MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

Kumar, Sudhir; Tamura, Koichiro; Nei, Masatoshi

doi:10.1093/bib/5.2.150

Cited by 10,725 publications

(7,567 citation statements)

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“…To investigate the relationship between the Edo Ainu and the other populations, neighbor‐joining (NJ) trees based on haplogroup frequency‐based pairwise F st were constructed in the program Mega 7.0.18 (Kumar, Tamura, & Nei, 2004). …”

Section: Methodsmentioning

confidence: 99%

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Adachi

Kakuda

Takahashi

et al. 2017

American J Phys Anthropol

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ObjectivesThe Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern‐day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large‐scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido.Materials and methodsMitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup‐defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations.ResultsOur findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.DiscussionOur results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual‐structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.

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Section: Methodsmentioning

confidence: 99%

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Adachi

Kakuda

Takahashi

et al. 2017

American J Phys Anthropol

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“…We constructed an unrooted neighbor-joining (NJ) tree of all sequences under the Tajima & Nei model using MEGA 4.1 software [14]. …”

Section: Methodsmentioning

confidence: 99%

Revealing fine scale subpopulation structure in the Vietnamese H'mong cattle breed for conservation purposes

Berthouly

Maillard

Doan³

et al. 2010

BMC Genet

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BackgroundDuring the last decades, there has been an acceleration of the loss of domestic animal biodiversity. For conservation purposes, the genetic diversity of the H'Mong cattle, an indigenous local breed was studied. Single-nucleotide polymorphisms (SNP) of the SRY gene and mtDNA D-Loop sequence were analysed to clarify the origin of the breed. The genetic diversity was assessed through genetic data with twenty-five FAO microsatellites, and morphometric data with five body measurements from 408 animals sampled from eight districts of the Ha Giang province.ResultsThe SRY genes were all of the zebu type. Among the 27 mtDNA haplotypes, 12 haplotypes were of the taurine type and the remaining 15 of the zebu type. This indicates female taurine introgression in the zebu H'Mong. The observed and expected heterozygosity ranged from 0.616 to 0.673 and from 0.681 to 0.729 respectively according to district, with low genetic differentiation (FST = 0.0076). Multivariate analysis on morphometric and genetic data shows a separation of districts into two groups following a south-west/north-east cline and admixture analysis confirmed the two clusters, but no differentiation of taurine introgression between clusters was observed. A possible admixture with the Yellow cattle breed from a neighbouring province was suggested through genetic data and householder interviews.ConclusionsIn this study we demonstrate the interest of fine-scale sampling for the study of genetic structure of local breeds. Such a study allows avoiding erroneous conservation policies and on the contrary, proposes measures for conserving and limiting crossbreeding between the H'Mong and the Yellow cattle breeds.

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“…Phylogenetic analysis of the sequences from the partial L gene and the complete N gene was carried out with MEGA 3 program ( 22 ) by using the Kimura 2 parameter model for nucleotides and amino model with Poisson correction for amino acids to calculate distances between sequences with confidence values of 1,000 bootstrapping trials. Phylogenetic trees of the L gene were constructed from TOSV obtained from sandflies and previous STIs and from different phleboviruses.…”

Section: Methodsmentioning

confidence: 99%