Is there any relationship between the haplotypes registered along the studied basin and those recorded in other distant basins? Two mitochondrial DNA markers, Cytochrome b and D-loop, were analyzed and four haplotypes were registered for both markers along the basin. H1 was present throughout all the river sections in high frequencies leading to a low genetic diversity. We suggest that only a few haplotypes tolerate the stressful conditions of mountain rivers. On the other hand, the presence of H4 at the site located downstream suggests a history of recent colonization from the southeast to the northwest of the biome. These results, together with the abundance decrease along the pollution gradient, and the non-migratory characteristic of C. decemmaculatus suggest that its populations may be at risk of local extinction.

Genetic Diversity of Mitochondrial DNA (mtDNA) D-Loop Sequences in Six Improved Tropically Adapted Chicken Breeds (iTABs) in Imo State, Nigeria

The improved tropically adapted chicken breeds (iTABs) are low-input-high-output chickens suitable for smallholder poultry (SHP). Six iTABs (Fulani, FUNAAB Alpha, Kuroiler, Noiler, Sasso and Shika Brown) were introduced, and were raised under semi-intensive management system and tested under the African Chicken Genetic Gains project in Nigeria. The objective of this study was to evaluate the genetic diversity of these iTABs tested in Imo State Nigeria using mitochondrial DNA (mtDNA), Blood samples were collected from 77 chickens belonging to these six populations of iTABs in the ratio (12:12:14:13:13:13), for Noiler, FUNAAB Alpha, Shika Brown, Kuroiler, Sasso and Fulani chickens, respectively. Genomic DNA was extracted from seventy-seven birds randomly selected from the six iTABs. A 450-bp mtDNA D-loop region was sequenced. The highest (H=5) and the lowest (H=2) number of haplotypes were found within Noiler, and Shika Brown/Fulani, respectively. Among the six populations, haplotype and nucleotide diversity was 0.558±0.063 and 0.0064±0.0013, respectively. A total of 8 haplotypes were identified from 15 polymorphic sites. These haplotypes clustered into three clades with 87.89% of the total maternal genetic variations occurring within population. Fulani and Shika Brown had the least (0.000) genetic distance. Tajima’s D was negative among populations and within Noiler, Kuroiler, Sasso and Fulani populations but was only statistically significant within the Noiler population. Diversity indices of this study revealed that mtDNA polymorphism was on the average both within populations and among populations. The results indicate the existence of two distinct maternal lineages from Southeast Asia, south central and Southeast China evenly distributed among the iTABs. The average genetic diversity observed within population can be utilized for the long-term genetic improvement and stabilization of the breeds.

Genetic diversity of Banat Naked Neck, indigenous chicken breed from Serbia, inferred from mitochondrial DNA D-loop sequence and microsatellite markers

Banat Naked Neck is the most important indigenous breed of chickens in Serbia. Marginalized until recently, it is becoming increasingly popular due to its adaptability and good productivity in alternative production systems. However, its history and the current breeding model pose challenges for breed preservation and future improvement. This study aimed to assess the genetic diversity and structure of four subpopulations of Banat Naked Neck from different districts in Serbia (West Backa, North Banat, South Banat and Kolubara) using D-loop mitochondrial DNA sequences and a set of 30 microsatellite markers. Seven haplotypes in the phylogenetic analysis of D-loop mitochondrial DNA suggested maternal origin related to the Indian subcontinent, while haplotype and nucleotide diversity averaged 0.731 ± 0.053 and 0.0067 ± 0.0018, respectively. Microsatellite genotyping showed an average detected number of alleles per locus of 5.129 ± 0.237, while the observed and expected heterozygosity averaged 0.560 ± 0.018 and 0.631 ± 0.014, respectively. Genetic differentiation estimated through FST was 0.051 (p < .001). Two clusters in STRUCTURE analysis showed possible separation of two older subpopulations (South Banat and Kolubara) from the two more recent ones (West Backa and North Banat). This first comprehensive study of genetic diversity serves as the basis for future preservation, use and improvement of the Banat Naked Neck breed.

