scholarly journals HIV-2 Diversity Displays Two Clades within group A with Distinct Geographical Distribution and Evolution

2021 ◽  
Author(s):  
Benoit Visseaux ◽  
Mélanie Bertine ◽  
Quentin Le Hingrat ◽  
Valentine Ferré ◽  
Charlotte Charpentier ◽  
...  
Keyword(s):  
Ivory Coast ◽  
Genetic Distances ◽  
Human Populations ◽  
Effective Population ◽  
African Countries ◽  
Guinea Bissau ◽  
Western Africa ◽  
Early Diversification ◽  
Population Sizes ◽  
Group A

Abstract Genetic diversity of HIV-2 groups A and B has not yet been fully described, especially in a few Western Africa countries such as Ivory-Coast or Mali. We collected 444 pol, 152 vif, 129 env, and 74 LTR sequences from patients of the French ANRS CO5 HIV-2 cohort completed by 221 pol, 18 vif, 377 env, and 63 LTR unique sequences from public databases. We performed phylogenetic reconstructions and revealed two distinct lineages within HIV-2 group A, herein called A1 and A2, presenting non-negligible genetic distances and distinct geographic distributions as A1 is related to coastal Western African countries and A2 to inland Western countries. Estimated early diversification times for groups A and B in human populations were 1940 [95% HPD: 1935-53] and 1961 [1952-70]. A1 experienced an early diversification in 1942 [1937-58] with two distinct early epidemics in Guinea-Bissau or Senegal, raising the possibility of group A emergence in those countries from an initial introduction from Ivory-Coast to Senegal, two former French colonies. Changes in effective population sizes over time revealed that A1 exponentially grew concomitantly to Guinea-Bissau independence war, but both A2 and B lineages experienced a latter growth, starting during the 80’s economic crisis. They all decreased after the 2000’s but at a slow rate for A2 and B lineages. This large HIV-2 genetic analysis provides suggest the existence of two distinct subtypes within group A and new data about HIV-2 early spreading patterns and recent epidemiologic evolution for which data are scarce outside Guinea-Bissau.

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

scholarly journals Changes in life history and population size can explain the relative neutral diversity levels on X and autosomes in extant human populations

2020 ◽  
Vol 117 (33) ◽  
pp. 20063-20069
Author(s):  
Guy Amster ◽  
David A. Murphy ◽  
William R. Milligan ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Population Size ◽  
Mutation Rates ◽  
Human Populations ◽  
Effective Population ◽  
Mutation Bias ◽  
Female Ratio ◽  
Generation Times ◽  
Population Sizes ◽  
Male Mutation Bias

In human populations, the relative levels of neutral diversity on the X and autosomes differ markedly from each other and from the naïve theoretical expectation of 3/4. Here we propose an explanation for these differences based on new theory about the effects of sex-specific life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly longer generation times in males than in females, are expected to have had multiple effects on human X-to-autosome (X:A) diversity ratios, as a result of male-biased mutation rates, the equilibrium X:A ratio of effective population sizes, and the differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for male mutation bias results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal that X:A ratios of effective population sizes are considerably greater than previously appreciated. Finally, we find that the joint effects of historical changes in life history and population size can explain the observed X:A diversity ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous, that non-African populations experienced a substantial reduction in polygyny and/or increase in the male-to-female ratio of generation times around the Out-of-Africa bottleneck, and that current diversity levels were affected by fairly recent changes in sex-specific life history.

Ecological Genetics of the Wild Rabbit in Australia. II. Protein Variation in British, French and Australian Rabbits and the Geographical Distribution of the Variation in Australia

1980 ◽  
Vol 33 (3) ◽  
pp. 371 ◽  
Author(s):  
BJ Richardson ◽  
PM Rogers ◽  
GM Hewitt
Keyword(s):  
Genetic Distances ◽  
Ecological Genetics ◽  
Wild Rabbit ◽  
Effective Population ◽  
Average Heterozygosity ◽  
Control Programs ◽  
Phosphogluconate Dehydrogenase ◽  
Protein Variation ◽  
Population Sizes ◽  
Mediterranean France

