scholarly journals Similar efficacies of selection shape mitochondrial and nuclear genes in Drosophila melanogaster and Homo sapiens

2014 ◽  
Author(s):  
Brandon S. Cooper ◽  
Chad Burrus ◽  
Chao Ji ◽  
Matthew W. Hahn ◽  
Kristi L. Montooth
Keyword(s):  
Drosophila Melanogaster ◽  
Homo Sapiens ◽  
Nuclear Genome ◽  
Nuclear Data ◽  
Nuclear Genes ◽  
Small Samples ◽  
Published Data ◽  
Effective Population ◽  
Synonymous Polymorphism ◽  
Linked Selection

Deleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (Ne) of the mtDNA, and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes from Drosophila melanogaster and nuclear data available from the same samples, we re-examine the hypothesis that non-recombining animal mtDNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction in Ne. Nevertheless, we find that the neutrality index (NI), a measure of the excess of nonsynonymous polymorphism relative to the neutral expectation, is not significantly different between mitochondrial and nuclear loci. Reanalysis of published data from Homo sapiens reveals the same lack of a difference between the two genomes, though small samples in previous studies had suggested a strong difference in both species. Thus, despite a smaller Ne, mitochondrial loci of both flies and humans appear to experience similar efficacies of selection as do loci in the recombining nuclear genome.

scholarly journals Similar Efficacies of Selection Shape Mitochondrial and Nuclear Genes in Both Drosophila melanogaster and Homo sapiens

2015 ◽  
Vol 5 (10) ◽  
pp. 2165-2176 ◽  
Author(s):  
Brandon S. Cooper ◽  
Chad R. Burrus ◽  
Chao Ji ◽  
Matthew W. Hahn ◽  
Kristi L. Montooth
Keyword(s):  
Drosophila Melanogaster ◽  
Homo Sapiens ◽  
Nuclear Genes

scholarly journals “Ghost Introgression” As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex

2019 ◽  
Vol 36 (11) ◽  
pp. 2375-2386 ◽  
Author(s):  
Dezhi Zhang ◽  
Linfang Tang ◽  
Yalin Cheng ◽  
Yan Hao ◽  
Ying Xiong ◽  
...  
Keyword(s):  
Bird Species ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Comparative Genomic ◽  
Genetic Introgression ◽  
Effective Population ◽  
Westward Expansion ◽  
Whole Genomes ◽  
Linked Selection ◽  
Two Populations

Abstract In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by “speciation reversal” or by mitochondrial capture through genetic introgression. Here, we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of “ghost introgression” as the cause of DMD, and we suggest that “ghost introgression” may be a widely overlooked phenomenon in nature.

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 The genomic landscape of recombination rate variation in Chlamydomonas reinhardtii reveals a pronounced effect of linked selection

2018 ◽  
Author(s):  
Ahmed R. Hasan ◽  
Rob W. Ness
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Recombination Rate ◽  
Natural Populations ◽  
Gc Content ◽  
Sexual Cycle ◽  
Rate Variation ◽  
Effective Population ◽  
Entire Genome ◽  
Recombination Rate Variation ◽  
Linked Selection

AbstractRecombination confers a major evolutionary advantage by breaking up linkage disequilibrium (LD) between harmful and beneficial mutations and facilitating selection. Here, we use genome-wide patterns of LD to infer fine-scale recombination rate variation in the genome of the model green alga Chlamydomonas reinhardtii and estimate rates of LD decay across the entire genome. We observe recombination rate variation of up to two orders of magnitude, finding evidence of recombination hotspots playing a role in the genome. Recombination rate is highest just upstream of genic regions, suggesting the preferential targeting of recombination breakpoints in promoter regions. Furthermore, we observe a positive correlation between GC content and recombination rate, suggesting a role for GC-biased gene conversion or selection on base composition within the GC-rich genome of C. reinhardtii. We also find a positive relationship between nucleotide diversity and recombination, consistent with widespread influence of linked selection in the genome. Finally, we use estimates of the effective rate of recombination to calculate the rate of sex that occurs in natural populations of this important model microbe, estimating a sexual cycle roughly every 770 generations. We argue that the relatively infrequent rate of sex and large effective population size creates an population genetic environment that increases the influence of linked selection on the genome.

