Habitat requirements affect genetic variation in three species of mayfly (Ephemeroptera, Baetidae) from South Africa

This study investigates genetic diversity in three species of Ephemeroptera, one eurytopic and therefore widespread (Afroptilum sudafricanum) and two stenotopic and thus endemic (Demoreptus natalensis and Demoreptus capensis) species, all of which co-occur in the southern Great Escarpment, South Africa. Mitochondrial DNA was analysed to compare the genetic diversity between the habitat generalist and the two habitat specialists. Afroptilum sudafricanum showed no indication of population genetic structure due to geographic location, while both Demoreptus species revealed clear genetic differentiation between geographic localities and catchments, evident from phylogenetic analyses and high FST values from AMOVA. In addition, the phylogenetic analyses indicate some deeper haplotype divergences within A. sudafricanum and Demoreptus that merit taxonomic attention. These results give important insight into evolutionary processes occurring through habitat specialisation and population isolation. Further research and sampling across a wider geographic setting that includes both major mountain blocks of the Escarpment and lowland non-Escarpment sites will allow for refined understanding of biodiversity and associated habitat preferences, and illuminate comparative inferences into gene flow and cryptic speciation.

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Investigation of Ongoing Recombination Through Genealogical Reconstruction for Sars-Cov-2

10.1101/2021.01.21.427579 ◽

2021 ◽

Author(s):

Anastasia Ignatieva ◽

Jotun Hein ◽

Paul A. Jenkins

Keyword(s):

South Africa ◽

Genetic Diversity ◽

Genetic Recombination ◽

Phylogenetic Analyses ◽

Evolutionary Process ◽

Recurrent Mutation ◽

Challenging Problem ◽

Sequencing Data ◽

Viral Pathogen ◽

History Of

AbstractThe evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem, and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables the analysis of recombination events that could have generated the data. We propose a framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and in South Africa, and find evidence of ongoing recombination.

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Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China

Current HIV Research ◽

10.2174/1570162x18666200415140652 ◽

2020 ◽

Vol 18 (3) ◽

pp. 210-218

Author(s):

Guolong Yu ◽

Yan Li ◽

Xuhe Huang ◽

Pingping Zhou ◽

Jin Yan ◽

...

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Reverse Transcriptase ◽

Phylogenetic Analyses ◽

Resistance Mutations ◽

Protease Inhibition ◽

Subtype B ◽

Primary Drug Resistance ◽

Hiv 1 ◽

Primary Drug

Background: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade’s polymorphisms in its functionally critical regions protease and reverse transcriptase. Objective: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B’s drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. Methods: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. Results: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE’s. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. Conclusions: CRF55_01B’s pol has different genetic diversity comparing to its counterpart in CRF55_01B’s parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

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Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽

10.3390/v13040545 ◽

2021 ◽

Vol 13 (4) ◽

pp. 545

Author(s):

Gédéon Prince Manouana ◽

Paul Alvyn Nguema-Moure ◽

Mirabeau Mbong Ngwese ◽

C.-Thomas Bock ◽

Peter G. Kremsner ◽

...

Keyword(s):

Genetic Diversity ◽

Preventive Measures ◽

Phylogenetic Analyses ◽

Enteric Viruses ◽

Study Cohort ◽

Viral Agent ◽

A Genome ◽

Stool Samples ◽

Pcr Techniques ◽

High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

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Enteroviruses in Respiratory Samples from Paediatric Patients of a Tertiary Care Hospital in Germany

Viruses ◽

10.3390/v13050882 ◽

2021 ◽

Vol 13 (5) ◽

pp. 882

Author(s):