Phylogenetic Analysis of Philippine Native Pigs (Sus scrofa L.) from Batanes, Quezon, and Marinduque Based on Mitochondrial DNA D-loop Markers

By analyzing the mitochondrial DNA (mtDNA) displacement loop (D-loop) region, we aimed to assess the genetic diversity of Philippine native pigs from Batanes, Quezon, and Marinduque and to determine the phylogenetic relationship between these subpopulations and other Asian and European pig breeds. Ear tissue samples were collected from the native pigs in Batanes (n = 17), Quezon (n = 37), and Marinduque (n = 40). Genomic DNA was extracted, and the D-loop sequences were amplified by PCR. The D-loop sequences of 94 Philippine samples were initially analyzed using the Kimura 2-parameter model and neighbor-joining method in MEGA7, identifying a total of 17 haplotypes designated as H1–H17. Notably, only eight haplotypes were specific to individuals coming from a particular province, whereas the remaining haplotypes were detected in samples from different provinces. Additional qualitative trait analysis that the majority of Philippine native pigs had black coat color, a plain coat pattern, short cylindrical snouts, straight head profiles, erect and forward-oriented ears, curly tails, and straight backlines. Phylogenetic analysis of the Philippine samples and 16 exotic pig breeds revealed that Philippine native pigs with H1 and H2 haplotypes formed a distinct clade with Taiwanese Type I Lanyu pig, whereas those with H3–H17 haplotypes clustered with other Asian and European pigs. Therefore, our findings suggest a close and unique relationship between Taiwanese Type I Lanyu and Philippine native pigs. The presence of several haplotypes also implies high genetic variation among Philippine native pigs. Specifically, the native pigs from Quezon and Marinduque are the most closely related, whereas those from Quezon and Batanes are the least closely related.

Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boars.

The Philippine archipelago was believed to have never been connected to the Asian continent even during the severe Quaternary sea-level drops. As a result, the history of domestic pig (Sus scrofa) dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine domestic pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boar corresponding to their geographic origin. The results revealed considerable genetic diversity (0.900±0.016) and widespread Asian pig-ancestry (94.60%) in the phylogenetic analysis, with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine domestic pigs corroborates our hypothesis of a genetic signal that may be associated with the recently reported multiple waves of human migrations to the Philippines. The Haplogroup D7, reported to occur only in Indo-Burma Biodiversity Hotspots, included a high frequency of Philippine domestic pig haplotypes (54.08%), which poses an interesting challenge because its distribution is not consistent with the hypothesized migration route of Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes (Asian major) on several Philippine islands. The analyses of mismatch distribution and neutrality test were consistent with the Bayesian skyline plot which showed a long stationary period of effective population size. The population decline was consistent with the pronounced population bottleneck in Asian and European pigs during the interglacial periods of the Pleistocene. The results of this study will support the conservation strategies and improvements of economically important genetic resources in the Philippines.

Endometrioid Cancer Associated With Endometriosis: From the Seed and Soil Theory to Clinical Practice.

Endometriosis is a benign condition characterized by the presence of ectopic endometrial tissue. It is still debated whether endometriosis is a disease that can predispose to the pathogenesis of endometrial cancer outside the uterus. Deficiencies in mismatch repair (MMR) genes are a known risk factor for developing endometrioid cancer. Starting from two cases of patients with abnormal MMR endometrioid carcinoma of the uterus and synchronous endometrioid carcinoma in non-ovarian and ovarian endometriosis, we performed a somatic mutation profile and phylogenetic analysis of the lesions in order to identify if they were metastasis or primary de novo tumors. In the first case, we identified de novo activating mutations in PIK3CA and KRAS in endometrioid cancer lesions but not in endometriosis. Although the acquisition of a de novo mutation in ESR1 and a decrease in mutant allele fraction (MAF) from the endometrial tumor to the localizations in the endometriosis lesions, the clonal relationship was confirmed by the limited number of heteroplasmic mutations in D-loop mitochondrial DNA region. In the other case, the clonal behavior was demonstrated by the overlap of MAF at each site. Our data support the hypothesis of a retrograde dissemination of tumor cells, moving from the primary carcinoma in the endometrium to ectopic sites of endometriosis where localizations of tumor arise.

Alcohol exacerbated biochemical and biophysical alterations in liver mitochondrial membrane of diabetic male wistar rats – A possible amelioration by green tea

Alcohol exacerbated biochemical and biophysical alterations in liver mitochondrial membrane of diabetic male wistar rats – A possible amelioration by green tea

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.

