scholarly journals Mitochondrial DNA D-Loop Diversity of the Helmeted Guinea Fowls in Kenya and Its Implications on HSP70 Gene Functional Polymorphism

2018 ◽  
Vol 2018 ◽  
pp. 1-12
Author(s):  
Philip Murunga ◽  
Grace Moraa Kennedy ◽  
Titus Imboma ◽  
Phillista Malaki ◽  
Daniel Kariuki ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Wild Population ◽  
Profile Analysis ◽  
Demographic History ◽  
Genetic Profile ◽  
Hsp70 Gene ◽  
Functional Polymorphisms ◽  
Mtdna Haplotypes ◽  
D Loop

We analyzed variations in 90 mitochondrial DNA (mtDNA) D-loop and heat shock protein 70 (HSP70) gene sequences from four populations of domesticated helmeted Guinea fowls (70 individuals) and 1 population of wild helmeted Guinea fowls (20 individuals) in Kenya in order to get information about their origin, genetic diversity, and traits associated with heat stress. 90 sequences were assigned to 25 distinct mtDNA and 4 HSP70 haplotypes. Most mtDNA haplotypes of the domesticated helmeted Guinea fowls were grouped into two main haplogroups, HgA and HgB. The wild population grouped into distinct mtDNA haplogroups. Two mtDNA haplotypes dominated across all populations of domesticated helmeted Guinea fowls: Hap2 and Hap4, while the dominant HSP70 haplotype found in all populations was CGC. Higher haplotype diversities were generally observed. The HSP70 haplotype diversities were low across all populations. The nucleotide diversity values for both mtDNA and HSP70 were generally low. Most mtDNA genetic variations occurred among populations for the three hierarchical categories considered while most variations in the HSP70 gene occurred among individuals within population. The lack of population structure among the domestic populations could suggest intensive genetic intermixing. The differentiation of the wild population may be due to a clearly distinct demographic history that shaped its genetic profile. Analysis of the Kenyan Guinea fowl population structure and history based on mtDNA D-loop variations and HSP70 gene functional polymorphisms complimented by archaeological and linguistic insight supports the hypothesis that most domesticated helmeted Guinea fowls in Kenya are related to the West African domesticated helmeted Guinea fowls. We recommend more molecular studies on this emerging poultry species with potential for poverty alleviation and food security against a backdrop of climate change in Africa.

scholarly journals Population structure and demographic history of Pacific herring Clupea pallasii around Japan inferred from mitochondrial DNA sequences

2017 ◽  
Vol 83 (2) ◽  
pp. 163-173 ◽  
Author(s):  
TOMONARI FUJITA ◽  
SHUICHI KITADA ◽  
YASUKO HARADA ◽  
YUKINO ISHIDA ◽  
SHOKO SANO ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Dna Sequences ◽  
Demographic History ◽  
Pacific Herring ◽  
Clupea Pallasii ◽  
History Of

scholarly journals Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9679
Author(s):  
Noorhani Syahida Kasim ◽  
Tun Nurul Aimi Mat Jaafar ◽  
Rumeaida Mat Piah ◽  
Wahidah Mohd Arshaad ◽  
Siti Azizah Mohd Nor ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Pacific Ocean ◽  
Goodness Of Fit ◽  
Demographic History ◽  
Population Expansion ◽  
Seasonal Migration ◽  
Likelihood Method ◽  
Recent Population Expansion ◽  
D Loop ◽  
Longtail Tuna

The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989–1.000; ND5 = 0.848–0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019–0.025; ND5 = 0.0017–0.003), “star-like” haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.

scholarly journals Mitochondrial Diversity of the East Balkan Swine (Sus scrofa f. domestica) in South-Eastern Bulgaria

2019 ◽  
Vol 69 (2) ◽  
pp. 229-236
Author(s):  
Nadezhda Palova ◽  
Iskra Yankova ◽  
Boyko Neov ◽  
Peter Hristov ◽  
Georgi Radoslavov
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Sus Scrofa ◽  
Genetic Profile ◽  
Scientific Center ◽  
Equal Distribution ◽  
Loop Region ◽  
D Loop ◽  
Purposeful Selection ◽  
Balkan Mountains

