Southern African Samples Research Articles

Rediscovery of Actinodontum lomaense: a range extension from Sierra Leone to southern Africa

The history of Actinodontum lomaense has been marked by taxonomic revisions since its initial discovery in samples from Sierra Leone during 1984. The reassignment from the genus Docidium to the genus Actinodontum primarily resulted from pronounced morphological differences, including variations in cell size and shape, ornamentations on the cell wall, and the presence of conical teeth-like structures at the isthmus. This article reports on the discovery of A. lomaense in two locations in southern Africa, marking a significant expansion of the geographical distribution range of the genus, from the tropical regions of Sierra Leone to sub-tropical environments in South Africa and the Kingdom of Lesotho. Additionally, the preference of Actinodontum species for relatively high altitudes, observed in this study, confirms a biogeographical pattern characterising this genus. Cell dimensions recorded in the southern African samples slightly exceeded dimensions previously reported in the literature. As a result, an extention of the dimension ranges for this species is proposed. Findings presented in this article, along with physico-chemical variables measured in their habitat, contribute to our understanding of the ecological preferences and distribution patterns of A. lomaense. It also provides valuable insights into the biogeography of desmid species on the African continent.

South African Buffalo-Derived Theileria parva Is Distinct From Other Buffalo and Cattle-Derived T. parva.

Theileria parva is a protozoan parasite transmitted by the brown-eared ticks, Rhipicephalus appendiculatus and Rhipicephalus zambeziensis. Buffaloes are the parasite’s ancestral host, with cattle being the most recent host. The parasite has two transmission modes namely, cattle–cattle and buffalo–cattle transmission. Cattle–cattle T. parva transmission causes East Coast fever (ECF) and January disease syndromes. Buffalo to cattle transmission causes Corridor disease. Knowledge on the genetic diversity of South African T. parva populations will assist in determining its origin, evolution and identify any cattle–cattle transmitted strains. To achieve this, genomic DNA of blood and in vitro culture material infected with South African isolates (8160, 8301, 8200, 9620, 9656, 9679, Johnston, KNP2, HL3, KNP102, 9574, and 9581) were extracted and paired-end whole genome sequencing using Illumina HiSeq 2500 was performed. East and southern African sample data (Chitongo Z2, Katete B2, Kiambu Z464/C12, Mandali Z22H10, Entebbe, Nyakizu, Katumba, Buffalo LAWR, and Buffalo Z5E5) was also added for comparative purposes. Data was analyzed using BWA and SAMtools variant calling with the T. parva Muguga genome sequence used as a reference. Buffalo-derived strains had higher genetic diversity, with twice the number of variants compared to cattle-derived strains, confirming that buffaloes are ancestral reservoir hosts of T. parva. Host specific SNPs, however, could not be identified among the selected 74 gene sequences. Phylogenetically, strains tended to cluster by host with South African buffalo-derived strains clustering with buffalo-derived strains. Among the buffalo-derived strains, South African strains were genetically divergent from other buffalo-derived strains indicating possible geographic sub-structuring. Geographic sub- structuring was also observed within South Africa strains. The knowledge generated from this study indicates that to date, ECF is not circulating in buffalo from South Africa. It also shows that T. parva has historically been present in buffalo from South Africa before the introduction of ECF and was not introduced into buffalo during the ECF epidemic.

Lip height estimation in a southern African sample

INTRODUCTION: The South African Police Service frequently relies on craniofacial approximation and superimposition to assist in identifying unknown deceased individuals. Standards to estimate lip height are however limited. Findings from this study share medical applications. Aims and objectives: Establish reliable standards for estimating lip height using dentoskeletal measurements. METHODS: Cone-beam CTs comprising 124 black and 39 white southern African adults were assessed. A series of dimensions were recorded using a DICOM viewer with an inbuilt measuring tool. Relationships between hard tissue structures (maxillary, mandibular and total central incisor heights, their corresponding root lengths, face height (N-Gn), and nose height (N-Sn)) and respective overlaying soft tissues (upper, lower and total lip heights) were evaluated. RESULTS AND CONCLUSIONS: Statistically significant differences were observed between population, sex and age groups. A selection of regression equations to estimate lip height was calculated that included population, sex and approximate age (20-39 and 40+ years) for improved goodness-of-fit (r2-value). Regression models using face height produced the strongest multiple correlation (r-value) and goodness-of-fit (r2-value). Validation testing indicated that regression models often improved upon mean measurements, while offering a degree of individuality that mean values do not.

Updating histological data on crown initiation and crown completion ages in southern Africans.

