Post on 19-May-2020
Assessing the relative ages of admixture in the bovine hybrid zones of Africa and the Near
East using X-chromosome haplotype mosaicism.
Abigail R. Freeman*, Clive J. Hoggart§, O. Hanotte† and Daniel G. Bradley*
*Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
§Imperial College, London, United Kingdom.
†International Livestock Research Institute, PO Box 00100, Nairobi, Kenya.
1
Genetics: Published Articles Ahead of Print, published on April 2, 2006 as 10.1534/genetics.105.053280
Running Title: Bovine X-chromosome haplotype mosaicism and linkage disequilibrium.
Keywords: admixture, haplotype mosaicism, linkage disequilibrium, Bos taurus.
Corresponding Author:
Professor Daniel Bradley
Smurfit Institute of Genetics,
Trinity College,
Dublin 2,
IRELAND.
Telephone: 00 353 1 608 1088
Fax: 00 353 1 679 8558
Email address: dbradley@tcd.ie
2
ABSTRACT
Historical hybridisation events between the two sub-species of cattle, Bos taurus and Bos
indicus, have occurred in several regions of the world, while other populations have remained
non-admixed. We typed closely linked X-chromosome microsatellites in cattle populations
with differing histories of admixture from Africa, Europe, the Near East and India.
Haplotype breakdown will occur as admixed populations age, and longer ancestral haplotypes
will remain intact in more recently admixed populations compared to older ones. We
genotyped male animals from these populations, obtaining unambiguous haplotypes, and
measured levels of linkage disequilibrium (LD) and ancestral mosaicism. Extensive LD,
likely to be the result of ongoing admixture, was discovered in hybrid cattle populations from
the perimeter of the tsetse zone in West Africa. A Bayesian method to assign microsatellite
allele ancestry was used to designate the likely origin of each chromosomal segment, and
assess the relative ages of admixture in the populations. A gradient of the age of admixture in
the African continent emerged, where older admixture has produced more fragmented
haplotypes in the south, and longer intact haplotypes, indicating more recent hybridisation,
feature in the northwest.
3
INTRODUCTION
Cattle have been domesticated at least twice from two distinct wild aurochs populations
(LOFTUS et al. 1994; BRADLEY et al. 1996; LOFTUS et al. 1999). The two extant taxa are Bos
taurus (taurine) and Bos indicus. The former were domesticated in the Middle East, Anatolia
and probably Africa about 10,000 years ago and are now found throughout northern Eurasia
and certain regions of Africa. Bos indicus or zebu cattle were domesticated from a different
variant of wild progenitor on the Indian sub-continent.
Substantial genetic exchange has taken place between the two types. Zebu cattle were
brought from southern Asia to the Middle East and the breeds that are found in this area
today are affected by hybridisation that took place perhaps over 3000 years ago (LOFTUS et
al. 1999). Nuclear genetic markers including Y-chromosome polymorphisms (BRADLEY et
al. 1994; HANOTTE et al. 2000) and autosomal microsatellites (MACHUGH et al. 1997) have
been used to show that there has been a widespread introgression of zebu cattle into the
African continent, which would have initially been inhabited only by African B. taurus, pure
examples of which remain only in certain parts of North and West Africa.
The genetic exchange between taurine and zebu cattle represents an appropriate model to
study the effects of post-admixture haplotypic decay through recombination, mutation and
genetic drift. Four of the domestic cattle hybrid zones; the Middle East, plus East, West and
Southern Africa, have breeds with roughly equal amounts, but different ages of admixture
(LOFTUS et al. 1999; HANOTTE et al. 2002). The first generation population created after an
admixture event will contain intact chromosomes from each of the inputting parental
populations. However, as mating occurs within the hybrid population these intact
chromosomes are mixed by recombination and gradually become more mosaic with each
4
generation. Therefore, the extent of genomic blocks undisturbed by hybrid recombination
will contain information about the history of admixture.