Genetic diversity in mitochondrial DNA D-loop region of indigenous pig breeds of India

India is home for at least 18 indigenous pig breeds; however, the genetic diversity of Indian pig, Sus scrofa domesticus, population is poorly known. Here, the hypervariable region (HVR) of mitochondrial DNA D-loop (~487 bp) of 214 pigs representing five indigenous and three exotic breeds was sequenced and analysed with reference sequences from other countries. A total of 54 segregating sites among the sequences revealed 56 different haplotypes. Two, 11, eight, seven and six haplotypes were identified with some haplotype sharing in indigenous breeds: Doom, Ghungroo, Mali, Niang-Megha and Tenyi-Vo, respectively. Population pairwise differences (PhiST) (0.409) were found significant (P<0.001), and variance within breeds (59.1%) was more than that of among breeds (40.9%). Similar topology was noted in phylogeny and median-joining network. Indian domestic pigs from this study were found to possess unique and highly differentiated haplotypes on network analysis. The diverse haplotypes and phylogenetic lineages identified here is the first report on Indian pig breeds that need to be further explored by complete mitochondrial DNA sequencing and analysis. These findings provide indicative insights for conservation and optimum utilization of the porcine genetic resources.

Genetic diversity and selection in Puerto Rican horses

Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the “Criollo”) horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the “gait-keeper” DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the “gait-keeper” DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant “gait-keeper” allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.

Decreased mitochondrial D-loop region methylation mediates an increase in mitochondrial DNA copy number in CADASIL

BackgroundCerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a typical neurodegenerative disease associated with mitochondrial dysfunction. Methylation of the D-loop region and mitochondrial DNA copy number (mtDNAcn) play a critical role in the maintenance of mitochondrial function. However, the association between D-loop region methylation, mtDNAcn and CADASIL remains unclear.MethodsOverall, 162 individuals were recruited, including 66 CADASIL patients and 96 age- and sex-matched controls. After extracting genomic DNA from the peripheral white blood cells, levels of D-loop methylation and mtDNAcn were assessed using MethylTarget sequencing and real-time PCR, respectively.ResultsWe observed increased mtDNAcn and decreased D-loop methylation levels in CADASIL patients compared to the control group, regardless of gender stratification. Besides, we found a negative correlation between D-loop methylation levels and mtDNAcn. Mediation effect analysis shows that the proportion of the association between mtDNAcn and CADASIL that is mediated by D-loop methylation is 11.6% (95% CI 5.6, 22.6). After gender stratification, the proportions of such associations that are mediated by D-loop methylation in males and females were 7.2% (95% CI 2.4, 19.8) and 22.0% (95% CI 7.4, 50.1), respectively.ConclusionDecreased methylation of the D-loop region mediates increased mtDNAcn in CADASIL, which may be caused by a compensatory mechanism of mitochondrial dysfunction in patients with CADASIL.

Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia.

Red junglefowl (RJF) is considered the ancestor of domestic chickens. However, the possible maternal origin, genetic diversity, and subspecies classification of the Philippine (PH) RJF remains uncertain. In this study, the complete mitochondrial DNA (mtDNA) D-loop sequence of 55 PH RJFs collected from the mountainous areas of Occidental Mindoro, Palawan, Agusan del Norte, Capiz, Leyte, Iloilo, and Guimaras were analyzed and compared with chicken reference sequences. Phylogenetic analysis revealed multiple maternal origins of the PH RJFs based on haplogroups D, E, and Y classification. This was supported by PH RJFs and RJFs from other Asian countries sharing a clade. A median-joining network also revealed the haplotype sharing of the PH RJFs and Indonesian RJF, demonstrating common maternal ancestry. High haplotype and nucleotide diversity were also observed at all sampling sites. Analysis of molecular variance indicated that the principal molecular variance existed within populations (81.23%) rather than among populations (18.77%). A population neutrality test and Bayesian skyline plot (BSP) analysis elucidated the RJF maternal effective population size expansion in the Philippines that possibly started approximately 2,800-3,000 years ago. The co-existence of Gallus gallus bankiva and Gallus gallus gallus in the Philippines was also verified. The haplotype sharing of the current RJF samples with commercial chickens suggested the need to formulate conservation programs that would protect the RJFs in the Philippines.

