Low genetic diversity in Wolbachia-Infected Culex quinquefasciatus (Diptera: Culicidae) from Brazil and Argentina

Culex quinquefasciatus is a vector of human pathogens, including filarial nematodes and several viruses. Although its epidemiological relevance is known to vary across geographical regions, an understanding of its population genetic structure is still incipient. In light of this, we evaluated the genetic diversity of Cx. quinquefasciatus and Cx. pipiens x Cx. quinquefasciatus hybrids collected from nine localities in Brazil and one site in Argentina. We used mitochondrial genes cox1 and nd4, along with the coxA and wsp genes of the maternally-inherited Wolbachia endosymbiont. The nd4 fragment was invariant between samples, whilst cox1 exhibited four haplotypes that separated two types of Cx. quinquefasciatus, one clustered in southern Brazil. Low sequence diversity was generally observed, being discussed. Both Brazilian and Argentinian mosquitoes were infected with a single Wolbachia strain. As reported in previous studies with these populations, cox1 and nd4 diversity is not congruent with the population structure revealed by nuclear markers or alar morphology. Future Cx. quinquefasciatus research should, if possible, evaluate mtDNA diversity in light of other markers.

Download Full-text

Genome typing and epidemiology of human listeriosis in New Zealand 1999-2018

Journal of Clinical Microbiology ◽

10.1128/jcm.00849-21 ◽

2021 ◽

Author(s):

Lucia Rivas ◽

Shevaun Paine ◽

Pierre-Yves Dupont ◽

Audrey Tiong ◽

Beverley Horn ◽

...

Keyword(s):

Genetic Diversity ◽

New Zealand ◽

Epidemiological Data ◽

Common Source ◽

Snp Analysis ◽

Whole Genome ◽

Single Nucleotide ◽

Low Genetic Diversity ◽

Geographical Regions ◽

Sequence Types

This study describes the epidemiology of listeriosis in New Zealand (NZ) between 1999 and 2018, as well as the retrospective whole genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population and non-pregnancy associated cases were more prevalent than pregnancy-associated cases (average 19 and 5 cases per annum, respectively). Analysis of WGS data was assessed using multi-locus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being, ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%) and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Amongst the 49 cgMLST types containing two or more isolates, 18 cgMLST types contained 2-4 isolates (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0-2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP-analysis also produced comparable results to wgMLST. The low genetic diversity within these clusters suggests a potential common source but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis, together with thorough exposure information from cases will potentially identify future outbreaks more rapidly and possibly those that have been undetected for some time over different geographically regions.

Download Full-text

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand

10.1101/201483 ◽

2017 ◽

Author(s):

Wibhu Kutanan ◽

Jatupol Kampuansai ◽

Piya Changmai ◽

Pavel Flegontov ◽

Roland Schröeder ◽

...

Keyword(s):

Genetic Diversity ◽

Mt Dna ◽

Mtdna Haplogroups ◽

The Past ◽

Low Genetic Diversity ◽

Related Group ◽

Recent Origin ◽

Mtdna Diversity ◽

Founder Event ◽

Northeastern Thailand

ABSTRACTThe Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non- recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely- related group.

Download Full-text

Genetic consequences of long-term isolation for the last French population of Eryngium viviparum (Apiaceae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz035 ◽

2019 ◽

Vol 191 (2) ◽

pp. 285-298 ◽

Cited By ~ 1

Author(s):

Pauline Rascle ◽

Elodie Flaven ◽

Frédéric Bioret ◽

Sylvie Magnanon ◽

Erwan Glemarec ◽

...

