scholarly journals Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

2019 ◽  
Vol 10 ◽  
Author(s):  
Xin-Hui Wang ◽  
Jie Li ◽  
Li-Min Zhang ◽  
Zi-Wen He ◽  
Qi-Ming Mei ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
South China ◽  
Dna Sequences ◽  
Population Differentiation ◽  
Demographic History ◽  
History Of

scholarly journals A genome epidemiological study of mycobacterium tuberculosis in subpopulations with high and low incidence rate in Guangxi, South China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dingwen Lin ◽  
Junning Wang ◽  
Zhezhe Cui ◽  
Jing Ou ◽  
Liwen Huang ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Incidence Rate ◽  
South China ◽  
Demographic History ◽  
Lineage Differentiation ◽  
A Genome ◽  
High Incidence ◽  
History Of ◽  
Lineage 2 ◽  
Low Incidence

Abstract Background Tuberculosis (TB) is caused by a bacterium called Mycobacterium tuberculosis (Mtb). China is the third in top 8 high TB burden countries and Guangxi is one of the high incidence areas in South China. Determine bacterial factors that affected TB incidence rate is a step toward Ending the TB epidemic. Results Genomes of M. tuberculosis cultures from a relatively high and low incidence region in Guangxi have been sequenced. 347 of 358(96.9%) were identified as M. tuberculosis. All the strains belong to Lineage 2 and Lineage 4, except for one in Lineage 1. We found that the genetic structure of the M. tuberculosis population in each county varies enormously. Low incidence rate regions have a lower prevalence of Beijing genotypes than other regions. Four isolates which harbored mutT4-48 also had mutT2-58 mutations. It is suggested that strains from the ancestors of modern Beijing lineage is circulating in Guangxi. Strains of modern Beijing lineage (OR=2.04) were more likely to acquire drug resistances than Lineage 4. Most of the lineage differentiation SNPs are related to cell wall biosynthetic pathways. Conclusions These results provided a higher resolution to better understand the history of transmission of M. tuberculosis from/to South China. And the incidence rate of tuberculosis might be affected by bacterial population structure shaped by demographic history. Our findings also support the hypothesis that Modern Beijing lineage originated in South China.

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 Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

2019 ◽  
Vol 125 (1) ◽  
pp. 105-117 ◽  
Author(s):  
Yixuan Kou ◽  
Li Zhang ◽  
Dengmei Fan ◽  
Shanmei Cheng ◽  
Dezhu Li ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Divergence ◽  
Evolutionary History ◽  
Isolation By Distance ◽  
Demographic History ◽  
East China ◽  
Population Divergence ◽  
Isolation By Environment ◽  
Late Neogene ◽  
History Of

Abstract Background and Aims Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). Methods DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). Key Results Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. Conclusions These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.

Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA

2013 ◽  
Vol 16 (2) ◽  
pp. 265-273 ◽  
Author(s):  
J. Zeyland ◽  
Ł. Wolko ◽  
J. Bocianowski ◽  
M. Szalata ◽  
R. Słomski ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Gradual Process ◽  
Mtdna Sequence ◽  
History Of

Abstract Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon- dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.

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