A survey for genetic variation was carried out using 21 proteins controlled by 26 loci in rabbits from Britain, Mediterranean France and Australia. Five enzymes, adenosine deaminase, phosphogluconate dehydrogenase, carboxylesterase, carbonate dehydratase and dihydrolipoamide reductase (NAD+) were found to be polymorphic. The average heterozygosity in wild rabbits was 6%. The genetic distances separating the various populations indicated that three different stocks were present in these populations. The rabbits from Britain and mainland Australia belonged to one group, those from France to a second group and the rabbits from southern Tasmania were a distinctive third group. Highly significant differences in gene frequency were found between the various local populations studied from mainland Australia. This variation showed no clear pattern and was attributed to genetic drift due to small effective population sizes. Bottlenecks in population size occur regularly in local rabbit populations in Australia through, for example, drought, myxomatosis outbreaks or rabbit control programs.

scholarly journals Isoenzymatic variability in tropical maize populations under reciprocal recurrent selection

2003 ◽  
Vol 60 (2) ◽  
pp. 291-297 ◽  
Author(s):  
Luciana Rossini Pinto ◽  
Maria Lúcia Carneiro Vieira ◽  
Cláudio Lopes de Souza Jr. ◽  
Rainério Meireles da Silva
Keyword(s):  
Genetic Variability ◽  
Recurrent Selection ◽  
Zea Mays L ◽  
Genetic Distances ◽  
Reciprocal Recurrent Selection ◽  
Tropical Maize ◽  
Effective Population ◽  
Selection Procedures ◽  
Maize Populations ◽  
Population Sizes

Maize (Zea mays L.) is one of the crops in which the genetic variability has been extensively studied at isoenzymatic loci. The genetic variability of the maize populations BR-105 and BR-106, and the synthetics IG-3 and IG-4, obtained after one cycle of a high-intensity reciprocal recurrent selection (RRS), was investigated at seven isoenzymatic loci. A total of twenty alleles were identified, and most of the private alleles were found in the BR-106 population. One cycle of reciprocal recurrent selection (RRS) caused reductions of 12% in the number of alleles in both populations. Changes in allele frequencies were also observed between populations and synthetics, mainly for the Est 2 locus. Populations presented similar values for the number of alleles per locus, percentage of polymorphic loci, and observed and expected heterozygosities. A decrease of the genetic variation values was observed for the synthetics as a consequence of genetic drift effects and reduction of the effective population sizes. The distribution of the genetic diversity within and between populations revealed that most of the diversity was maintained within them, i.e. BR-105 x BR-106 (G ST = 3.5%) and IG-3 x IG-4 (G ST = 4.0%). The genetic distances between populations and synthetics increased approximately 21%. An increase in the genetic divergence between the populations occurred without limiting new selection procedures.

Political Regimes, Contentious National Identity Question, and Nation-Building in African Countries: The Kenyan Case (1963 – 2020)

2020 ◽  
Vol 7 (11) ◽  
pp. 213-230
Author(s):  
Peter SAKWE MASUMBE
Keyword(s):  
National Identity ◽  
Ivory Coast ◽  
Cultural Landscapes ◽  
Nation Building ◽  
National Identities ◽  
Political Regimes ◽  
African Countries ◽  
Elite Theory ◽  
Guinea Bissau ◽  
Election Violence

Kenya’s successive political regimes’ contentiousness, like elsewhere in Africa, breeds the dearth of national identity, notwithstanding national identity’s relevance in characterising countries’ politico-economic and socio-cultural landscapes. National identity accelerates nation-building, hence, its inevitability for African countries; given their irrefutable need for statehoods. Arguably, the dearth of national identity constructs gratuitous upheavals as illustrated by post-election violence and contestations, in Kenya 2007, Ivory Coast 2010-2011, Cameroon 2018-2019, Nigeria 2018, Guinea Bissau 2020, etcetera. While seeking to divulge how Kenya’s national identity could emerge with its 4th President in 2017; this paper argues that, in African countries, the dearth of national identities propels political and economic failures, destroys citizens’ senses of belonging, undermines nation-building and enhances national disunity. Irked by these peccadilloes, fashioned by African leaders’ self-centredness; this work grounds on the elite theory to conclude that, leaders of African political regimes generate national identities’ dearth and their countries’ disunity and underdevelopment.

scholarly journals Population dynamics of GC-changing mutations in humans and great apes

2020 ◽  
Author(s):  
Juraj Bergman ◽  
Mikkel Heide Schierup
Keyword(s):  
Gene Conversion ◽  
Nucleotide Composition ◽  
Human Populations ◽  
Great Ape ◽  
Effective Population ◽  
Biased Gene Conversion ◽  
Repair Mechanisms ◽  
Nucleotide Context ◽  
Population Sizes ◽  
Transitions And Transversions