Keyword(s):

Genetic Diversity ◽

Conservation Status ◽

Disjunct Distribution ◽

French Population ◽

Endemic Plant ◽

Evolutionary Potential ◽

The North ◽

Low Genetic Diversity ◽

Geographical Regions ◽

Seasonally Flooded

Abstract Eryngium viviparum (Apiaceae) is an endangered endemic plant of the Atlantic region of Europe, growing in seasonally flooded sites, and is characterized by a highly disjunct distribution. It occurs in just a few sites in the north-western part of the Iberian Peninsula and in a single locality in France. To improve the conservation status of E. viviparum in France, a conservation programme has been implemented to reintroduce the species. Before considering such an operation, genetic studies were conducted to determine the genetic status of the last French population and to identify the genetic source that should be considered for the best reintroduction strategy. Using microsatellite markers, we documented the genetic structure of the last French population and compared its genetic diversity with that of ten Iberian populations, which cover the three geographical regions where the species occurs. As expected, the French population of E. viviparum shows low genetic diversity due to a bottleneck and geographical isolation. The evolutionary potential appears low, with no private alleles in this population. Furthermore, this population is highly differentiated from the Iberian populations in terms of genetic variation and ecological niche. These results bring new questions regarding the conservation of E. viviparum in France, especially for management and reintroduction aimed at favouring genetic diversity and avoiding extinction.

Download Full-text

Molecular Epidemiology Surveillance of SARS-Cov-2: Mutations and Genetic Diversity One Year After Emerging

10.20944/preprints202101.0173.v1 ◽

2021 ◽

Author(s):

Alejandro Flores-Alanis ◽

Armando Cruz-Rangel ◽

Flor Rodríguez-Gómez ◽

James González ◽

Carlos Alberto Torres-Guerrero ◽

...

Keyword(s):

Genetic Diversity ◽

Genomic Analysis ◽

Viral Fitness ◽

Spike Protein ◽

Molecular Surveillance ◽

Low Genetic Diversity ◽

Geographical Regions ◽

Frequent Mutations ◽

One Year ◽

Over Time

In December 2019, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the province of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. We performed genomic analysis to identify the changes in genetic diversity of SARS-CoV-2 between December 2019 and November 2020, and through molecular surveillance, we monitored the mutations that could be involved in viral fitness. We analyzed 2,213 complete genomes from 6 geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified 7 frequent mutations that resulted in non-synonymous substitutions (dN). Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein emerged recently and have spread in Oceania and Europe. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Download Full-text

Genetic Diversity Within and Among Populations of Shorea Robusta Roxb. Ex Gaertn. In Bangladesh and Its Implications for Conservation

Bangladesh Journal of Botany ◽

10.3329/bjb.v50i2.54098 ◽

2021 ◽

Vol 50 (2) ◽

pp. 405-412

Author(s):

Pragga Saha Sharmi ◽

Md Abul Kashem ◽

Rifat Samad ◽

Mohammad Zabed Hossain

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Isolation By Distance ◽

Genetic Erosion ◽

Mantel Test ◽

Small Population ◽

Deciduous Forests ◽

Shorea Robusta ◽

Low Genetic Diversity ◽

Geographical Regions

Fragmentation and reduction of natural population size render threats to the conservation of forest resources through depletion of genetic diversity. Hence, information on genetic structure of Sal (Shorea robusta Roxb. ex Gaertn.) populations is relevant for proper management and conservation of the tropical deciduous forests. The present study focused on assessing the genetic diversity of the populations of Sal which was the dominant tree species of the deciduous forests of Bangladesh. Plant leaf samples were collected from the three populations of Sal distributed in the three geographical regions including Madhupur tract in the districts Tangail and Gazipur and that of the districts of Cumilla and Dinajpur. DNA band profiles were generated using eight ISSR primers for a total of 13 samples taken from the three populations. Statistical analysis was done using PopGen 32 and GenAlEx 6.5 softwares. Principal coordinate analysis done on the DNA band profiles revealed that Sal populations of Madhupur tract and Cumilla positioned nearby while Dinajpur showed maximum genetic distance with that of Cumilla. Mantel test showed significant (p=0.05) correlation between genetic and geographic distances indicating “Isolation by Distance”. Data of the present study indicated higher genetic polymorphism (68.87%) in the Sal population of Madhupur tract compared to other two populations. Small population size of Sal of Dinajpur forest might be related with its low genetic diversity. Data of the present study suggest immediate attention for the conservation of Sal forests in Bangladesh before further genetic erosion occurs. Bangladesh J. Bot. 50(2): 405-412, 2021 (June)

Download Full-text

Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging

Pathogens ◽

10.3390/pathogens10020184 ◽

2021 ◽

Vol 10 (2) ◽

pp. 184

Author(s):

Alejandro Flores-Alanis ◽

Armando Cruz-Rangel ◽

Flor Rodríguez-Gómez ◽

James González ◽

Carlos Alberto Torres-Guerrero ◽

...

