Characterizing the admixed African ancestry of African Americans

Background

Accurate, high-throughput genotyping allows the fine characterization of genetic ancestry. Here we applied recently developed statistical and computational techniques to the question of African ancestry in African Americans by using data on more than 450,000 single-nucleotide polymorphisms (SNPs) genotyped in 94 Africans of diverse geographic origins included in the HGDP, as well as 136 African Americans and 38 European Americans participating in the Atherosclerotic Disease Vascular Function and Genetic Epidemiology (ADVANCE) study. To focus on African ancestry, we reduced the data to include only those genotypes in each African American determined statistically to be African in origin.

Results

From cluster analysis, we found that all the African Americans are admixed in their African components of ancestry, with the majority contributions being from West and West-Central Africa, and only modest variation in these African-ancestry proportions among individuals. Furthermore, by principal components analysis, we found little evidence of genetic structure within the African component of ancestry in African Americans.

Conclusions

These results are consistent with historic mating patterns among African Americans that are largely uncorrelated to African ancestral origins, and they cast doubt on the general utility of mtDNA or Y-chromosome markers alone to delineate the full African ancestry of African Americans. Our results also indicate that the genetic architecture of African Americans is distinct from that of Africans, and that the greatest source of potential genetic stratification bias in case-control studies of African Americans derives from the proportion of European ancestry.     

Measuring physical traits of primates remotely: the use of parallel lasers

Physical traits, such as body size, and processes like growth can be used as indices of primate health and can add to our understanding of life history and behavior. Accurately measuring physical traits in the wild can be challenging because capture is difficult, disrupts animals, and may cause injury. To measure physical traits of arboreal primates remotely, we adapted a parallel laser technique that has been used with terrestrial and marine mammals. Two parallel lasers separated by a known distance (4 cm) and mounted onto a digital camera are projected onto an animal. When a photograph is taken, the laser projections on the target provide a scale bar. We validated the technique for measuring the physical traits of identifiable red colobus monkeys (Procolobus rufomitratus) in Kibale National Park, Uganda. First, we photographed the tails of monkeys with laser projections and compared these with measurements previously obtained when the animals were captured. Second, we manually measured the distance between two markers placed on tree branches at similar heights to those used by monkeys, and compared them with the measurements obtained through digital photographs of the markers with parallel laser projections. The mean tail length of the monkeys via manual measurements was 63.3+/-4.4 cm, and via remote measurements was 63.0+/-4.1 cm. The mean distance between the markers on tree branches via manual measurements was 13.8+/-3.59 cm, and via remote measurements was 13.9+/-3.58 cm. The mean error using parallel lasers was 1.7% in both cases. Although the needed precision will depend on the question asked, our results suggest that sufficiently precise measurements of physical traits or substrates of arboreal primates can be obtained remotely using parallel lasers.     

New facial measurement used in the determination of palatine index and thickness of the mandibular body index

Measurements of the height of the mandibular body and the length of the palate rest on the assumption that the alveolar parts of the mandible and maxilla are not altered. Unfortunately, in the skeletal remains of the past population most of the molar teeth are often antemortem lost and this tooth loss is followed by resorption of the alveolar ridge. A new method of taking mandibular and palate measurements, which could be used in these cases is proposed in the study.     

Classification of the southern African sanga and East African shorthorned zebu

Humped African cattle, which are differentiated into zebu and sanga types, have traditionally been classified as Bos indicus . This paper discusses existing evidence and presents new evidence supporting the classification of southern African sangas as Bos taurus and East African zebus as ' taurindicus '. Classification is based on karyotype, frequencies of DNA markers and protein polymorphisms. The Boran, an East African zebu, has an acrocentric Y chromosome typical of Bos indicus . The southern African sanga breeds have a submetacentric Y chromosome typical of Bos taurus . Frequencies of four DNA markers support the hypothesis that the Tuli, a southern African sanga, had taurine ancestors and the Boran had both taurine and indicine ancestors. Frequencies for several protein polymorphisms strongly suggest that southern African sangas have more in common with taurine than with indicine breeds, while East African zebus are an admixture of African taurine and Asian indicine breeds.     

Assessing the health of sediment ecosystems: use of chemical measurements

1. This paper outlines the use of chemical measurements as surrogate indicators of the health of sediment ecosystems. 2. For chemical measurements to be used for this purpose, links must be able to be made between adverse biological effects and the chemical composition of sediments. 3. Benchmark sediment quality guidelines allow decisions to be made about whether or not a sediment ecosystem is likely to be impacted. These guidelines are established using an effects database and a weight-of-evidence approach that gives ranges of chemical concentrations associated with known adverse biological effects. 4. If guidelines are exceeded the measured values are compared to concentrations of that contaminant in a comparable background or reference sediment. Exceedance of these concentrations leads to site-specific estimates of contaminant bioavailability. If a potential problem is indicated, laboratory sediment bioassays are used to assess the likelihood that the sediment will harm biota. 5. Trace metals are used as an example of a sediment contaminant.     

