scholarly journals Schizophrenia-associated HapICE haplotype is associated with increased NRG1 type III expression and high nucleotide diversity

2012 ◽  
Vol 2 (4) ◽  
pp. e104-e104 ◽  
Author(s):  
C S Weickert ◽  
Y Tiwari ◽  
P R Schofield ◽  
B J Mowry ◽  
J M Fullerton
Keyword(s):  
Nucleotide Diversity ◽  
Type Iii ◽  
High Nucleotide Diversity

New insights on the genetic diversity of the honeybee parasiteNosema ceranaebased onmultilocussequence analysis

Parasitology ◽  
2013 ◽  
Vol 140 (11) ◽  
pp. 1346-1356 ◽  
Author(s):  
MATHIEU ROUDEL ◽  
JULIE AUFAUVRE ◽  
BRUNO CORBARA ◽  
FREDERIC DELBAC ◽  
NICOLAS BLOT
Keyword(s):  
Ribosomal Rna ◽  
Evolutionary History ◽  
Nucleotide Diversity ◽  
Selective Pressure ◽  
Population Divergence ◽  
Environmental Cues ◽  
Microsporidian Parasite ◽  
High Nucleotide Diversity ◽  
Single Host ◽  
Parasite Populations

SUMMARYThe microsporidian parasiteNosema ceranaeis a common pathogen of the Western honeybee (Apis mellifera) whose variable virulence could be related to its genetic polymorphism and/or its polyphenism responding to environmental cues. Since the genotyping ofN. ceranaebased on unique marker sequences had been unsuccessful, we tested whether amultilocusapproach, assessing the diversity of ten genetic markers – encoding nine proteins and the small ribosomal RNA subunit – allowed the discrimination betweenN. ceranaevariants isolated from singleA. melliferaindividuals in four distant locations. High nucleotide diversity and allele content were observed for all genes. Most importantly, the diversity was mainly present within parasite populations isolated from single honeybee individuals. In contrast the absence of isolate differentiation precluded anytaxadiscrimination, even through amultilocusapproach, but suggested that similar populations of parasites seem to infect honeybees in distant locations. As statistical evolutionary analyses showed that the allele frequency is under selective pressure, we discuss the origin and consequences ofN. ceranaeheterozygosity in a single host and lack of population divergence in the context of the parasite natural and evolutionary history.

Cytoplasmic DNA disclose high nucleotide diversity and different phylogenetic pattern in Taihangia rupestris Yu et Li

2016 ◽  
Vol 66 ◽  
pp. 201-208 ◽  
Author(s):  
Yueqin Cheng ◽  
Jingmian Duan ◽  
Zhenbin Jiao ◽  
G. Geoff Wang ◽  
Fengming Yan ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Phylogenetic Pattern ◽  
High Nucleotide Diversity ◽  
Cytoplasmic Dna

Molecular Variation at the In(2L)t Proximal Breakpoint Site in Natural Populations of Drosophila melanogaster and D. simulans

Genetics ◽  
2000 ◽  
Vol 154 (4) ◽  
pp. 1681-1691 ◽  
Author(s):  
Peter Andolfatto ◽  
Martin Kreitman
Keyword(s):  
Drosophila Melanogaster ◽  
Nucleotide Diversity ◽  
Natural Populations ◽  
Costa Rican ◽  
Homologous Region ◽  
Nucleotide Polymorphism ◽  
Major Haplotype ◽  
High Nucleotide Diversity ◽  
Interspecific Divergence ◽  
Proximal Breakpoint