To update histological data on crown initiation and completion ages in southern Africans. To evaluate implications of these data for studies that: (a) rely on these data to time linear enamel hypoplasias (LEHs), or, (b) use these data for comparison to fossil hominins. Initiation ages were calculated on 67 histological sections from southern Africans, with sample sizes ranging from one to 11 per tooth type. Crown completion ages for southern Africans were calculated in two ways. First, actual derived initiation ages were added to crown formation times for each histological section to obtain direct information on the crown completion ages of individuals. Second, average initiation ages from this study were added to average crown formation times of southern Africans from the Reid and coworkers previous studies that were based on larger samples. For earlier-initiating tooth types (all anterior teeth and first molars), there is little difference in ages of initiation and crown completion between this and previous studies. Differences increase as a function of initiation age, such that the greatest differences between this and previous studies for both initiation and crown completion ages are for the second and third molars. This study documents variation in initiation ages, particularly for later-initiating tooth types. It upholds the use of previously published histological aging charts for LEHs on anterior teeth. However, this study finds that ages of crown initiation and completion in second and third molars for this southern African sample are earlier than previously estimated. These earlier ages reduce differences between modern humans and fossil hominins for these developmental events in second and third molars.

Perikymata numbers and enamel extension rates in the incisors of three archaeological modern human populations from two caves located in Spain: Maltravieso Cave (Cáceres) and Mirador Cave (Burgos)

Abstract A number of authors have studied the variability of total perikymata counts on permanent incisors in different modern human populations, finding that some populations show a significantly lower number of perikymata than others. However, little is known about the overall variability of these traits in archaeological populations of modern humans. Our aim was to broaden the available data on total perikymata counts on incisors, and to further discuss enamel extension rate variability in modern human incisors. Our sample consisted of 15 incisors from three different archaeological populations belonging to the Holocene: two populations from Mirador Cave (Sierra de Atapuerca, Burgos) assigned to two different chronological periods, and a population from Maltravieso Cave (Caceres). We refer to these populations as the MTV–MIR sample. Perikymata were counted from several images obtained using an environmental scanning electron microscope (ESEM). Our results suggest the total number of perikymata of the MTV–MIR incisors fall most comfortably within the distribution of counts reported for modern Europeans and Inuit rather than those representing southern African samples of incisors. Furthermore, the percentage of the perikymata numbers in the last five deciles into which the crowns were divided (the cervical half) did not show statistically significant differences when compared to the other modern human populations. This suggests that enamel extension rates among modern human incisors share a common pattern, which might differ from that present in other species. More data from other modern and archaeological sub-Saharan African samples are needed to test whether low perikymata counts are exclusive to the southern African group or are indeed truly representative of sub-Saharan African populations as a whole today and in the past.

Significant population genetic structuring of the holoplanktic scyphozoan Pelagia noctiluca in the Atlantic Ocean

Pelagia noctiluca is thought to have a global distribution, yet our understanding of genetic connectivity across the range of this problem animal is poor. Here, we investigate the genetic structure of populations off southern Africa using mitochondrial COI and nuclear ITS1 and ITS2 genes, and compare the results to recent work conducted in the North-East Atlantic. Analyses showed significant differentiation between the southern and northern Atlantic population groups (COI Φ st = 0.72, ITS2 Φ st = 0.23, p < 0.001), which suggests historical rather than contemporary gene flow. Southern African samples showed high haplotypic (h = 1) and low nucleotide (π = 0.008) diversity, similar to those from Europe. Phylogenetic analyses suggest South African samples to have diverged earlier than those from the northern Atlantic.

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ~3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ~60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.

A review of early Homo in southern Africa focusing on cranial, mandibular and dental remains, with the description of a new species ( Homo gautengensis sp. nov.)

The southern African sample of early Homo is playing an increasingly important role in understanding the origins, diversity and adaptations of the human genus. Yet, the affinities and classification of these remains continue to be in a state of flux. The southern African sample derives from five karstic palaeocave localities and represents more than one-third of the total African sample for this group; sampling an even wider range of anatomical regions than the eastern African collection. Morphological and phenetic comparisons of southern African specimens covering dental, mandibular and cranial remains demonstrate this sample to contain a species distinct from known early Homo taxa. The new species Homo gautengensis sp. nov. is described herein: type specimen Stw 53; Paratypes SE 255, SE 1508, Stw 19b/33, Stw 75–79, Stw 80, Stw 84, Stw 151, SK 15, SK 27, SK 45, SK 847, SKX 257/258, SKX 267/268, SKX 339, SKX 610, SKW 3114 and DNH 70. H. gautengensis is identified from fossils recovered at three palaeocave localities with current best ages spanning ∼2.0 to 1.26–0.82 million years BP. Thus, H. gautengensis is probably the earliest recognised species in the human genus and its longevity is apparently well in excess of H. habilis.