Abstract The East Balkan Swine (EBS) is the only preserved local swine breed in Bulgaria and one of the few indigenous pig breeds in Europe. The EBS is distributed in the region of Eastern Balkan Mountains and the Strandja Mountain. To reveal the breed’s genetic profile, we analyzed 50 purebred individuals according to mitochondrial DNA (D-loop region, HVR1) and sequence analysis in the Scientific Center of Agriculture (Sredets region) in the country. The obtained results show the presence of four haplotypes: three Asian specific haplotypes (H1, H2, and H3) and the European specific E1a1. The haplotypes H2 (6 %) and H3 (2 %) were newly described and were branched from the basic clade H1 (90 %). All haplotypes belong to the Asiatic clade A (98 %), except one sample assigned to the European haplogroup E1 (2 %) in contrast to samples from East North Bulgaria where Asiatic and Europen clades were with almost equal distribution. The coexistence of two mtDNA clades in EBS in Bulgaria may be related to the source of the pig populations and/or the historical crossbreeding with imported pigs. In conclusion, due to its native origin, the East Balkan Swine may be the only possible option for a solution to the exhaustion of the beneficial genetic variation of available cultural breeds. With its participation, high-productive populations can be restored and established after a long and purposeful selection.

scholarly journals Mitochondrial DNA variation and phylogeography of native Mongolian goats

2020 ◽  
Vol 33 (6) ◽  
pp. 902-912 ◽  
Author(s):  
Onolragchaa Ganbold ◽  
Seung-Hwan Lee ◽  
Woon Kee Paek ◽  
Munkhbaatar Munkhbayar ◽  
Dongwon Seo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Nucleotide Diversity ◽  
Demographic History ◽  
Hypervariable Region ◽  
Dna Variation ◽  
Hypervariable Region 1 ◽  
Phylogenetic Status

Objective: Mongolia is one of a few countries that supports over 25 million goats, but genetic diversity, demographic history, and the origin of goat populations in Mongolia have not been well studied. This study was conducted to assess the genetic diversity, phylogenetic status and population structure of Mongolian native goats, as well as to discuss their origin together with other foreign breeds from different countries using hypervariable region 1 (HV1) in mtDNA.Methods: In this study, we examined the genetic diversity and phylogenetic status of Mongolian native goat populations using a 452 base-pair long fragment of HVI of mitochondrial DNA from 174 individuals representing 12 populations. In addition, 329 previously published reference sequences from different regions were included in our phylogenetic analyses.Results: Investigated native Mongolian goats displayed relatively high genetic diversities. After sequencing, we found a total of 109 polymorphic sites that defined 137 haplotypes among investigated populations. Of these, haplotype and nucleotide diversities of Mongolian goats were calculated as 0.997±0.001 and 0.0283±0.002, respectively. These haplotypes clearly clustered into four haplogroups (A, B, C, and D), with the predominance of haplogroup A (90.8%). Estimates of pairwise differences (Fst) and the analysis of molecular variance values among goat populations in Mongolia showed low genetic differentiation and weak geographical structure. In addition, Kazakh, Chinese (from Huanghuai and Leizhou), and Arabian (Turkish and Baladi breeds) goats had smaller genetic differentiation compared to Mongolian goats.Conclusion: In summary, we report novel information regarding genetic diversity, population structure, and origin of Mongolian goats. The findings obtained from this study reveal that abundant haplogroups (A to D) occur in goat populations in Mongolia, with high levels of haplotype and nucleotide diversity.

scholarly journals Population structure and demographic history of Pacific herring Clupea pallasii around Japan inferred from mitochondrial DNA sequences

2018 ◽  
Vol 84 (4) ◽  
pp. 585-585
Author(s):  
TOMONARI FUJITA ◽  
SHUICHI KITADA ◽  
YASUKO HARADA ◽  
YUKINO ISHIDA ◽  
SHOKO SANO ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Dna Sequences ◽  
Demographic History ◽  
Pacific Herring ◽  
Clupea Pallasii ◽  
History Of
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