Incorporating parasite data in population structure studies of South African sardine Sardinops sagax

Parasitology ◽  
2014 ◽  
Vol 142 (1) ◽  
pp. 156-167 ◽  
Author(s):  
CARL DAVID VAN DER LINGEN ◽  
LAURA FRANCES WESTON ◽  
NURUDEAN NORMAN SSEMPA ◽  
CECILE CATHARINE REED
Keyword(s):  
South Africa ◽  
Population Structure ◽  
South African ◽  
Infection Intensity ◽  
Distribution Patterns ◽  
Convincing Evidence ◽  
Spatial Gradients ◽  
Spatial Differences ◽  
Sardine Population ◽  
Sardinops Sagax

SUMMARYA multidisciplinary approach has been applied to examine the population structure of sardine Sardinops sagax off South Africa, where this species supports significant fisheries and is also of ecological and eco-tourism importance. Observations of discontinuous sardine distribution patterns, discrete spawning grounds and significant spatial differences in a variety of phenotypic characteristics have suggested the existence of discrete western, southern and eastern sardine sub-populations or stocks. The use of parasites as biological tags to elucidate sardine population structure has recently been investigated, and strong spatial gradients around South Africa in the prevalence, mean infection intensity and mean abundance of a digenean ‘tetracotyle’ type metacercarial endoparasite considered to be of the genus Cardiocephaloides and found in the humours of fish eyes support and have proved particularly convincing evidence for the sardine multiple stock hypothesis. A discontinuous distribution in the occurrence of another parasite, the coccidean Eimeria sardinae found in fish testes, has provided additional but weaker evidence of discrete stocks. These results have contributed to a changed understanding of the population structure of South African sardine and have significant implications for management of the fisheries for this species.

The quantitative use of parasite data in multistock modelling of South African sardine (Sardinops sagax)

2017 ◽  
Vol 74 (11) ◽  
pp. 1895-1903 ◽  
Author(s):  
Carryn L. de Moor ◽  
Douglas S. Butterworth ◽  
Carl D. van der Lingen
Keyword(s):  
South Africa ◽  
Population Structure ◽  
South African ◽  
Parasite Prevalence ◽  
Parasite Infection ◽  
Stock Structure ◽  
The West ◽  
Fish Stocks ◽  
Length Data ◽  
Stock Mixing

Differences in parasite infection have previously been used to distinguish between fish stocks. We demonstrate a novel use of parasite prevalence-by-length data to inform quantitatively on stock mixing. An initial two mixing stock hypothesis proved consistent with biological and survey data, suggesting that there are different stocks of sardine off the west and south coasts of South Africa. That hypothesis assumed that only recruits moved from the west to the south stock. However, new “tetracotyle”-type metacercarian parasite bio-tag data indicate a need to allow older fish to move between the stocks as well. We demonstrate extension of bio-tagging to inform on the plausibility of population structure hypotheses by including parasite prevalence-by-length data in the model’s likelihood. Our method enables the estimation of the magnitude of mixing between semidiscrete stocks, providing more precise estimates of annual movement. Such improved precision may be important in better informing future movement hypotheses and thereby management. Our research provides a framework to use to inform quantitatively on stock structure and movement hypotheses for other fish species with bio-tagging data.

scholarly journals Morpho-agronomic and genetic variation among Phaseolus vulgaris landraces from selected provinces of South Africa

2021 ◽  
Author(s):  
Valencia Vuyisile Ndlangamandla ◽  
Nontuthuko Rosemary Ntuli
Keyword(s):  
South Africa ◽  
Population Structure ◽  
Phaseolus Vulgaris ◽  
South African ◽  
Agronomic Traits ◽  
Block Design ◽  
Reproductive Traits ◽  
High Level ◽  
Clustering Pattern ◽  
Or Genes

