Analysis Of Mitochondrial DNA Control Region Research Articles

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.

Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy

Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Europe, the S. trutta complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the S. trutta complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term Salmo macrostigma should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena.

Population genetics and taxonomic signatures of wild Tilapia in Japan based on mitochondrial DNA control region analysis

Non-native tilapia species were repeatedly introduced to Asian and South American countries because of their adaptiveness to new environments and new environmental conditions. Such founder populations rapidly adapted by evolving outstanding ecological and physiological features, making them highly successful invaders throughout the tropical and subtropical regions. In Japan, nine tilapia species were introduced. In recent years, several established populations were introgressed by accidental release of aquaculture strains of Oreochromis niloticus, causing reductions in population sizes, genetic diversity, and genetic perturbation upon introgressive hybridization. This study aimed to assess the levels of genetic integrity, genetic population structure, and biogeographic relationships of wild tilapia species found in Japan. Phylogenetic and phylogeographic analysis based on mtDNA control region sequences yielded 52 distinct haplotypes, indicating significant differences in genetic variability among the analyzed populations. Analysis of molecular variance showed high levels of variation within populations, except for tilapia species representing reproductively incompatible taxonomic units to O. niloticus aquaculture stains. Overall, a significant genetic structure emerged among the 11 populations analyzed. Our results indicated that accidental release of O. niloticus via aquaculture contributed significantly to the current genetic differentiation among populations within a few generations, showing clear signals of mtDNA introgression across species boundaries.

Genetic Differentiation of the Steppe Field Mouse Sylvaemus witherbyi Populations: The Results of the Mitochondrial DNA Control Region Analysis.

The degree of genetic diversity of the steppe field mouse was estimated on the basis of the mtDNA control region variability data. Polymorphism of this mtDNA marker in S. witherbyi was more pronounced than previously assumed. The steppe field mouse population from the northern shore of Lake Manych-Gudilo includes several mitochondrial lines, which may be due to the existence of several migration flows to this area from Southwest Asia.

Two ovine mitochondrial DNAs harboring a fifth 75/76 bp repeat motif without altered gene expression in Northern Spain.

The Basque Country is home to the Latxa sheep breed, which is divided in several varieties such as Latxa Black Face (LBKF) and Latxa Blonde Face (LBLF). Mitochondrial DNA control region analysis of 174 male sheep (97 LBKF and 77 LBLF) was performed with the objective of characterizing the maternal lineages of these two varieties that are the basis to produce the cheese with Idiazabal quality label. The percentage of unique haplotypes was 77.32% in LBKF and 67.53% in LBLF. Most of the individuals were classified into B haplogroup (98.85%), while A haplogroup was much less frequent. Two Latxa individuals (one LBKF and one LBLF), both belonging to B haplogroup, displayed an additional 75/76 bp tandem repeat motif. Only 33 other sequences with this repeat motif were found among 11 061 sheep sequences included in the GenBank database. Gene expression was analyzed in peripheral blood leukocytes since the additional 75/76 bp repeat motif falls within ETAS1, a domain with a possible function in regulation of replication and transcription. The mRNA expression from four mitochondrial genes (COI, cyt b, ND1, and ND2) was analyzed in the two individuals of this study with a fifth repeat motif and in four without it. Although lower transcription was observed when the additional 75/76 bp repeat motif was present, no statistically significant differences were observed. Therefore, the variation in the number of the 75/76 repeat motif does not seem to modify the gene expression rate in mitochondrial genes.

Research Article Mitochondrial DNA control region analysis of three ethnic populations in lower Northern part of Thailand.

The lower northern part of Thailand contains various genetically diverse ethnic populations. The sequences of the mitochondrial DNA hypervariable region were studied in three ethnic populations inhabiting Phitsanulok Province. One hundred and nine nucleotide sequences - 53, 29, and 27 from Hmongs (Hill tribe), Lao Songs, and Thai-Siams, respectively - were collected. The haplotypes were generated from 1130 nucleotides of the entire control region. Eighty-six haplotypes were found in the three ethnic populations, and no shared haplotypes were found between populations. Point heteroplasmy was noted at position 311 (C→Y). Haplotypes with ACAC-insertion at position 512 were observed in immigrant individuals from the Lao Song population. The Thai-Siam population showed higher genetic diversity than the other populations. The Hmong and Lao Song populations showed less genetic diversity than those living in their original area. The neutrality testing suggested that the result might be influenced by genetic drift.

Genetic structure and differentiation of the fire salamander Salamandra salamandra at the northern margin of its range in the Carpathians

Amphibian populations occurring at the margin of the species range exhibit lower genetic variation due to strong genetic drift and long-term isolation. Limited mobility and site fidelity together with habitat changes may accelerate genetic processes leading to local extinction. Here, we analyze genetic variation of the fire salamander subspeciesSalamandra s. salamandrainhabiting the Outer Carpathian region in Poland, at the northern border of its distribution. Nuclear DNA polymorphism based on 10 microsatellite loci of 380 individuals sampled in 11 populations were analysed to measure gene flow between subpopulations and possible long-term isolation. Mitochondrial DNA control region analysis among 17 individuals representing 13 localities was used to detect the origin of populations which colonized Northern Europe after the last glaciation. Overall, pairwise FST’s and AMOVA test of ‘among group’ variation showed little differences in the allele frequencies and relatively high local gene flow. However, Bayesian clustering results revealed subtle structuring between eastern and western part of the studied region. Two extreme marginal populations from the Carpathian Piedmont revealed reduced genetic variation which may be attributed to strong influence of genetic drift. Only one mitochondrial DNA haplotype (type IIb) was found in all individuals and suggest that after the Last Glacial MaximumSalamandra salamandramigrated to the North-Western Europe from the single glacial refugium placed in the Balkan Peninsula.