What molars contribute to an emerging understanding of lateral enamel formation in Neandertals vs. modern humans

Two hypotheses, based on previous work on Neandertal anterior and premolar teeth, are investigated here: (1) that estimated molar lateral enamel formation times in Neandertals are likely to fall within the range of modern human population variation, and (2) that perikymata (lateral enamel growth increments) are distributed across cervical and occlusal halves of the crown differently in Neandertals than they are in modern humans. To investigate these hypotheses, total perikymata numbers and the distribution of perikymata across deciles of crown height were compared for Neandertal, northern European, and southern African upper molar mesiobuccal (mb) cusps, lower molar mesiobuccal cusps, and the lower first molar distobuccal (db) cusp. Sample sizes range from five (Neandertal M 1db) to 29 (southern African M 1mb). Neandertal mean perikymata numbers were found to differ significantly from those of both modern human samples (with the Neandertal mean higher) only for the M 2mb. Regression analysis suggests that, with the exception of the M 2mb, the hypothesis of equivalence between Neandertal and modern human lateral enamel formation time cannot be rejected. For the M 2mb, regression analysis strongly suggests that this cusp took longer to form in the Neandertal sample than it did in the southern African sample. Plots of perikymata numbers across deciles of crown height demonstrate that Neandertal perikymata are distributed more evenly across the cervical and occlusal halves of molar crowns than they are in the modern human samples. These results are integrated into a discussion of Neandertal and modern human lateral enamel formation across the dentition, with reference to issues of life history and enamel growth processes.

Mammalian body size changes and Plio-Pleistocene environmental shifts: implications for understanding hominin evolution in eastern and southern Africa

This study examines geographic and temporal variation in three mammalian taxa co-occurring in eastern and southern Africa. The selected taxa—the spotted hyena ( Crocuta crocuta), the plains zebra ( Equus burchellii), and the impala ( Aepyceros melampus)—are geographically widespread in modern times and are abundant in eastern and southern African Plio-Pleistocene fossil sites. Craniodental measurements of modern conspecifics from known geographic locations are compared using multivariate statistical methods to discern patterns of modern geographic variation within taxa. Modern and fossil samples are statistically compared to assess the nature and extent of inferred shifts in body size, both between modern samples and through time in each region. These results indicate that modern spotted hyenas and plains zebras exhibit mainly size variation between regions, with southern African samples possessing statistically larger craniodental metrics than eastern African samples. Comparison of fossil and modern samples reveals that the fossil assemblages do not show the same pattern of geographic variation. Significant temporal changes are more numerous between fossil and modern eastern African samples, and these changes are not mirrored by similar changes in the southern African samples. The changes experienced by taxa in eastern Africa appear to have been more extreme and wide-ranging than those in southern Africa, a presumed refugium. This result accords well with genetic studies of several large mammal species and paleoenvironmental studies suggesting that eastern African localized environments were more affected by tectonism and volcanism than were those in southern Africa. This study suggests that different evolutionary scenarios may have existed within Africa during the Plio-Pleistocene, but that both regions played unique and complementary roles in the evolution of African hominins and the broader faunal community.

Anterior tooth growth periods in Neandertals were comparable to those of modern humans

A longstanding controversy in paleoanthropology surrounds the question of whether Neandertals shared the prolonged growth periods of modern humans. To address this question, this investigation compares the duration of enamel formation in Neandertals with that of three comparative modern human groups. Because dental and somatic growth are correlated with each other, dental growth periods are indicative of overall periods of growth. Growth increments on the anterior teeth of Neandertals, modern Inuit, and modern people from Newcastle and southern Africa were counted and their means compared. In addition, potential variation in the time spans represented by growth increments was considered and incorporated into the analysis of enamel formation times. These analyses show that Neandertal imbricational enamel formation times, although likely to have been faster than those of the Inuit, are not likely to have been faster than those of the Newcastle sample and for some teeth are clearly slower than those of the southern African sample. Thus, Neandertal tooth growth and, by extension, somatic growth, appears to be encompassed within the modern human range of interpopulation variation.

A Cross-cultural Study with Culture Fair Normative Indications on WAIS-III Digit Symbol―Incidental Learning

ABSTRACT The WAIS-III Digit Symbol-Incidental Learning optional procedure, including Pairing and Free Recall, was administered to a southern African sample (N = 68, age range 19–30), which was stratified for ethnicity in association with language of origin (white English first language versus black African first language), educational level (Grade 12 and Graduate), and quality of education (advantaged and disadvantaged). (‘African language’ is the term used to denote the indigenous languages of black populations in southern Africa). Results yielded no significant differences for ethnicity/language of origin, level or quality of education, indicating that Digit Symbol-Incidental Learning may be a relatively culture independent task with utility as a neuropsychological screening instrument. Broad normative guidelines are provided for diagnostic purposes, and comparisons are made with available norms.