Abstract Key message The morpho-agronomic and genetic studies recorded variations in vegetative and reproductive traits, and in molecular information through population structure and clustering approaches among South African Phaseolus vulgaris landraces. Abstract Phaseolus vulgaris L., commonly known as common beans, is widely used for its edible leaves, immature pods, and dry seeds. Studies on variation in morphology and genetics among P. vulgaris landraces are limited in South Africa. Therefore, the current study aimed to determine the morpho-agronomic and genetic variations among P. vulgaris landraces. Thirty-eight landraces from different agro-ecological origins, planted in a randomized complete block design, had their variation in vegetative and reproductive traits determined. These landraces were studied for their genetic diversity using simple sequence repeat (SSR) markers. The landraces were clustered in a biplot and dendrogram based on their seed coats, shape, similar morpho-agronomic traits, and their areas of origin. A total of 57 alleles were produced with a mean of 3.64 per SSR locus. The polymorphism information content ranged from 0.00 to 0.58. The population structure had the highest delta value K = 2, thus the 38 landraces were divided into two subpopulations based on the Bayesian approach. The population structure showed an overlap among the landraces as several from the Mesoamerican carried some seed traits or genes from the Andean gene pool, and showed a high level of admixtures. The principal coordinate analysis and the dendrogram had a similar clustering pattern as the population structure. This study revealed the potential markers with high diversity that can be used to determine genetically homogenous/heterogeneous landraces. Therefore, the use of PV-ctt001, PV-ag001, and PV-at003 could be beneficial in future breeding, conservation, and marker-assisted selection studies.

scholarly journals Online appendix 1:South African National Survey of Arachnida: A checklist of the spiders (Arachnida, Araneae) of the Lekgalameetse Nature Reserve, Limpopo province, South Africa

Koedoe ◽  
2016 ◽  
Vol 58 (1) ◽  
Author(s):  
Stefan H. Foord ◽  
Anna S. Dippenaar-Schoeman ◽  
Rudy Jocqué ◽  
Charles R. Haddad ◽  
Robin Lyle ◽  
...  
Keyword(s):  
South Africa ◽  
South African ◽  
National Survey ◽  
Nature Reserve ◽  
Conservation Status ◽  
Distribution Patterns ◽  
Limpopo Province ◽  
Specific Information ◽  
Spider Species ◽  
Online Appendix

The aim of the South African National Survey of Arachnida (SANSA) is to document the Arachnida fauna of South Africa. One of the focus areas of SANSA is to survey protected areas to obtain species-specific information, and species distribution patterns for Red Data assessments. Here, we provide the first checklist of the spider species of Lekgalameetse Nature Reserve (LNR) in the Limpopo province of South Africa collected during five surveys between 2009 and 2016 using methods targeting both the ground and field layers. Forty-five families, represented by 168 genera and 268 species, have been collected so far. The most species-rich families were the Salticidae (41 spp.) and Araneidae (38 spp.), followed by the Thomisidae (33 spp.), while 11 families were represented by one species. Information on spider guilds, endemicity value and conservation status are provided. The LNR protects approximately 12.2% of the total South African spider fauna. Two species, Hasarinella distincta Haddad & Wesołowska, 2013 (Salticidae) and Ballomma legala Jocqué & Henrard, 2015 (Zodariidae), are presently known to be endemic to the reserve.Conservation implications: The LNR falls within the Savanna Biome in the Limpopo province. Only five spider species were previously known from the reserve and 263 spp. are reported from the reserve for the first time. Thirteen species are possibly new to science and 2 species represent new distribution records for South Africa.

scholarly journals South African National Survey of Arachnida: A checklist of the spiders (Arachnida, Araneae) of the Lekgalameetse Nature Reserve, Limpopo province, South Africa

Koedoe ◽  
2016 ◽  
Vol 58 (1) ◽  
Author(s):  
Stefan H. Foord ◽  
Anna S. Dippenaar-Schoeman ◽  
Rudy Jocqué ◽  
Charles R. Haddad ◽  
Robin Lyle ◽  
...  
Keyword(s):  
South Africa ◽  
South African ◽  
National Survey ◽  
Nature Reserve ◽  
Conservation Status ◽  
Distribution Patterns ◽  
Limpopo Province ◽  
Specific Information ◽  
Spider Species ◽  
Species Specific