AbstractA previous study of nucleotide polymorphism in a Costa Rican population of Drosophila melanogaster found evidence for a nonneutral deficiency in the number of haplotypes near the proximal breakpoint of In(2L)t, a common inversion polymorphism in this species. Another striking feature of the data was a window of unusually high nucleotide diversity spanning the breakpoint site. To distinguish between selective and neutral demographic explanations for the observed patterns in the data, we sample alleles from three additional populations of D. melanogaster and one population of D. simulans. We find that the strength of associations among sites found at the breakpoint varies between populations of D. melanogaster. In D. simulans, analysis of the homologous region reveals unusually elevated levels of nucleotide polymorphism spanning the breakpoint site. As with American populations of D. melanogaster, our D. simulans sample shows a marked reduction in the number of haplotypes but not in nucleotide diversity. Haplotype tests reveal a significant deficiency in the number of haplotypes relative to the neutral expectation in the D. simulans sample and some populations of D. melanogaster. At the breakpoint site, the level of divergence between haplotype classes is comparable to interspecific divergence. The observation of interspecific polymorphisms that differentiate major haplotype classes in both species suggests that haplotype classes at this locus are considerably old. When considered in the context of other studies on patterns of variation within and between populations of D. melanogaster and D. simulans, our data appear more consistent with the operation of selection than with simple demographic explanations.

scholarly journals Two divergent haplogroups of a sacsin-like gene in Acropora corals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shiho Takahashi-Kariyazono ◽  
Yohey Terai
Keyword(s):  
Nucleotide Diversity ◽  
Environmental Changes ◽  
Keystone Species ◽  
Genomic Region ◽  
The Other ◽  
Acropora Millepora ◽  
Functional Differences ◽  
High Nucleotide Diversity ◽  
Candidate Protein ◽  
Shock Proteins

AbstractReef-building corals are declining due to environmental changes. Sacsin is a member of the heat shock proteins and has been reported as a candidate protein associated with the stress response in Acropora corals. Recently, high nucleotide diversity and the persistence of two divergent haplogroups of sacsin-like genes in Acropora millepora have been reported. While it was not clear when the two haplogroups have split and whether the haplogroups have persisted in only A. millepora or the other lineages in the genus Acropora. In this study, we analyzed a genomic region containing a sacsin-like gene from Acropora and Montipora species. Higher nucleotide diversity in the sacsin-like gene compared with that of surrounding regions was also observed in A. digitifera. This nucleotide diversity is derived from two divergent haplogroups of a sacsin-like gene, which are present in at least three Acropora species. The origin of these two haplogroups can be traced back before the divergence of Acropora and Montipora (119 Ma). Although the link between exceptionally high genetic variation in sacsin-like genes and functional differences in sacsin-like proteins is not clear, the divergent haplogroups may respond differently to envionmental stressors and serve in the adaptive phsiological ecology of these keystone species.

scholarly journals High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Heredity ◽  
2015 ◽  
Vol 115 (5) ◽  
pp. 460-470 ◽  
Author(s):  
S V Song ◽  
S Downes ◽  
T Parker ◽  
J G Oakeshott ◽  
C Robin
Keyword(s):  
Linkage Disequilibrium ◽  
Helicoverpa Armigera ◽  
Nucleotide Diversity ◽  
Selective Sweep ◽  
High Nucleotide Diversity ◽  
Helicoverpa Armígera

csd alleles in the red dwarf honey bee (Apis florea, Hymenoptera: Apidae) show exceptionally high nucleotide diversity

2011 ◽  
Vol 18 (6) ◽  
pp. 645-651 ◽  
Author(s):  
Zhi-Yong Liu ◽  
Zi-Long Wang ◽  
Xiao-Bo Wu ◽  
Wei-Yu Yan ◽  
Zhi-Jiang Zeng
Keyword(s):  
Honey Bee ◽  
Nucleotide Diversity ◽  
Apis Florea ◽  
High Nucleotide Diversity

scholarly journals Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Chungang Feng ◽  
Mats Pettersson ◽  
Sangeet Lamichhaney ◽  
Carl-Johan Rubin ◽  
Nima Rafati ◽  
...  
Keyword(s):  
Population Size ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
De Novo ◽  
Large Fraction ◽  
Atlantic Herring ◽  
De Novo Mutations ◽  
High Nucleotide Diversity ◽  
Census Population Size ◽  
High Degree

The Atlantic herring is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π = 0.3%), only three-fold higher than in human. Here, we present a pedigree-based estimation of the mutation rate in this species. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 2.0 × 10-9 per base per generation. We observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development. The estimated mutation rate – the lowest among vertebrates analyzed to date – partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size. But a species like the herring will never reach its expected nucleotide diversity because of fluctuations in population size over the millions of years it takes to build up high nucleotide diversity.

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