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Enabling the Genomic Revolution in Africa

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Enabling the Genomic Revolution in Africa INSIGHTS | PERSPECTIVES barrier that culminated in the RESEARCH CAPACITY speciation of these two crow taxa. Armed with this new very detailed genetic informa- Enabling tion, it is clear that none of the currently formulated species concepts fully apply to these the genomic two crow taxa (unless one is willing relax some stringency Sw in the various definitions). In- revolution deed, the genomes of German carrion crows are much more in Africa similar to those of hooded Po crows than to Spanish car- rion crows. Put simply, apart H3Africa is developing from the few carrion crow type capacity for health-related “speciation islands,” German Ge carrion crows could be con- genomics research in Africa sidered to represent hooded Sp crows with a black (carrion By The H3Africa Consortium * † crow) phenotype. There is a clear need for ad- ur understanding of genome biology, ditional population genomic genomics, and disease, and even hu- studies using a more dense man history, has advanced tremen- sampling, especially among dously with the completion of the 1.0 the fully black carrion crows, Human Genome Project. Technologi- on August 3, 2014 Ancestry 0.5 Sp Ge Po Sw before the complexity of repro- cal advances coupled with significant 0.0 ductive isolation and speciation Ocost reductions in genomic research have among these two taxa can be yielded novel insights into disease etiol- Speciation battleground. On either side of the narrow hybridization fully understood. The specia- ogy, diagnosis, and therapy for some of zone (dark brown), the carrion crow (Corvus corone) (dark area) tion genomics strategy already the world’s most intractable and devastat- and hooded crow (Corvus cornix) (pale area) ( 2) maintain their proved itself in unraveling the ing diseases—including ma- marked phenotypic differentiation, despite apparent lack of genetic complexities of mimicry among POLICY laria, HIV/AIDS, tuberculosis, differentiation. Genome-wide admixture analyses (inset at bottom) show many Heliconius butterfly cancer, and diabetes. Yet, de- that German carrion crows most closely resemble (80%) hooded crows, taxa ( 7) and, as in the study of spite the burden of infectious diseases and, www.sciencemag.org and are quite distinct from Spanish carrion crows. Sampling sites for Poelstra et al., stresses the im- more recently, noncommunicable diseases the present study ( 6) are shown as circles. Sp, Spain; Ge, Germany; Po, portance of using RNA-based (NCDs) in Africa, Africans have only par- Poland; Sw, Sweden. information in addition to ticipated minimally in genomics research. Of DNA. Only time will tell if, and the thousands of genome-wide association Yet, roughly a decade ago, newly pro- when, German carrion crows will adopt the studies (GWASs) that have been conducted posed DNA-based taxonomy ( 11) promised “hooded phenotype,” a fate that seems un- globally, only seven (for HIV susceptibility, to solve the species debate. A Barcode of avoidable. Until then, we can only applaud malaria, tuberculosis, and podoconiosis) Life Data Systems (BOLD) ( 12) quickly these crows for defeating Linnaeus’s curse. ■ have been conducted exclusively on Afri- Downloaded from emerged, seeking to provide a reliable, can participants; four others (for prostate cost-effective solution to the problem of REFERENCES cancer, obsessive compulsive disorder, and 1. C. Linnaeus, Systema Naturae (Tomus I, Holmiae, species identification ( 12) and a standard Impensis Laurentii Salvii, Stockholm, 1758). anthropometry) included some African screening threshold of sequence differ- 2. S. Cramp, C. M. Perrins, Eds., The Birds of the Western participants (www.genome.gov/gwastudies/). ence (10× average intraspecific difference) Palearctic (Oxford Univ. Press, Oxford, 1994), vol. 8. As discussed in 2011 (www.h3africa.org), if to speed the discovery of new animal spe- 3. E. Haring, B. Däubl, W. Pinsker, A. Kryukov, A. Gamauf, J. the dearth of genomics research involving Zoological Syst. Evol. Res. 50, 230 (2012). cies ( 13). Sometimes considered a “carica- 4. J. B. W. Wolf et al., Mol. Ecol. 19 (suppl. 1), 162 (2010). Africans persists, the potential health and ture of real taxonomy” ( 14), this approach 5. D. T. Parkin et al., Br. Birds 96, 274 (2003). economic benefits emanating from genomic failed to identify, perhaps not surprisingly, 6. J. W. Poelstra et al., Science 344, 1410 (2014). science may elude an entire continent. two American crow species and a number 7. O. Seehausen et al., Nat. Rev. Genet. 