The aim of the South African National Survey of Arachnida (SANSA) is to document the Arachnida fauna of South Africa. One of the focus areas of SANSA is to survey protected areas to obtain species-specific information, and species distribution patterns for Red Data assessments. Here, we provide the first checklist of the spider species of Lekgalameetse Nature Reserve (LNR) in the Limpopo province of South Africa collected during five surveys between 2009 and 2016 using methods targeting both the ground and field layers. Forty-five families, represented by 168 genera and 268 species, have been collected so far. The most species-rich families were the Salticidae (41 spp.) and Araneidae (38 spp.), followed by the Thomisidae (33 spp.), while 11 families were represented by one species. Information on spider guilds, endemicity value and conservation status are provided. The LNR protects approximately 12.2% of the total South African spider fauna. Two species, Hasarinella distincta Haddad & Wesołowska, 2013 (Salticidae) and Ballomma legala Jocqué & Henrard, 2015 (Zodariidae), are presently known to be endemic to the reserve.Conservation implications: The LNR falls within the Savanna Biome in the Limpopo province. Only five spider species were previously known from the reserve and 263 spp. are reported from the reserve for the first time. Thirteen species are possibly new to science and 2 species represent new distribution records for South Africa.

scholarly journals Population Structure of Non-ST6 Listeria monocytogenes Isolated in the Red Meat and Poultry Value Chain in South Africa

2020 ◽  
Vol 8 (8) ◽  
pp. 1152
Author(s):  
Itumeleng Matle ◽  
Thendo Mafuna ◽  
Evelyn Madoroba ◽  
Khanyisile R. Mbatha ◽  
Kudakwashe Magwedere ◽  
...  
Keyword(s):  
South Africa ◽  
Population Structure ◽  
South African ◽  
Value Chain ◽  
Meat Products ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Processed Meat ◽  
Main Lineage ◽  
High Level

Meat products have been implicated in many listeriosis outbreaks globally, however there is a dearth of information on the diversity of L. monocytogenes isolates circulating in food products in South Africa. The aim of this study was to investigate the population structure of L. monocytogenes isolated in the meat value chain within the South African market. Based on whole-genome sequence analysis, a total of 217 isolates were classified into two main lineage groupings namely lineages I (n = 97; 44.7%) and II (n = 120; 55.3%). The lineage groups were further differentiated into IIa (n = 95, 43.8%), IVb (n = 69, 31.8%), IIb (n = 28, 12.9%), and IIc (n = 25, 11.5%) sero-groups. The most abundant sequence types (STs) were ST204 (n = 32, 14.7%), ST2 (n = 30, 13.8%), ST1 (n = 25, 11.5%), ST9 (n = 24, 11.1%), and ST321 (n = 21, 9.7%). In addition, 14 clonal complex (CCs) were identified with over-representation of CC1, CC3, and CC121 in “Processed Meat-Beef”, “RTE-Poultry”, and “Raw-Lamb” meat categories, respectively. Listeria pathogenic islands were present in 7.4% (LIPI-1), 21.7% (LIPI-3), and 1.8% (LIPI-4) of the isolates. Mutation leading to premature stop codons was detected in inlA virulence genes across isolates identified as ST121 and ST321. The findings of this study demonstrated a high-level of genomic diversity among L. monocytogenes isolates recovered across the meat value chain control points in South Africa.

scholarly journals South African National Survey of Arachnida: A checklist of the spiders (Arachnida, Araneae) of the Tswalu Kalahari Reserve in the Northern Cape province, South Africa