The examination of closely linked markers can be used to estimate how parental haplotypes
have been broken down over time in the hybrid population. Microsatellite allele frequency
spectra have been shown to differ sharply between B. indicus and B. taurus, facilitating the
assignment of ancestry at specific chromosome positions. Moreover extended haplotypes
may be unambiguously assigned to X-chromosomes in males.
Here we investigate differences in haplotypic mosaicism among 346 X-chromosomes typed
in male cattle from regions of differing phylogeographic history. We estimate microsatellite
allele ancestry at ten loci within a 10cM region to examine the breakdown of genomic blocks,
and assess levels of linkage disequilibrium (LD) in populations with differing histories of
admixture. We relate the different levels of haplotypic mosaicism and LD to the different
time depths and manners of introgression. For simplicity, we use the term LD to describe
both traditional linkage disequilibrium, and pairwise disequilibrium between non-linked
markers.
5
MATERIALS AND METHODS
346 male cattle DNA samples from 22 breeds were obtained as described previously (Table
1) (MACHUGH et al. 1997; LOFTUS et al. 1999; RITZ et al. 2000; HANOTTE et al. 2002). The
approximate locations of the sample sites and previously calculated admixture estimates (mR)
are shown in Figure 1 (MACHUGH et al. 1997; LOFTUS et al. 1999; HANOTTE et al. 2002;
FREEMAN et al. 2004). For LD analysis, the novel data obtained here were combined with
microsatellite data from previously published studies (MACHUGH et al. 1997; LOFTUS et al.
1999; HANOTTE et al. 2002; FREEMAN et al. 2004). Of the 22 breeds, two were unadmixed
European B. taurus, three were primarily unadmixed West African B. taurus and two were
primarily unadmixed B. indicus. The remaining 15 breeds were known to have been formed
by admixture between Bos taurus and Bos indicus. Figure 1 shows the geographic location of
the breeds
10 X-chromosome microsatellites were selected from the Meat Animal Research Center
(MARC) database http://sol.marc.usda.gov/genome/genome.html (BISHOP et al. 1994; SUN et
al. 1994; KAPPES et al. 1997). All of the microsatellites selected have been linkage mapped
to a 10 cM region on the X chromosome (KAPPES et al. 1997; SØNSTEGARD et al. 1997;
SØNSTEGARD et al. 2001; IHARA et al. 2004). Six of the markers have also been included in
radiation hybrid maps of the bovine X chromosome (BtaX) (AMARAL et al. 2002; WILLIAMS
et al. 2002), and all but one of the markers can be found in the Pre! ensembl bovine genome
assembly (http://pre.ensembl.org/Bos_taurus/index.html). Approximate distances between
markers and marker order were taken from the genome assembly after observing agreement
between this and the linkage and radiation hybrid maps for most markers. To control for
potential mis-orientation of contigs in the preliminary assembly, a comparison with the
syntenic chromosomal region in humans was examined. Again, order seemed to be mostly
6
conserved. Thus, for the purposes of this paper, the marker order and positions listed in
Table 2 were used. Two methods of genotyping were used, with common standards enabling
combination of the data. Populations marked with an asterisk in Table 1 were genotyped
using a radioactive PCR method described in MacHugh et al (1997), while the remaining
populations were genotyped using an ABI 377™ system following the protocol of Hanotte
and colleagues (2002).
Pairwise linkage disequilibrium between locus pairs was carried out using an extension of
Fisher’s exact test implemented by the GENEPOP program (v3.2a) (RAYMOND and ROUSSET
1995). Populations were defined according to the regional groups in table 1. For a given pair
of loci within one population, the possible genotypes are represented by GENEPOP in a
contingency table. For each locus pair within each population, the unbiased estimate of the
p-value is calculated using a Markov chain as the sum of the probabilities of all tables (with
the same marginal values as the observed one) with a lower or equal probability than the
observed table.