Cross-cultural Effects on IQ Test Performance: A Review and Preliminary Normative Indications on WAIS-III Test Performance

ABSTRACT This article presents a review of cross-cultural influences on Wechsler IQ tests, together with a preliminary investigation into WAIS-III test performance (English administration) for a southern African sample (age range 19–30) stratified for white English first language and black African first language, level and quality of education. (‘African language’ is the term used to denote the indigenous languages of black populations in southern Africa). A two-way ANOVA revealed highly significant effects for both level and quality of education within the black African first language group. Scores for the white English and black African first language groups with advantaged education were comparable with the US standardization, whereas scores for black African first language participants with disadvantaged education were significantly lower than this. Thus indications from this research are that normative studies should take account of the influential variable of quality of education, in addition to level of education. Alternatively faulty conclusions may be drawn about the effects of ethnicity, with the potential for neuropsychological misdiagnosis.

Comparative meta-analysis of the impact of offshore marine mining on macrobenthic communities versus organic pollution studies

The phylum-level meta-analysis approach has been proposed as a way of comparing geographically different areas along a common scale of disturbance. However, the training data set which establishes the scale of disturbance and all subsequent studies using the approach have been exposed to some sort of organic or inorganic pollution. Using macrobenthic communities subjected to a short-lived but intense physical disturbance from offshore mining off the west coast of Southern Africa, we tested the applicability of the meta-analysis approach for assessing the severity of disturbance in physically disturbed communities. The positioning of the original data set along a primary axis of disturbance was maintained; however, a second significant separation, along the vertical axis, distinguishes between macrobenthic assemblages from southern Africa and the NE Atlantic Shelf. The southern African samples are characterised by a larger proportion of Crustacea, and in the case of mined samples Mollusca, whereas the NE Atlantic data contain relatively more Echinodermata in the unpolluted samples and are dominated by Annelida in the organically enriched areas. The proportion of annelids decreased by about 50% in mined areas compared to the non-mined areas and the NE Atlantic samples. Conversely, bivalves and gastropods exhibited a notable increase in proportion in the mined patches compared to the adjacent non-mined areas, possibly as a result of their preferential ability to survive the mining process or their better ability to recolonise after mining, or an interplay of both factors. The mining activity may result in the selection of species for their physical robustness and tolerance to mining rather than their resistance to pollution in the conventional sense. The failure of the meta-analysis to ordinate the mined samples along the primary horizontal axis of disturbance, as defined by Warwick & Clarke¹s original study (Mar Ecol Prog Ser 92:221-231), does not reflect a failure of the meta-analysis to detect disturbance, but rather shows that the primary axis is strongly determined by the opportunistic species characteristic of organically enriched areas. It appears that phylum-level meta-analysis is better suited to assessing the impact of organic and chemical pollution on an ocean-basin scale than it is to physical disturbance caused by offshore mining.

Relationship between size of distal accessory tubercles and hypocones in permanent maxillary molar crowns of southern Africans

The relationships between total occlusal crown area and the basal cusp areas of the accessory distal tubercle (C5) and the hypocone were analysed in molars of complete upper tooth rows of a southern African sample. While non-parametric tests between hypocone and C5 sizes did not yield statistically significant results, analyses of metrical data revealed a trend towards compensatory interaction between both cusps. Contrary to previous reports the size of C5 was found to be independent of total crown area. As enamel is thickest on cusp tips there may be a functional reason for the frequency of occurrence of the distal accessory tubercle. The pattern of distribution of the hypocone and C5 within a tooth row may be related to the occlusal wear pattern in Homo, which exhibits a marked lingual slope of wear in anterior molars and a horizontal or even buccal slope in posterior teeth.

On the relative frequencies of hominid maxillary and mandibular teeth and jaws as taphonomic indicators

In southern African samples of early hominid remains, maxillary and mandibular teeth (deciduous-plus-permanent) have a virtually equal chance of accumulating in the dolomitic limestone cave deposits, of being preserved therein and recovered therefrom. Thus, of 1066 fossil teeth ofAustralopithecus spp. plusHomo habilis, 51.9 per cent are maxillary and 48.1 per cent mandibular. On the other hand, the East African sample of 847 early hominid, deciduous-plus-permanent teeth, departs more strikingly from a 1∶1 ratio: it comprises 41.0 per cent maxillary and 59.0 per cent mandibular teeth. It is inferred that mandibular teeth have a somewhat better chance of accumulating and being preserved in, and being recovered from, the open, fluvial, lacustrine and deltaic sedimentary environments of the East African sites. The dental proportions are approximately matched by the proportions of jaws. For example, the maxilla: mandible proportions at Koobi fora in northern Kenya are 33.0∶67.0 for teeth and 21.6∶78.4 for jaws. In other words, the preponderance in favour of mandibular remains is somewhat more marked in the case of jaws than of teeth, this distinction doubtless reflecting the more fragile bony structure of the maxilla and the sturdier construction of the mandible.