Koedoe ◽  
2018 ◽  
Vol 60 (1) ◽  
Author(s):  
Anna S. Dippenaar-Schoeman ◽  
Charles R. Haddad ◽  
Robin Lyle ◽  
Leon N. Lotz ◽  
Stefan H. Foord ◽  
...  
Keyword(s):  
South Africa ◽  
South African ◽  
National Survey ◽  
New Records ◽  
Conservation Status ◽  
Distribution Patterns ◽  
Specific Information ◽  
Spider Species ◽  
Northern Cape ◽  
Species Specific

One of the aims of South African National Survey of Arachnida (SANSA) is to survey protected areas to obtain species-specific information and compile inventories to determine species distribution patterns and evaluate their conservation status for Red Data assessments. The aim of this study, the first in a series of surveys of the Diamond Route Reserves, was to compile the first checklist of the spider species in the Northern Cape at the Tswalu Kalahari Reserve. Spiders were collected during three survey periods (2005−2013) using different collecting methods to sample both the ground and field layers. In total, 32 families represented by 108 genera and 136 species have been collected so far. The most species-rich families are the Salticidae (20 spp.) and Thomisidae (18 spp.), followed by the Gnaphosidae and Araneidae (11 spp. each), while nine families are represented by singletons. The free-living wandering spiders represent 97 spp., while 39 spp. are web-builders. Information on spider guilds, endemicity value and conservation status are provided. The Tswalu Kalahari Reserve protects approximately 6.1% of the total South African spider fauna, while 24.3% of the species found in the reserve are South African endemics, of which 5.9% are Northern Cape endemics. Approximately 6.0% of the species sampled are possibly new to science or represent new records for South Africa.Conservation implications: The Tswalu Kalahari Reserve falls within the Savanna Biome in the Northern Cape province. Only one spider species was previously known from the reserve; a further 135 spp. are reported for the first time, with 5.9% of the species being Northern Cape endemics and 24.3% South African endemics. Approximately 6.0% of the species may be new to science or represent new records for South Africa.

scholarly journals Spider checklist for the Blouberg, in the Vhembe Biosphere Reserve, South Africa

Bothalia ◽  
2019 ◽  
Vol 49 (1) ◽  
Author(s):  
Stefan Foord ◽  
Anna S. Dippenaar-Schoeman ◽  
Charles R. Haddad ◽  
Colin Schoeman ◽  
Norbert Hahn ◽  
...  
Keyword(s):  
South Africa ◽  
South African ◽  
Biosphere Reserve ◽  
Distribution Patterns ◽  
African Species ◽  
Species List ◽  
The North ◽  
North Eastern ◽  
Collecting Methods ◽  
Conservation Concern

Background: The north-eastern mountainous region of South Africa has been identified as a spider diversity hotspot and centre of endemisim. The Blouberg is an isolated inselberg that forms part of the Soutpansberg geological complex, the northernmost mountain in South Africa.Objectives: This article provides an updated species list of the Blouberg spiders, which includes details of the distribution patterns and conservation statuses of all taxa. Exotic species and species of special conservation concern are identified.Method: Surveys were conducted between 2005 and 2012, and a range of collecting methods were used to sample both the ground and field layers.Results: A total of 47 families were sampled in 210 genera and 346 species. The families of Salticidae (45 spp.), Gnaphosidae (32 spp.), Thomisidae (31 spp.), Araneidae (26 spp.) and Lycosidae (24 spp.) were the most diverse. Five species are of conservation concern, one species is Vulnerable, one is possibly exotic and 62 species are South African endemics.Conclusion: Presently, 17% of South African species are protected on the mountain and its surrounding foothills. The latter are of particular conservation concern, while the mountaintop and its associated habitats are under-sampled.

scholarly journals Borassus aethiopum Mart. (Arecaceae) in Limpopo province with a key to South African palms

Bothalia ◽  
2019 ◽  
Vol 49 (1) ◽  
Author(s):  
Stefan J. Siebert ◽  
Madeleen Struwig
Keyword(s):  
South Africa ◽  
Population Structure ◽  
South African ◽  
Leaf Shape ◽  
Fruit Size ◽  
Size Class ◽  
Limpopo Province ◽  
Disjunct Distribution ◽  
Palm Species ◽  
Borassus Aethiopum