Statistical inference on admixture and the ancestry crossover rate in the admixed cattle
populations was made in the computer program ADMIXMAP by simulating posterior
samples of the model parameters using Markov chain Monte Carlo simulation (HOGGART et
al. 2003; HOGGART et al. 2004). ADMIXMAP implements a full Bayesian hierarchical
model for admixture at the population, individual and locus level and also models the allele
frequencies in the unadmixed subpopulations that have contributed to the admixed population
under study. The stochastic variation of ancestry between loci on each chromosome is
modelled by independent Poisson arrival processes, one for each unadmixed population
contributing to the admixed population under study, in our case B. taurus and B. indicus.
7
Thus inference is made on parameters representing population and individual admixture,
indicator parameters for locus ancestry for all loci and all individuals, parameters of
multinomial distributions representing allele and haplotype frequencies in the two
populations and τ, the sum-of-intensities of the two Poisson arrival processes. Whilst
admixture was modelled separately for each individual in a population (independent and
identically distributed from the population level admixture distribution) τ was assumed to be
the same for all individuals in the population.
For an individual with admixture proportion θ from B. taurus the intensities per Morgan of
the arrival processes for B. taurus and B. indicus are θτ and τθ)1( − respectively. The
ancestry crossover rate ρ (the rate per Morgan of transitions between ancestry of one
subpopulation to ancestry of the other) is given by )2 1( θτθρ −= , thus the larger τ the more
frequent the crossovers. Since the X chromosome only undergoes recombination in female
gametes, a different τ will be applicable to the X chromosome than the autosomes. However,
in our data sets the autosomal markers are unlinked thus τ was estimated from the linked
markers typed in the 10cM region of the X chromosome alone. In contrast individual
admixture proportions (θ) were estimated from both the autosomal and X chromosome
markers. When introgression occurs in a single pulse the expectation of τ on the autosomes is
equal to the number of generations since admixture, (FALUSH et al. 2003). However,
admixture in the cattle populations is not believed to have occurred as a single event but
rather through continuous gene flow of B. indicus into B. taurus populations. The effect of
continuous gene flow on τ is unclear thus it cannot be interpreted as the number of
generations since admixture but as a relative measure of the age of admixture among the
populations studied. Given the lack of interpretation of τ it was assigned an uninformative
prior, log τ uniform. Prior distributions for population specific allele frequencies for Bos
8
taurus and Bos indicus were set from allele counts in the five Bos taurus populations (both
European and west African) and two Bos indicus populations listed in Table 1. Whilst it is
known that the West African Bos taurus populations contain a degree of indicus admixture
this is very small (mR = 3%, 7% and 10% in Guinean N’Dama, Guinea Bissau N’Dama and
Somba respectively) and thus will have minimal effect on the allele counts. Furthermore,
specifying prior distributions from the allele counts rather than fixing them at their mean
values allows for error in the frequencies to be accounted for. Uninformative uniform priors
were assigned for the population level admixture.
The ADMIXMAP analyses assumes that all LD between markers can be attributed to
admixture LD and LD due to ancestral mosaicism but ignores background LD. The X
chromosome markers used in our analyses are between 0.1 Mb and 2.5 Mb apart (Table 2),
and at such distances it is a reasonable approximation to ignore background LD.
Statistical testing was carried out using SPSS (v. 12.0) and values of τ were plotted with
sampling location using the ARCVIEW GIS software package. Equal interval contours join
areas with similar values of τ (Environmental Systems Research Institute, ESRI, Redlands,
CA). A synthetic map was finalised using the Adobe Illustrator (v. 8.0) package.
9
RESULTS
A set of ten linked X-chromosome microsatellites that have been mapped within a 10cM
region of BtaX were genotyped in 346 male cattle samples from geographical locations
shown in Figure 1 and detailed in Table 1. The data were combined with unlinked autosomal
microsatellite genotypic data from previous publications.