External Morphological and Molecular Evidence of Natural Intrageneric Hybridization between Common and Indo-Pacific Bottlenose Dolphins (Tursiops truncatus × T. aduncus) from Japanese Waters

Hybrid cetaceans occur in both captive and natural environments. This study is the first to describe the external morphological and genetic characterizations of natural intrageneric hybridization between the common bottlenose dolphin, Tursiops truncatus, and the Indo-Pacific bottlenose dolphin, T. aduncus, in Japanese waters. In November 2019, a stray dolphin was seen in Moriura Bay, Wakayama, Japan, and was a male that measured 241.5 cm in body length in July 2020, after an incidental catch in February 2020. Moderate speckles in the genital area of the dolphin were observed, which is a characteristic of T. aduncus. The dolphin had 22–23 pairs of teeth in each jaw, a quantity consistent for both species. The length of the rostrum and the size of flippers were within the range of T. aduncus. The mitochondrial DNA D-loop region haplotype was 99% homology with those from T. aduncus found in Chinese and Japanese waters. Microsatellite analysis revealed that the dolphin contained ratios of approximately 50% of both T. truncatus and T. aduncus lineages; the dolphin could therefore be an F1 hybrid between a female T. aduncus and a male T. truncatus. Further genetic studies are required to elucidate the origin of this hybrid dolphin.

DNA marking of the rate of maturation of gonads in female sterlet x beluga (A. ruthenus x H. huso) hybrid under conditions of recirculation systems

To create a theoretical basis for the development of new technologies for the formation of highly productive sturgeon herds, work has begun on conducting research on DNA - markers associated with economically useful traits. At the first stage of the work, polymorphic regions of the mitochondrial DNA (mtDNA) D-loop were investigated in order to search for promising molecular genetic markers associated with the production properties of sturgeon hybrids. Along with point polymorphisms in mtDNA hybrids, variability in the length of the D-loop was observed, as well as the presence of heteroplasmy in length. The length variability of the D-loop is due to the presence of tandem repeating units in multiples of 80 base pairs (bp). Using Fisher’s exact test, it was shown that the proportion of individuals with four tandem repeating units of 80 bp eachsignificantly higher (p = 0.030) in the group of highly productive hybrids. The obtained data suggest that such a trait as the accelerated maturation of female hybrids (A. ruthenus x H. huso) grown in a closed water supply can be associated with the mitochondrial DNA haplotype, in the D-loop of which there are fourrepeating units.

A Matrilineal Study on the Origin and Genetic Relations of the Ecuadorian Pillareño Creole Pig Population through D-Loop Mitochondrial DNA Analysis.

Simple SummaryMitochondrial DNA (mtDNA) analysis is a tool in assessing the maternal origin, phylogeny, and population structure of domestic animals. The Ecuadorian Pillareño Creole pig is a creole breed that comes from the descendants of Iberian pig introduced to Ecuador by the Spanish conquerors. This creole population represents important reservoirs of genetic diversity that are very essential to preserve; however, the introduction of new breeds of pigs has displaced this creole pig from Ecuador to the background. The objective of the mitochondrial DNA analysis was to identify the Ecuadorian Pillareño Creole pig populations, their origins, and their maternal lines. For this study, DNA samples from 34 Ecuadorian Pillareño Creole pigs were used, with the animals belonging to seven rural regions of Ecuador. The haplogroup network suggested that the Pillareño creole pig population can be grouped into a single haplotype and that it belongs to the European pig clades. The genetic relationship between the Ecuadorian Pillareño Creole and the European pigs, particularly the Iberian pigs from Spain, can be used to establish of an official breeding program for the conservation and valuation of these creole populations, with this genetic mitochondrial analysis potentially providing a better approach for the rescue of the Ecuadorian Pillareño Creole pig populations.Domestic pig breeds reached America on the second Columbus trip; from this date, Iberian pig genetic resources were disseminated throughout the continent, forming diverse creole breeds. These Ecuadorian Creole pigs are important for food production but have been genetically eroded since the introduction of transboundary breeds. In this study, we sought to characterize this erosion more thoroughly through mitochondrial DNA D-Loop analysis of Ecuadorian Pillareño Creole pigs from seven regions of Ecuador. To allow comparison, we also included in our analysis sequences from wild species, commercial lines, and domestic pigs, which were obtained from the NCBI GenBank database. Creole pigs’ population showed overall moderate Hd values and low π values, and a negative value of Tajima’s D was observed. The greatest differentiation from the Ecuadorian Pillareño Creole pigs was observed between Asian wild and Asian domestic pigs. The haplotype analysis revealed three different phylogenetic clades (A, E I, and E II) and 65 haplotypes. Ecuadorian Creole populations were grouped into nine haplotypes for Clade E I and E II, which have not previously been reported for Creole Pillareño populations. Our analysis indicates that in the establishment of Creole Pillareño pigs, individuals most likely separated from the Asian pig population and appear to be genetically influenced by European and Iberian populations raised in Spain.