Conserving the African rhinoceros

The Southern African rhinoceros population has been dwindling through the years. A lot of effort has been put toward coming up with the most effective way of protecting the black and white rhinoceros population in the world yet still the animals remain endangered despite the enormous global efforts to protect the species. Such conservation efforts include; establishment of sanctuaries, wildlife farming, dehorning, trade and market controls, listing of species as endangered, use of biotechnology and biotelemetry. However useful, each of these methods has its own strengths and weaknesses relative to the success of rhinoceros conservation. It however has been noted in this review that dehorning is the most effective method as it involves removal of the horn hence extinguishing the need for poaching. Despite the high success rate it has also been noted that this requires a great deal of skill and finance hence limiting the application of this technique in developing nations. Sanctuaries provide an ideal breeding environment that is better than the wild and enhanced breeding accounted for a significant increase in rhinoceros population where it has been applied. It was however been conclude that a holistic conservation approach is required to conserve the African rhinoceros.     

African and European perception of African female attractiveness

Majority of research on attractiveness is restricted to faces of European origin. The perception of attractiveness may, however, vary across communities due to variations in both facial morphology and local standards of beauty. We investigated the relative contribution of four facial markers of attractiveness based on 101 female facial portraits (standardized, non-manipulated) from Cameroon and Namibia, which were assessed by local male raters and by raters from a distant European population, the Czech Republic. Images from Cameroon include only women of Bantu origin, while Namibians are represented by women of both Bantu (Owambo/Herero) and Nama origin. While controlling for age and BMI, we explored the relationship between female attractiveness and a set of facial traits: fluctuating asymmetry, averageness, shape sexual dimorphism, and skin color (rated and measured in CIELab color space).In the Cameroonian sample, local male raters favored lighter-skinned female faces with morphology closer to average. The attractiveness of Nama women as rated by Nama men positively correlated with lighter complexion, but this did not extend to rating by Cameroonian men. The attractiveness of Namibian Owambo/Herero women was positively associated with facial femininity and lighter complexion when judged by both Cameroonian and Nama male raters. In all samples, the attractiveness as rated by Czech men was predicted by age and BMI, but not by skin color. We found no significant association between attractiveness and fluctuating asymmetry in any of the tested samples. When controlling for age, the effect of skin color on attractiveness turned to be non-significant in the Owambo/Herrero and Nama sample, but remained significant in the Cameroonian sample. Variations in skin color thus represent an important factor of African female attractiveness within the African context, but they do not seem to affect judgements made by European raters. Sensitivity to some facial markers of female attractiveness thus seems to be restricted to regional populations and/or constrained by shared ethnicity.     

Distribution and abundance of African waterfowl: examples from the African Waterfowl Census

Dodman, T. & Rose, P. 2000. Distribution and abundance of African waterfowl: examples from the African Waterfowl Census. Ostrich 71 (1 & 2): 235–243.

Wetlands International coordinates waterfowl counts in Africa. Counts from 1958–1990 were analysed in 1991, when the African Waterfowl Census (AfWC) was also launched. By 1996, 25 countries were participating. This preliminary appraisal of the AfWC shows that resulting data can be used to identify distribution and abundance patterns, although there are still significant gaps in AfWC coverage and focus. The degree to which AfwC data may be used to assess the conservation status of African waterfowl populations depends on a function of data quality, quantity and reliability. To enable this practical use of data, several priorities for future work are identified, based on the strengths and weaknesses of the current information: (1) simultaneous co-ordinated counts, (2) regular annual or biannual monitoring of the same sites, (3) development of priority list of sites for regular survey, (4) frequent monitoring of particularly important sites (e.g. every three months), (5) building waterbird surveys into broader programmes of ecological monitoring, (6) planning of special internationally coordinated surveys, (7) planning regular complete surveys in major wetlands, e.g. every five years, and (8) extending the AfWC to other taxa and broader surveys of wetland use by man. In Africa, 522 discrete waterbird populations have been identified. Over half the populations for which trends have been established are in decline. Results from a recent atlas of Anatidae are illustrated by the Fulvous Whistling-Duck Dendrocygnu bicolor, for which three discrete populations and 21 key sites are identified. Wetlands are the most important habitats for waterbirds. Many species (e.g. Grey Heron Ardea cinema) exploit a variety of wetland types and are geographically widespread; those with special habitat requirements (e.g. Blue-winged Goose Cyanochen cyanopterus) oh have restricted ranges. Hartlaub's Duck Pteronetta hartlaubi is one of the few waterbirds specific to the tropical forest biome. The movements of Abdim's Stork Ciconia abdimii in southern Africa show a clear response to rainfall.     

Growth of rhesus monkeys during the first 54 months of life

As part of a study of the long-term effects of environmental conditions on the health and development of non-human primates, the growth of 60 rhesus monkeys (Macaca mulatta, 34 males and 26 females) was determined longitudinally with biweekly or triweekly measurements of eight body dimensions from one to 54 months of age. Our data showed similar growth to previous studies and provide additional data defining normal rhesus monkey growth under more precisely defined living conditions than were reported in previously published studies on this species.     

