Demographic history of Trinorchestia longiramus (Amphipoda, Talitridae) in South Korea inferred from mitochondrial DNA sequence variation

Crustaceana ◽  
2016 ◽  
Vol 89 (13) ◽  
pp. 1559-1573 ◽  
Author(s):  
Jiyoung Woo ◽  
Hyesuck An ◽  
Byung-Jin Lim ◽  
Ha Yeun Song ◽  
Min-Seop Kim ◽  
...  
Keyword(s):  
Demographic History ◽  
Haplotype Diversity ◽  
Nucleotide Sequence Analysis ◽  
Distribution Analysis ◽  
Demographic Bottleneck ◽  
Dna Sequence Variation ◽  
Mismatch Distribution Analysis ◽  
History Of ◽  
Amova Analysis ◽  
Mitochondrial Cytochrome Oxidase

We investigated the demographic history ofTrinorchestia longiramusJo, 1988 using the nucleotide sequence analysis of the mitochondrial cytochrome oxidase subunit I (COI) gene from 277 individuals collected from eight Korean populations. From the low haplotype diversity and nucleotide diversity in all populations, a neutrality test, and mismatch distribution analysis, the species appears to have recently experienced a prolonged or severe demographic bottleneck. Pairwise populationFSTestimates and AMOVA [= Analysis of Molecular Variance] results showed that substantial differentiation is present between the southern and eastern populations. The population structure ofT. longiramusmay have been influenced by glacial population extinctions and interglacial colonization during the Pleistocene ice-ages.

Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Heliothis Virescens ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Haplotype Network ◽  
Demographic Expansion ◽  
Significant Genetic Structure ◽  
History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation

2019 ◽  
Vol 110 (7) ◽  
pp. 844-856 ◽  
Author(s):  
Chin-Hong Ng ◽  
Soon-Leong Lee ◽  
Lee-Hong Tnah ◽  
Kevin K S Ng ◽  
Chai-Ting Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Gene Diversity ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population History ◽  
Conservation Strategy ◽  
Ex Situ ◽  
History Of ◽  
Shorea Platyclados

Abstract Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.

scholarly journals Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1480
Author(s):  
Adam Abied ◽  
Lei Xu ◽  
Bahlibi W. Sahlu ◽  
Feng Xing ◽  
Abulgasim Ahbara ◽  
...  
Keyword(s):  
Demographic History ◽  
Adaptive Immune Response ◽  
Conservation Strategies ◽  
Distribution Analysis ◽  
Runs Of Homozygosity ◽  
Sheep Breeds ◽  
Indigenous Sheep ◽  
Genome Wide ◽  
History Of ◽  
Genomic Regions

Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (5S_rRNA), the innate and adaptive immune response (HERC2 and CYFIP1), digestion and metabolism (CENPJ), growth (SPP1), body size and developments (GJB2 and GJA3). This study highlighted new insights into the ROH patterns and provides a basis for future breeding and conservation strategies of Chinese sheep breeds.

scholarly journals Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean

ZooKeys ◽  
2019 ◽  
Vol 830 ◽  
pp. 127-144 ◽  
Author(s):  
Lu Liu ◽  
Xiumei Zhang ◽  
Chunhou Li ◽  
Hui Zhang ◽  
Takashi Yanagimoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Fishery Management ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Northwestern Pacific ◽  
Distribution Analysis ◽  
Recent Population Expansion

Sebastiscusmarmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S.marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S.marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S.marmoratus.

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 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 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)

Sign in / Sign up

Export Citation Format

Share Document