Genetic Structure of Nomadic Bedouin from Kuwait
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Heredity (2009) 103, 425–433 & 2009 Macmillan Publishers Limited All rights reserved 0018-067X/09 $32.00 www.nature.com/hdy ORIGINAL ARTICLE Genetic structure of nomadic Bedouin from Kuwait T Mohammad1,2, Y Xue3, M Evison4 and C Tyler-Smith3 1Division of Genomic Medicine, University of Sheffield, Sheffield, UK; 2The Leverhulme Centre for Evolutionary Studies, University of Cambridge, Cambridge, UK; 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK and 4Department of Anthropology, University of Toronto, Toronto, Ontario, Canada Bedouin are traditionally nomadic inhabitants of the Persian samples clustered with their geographical neighbours in both Gulf who claim descent from two male lineages: Adnani and the autosomal and Y-chromosomal analyses, and showed Qahtani. We have investigated whether or not this tradition is strong evidence of genetic isolation and drift. Although there reflected in the current genetic structure of a sample of 153 was no evidence of segregation into the two male lineages, Bedouin males from six Kuwaiti tribes, including three tribes other aspects of genetic structure were in accord with tradition. from each traditional lineage. Volunteers were genotyped Heredity (2009) 103, 425–433; doi:10.1038/hdy.2009.72; using a panel of autosomal and Y-STRs, and Y-SNPs. The published online 29 July 2009 Keywords: Bedouin; Adnani and Qahtani lineages; Y chromosome; autosomal STRs Introduction it generally highly informative regarding genetic struc- ture and differentiation (Jobling and Tyler-Smith, 2003). Kuwait lies in the Arabian Peninsula at the head of the In addition, its strict paternal inheritance allows compar- Persian Gulf. Although it is located near a possible isons to be made between traditional male-line descent migration route out of Africa that may have been used groups and observed male-line genetic structures. It is a over 50 000 years ago (Jobling et al., 2004), such early single locus, however, and conclusions based on it may events seem to have had little impact on the current not be representative of the rest of the genome. We, populations of Kuwait and the first known settlement therefore, complemented the Y-chromosome analysis dates only to the third century BCE when the Ancient with that of a widely used panel of autosomal STRs Greeks colonized the island of Failaka under Alexander (Collins et al., 2004). the Great. Historians believe that the current settlement Samples for DNA analysis were collected from was established between the late 16th and 18th centuries volunteers from the Adnani tribes of Al-Aniza, Mutran CE (Dickson, 1956). The population of Kuwait is divided and Awazim (a Suluba tribe), and the Qahtani tribes of into two main groups: townspeople and Bedouin tribal Ajman, Shimar and Murrah. This selection is representa- groups ( Qaba’il) with affiliations to their ‘cousins’ tive of the most prominent tribes of Adnani and Qahtani ( wild ‘am) who inhabit other parts of the Arabian lineages of Arabia. The results from the sample were Peninsula. The Bedouin are not geographically isolated compared with data from other populations derived from each other and are traditionally nomadic, moving from the literature. from one region to another seeking pasture for their herds to graze and water for survival (Dickson, 1967). Materials and methods The Bedouin conventionally claim descent from two main lineages: from Adnan son of Ishmael—the Adnani Samples lineage—or from Qahtan (or Joktan)—the Qahtani One hundred and fifty-three distantly related male (or Joktani) lineage. subjects—known not to share a common ancestor within We wished to investigate the genetic structure of the the last three generations—were collected from six Kuwaiti Bedouin and consider how they compare with Bedouin tribes. Ethical review was completed by a neighbouring populations, what the genetic conse- research ethics committee of The University of Sheffield quences of their traditional lifestyle might be, and (UK) and The Kuwait University ethical review board whether the social lineages that identify their descent (Kuwait). Informed consent was obtained from all groups are also reflected in their genetic lineages. participants. Specimens were collected as buccal swabs. The non-recombining part of the Y chromosome was The Bedouin were from the two traditional lineages— chosen for analysis. Its high levels of population Adnani: Mutran (n ¼ 30), Aniza (n ¼ 21) and Awazim differentiation—a consequence of its low effective (n ¼ 37), and Qahtani: Ajman (n ¼ 39), Shimar (n ¼ 21) population size and, sometimes, of patrilocality—make and Murrah (n ¼ 5; because of the small sample size, Murrah specimens were used only in the autosomal Correspondence: Dr C Tyler-Smith, The Wellcome Trust Sanger Institute, analysis). Samples were collected from four main Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. E-mail: [email protected] Kuwaiti Governorates: Awazim and Aniza tribes from Received 2 December 2008; revised 8 June 2009; accepted 15 June the Al-Assima (capital) Governorate (29.4 Lat, 42.2 2009; published online 29 July 2009 Long.), Ajman and Murrah from the Al-Ahmadi Genetic structure of nomadic Bedouin from Kuwait T Mohammad et al 426 Governorate (28.7 Lat, 48.3 Long.), the Mutran sample tions. Y-STR variation was used to calculate population from the Al-Farwaniyah Governorate (29.2 Lat, 47.9 pairwise RST values. Similarly, SNP variation was used to Long.) and the Shimar sample from both the Al-Jahrah calculate pairwise fST values. In addition, autosomal (29.3 Lat, 47.6 Long.) and Al-Ahmadi Governorates. allele frequencies were used to calculate FST pairwise- Locations are shown in Supplementary Figure 1. Kuwaiti genetic distances. The distance matrix used consisted of Bedouin do not marry outside their own tribe and the number of steps by which each pair of STR samples collected in the capital are not admixed. DNA haplotypes or SNP haplogroups differed. Multidimen- was extracted from buccal cells using the BuccalAmp sional scaling (MDS) plots were constructed using SPSS DNA Extraction Kits and protocol (Epicentre, Madison, version 12.0. WI, USA). STRUCTURE 2.1 (Pritchard et al., 2000) was used to infer clusters of individuals on the basis of the genetic Autosomal STR typing data from unlinked loci alone. The model assumes the Amplification with the identifiler multiplex was per- presence of K populations (where K is unknown and is formed directly on 5 ml (0.1 ng ml–1) of the DNA extract specified in advance for each run of the program). Allele using a 12.5-ml reaction volume following the recom- frequencies at each locus characterize each assumed K. mendations of the manufacturer (Collins et al., 2004) on a For all simulations and calculations, a no-admixture GeneAmp PCR System 2400 (Applied Biosystems, Foster model was assumed, with allele frequencies correlated City, CA, USA). PCR cycle conditions were set at 95 1C among groups. In the no-admixture model, each indivi- for 11 min; 28 cycles: 94 1C for 1 min, 59 1C for 1 min, dual comes from one of the K populations—that is 72 1C for 1 min; then 60 1C for 60 min. The amplified populations do not have mixed ancestry; anticipating products were electrophoretically separated on an ABI that the volunteers are either of a Qahtani or Adnani Prism 3730 Genetic Analyzer (Applied Biosystems). ancestry. The program was run twice, once with K ¼ 1–6 After separation, the fluorescent fragments were as the predetermined number of Bedouin populations, analysed using GeneMapper-ID version 3.1 (Applied and once comparing the Bedouin sample to worldwide Biosystems). populations also predetermined at K ¼ 1–6. Both runs used 50 000 iterations for the burn-in period and 100 000 Y-STR typing additional iterations to obtain parameter information. Each run was carried out five times and posterior Amplification with the Y-filer multiplex was performed probabilities for each K were computed for each set of directly on 5 ml (0.1 ng ml–1) of the DNA extract using a runs. 12.5-ml reaction volume following the recommendations Median-joining networks were constructed using Net- of the manufacturer (Mulero et al., 2006) on a GeneAmp work version 4.1.1.2 or 4.5.1.0 (Bandelt et al., 1999). A PCR System 2400 (Applied Biosystems). PCR conditions weighting method with a four-fold range was used in the were 95 1C for 11 min; 30 cycles: 94 1C for 1 min, 61 1C for construction of the networks, with specific weights 1 min, 72 1C for 1 min; then 60 1C for 80 min. The assigned for each STR locus (Qamar et al., 2002) taking amplified products were electrophoretically separated into account the Y-STR variation across the Bedouin on an ABI Prism 3730 Genetic Analyzer (Applied samples. The network for haplogroup J contained many Biosystems). After separation, the fluorescent fragments high-dimensional reticulations. This was resolved by were analysed using GeneMapper-ID version 3.1 applying the reduced median followed by median- (Applied Biosystems). Y-STR typing was carried out joining network methods. according to the manufacturer’s protocol. Bayesian Analysis of Trees With Internal Node Gen- eration (BATWING) (Wilson et al., 2003) was used to Binary polymorphism typing estimate population-genetic parameters and the time to Y-SNP typing was carried out with a 96 Y-SNP kit most recent common ancestor (TMRCA) of a set of (version 2.0) manufactured by Marligen Biosciences chromosomes. The model assumes the single-step muta- (Ijamsville, MD, USA). The kit comprised a core tions of STRs and the demographic model chosen was detection kit (Haplogroups A-R), a broad screening kit exponential growth from an initially constant-sized and 11 individual genotyping kits (Supplementary Table population, with or without subdivision in different 1). Y-SNP fragments were amplified by multiplex PCR, in runs of the program.