Nucleotide diversity and demographic history of Pinus bungeana , an endangered conifer species endemic in China

2019 ◽  
Vol 58 (3) ◽  
pp. 282-294
Author(s):  
Yi‐Xin Yang ◽  
Li‐Qiang Zhi ◽  
Yun Jia ◽  
Qiu‐Yi Zhong ◽  
Zhan‐Lin Liu ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Demographic History ◽  
Conifer Species ◽  
History Of ◽  
Pinus Bungeana

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

scholarly journals Multilocus Patterns of Nucleotide Diversity, Linkage Disequilibrium and Demographic History of Norway Spruce [Picea abies(L.) Karst]

Genetics ◽  
2006 ◽  
Vol 174 (4) ◽  
pp. 2095-2105 ◽  
Author(s):  
Myriam Heuertz ◽  
Emanuele De Paoli ◽  
Thomas Källman ◽  
Hanna Larsson ◽  
Irena Jurman ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Picea Abies ◽  
Norway Spruce ◽  
Nucleotide Diversity ◽  
Demographic History ◽  
History Of

Nucleotide polymorphism and phylogeographic history of an endangered conifer species Pinus bungeana

2016 ◽  
Vol 64 ◽  
pp. 89-96 ◽  
Author(s):  
Yi-Xin Yang ◽  
Ma-Li Wang ◽  
Zhan-Lin Liu ◽  
Juan Zhu ◽  
Meng-Ying Yan ◽  
...  
Keyword(s):  
Nucleotide Polymorphism ◽  
Conifer Species ◽  
Phylogeographic History ◽  
History Of ◽  
Pinus Bungeana

scholarly journals Corrigendum to: Demographic history of the human commensal Drosophila melanogaster

2021 ◽  
Vol 13 (3) ◽  
Author(s):  
J Roman Arguello ◽  
Stefan Laurent ◽  
Andrew G Clark
Keyword(s):  
Drosophila Melanogaster ◽  
Demographic History ◽  
History Of

scholarly journals Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 155 (2) ◽  
pp. 863-872 ◽  
Author(s):  
Helmi Kuittinen ◽  
Montserrat Aguadé
Keyword(s):  
Nucleotide Diversity ◽  
Direct Relationship ◽  
Selective Sweep ◽  
Balancing Selection ◽  
Neutral Theory ◽  
Low Frequency ◽  
The Other ◽  
Nucleotide Variation ◽  
Rapid Population Growth ◽  
History Of

AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

scholarly journals Reference genome and demographic history of the most endangered marine mammal, the vaquita

2020 ◽  
Author(s):  
Phillip A. Morin ◽  
Frederick I. Archer ◽  
Catherine D. Avila ◽  
Jennifer R. Balacco ◽  
Yury V. Bukhman ◽  
...  
Keyword(s):  
Marine Mammal ◽  
Reference Genome ◽  
Demographic History ◽  
History Of

scholarly journals Temporal fluctuations of Y-chromosomal variation in Bos taurus

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Demographic History ◽  
Northern Europe ◽  
Chromosomal Gene ◽  
Chromosomal Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Domestic Species ◽  
History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

Dialect contact and phonological reallocation: “Canadian Raising” in the English Fens

1997 ◽  
Vol 26 (1) ◽  
pp. 15-46 ◽  
Author(s):  
David Britain
Keyword(s):  
Social Networks ◽  
Demographic History ◽  
Structuration Theory ◽  
Compelling Evidence ◽  
Dialect Contact ◽  
British English ◽  
Speech Communities ◽  
Allophonic Variation ◽  
History Of ◽  
Local Variable

ABSTRACTThis article reports on research carried out in the Fens in Eastern England, a region noted in the dialectological literature as the site of a number of important phonological transitions, most notably [] and [a – a:], which separate northern and southern varieties of British English. Recordings of 81 speakers from across the Fens were analyzed for the use of (ai), a particularly salient local variable. A “Canadian Raising” type of allophonic variation was found in the central Fenland: speakers in this area used raised onsets of (ai) before voiceless consonants but open onsets before voiced consonants, morpheme boundaries, and //. The article weighs a number of possible explanations for the emergence of this variation in the Fens. Based on compelling evidence from the demographic history of the area, it supports a view that such an allophonic distribution, previously thought not to be found in Britain, emerged as the result of dialect contact. The sociolinguistic process of koinéization that is commonly associated with post-contact speech communities (Trudgill 1986) is held responsible for the focusing of this allophonic variation from the input dialects of an initially mixed variety. The article concludes by suggesting a socially based explanatory model to account for the way that speakers implement processes of focusing and koinéization in areas of dialect contact. [English, dialects, contact, koiné, geographical linguistics, social networks, structuration theory)

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