15, 176 (2014). The lack of large-scale genomics studies 8. J. L. Feder, S. P. Egan, P. Nosil, Trends Genet. 28, 342 of members of the herring gull Larus ar- (2012). in Africa is the result of many deep-seated gentatus species assemblage above the set 9. C. Darwin, On the Origin of Species by Means of Natural issues, including a shortage of African scien- threshold ( 13). Furthermore, despite past Selection (Murray, London, 1859). tists with genomic research expertise, lack 10. K. Winkler et al., Ornithol. Monogr. 63, 30 (2007). ( 3) and present ( 6) sequencing projects, 11. D. Tautz, P. Arctander, A. Minelli, R. H. Thomas, A. P. Vogler, of biomedical research infrastructure, lim- JELMER FROM POELSTRA ADAPTED , carrion crows and hooded crows can also Trends Ecol. 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ILLUSTRATION: 1346 20 JUNE 2014 • VOL 344 ISSUE 6190 sciencemag.org SCIENCE Published by AAAS scientists acquiring the expertise and facili- ties necessary to lead high-quality genom- National Institutes of Health ics research aimed at understanding health problems relevant to African populations Wellcome Trust H3Africa Research Network and to become internationally competitive in genomic science and its applications. Tunisia In June 2010, the U.S. National Institutes of Health (NIH) and UK-based Wellcome Trust, in partnership with the African Soci- Morocco ety of Human Genetics, announced a plan to enhance the ability of African scientists Egypt to apply genomic and epidemiological ap- proaches to shed light on the determinants of chronic and infectious diseases in Africa Senegal Mali Niger ( 1). The Human Heredity and Health in Af- The Gambia Sudan Nigeria rica (H3Africa) initiative, now funded at $76 Guinea million over 5 years, is focused on capacity Sierra Leone Ethiopia building, as well as specific scientific goals. H3Africa research grants are awarded di- Benin Uganda Côte d’Ivoire Ghana rectly to African institutions where principal Democratic Burkina Faso Cameroon investigators are based (table S1), which al- Republic Kenya lows African scientists to develop and direct of Congo their independent research agendas. The Tanzania NIH primary award institution program encourages formation of intra- Malawi WT primary award institution continental collaborations and development Collaborating institution of specific infrastructural elements, i.e., Zambia African-based biorepositories and a pan- African bioinformatics network (H3ABio- Other collaborating institutions are in Belgium, Canada, France, the United Net). H3Africa also includes training pro- Namibia Kingdom, and the United States Botswana Mauritius grams aimed at retaining African scientists on the continent to help build a sustainable Boundaries as depicted at Mozambique un.org/Depts/Cartographic/map/ critical mass of researchers. Open calls for profle/africa research proposals have emphasized col- South Africa laborations within Africa, plus accessible biorepositories and a bioinformatics net- work with nodes across the continent (table velopment of end-stage renal disease, that genes interact with life style (barefoot farm- S2). The footprint of H3Africa extends across is two to five times normal, respectively ( 2, ing practices) to increase susceptibility to Africa (see the map), comprising 21 grants 3). These variants also confer 29 times the podoconiosis, a neglected tropical disease in (table S1). It is anticipated that, together, risk of HIV-associated nephropathy (HIVAN) Ethiopia and Cameroon ( 9). H3Africa projects will analyze samples from ( 4). Despite these renal outcomes, the preva- A key challenge to building critical mass 50,000 to 75,000 participants. lence of the risk genotype is 13% among AA for genomic research in Africa is the reten- H3Africa is predicated on the belief that and virtually absent among those of non- tion of scientific leadership capable of devel- diseases and nonmedical issues relevant to African ancestry. The prevailing hypothesis oping and maintaining sustainable research Africans can be best explored in partnership is that APOL1 renal risk variants evolved in programs. The dearth of research-intensive with inhabitants of Africa (both researchers sub-Saharan Africa about 10,000 years
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