Keyword(s):

Genetic Diversity ◽

Spike Protein ◽

The Novel ◽

Molecular Surveillance ◽

Low Genetic Diversity ◽

Geographical Regions ◽

Frequent Mutations ◽

One Year ◽

The City ◽

Over Time

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Download Full-text

CARACTERIZACIÓN GENÉTICA DE LA COLONIA REPRODUCTIVA DE LA TORTUGA MARINA GOLFINA –LEPIDOCHELYS OLIVACEA– en el PARQUE NACIONAL NATURAL GORGONA (PACÍFICO COLOMBIANO) A PARTIR DE SECUENCIAS DE ADN MITOCONDRIAL

Bulletin of Marine and Coastal Research ◽

10.25268/bimc.invemar.2008.37.1.183 ◽

2016 ◽

Vol 37 (1) ◽

Author(s):

Lindamar Camacho Mosquera ◽

Diego Amorocho ◽

Luz M. Mejía Ladino ◽

Juan D. Palacio Mejía ◽

Fernando Rondón González

Keyword(s):

Genetic Diversity ◽

Eastern Pacific ◽

Conservation Strategies ◽

Lepidochelys Olivacea ◽

Natal Homing ◽

Low Genetic Diversity ◽

Natural Park ◽

Geographical Regions ◽

D Loop ◽

Definition Of

To genetic characterize the nesting colony of L. olivacea in Palmeras beach-Gorgona National Natural Park- and to contribute to the implementation of strategies of conservation for the species, a fragment of the mitocondrial DNA control region (D-loop) was sequenced in 29 individuals for studying the genetic diversity and phylogenetic relationships in comparison with data published in GenBank. The analysis of the sequences revealed the presence of two haplotypes N (96.55%) and E (3.45%), according to the sequences reported for this species. The genetic (h) and nucleotide (π) diversity of the studied colony was h=0.069 and π =0.023%, these results corroborate that the Testudines presents a low genetic diversity. These values of diversity are low when they were compared with continental populations of L. olivacea of the South of Baja California (h=0.16 and π=0.06%), Eastern Pacific (h=0.60 and π =0.26%) and east of India (Sri Lanka with h=0.72 and π =2.07%; Orissa with h=0.27 and π=0.3%) in spite of different number of colonies. The analyses of phylogenetic inference, using the Neighbour- Joining method, confirm the cluster of the haplotypes in two geographical regions (eastern Pacific and east India). We conclude that the presence of the haplotype N corroborate the hypothesis of natal homing (adult females return to lay eggs in the general region where they were born) of L. olivacea in Palmeras beach, this information contribute in the definition of management units required for the implementation of conservation strategies for the species.

Download Full-text

KERAGAMAN GENETIK INDUK UDANG WINDU DI PERAIRAN SELATAN PANGANDARAN DAN BINUANGEUN, JAWABARAT

Jurnal Rekayasa Lingkungan ◽

10.29122/jrl.v5i3.1896 ◽

2018 ◽

Vol 5 (3) ◽

Author(s):

Ratu Siti Aliah

Keyword(s):

Genetic Diversity ◽

Population Genetic ◽

Gene Locus ◽

Penaeus Monodon ◽

12S Rrna ◽

Brood Stock ◽

Population Genetic Diversity ◽

Result Show ◽

Mtdna Diversity

An evaluation of the Black Tiger Brood Stock (Penaeus monodon) genetic diversity of Pangandaran and Binuangeun was conducted by using the mtDNA diversity of two gene locus of CO I and 12S rRNA to understand their population genetic diversity. The result show that the brood stock of Pangandaran has 17 haplotipe, while from Binuangeun has 13 haplotipe. The result indicated that the genetic diversity of the Balck Tiger brood stock of Pangandaran was higher than thatBinuangeun.Key words : Genetic diversity, Black Tiger brood stock, Pangandaran, Binuangeun

Download Full-text