African Roots of the Amistad Revolt

Sierra Leone: The African Roots of the Amistad Revolt: Masks of the Sacred Bush. Peabody Museum of Natural History, Yale University, July 15, 2000– December 2000.     

Charting the ancestry of African Americans

The Atlantic slave trade promoted by West European empires (15th-19th centuries) forcibly moved at least 11 million people from Africa, including about one-third from west-central Africa, to European and American destinations. The mitochondrial DNA (mtDNA) genome has retained an imprint of this process, but previous analyses lacked west-central African data. Here, we make use of an African database of 4,860 mtDNAs, which include 948 mtDNA sequences from west-central Africa and a further 154 from the southwest, and compare these for the first time with a publicly available database of 1,148 African Americans from the United States that contains 1,053 mtDNAs of sub-Saharan ancestry. We show that >55% of the U.S. lineages have a West African ancestry, with <41% coming from west-central or southwestern Africa. These results are remarkably similar to the most up-to-date analyses of the historical record.     

The surface of the African trypanosomes

The African trypanosomes bear on the outside of their cell membrane a single 10-15 nm thick coat of a glycoprotein. This glycoprotein may differ in structure in the predominant populations of parasitemic waves found in relapsing infections. Variant Specific Glycoprotein (VSG) range in MW between 53,000-63,000 d and may have variable amounts of carbohydrate attached at one, two, or several loci. Such differences in carbohydrate content may account in part for their range in molecular size. Approximately 30 C-terminal residues demonstrate isotypy ; i.e. these regions fall into classes having similar amino acid sequence. Modest homology has been demonstrated in two VSGs of T. congolense arising in relapsing infections although comparison of many VSG show little or no obvious homology. More recently, lipid-associated forms of VSG have been described and it is believed that these forms may be transmembrane proteins. Different VSGs appear to have different amounts of the primary sequence which have alpha-helix-forming potential. In some VSG, in excess of 80% of the structure is helical as judged by both Chou-Fasman calculations and by circular dichroism. This raises the possibility that different VSG may have different folding patterns. The arrangement of VSG on the trypanosome surface probably places the basic amino acid-rich carbohydrate-bearing C-terminus of the polypeptide chain close to the membrane. There is some protein-protein association between VSGs for which (in T. evansi) the C-terminal tail is not required. The importance of VSG structure lies not only in the fact that the molecule mediates the phenomenon of antigenic variation but also in the recent observation that VSG may act on the cellular immune system to suppress the humoral immune responses of the host.     

Ticks of the Central African Republic

A review is presented of the ticks of the Central African Republic (C.A.R.), based on unpublished data and a literature review. We consider as established in the C.A.R. two species of Argasidae (one species of each of the genera Carios and Ornithodoros) and 49 species of Ixodidae: 5 Ixodes, 11 Amblyomma, 2 Dermacentor, 9 Haemaphysalis, 4 Hyalomma, and 18 Rhipicephalus species, 3 of which belong to the subgenus Boophilus. Two of these species, one Amblyomma and one Dermacentor, may by now have disappeared from the country together with their hosts, the black and white rhinoceroses. Moreover, four other species of Ixodidae have been recorded, but are not necessarily established in the country, and 6 species of Ixodidae have apparently been reported incorrectly; the data for the occurrence of three other species of Ixodidae are uncertain. Rhipicephalus species in the C.A.R. present the greatest difficulties in identification, on the one hand because of uncertainties in taxonomy, particularly in the capensis group, on the other hand because of individual variability, which means that individual specimens cannot always be reliably identified to species. Examining the dissected and cleared gonopore structure of females helps, but is very time-consuming where large numbers are involved. Some of the species of the genus Haemaphysalis are also difficult to identify with certainty. There are only a few species of Hyalomma in the country. We revised also some old records of ticks in C.A.R., which we consider as unreliable and should be disregarded because of subsequent changes in taxonomy and nomenclature, unless the material is still available for examination.     

Elevated male European and female African contributions to the genomes of African American individuals

The differential relative contribution of males and females from Africa and Europe to individual African American genomes is relevant to mapping genes utilizing admixture analysis. The assessment of ancestral population contributions to the four types of genomic DNA (autosomes, X and Y chromosomes, and mitochondrial) with their differing modes of inheritance is most easily addressed in males. A thorough evaluation of 93 African American males for 2,018 autosomal single nucleotide polymorphic (SNP) markers, 121 X chromosome SNPs, 10 Y chromosome haplogroups specified by SNPs, and six haplogroup defining mtDNA SNPs is presented. A distinct lack of correlation observed between the X chromosome and the autosomal admixture fractions supports separate treatment of these chromosomes in admixture-based gene mapping applications. The European genetic contributions were highest (and African lowest) for the Y chromosome (28.46%), followed by the autosomes (19.99%), then the X chromosome (12.11%), and the mtDNA (8.51%). The relative order of admixture fractions in the genomic compartments validates previous studies that suggested sex-biased gene flow with elevated European male and African female contributions. There is a threefold higher European male contribution compared with European females (Y chromosome vs. mtDNA) to the genomes of African American individuals meaning that admixture-based gene discovery will have the most power for the autosomes and will be more limited for X chromosome analysis. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.