Susanne Baertl ◽

Corinna Pietsch ◽

Melanie Maier ◽

Mario Hönemann ◽

Sandra Bergs ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analyses ◽

Tertiary Care ◽

Oxygen Demand ◽

Care Hospital ◽

Paediatric Patients ◽

Enterovirus A71 ◽

Coxsackievirus A6 ◽

Enterovirus D68 ◽

Tract Infections

Enteroviruses are associated with various diseases accompanied by rare but severe complications. In recent years, outbreaks of enterovirus D68 and enterovirus A71 associated with severe respiratory infections and neurological complications have been reported worldwide. Since information on molecular epidemiology in respiratory samples is still limited, the genetic diversity of enteroviruses was retrospectively analysed over a 4-year period (2013–2016) in respiratory samples from paediatric patients. Partial viral major capsid protein gene (VP1) sequences were determined for genotyping. Enteroviruses were detected in 255 (6.1%) of 4187 specimens. Phylogenetic analyses of 233 (91.4%) strains revealed 25 different genotypes distributed to Enterovirus A (39.1%), Enterovirus B (34.3%), and Enterovirus D (26.6%). The most frequently detected genotypes were enterovirus D68 (26.6%), coxsackievirus A6 (15.9%), and enterovirus A71 (7.3%). Enterovirus D68 detections were associated with lower respiratory tract infections and increased oxygen demand. Meningitis/encephalitis and other neurological symptoms were related to enterovirus A71, while coxsackievirus A6 was associated with upper respiratory diseases. Prematurity turned out as a potential risk factor for increased oxygen demand during enterovirus infections. The detailed analysis of epidemiological and clinical data contributes to the non-polio enterovirus surveillance in Europe and showed high and rapidly changing genetic diversity of circulating enteroviruses, including different enterovirus D68 variants.

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Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Diversity ◽

10.3390/d13030126 ◽

2021 ◽

Vol 13 (3) ◽

pp. 126

Author(s):

Emily K. Latch ◽

Kenneth L. Gee ◽

Stephen L. Webb ◽

Rodney L. Honeycutt ◽

Randy W. DeYoung ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Wildlife Management ◽

Field Observations ◽

Adaptive Potential ◽

Population Isolation ◽

Potential Benefits ◽

Wildlife Populations ◽

Mtdna Diversity

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

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Erosion rates and weathering timescales in the eastern Great Escarpment, South Africa

Chemical Geology ◽

10.1016/j.chemgeo.2021.120368 ◽

2021 ◽

pp. 120368

Author(s):

Tebogo V. Makhubela ◽

Jan D. Kramers ◽

Sibusiso M. Konyana ◽

Herman S. van Niekerk ◽

Stephan R. Winkler

Keyword(s):

South Africa ◽

Erosion Rates ◽

Great Escarpment

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Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315420001319 ◽

2021 ◽

pp. 1-11

Author(s):

Andrea Highfield ◽

Angela Ward ◽

Richard Pipe ◽

Declan C. Schroeder

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Dunaliella Salina ◽

Phylogenetic Analyses ◽

Ssu Rdna ◽

Lsu Rdna ◽

Hypersaline Environments ◽

Rdna Its ◽

Β Carotene ◽

Selection Of

Abstract Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

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Genetic diversity of the extremely rare Habenaria dentata and the rare Habenaria linearifolia (Orchidaceae) in South Korea: implications for population history and conservation

Plant Ecology and Evolution ◽

10.5091/plecevo.2018.1366 ◽

2018 ◽

Vol 151 (1) ◽

pp. 48-60

Author(s):

Mi Yoon Chung ◽

Hoa Thi Quynh Le ◽

Sungwon Son ◽

Huai Zhen Tian ◽

Myong Gi Chung

Keyword(s):