Mitochondrial DNA control region analysis of three ethnic groups in the Republic of Macedonia.

A total of 444 individuals representing three ethnic groups (Albanians, Turks and Romanies) in the Republic of Macedonia were sequenced in the mitochondrial control region. The mtDNA haplogroup composition differed between the three groups. Our results showed relatively high frequencies of haplogroup H12 in Albanians (8.8%) and less in Turks (3.3%), while haplogroups M5a1 and H7a1a were dominant in Romanies (13.7% and 10.3%, respectively) but rare in the former two. This highlights the importance of regional sampling for forensic mtDNA databasing purposes. These population data will be available on EMPOP under accession numbers EMP00644 (Albanians), EMP00645 (Romanies) and EMP00646 (Turks).

동해 강도다리(Platichthys stellatus) 2개체군의 형태 및 분자변이

Morphological and genetic variation of two populations of Platichthys stellatus were investigated based on 30 individuals each, collected from Uljin (seedling release area) and Pohang (control) in Korea. Morphological analyses demonstrated that the two populations of P. stellatus were well distinguishable in body color of the blind side and fin shape. Mitochondrial DNA control region analysis indicated no significant differences between the two populations (<TEX>$F_{ST}=-0.00849$</TEX>, P>0.05). We also analyzed microsatellite DNA loci of the two populations using six markers. Observed heterozygosity (<TEX>$H_O$</TEX>) and expected heterozygosity (<TEX>$H_E$</TEX>) were 0.550 and 0.592, respectively, in P. stellatus from Uljin, but 0.700 and 0.737 in P. stellatus from Pohang. An index of differentiation in genetic structure revealed significant differences between the two populations (<TEX>$F_{ST}=0.0208$</TEX>, P<0.05). Our results suggest that the Uljin population may be comprised of released P. stellatus, whereas the Pohang population may be wild P. stellatus, highlighting the necessity of continuous monitoring of the two populations.

Phylogeographic study of brown trout from Serbia, based on mitochondrial DNA control region analysis

In order to illuminate the phylogeography of brown trout (Salmo trutta) populations in the Balkan state of Serbia, the 561 bp 5'-end of mtDNA control region of 101 individuals originating from upland tributaries of the Danubian, Aegean and Adriatic drainages were sequenced and compared to corresponding brown trout sequences obtained in previous studies. Among 15 haplotypes found, 14 were considered native, representing the Danubian and Adriatic lineages of the brown trout, while one haplotype (ATcs1), found only in two individuals originating from two stocked rivers, corresponded to the Atlantic lineage and was considered introduced. Native haplotypes exhibited a strong geographic pattern of distribution: the Danubian haplotypes were strictly confined to the Danubian drainage, while the Adriatic haplotypes dominated in the Aegean and Adriatic drainages; most of the total molecular variance (69%) was attributed to differences among the drainages. Phylogenetic reconstruction, supplemented with seven haplotypes newly described in this study, suggested a sister position of the Atlantic-Danubian and Adriatic-Mediterranean-marmoratus ("southern") phylogenetic group, and pointed to the existence of a distinct clade, detected within the "southern" group. The data obtained confirmed our expectation of the existence of high genetic diversity in Balkan trout populations, and we recommend more widespread surveys covering trout stocks from the region.

Phylogeographic study of brown trout from Serbia, based on mitochondrial DNA control region analysis

Phylogeographic study of brown trout from Serbia, based on mitochondrial DNA control region analysis

Genetic Variation of the MHCDQBLocus in the Finless Porpoise (Neophocaena phocaenoides)

The Major Histocompatibility Complex (MHC) is a large multigene coding for glycoproteins that play a key role in the initiation of immune responses in vertebrates. The exon 2 region of the MHC DQB locus was analyzed using 160 finless porpoises from 5 populations in Japanese waters. The 5 populations were based on a previous mitochondrial DNA control region analysis, which showed distinct geographical separation. Eight DQB alleles were detected, and the geographical distribution of the alleles indicated that most of them are shared among the populations. Heterozygosity of the DQB alleles in each population ranged from 0.55 to 0.78, and for all 5 populations was 0.78. Low MHC variability is not a common feature in marine mammals, but the finless porpoise populations inhabiting coastal waters had a relatively high MHC heterozygosity. Balancing selection in the MHC DQB alleles of the finless porpoise was indicated by the higher rate of nonsynonymous than synonymous substitutions for PBR; however, an excess of hetrozygotes compared to expectation was not observed. This suggests that the MHC DQB locus in the finless porpoise may have been under balancing selection for a long evolutionary time period, and is influenced by genetic drift beyond the effect of balancing selection for short time periods in small local populations.