AbstractBackgroundThe nucleotide composition of the genome is a balance between origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and among great ape species.ResultsWe report a stronger correlation between GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC. We show that the strength of gBGC differs for transitions and transversions but that its overall strength is positively correlated with effective population sizes of human populations and great ape species, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. We study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to hypermutability of specific nucleotide contexts.ConclusionsDifferences in GC-biased gene conversion are evident between different mutation types, and dependent on sex-specific recombination, population size and flanking nucleotide context. Our results therefore highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.

scholarly journals Genotype Profiles of Rotavirus Strains from Children in a Suburban Community in Guinea-Bissau, Western Africa

2000 ◽  
Vol 38 (1) ◽  
pp. 264-267
Author(s):  
Thea Kølsen Fischer ◽  
Hans Steinsland ◽  
Kåre Mølbak ◽  
Rui Ca ◽  
Jon R. Gentsch ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Mixed Infections ◽  
Group A Rotavirus ◽  
Guinea Bissau ◽  
Reverse Transcription Pcr ◽  
Western Africa ◽  
Suburban Community ◽  
Group A ◽  
Unusual Type

ABSTRACT The P (VP4) and G (VP7) genotypes of 167 group A rotavirus strains obtained during the period 1996 to 1998 from 149 children living in a suburban community in Guinea-Bissau, western Africa, were determined by the reverse transcription-PCR technique. A total of nine combinations including five different P types and five different G types were identified. The globally common genotype pairs P[8], G1; P[4], G2; P[8], G3 and P[8], G4 were underrepresented in this study area. We found a substantial year-to-year variation in the occurrence of the genotype combinations. In 1996 and 1997, P[6], G2 was the most frequent, whereas P[8], G1 was more common in 1998. The unusual type P[9], G3 and a few mixed infections were detected. Sixteen percent of the rotavirus-positive samples were nontypeable.

scholarly journals Changes in life history and population size can explain relative neutral diversity levels on X and autosomes in extant human populations

2019 ◽  
Author(s):  
Guy Amster ◽  
David A. Murphy ◽  
William M. Milligan ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Population Size ◽  
Mutation Rates ◽  
Human Populations ◽  
Effective Population ◽  
Mutation Bias ◽  
Historical Changes ◽  
Generation Times ◽  
Population Sizes ◽  
Male Mutation Bias

AbstractIn human populations, relative levels of neutral polymorphism on the X and autosomes differ markedly from each other and from the naive theoretical expectation of ¾. These differences have attracted considerable attention, with studies highlighting several potential causes, including male biased mutation and reproductive variance, historical changes in population size, and selection at linked loci. We revisit this question in light of our new theory about the effects of life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly higher generation times in males than females, likely had multiple effects on human X-to-autosomes (X:A) polymorphism ratios, through the extent of male mutation bias, the equilibrium X:A ratios of effective population sizes, and differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for the male bias in mutation results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal X:A ratios of effective population sizes to be considerably greater than previously appreciated. We then show that the joint effects of historical changes in life history and population size can explain X:A polymorphism ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous; that non-African populations experienced a substantial reduction in polygyny and/or increase in male-biased generation times around the out of Africa bottleneck; and that extant diversity levels were affected by fairly recent changes in sex-specific life history.Significance StatementAll else being equal, the ratio of diversity levels on X and autosomes at selectively neutral sites should mirror the ratio of their numbers in the population and thus equal ¾. In reality, the ratios observed across human populations differ markedly from ¾ and from each other. Because from a population perspective, autosomes spend an equal number of generations in both sexes while the X spends twice as many generations in females, these departures from the naïve expectations likely reflect differences between male and female life histories and their effects on mutation processes. Indeed, we show that the ratios observed across human populations can be explained by demographic history, assuming plausible, sex-specific mutation rates, generation times and reproductive variances.

scholarly journals First Report of Zucchini yellow mosaic virus in Cucurbits in Ivory Coast

Plant Disease ◽  
2010 ◽  
Vol 94 (11) ◽  
pp. 1378-1378 ◽  
Author(s):  
D. Koné ◽  
S. Aké ◽  
K. Abo ◽  
S. Soro ◽  
C. A. N'Guessan ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Ivory Coast ◽  
Zucchini Yellow Mosaic Virus ◽  
Yellow Mosaic Virus ◽  
Watermelon Mosaic Virus ◽  
African Countries ◽  
Cucumis Sativus L ◽  
First Report ◽  
Phylogenetic Cluster ◽  
Group A