Genetic Diversity ◽

Southern China ◽

Geographic Location ◽

Population History ◽

Population Variation ◽

Conservation Strategies ◽

Ancestral Population ◽

Allozyme Diversity ◽

Glacial Origin

Background and aims – Since historical events often leave an indelible mark on levels of genetic diversity of plant populations, one may indirectly infer their evolutionary history with the help of current patterns of genetic diversity. The terrestrial orchid Habenaria dentata, an element of warm-temperate/subtropical vegetation, reaches its northernmost limits in the Korean Peninsula, and thus it is extremely rare there. As H. dentata was absent from the Peninsula during the Last Glacial Maximum (LGM), it is likely to be of post-glacial origin having arrived from either a single refugium or multiple refugia. However, its rare, temperate/boreal congener H. linearifolia might have persisted in situ in either macrorefugia or microrefugia on the Peninsula during the LGM.Methods – To test which hypothesis is most appropriate for each species, we investigated levels of allozyme-based (17 loci) genetic diversity and population genetic structure in the two only known populations of H. dentata and in 12 populations of H. linearifolia.Key results – No allozyme diversity was found in H. dentata (He = 0.000), whereas H. linearifolia exhibited low within-population variation (He = 0.060) and high among-population differentiation (FST = 0.237). We found little association between populations in relation to their geographic location; several populations presented individuals belonging to different clusters.Conclusions – Our results suggest that H. dentata likely originated from a single ancestral population (perhaps from southern Japan or southern China) through post-glacial dispersal, whereas H. linearifolia probably survived the LGM in situ in microrefugia situated at low to mid-elevated regions. We further suggest that separate conservation strategies for each species should be employed, given that the two taxa have different ecological and demographic traits and harbour different levels of genetic diversity.

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Biological and Phylogenetic Analyses Suggest that Two Cryphonectria spp. Cause Cankers of Eucalyptus in Africa

Plant Disease ◽

10.1094/pdis.2003.87.11.1329 ◽

2003 ◽

Vol 87 (11) ◽

pp. 1329-1332 ◽

Cited By ~ 18

Author(s):

J. Roux ◽

H. Myburg ◽

B. D. Wingfield ◽

M. J. Wingfield

Keyword(s):

South Africa ◽

South America ◽

South African ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Eucalyptus Grandis ◽

Its Region ◽

South African Isolate ◽

Dna Sequence Data ◽

The Republic

Cryphonectria cubensis is an economically important pathogen of commercial Eucalyptus spp. Differences have been reported for disease symptoms associated with Cryphonectria canker in South Africa and other parts of the world, and recent DNA-based comparisons have confirmed that the fungus in South Africa is different from that in South America and Australasia. During a disease survey in the Republic of Congo, Cryphonectria canker was identified as an important disease on Eucalyptus grandis and E. urophylla. In this study, we compared Congolese and South African isolates of C. cubensis using DNA sequence data and pathogenicity under greenhouse conditions. The β-tubulin and internal transcribed spacer (ITS) region sequences show that C. cubensis in Congo is different from the fungus in South Africa and that Congolese isolates group most closely with South American isolates. Furthermore, pathogenicity tests showed that a South African isolate was more aggressive than two Congolese isolates. We conclude that two distinct Cryphonectria spp. occur in Africa and hypothesize that the fungus in the Congo probably was introduced into Africa from South America. Both fungi are important pathogens causing disease and death of economically important plantation trees. However, they apparently have different origins and must be treated separately in terms of disease management and quarantine considerations.

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Language and the geopolitics of (dis)location: A study of Zimbabwean Shona and Ndebele speakers in Johannesburg

Language in Society ◽

10.1017/s0047404517000793 ◽

2018 ◽

Vol 47 (1) ◽

pp. 115-139 ◽

Cited By ~ 1

Author(s):

Gugulethu Siziba ◽

Lloyd Hill

Keyword(s):

South Africa ◽

South African ◽

Census Data ◽

Strong Association ◽

Geographic Location ◽

Migration Literature ◽

African Migrants ◽

Social Positioning ◽

Language And Ethnicity ◽

The City

AbstractThe Zimbabwean diaspora is a well-documented phenomenon. While much research has been done on Zimbabwean migration to South Africa, the role that language plays in this process has not been well researched. This article draws on South African census data and qualitative fieldwork data to explore the manner in which Zimbabwean migrants use languages to appropriate spaces for themselves in the City of Johannesburg. The census data shows that African migrants tend to concentrate in the Johannesburg CBD, and fieldwork in this area reveals that Zimbabwean migrants are particularly well established in two suburbs—Yeoville and Hillbrow. The article explores migrant language repertoires, which include English, Shona, Ndebele, and a variant of Zulu. While many contributions to the migration literature tend to assume a strong association between language and ethnicity, the article shows how this relationship is mediated by geographic location and social positioning within the city. (Language, migration, Johannesburg, South Africa, Zimbabwe)*

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