scholarly journals A SURVEY OF ISOZYME POLYMORPHISM IN A DROSOPHILA MELANOGASTER NATURAL POPULATION

Genetics ◽  
1975 ◽  
Vol 80 (4) ◽  
pp. 761-771
Author(s):  
H T Band
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Population ◽  
Published Data ◽  
The South ◽  
Biochemical Polymorphism ◽  
Metabolizing Enzymes ◽  
Animal Populations ◽  
Isozyme Polymorphism ◽  
The Right

ABSTRACT A survey of biochemical polymorphism among glucose- and non-glucose-metabolizing enzymes was carried out on the June 1973 collection from the South Amherst, Mass. Drosophila melanogaster natural population. Polymorphic levels are among the highest recorded for this species; polymorphism among glucose-metabolizing enzymes did not differ significantly from that among non-glucose-metabolizing enzymes. Two loci, G6Pd on the × and Est-6 on the 3rd chromosome, displayed significant excesses of heterozygotes. Adh on the 2nd and Idh, Odh and Ao on the 3rd chromosome showed significant heterozygote deficiencies. Idh is ten map units to the left of Est-6, Odh twelve map units to the right and Ao is seven units beyond Odh. Temperatures in the two-week June period prior to collection were exceedingly variable. Daily high/low ranged between 76°/40° and 97°/65°F. These results support the findings of Frydenberg and Simonsen (1973) that in some populations glucose-metabolizing enzymes tend to be as polymorphic as non-glucose-metabolizing ones. They also add to the evidence obtained from other plant and animal populations that increased biochemical polymorphism is associated with more variable and/or colder climates. The increase may in part be due to increased polymorphism among glucose-metabolizing enzymes. Comparisons utilizing published data on other D. melanogaster populations and on D. robusta indicate a clinal increase in heterozygosity among glucose-metabolizing enzymes as one moves northward.

scholarly journals Comprehensive Overview and Assessment of microRNA Target Prediction Tools in Homo sapiens and Drosophila melanogaster

2019 ◽  
Vol 14 (5) ◽  
pp. 432-445 ◽  
Author(s):  
Muniba Faiza ◽  
Khushnuma Tanveer ◽  
Saman Fatihi ◽  
Yonghua Wang ◽  
Khalid Raza
Keyword(s):  
Drosophila Melanogaster ◽  
Mirna Target ◽  
Homo Sapiens ◽  
Target Prediction ◽  
Computational Prediction ◽  
Transcriptional Level ◽  
Mirna Target Prediction ◽  
Microrna Target ◽  
Prediction Tools ◽  
Mirna Targets

Background: MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression at the post-transcriptional level through complementary base pairing with the target mRNA, leading to mRNA degradation and blocking translation process. Many dysfunctions of these small regulatory molecules have been linked to the development and progression of several diseases. Therefore, it is necessary to reliably predict potential miRNA targets. Objective: A large number of computational prediction tools have been developed which provide a faster way to find putative miRNA targets, but at the same time, their results are often inconsistent. Hence, finding a reliable, functional miRNA target is still a challenging task. Also, each tool is equipped with different algorithms, and it is difficult for the biologists to know which tool is the best choice for their study. Methods: We analyzed eleven miRNA target predictors on Drosophila melanogaster and Homo sapiens by applying significant empirical methods to evaluate and assess their accuracy and performance using experimentally validated high confident mature miRNAs and their targets. In addition, this paper also describes miRNA target prediction algorithms, and discusses common features of frequently used target prediction tools. Results: The results show that MicroT, microRNA and CoMir are the best performing tool on Drosopihla melanogaster; while TargetScan and miRmap perform well for Homo sapiens. The predicted results of each tool were combined in order to improve the performance in both the datasets, but any significant improvement is not observed in terms of true positives. Conclusion: The currently available miRNA target prediction tools greatly suffer from a large number of false positives. Therefore, computational prediction of significant targets with high statistical confidence is still an open challenge.

scholarly journals Mitochondrial DNA polymorphism and cardiovascular continuum diseases