Background: Borassus aethiopum Mart. commonly occurs in many parts of tropical Africa and in South Africa it is restricted to the Leydsdorp region where it is conspicuous along the Selati River. The species is sometimes considered to have been introduced to South Africa due to its disjunct distribution. It has remained poorly studied and little is known about the local populations of this palm.Objectives: This study provides a descriptive treatment and documents the population structure of B. aethiopum in this area, and presents a key to the six indigenous palm species of South Africa.Methods: All accessible populations were surveyed and documented, and eight transects were randomly placed to gather data on size class distributions. B. aethiopum and other indigenous palm species were compared morphologically.Results: The population structure analyses of B. aethiopum revealed a monotonic decline, but the permutation index suggested that the species is prone to recruitment events. This is supported by patches that are dominated by specific height classes. Leaf shape and size, fruit size and geographical distribution were the diagnostic characters most useful to recognize the species of South African indigenous palms.Conclusion: Borassus aethiopum is distinguishable from other South African palms based on stem, leaf and fruit characters. It is considered as indigenous to Granite Lowveld as the palm is part of the natural vegetation and is characterized by a size class distribution reflecting a stable population. 

Reframing Xenophobia in South Africa as Colour-Blind: The Limits of the Afro Phobia Thesis

2020 ◽  
Vol 17 (3) ◽  
pp. 433-444
Author(s):  
Amanuel Isak Tewolde
Keyword(s):  
South Africa ◽  
South African ◽  
Analytical Framework ◽  
Conflict Theory ◽  
Black African ◽  
South Africans ◽  
Theoretical Perspectives ◽  
Online Newspaper ◽  
Close Proximity ◽  
Realistic Conflict Theory

Many scholars and South African politicians characterize the widespread anti-foreigner sentiment and violence in South Africa as dislike against migrants and refugees of African origin which they named ‘Afro-phobia’. Drawing on online newspaper reports and academic sources, this paper rejects the Afro-phobia thesis and argues that other non-African migrants such as Asians (Pakistanis, Indians, Bangladeshis and Chinese) are also on the receiving end of xenophobia in post-apartheid South Africa. I contend that any ‘outsider’ (White, Asian or Black African) who lives and trades in South African townships and informal settlements is scapegoated and attacked. I term this phenomenon ‘colour-blind xenophobia’. By proposing this analytical framework and integrating two theoretical perspectives — proximity-based ‘Realistic Conflict Theory (RCT)’ and Neocosmos’ exclusivist citizenship model — I contend that xenophobia in South Africa targets those who are in close proximity to disadvantaged Black South Africans and who are deemed outsiders (e.g., Asian, African even White residents and traders) and reject arguments that describe xenophobia in South Africa as targeting Black African refugees and migrants.

Region of Birth and Child Mortality among Black Migrants to South Africa: Is there a foreign-born advantage?

2016 ◽  
Vol 13 (3) ◽  
pp. 359-376 ◽  
Author(s):  
Tiffany L Green ◽  
Amos C Peters
Keyword(s):  
South Africa ◽  
South African ◽  
Child Mortality ◽  
Southern Africa ◽  
Strong Relationship ◽  
Developed Countries ◽  
Black Immigrants ◽  
Foreign Born ◽  
Region Of Origin ◽  
Child Deaths

Much of the existing evidence for the healthy immigrant advantage comes from developed countries. We investigate whether an immigrant health advantage exists in South Africa, an important emerging economy.  Using the 2001 South African Census, this study examines differences in child mortality between native-born South African and immigrant blacks.  We find that accounting for region of origin is critical: immigrants from southern Africa are more likely to experience higher lifetime child mortality compared to the native-born population.  Further, immigrants from outside of southern Africa are less likely than both groups to experience child deaths.  Finally, in contrast to patterns observed in developed countries, we detect a strong relationship between schooling and child mortality among black immigrants.

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