During a field survey conducted in December 2008 and January 2009 in southern Ivory Coast, zucchini squash (Cucurbita pepo L.) and cucumber (Cucumis sativus L.) plants were observed showing severe symptoms of leaf mosaic and distortions, filiformism, and fruit deformations. Nine samples were collected from symptomatic plants in four locations (Adzopé, Songon, Ayamé, and Gagnoa) and dried over CaCl2. Double-antibody sandwich (DAS)-ELISA tests were performed directly on dried samples with antisera against nine cucurbit-infecting viruses: Zucchini yellow mosaic virus (ZYMV, Potyvirus); Papaya ringspot virus (PRSV, Potyvirus); Watermelon mosaic virus (WMV, Potyvirus); Moroccan watermelon mosaic virus (MWMV, Potyvirus); Cucumber vein yellowing virus (CVYV, Ipomovirus); Cucumber mosaic virus (CMV, Cucumovirus); Cucurbit aphid borne yellows virus (CABYV, Polerovirus); Squash mosaic virus (SqMV, Comovirus); and Cucumber green mottle mosaic virus (CGMMV, Tobamovirus). ZYMV was detected alone in four of six zucchini squash samples and in mixed infection with CMV and PRSV in two of three cucumber samples. A cucumber sample (CI09-09) collected at Songon and infected by ZYMV, CMV, and PRSV was inoculated to zucchini squash. ZYMV was separated from CMV and PRSV by inoculating zucchini squash plantlets with one Myzus persicae Sulzer per plant with 2-min acquisition and 2-h inoculation access periods. Plants infected by ZYMV only developed typical symptoms of severe mosaic, distortion, and filiformism on leaves. Total RNA was extracted from the original dried sample of CI09-09 using TRI-Reagent (Molecular Research Center Inc., Cincinnati, OH) (2). One-step reverse transcription (RT)-PCR was performed with our standard protocol and specific primers (2), yielding a 605-bp fragment corresponding to part of the polymerase (NIb) and coat protein (CP) coding regions. The nucleotide sequence of the NIb-CP fragment of Ivory Coast ZYMV isolate CI09-09 (GenBank No. HM450303) shared 98.5, 92.7, 80.5, and 75.7% identity with ZYMV isolates from France (isolate E9, HM641798), Florida (D13914), Singapore (AF014811), and Vietnam (DQ925449), respectively. Sequence comparison indicated that CI09-09 belongs to the phylogenetic cluster 1 of group A of ZYMV (2). ZYMV, first described in 1981, is now one of the most damaging viruses in cucurbit crops worldwide and is characterized by an important biological and molecular diversity (1,3). ZYMV has already been reported in several African countries, mostly in the northern and southern parts of the continent (1), but to our knowledge, this is the first report of ZYMV in Ivory Coast. Among African isolates, CI09-09 shared 97.5% identity with isolate Su06-22 from Sudan (HM641799) belonging to the phylogenetic cluster 1 of group A of ZYMV, 94 to 95% identity with isolates from neighboring Mali (HM005307–HM005312) belonging to cluster 2 of group A, and 79.6% identity with the divergent isolate R5A from Réunion Island (L29569) belonging to phylogenetic group B of ZYMV. The presence of ZYMV in four distant locations in southern Ivory Coast suggests that this virus constitutes a serious threat to cucurbit production in this country. References: (1) C. Desbiez and H. Lecoq. Plant Pathol. 46:809, 1997, (2) C. Desbiez et al. Virus Res. 85:5, 2002, (3) H. Lecoq et al. Virus Res. 141:190, 2009.

scholarly journals Population dynamics of GC-changing mutations in humans and great apes

Genetics ◽  
2021 ◽  
Author(s):  
Juraj Bergman ◽  
Mikkel Heide Schierup
Keyword(s):  
Great Apes ◽  
Nucleotide Composition ◽  
Human Populations ◽  
Great Ape ◽  
Effective Population ◽  
European Descent ◽  
Cpg Sites ◽  
Biased Gene Conversion ◽  
Repair Mechanisms ◽  
Population Sizes

Abstract The nucleotide composition of the genome is a balance between origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and great ape species. We report a stronger correlation between segregating GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC in humans and chimpanzees. We show that the overall strength of gBGC is generally correlated with effective population sizes in humans, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. Furthermore, species of the Gorilla and Pongo genus have a greatly reduced gBGC effect on CpG sites. We also study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to hypermutability of specific nucleotide contexts. Our results highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.

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