2018 ◽  
pp. 9-13
Author(s):  
М.В. Голубенко ◽  
Р.Р. Салахов ◽  
Т.В. Шумакова ◽  
С.В. Буйкин ◽  
О.А. Макеева ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Cardiovascular Diseases ◽  
Mitochondrial Genome ◽  
Dna Polymorphism ◽  
Nuclear Genome ◽  
Published Data ◽  
Human Populations ◽  
Mitochondrial Dna Polymorphism ◽  
Polymorphism Level ◽  
Cardiovascular Continuum

Митохондриальный геном кодирует жизненно важные белки субъединиц дыхательной цепи и характеризуется высоким уровнем полиморфизма в популяциях человека. Однако работы по поиску генов предрасположенности к многофакторным заболеваниям, в том числе сердечно-сосудистым, часто ограничиваются анализом ядерного генома. В то же время показано, что отдельные генотипы мтДНК могут отличаться более высокой или низкой эффективностью окислительного фосфорилирования. Выявлены ассоциации популяционного полиморфизма мтДНК с сердечно-сосудистыми заболеваниями. Согласно результатам наших исследований, а также опубликованных другими авторами результатам ассоциативных и функциональных исследований, можно говорить о том, что эффект полиморфизма мтДНК проявляется чаще не в предрасположенности к сердечно-сосудистым заболеваниям в целом, а в риске развития осложнений и коморбидных фенотипов в пределах синтропии сердечно-сосудистого континуума. Mitochondrial genome, encoding respiratory chain subunits, is characterized by high polymorphism level in human populations. In most studies for susceptibility genes for common diseases, including cardiovascular diseases, the analysis is limited to the nuclear genome. It was shown that particular mtDNA genotypes may differ by oxidative phosphorylation efficiency. Some associations of mtDNA polymorphisms with cardiovascular diseases have been found. According to our results and published data, we suggest that mtDNA effect on cardiovascular system does not manifest in predisposition to cardiovascular diseases themselves but rather in risk of complications and comorbidities in the cardiovascular continuum.

Genetically effective population sizes of Antarctic seals estimated from nuclear genes

2011 ◽  
Vol 12 (6) ◽  
pp. 1435-1446 ◽  
Author(s):  
Caitlin Curtis ◽  
Brent S. Stewart ◽  
Stephen A. Karl
Keyword(s):  
Nuclear Genes ◽  
Effective Population ◽  
Antarctic Seals ◽  
Population Sizes

scholarly journals Selection using assortative mating in Drosophila melanogaster

1963 ◽  
Vol 4 (3) ◽  
pp. 356-369 ◽  
Author(s):  
Glenorchy McBride ◽  
Alan Robertson
Keyword(s):  
Drosophila Melanogaster ◽  
Assortative Mating ◽  
Random Mating ◽  
Selection Response ◽  
Index Selection ◽  
Individual Selection ◽  
Effective Population ◽  
Selected Lines ◽  
The Individual ◽  
Rate Of Response

The effectiveness of the assortative mating of selected individuals in increasing selection response was tested, using abdominal chaeta score in Drosophila melanogaster. Three paired comparisons were made. In two sets of lines with 10 matings per line, individual score was used for selection and as the basis for the assortative mating. In the third set with 20 matings per line an index of individual and family score, designed to maximize rate of response, was used.The intensity of selection was one in ten in all lines. Flies were raised in vials and individual pedigrees were kept.In all comparisons, assortative mating gave a greater selection response, this being partly due to a greater realized heritability and partly to a greater selection differential. The effect of the assortative mating was largest in the index selected lines. With random mating, the effectiveness of the index selection itself when compared to individual selection was in accordance with theory.In two comparisons, assortative mating increased the rate of inbreeding. The highest rate of inbreeding was observed with index selection and assortative mating, even though there were here twice as many matings as in the individually selected lines.In the individual selection lines, the effective population size was 7·4 pairs of parents, compared to the actual value of 10 and in the index lines 7·0 compared to 20. In the former, only one-half of the matings in the initial generations made any permanent contributions to the line and in the index lines only one-third. Within generations and lines, there was a significant positive correlation between the mean score of a family and its inbreeding coefficient.It is suggested that assortative mating is a method of increasing selection response in some situations. Its particular characteristic is that it becomes more powerful when the heritability is high whereas all of the other environmental aids to individual selection are more effective when the heritability is low.

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