The strength of pairwise linkage disequilibrium (LD) between all typed markers was
estimated and the results divided into two groups according to the significance of association
between pairs of markers: p<0.05 and p<0.01. Figure 2 shows matrices of LD significance
levels for all possible pairwise comparisons of the 10 X-chromosome loci in their
chromosomal order, and for the unlinked markers. The samples were divided into regional
groupings according to Table 1, excluding the Zebu Malagasy breed which does not easily
fall into an appropriate category and which is only represented by 4 individuals. The
unlinked autosomal microsatellite markers provide a measure of the background levels of LD
in each regional group. LD measures for linked markers are shown on the left hand side of
the heavy black line, in the order that they are located on the X-chromosome.
In general, and as expected, physically linked markers tend to have higher levels of
association than markers from different chromosomes. This trend is evident in all groups
except European B. taurus. This group exhibits slightly lower levels of LD among linked
markers than unlinked markers, but the difference is small. The trend is apparent in all of the
hybrid populations (Near Eastern, West African, East African, South African), but most
especially in the West African hybrid population which exhibits especially high levels of LD
among the X-chromosome microsatellites. Nearly 45% of all possible pairwise comparisons
10
between linked markers are in LD at a significance level of 0.01 in this group. This is over
three times as many as is seen in any of the other population groups.
Estimates of τ obtained from ADMIXMAP enable comparison of time since admixture
among the different sampled populations, but cannot be taken as absolute values, as a single
event is unlikely to be an accurate model of past hybridisation processes. Values of τ are
shown on a synthetic contour map (Figure 3). Despite the relatively small number of hybrid
breeds (fifteen), some geographical congruency can be observed for values of τ.
The posterior means and standard deviations of the sum-of-intensities parameter τ for the
admixed breeds are shown in Table 1. We see that within the African continent there are two
main trends among the hybrid populations. Firstly, values of τ tend to be higher in the south
of the continent, and secondly there is a decreasing cline in values of τ from east to west in
the northern part of the continent. To test for significant difference between hybrid breeds in
the north and south we pooled the estimates of τ using the inverse variance method (DEEKS et
al. 2001). The pooled estimate of τ for hybrid breeds in the northern part of the continent
(Mbororo, Gobra, Sokoto Gudali, Arashie, Kuri) is 7.6 (standard deviation 1.66), and the
pooled estimate for hybrids in the south (Ogaden, Ankole, Afrikaner, Nguni, Watusi, Zebu
Malagasey, Barotse, Kavango) is 13.9 (standard deviation 1.85). The test for difference
between the means of the groups is significant, p=0.012. The pooled estimate for τ in the two
Near Eastern hybrids is 15.4 (standard deviation 3.54), with the highest value being observed
in the eastern-most Iraqi breed (τ =17.8).
11
DISCUSSION
Cattle populations represent an ideal model for the study of admixture generated linkage
disequilibrium and haplotype decay, as it is well established that they were domesticated
from divergent wild progenitors leading to two main interfertile lineages: Bos taurus and Bos
indicus. Since domestication, the two types have been combined in many different hybrid
breeds but there are also pure extant taurine and zebu populations that provide good proxies
for the original ancestral populations (MACHUGH et al. 1997).
The amount of admixture in the breeds used in this study had previously been estimated using
autosomal microsatellites (MACHUGH et al. 1997; LOFTUS et al. 1999; HANOTTE et al. 2002;
FREEMAN et al. 2004)(Figure 1). Here we set out to examine the pattern of haplotype decay
in the bovine genome after admixture by genotyping closely linked microsatellite markers.
The level of divergence between the contributing parental populations will determine whether
it is possible to assign definite ancestry to an allele in a hybrid individual. In a previous
study, we found that over 80% of microsatellite alleles surveyed at 20 loci in European, Near
Eastern and Indian cattle populations showed greater than 50% frequency differential (scaled
by the absolute allele frequency) between B. indicus and B. taurus (KUMAR et al. 2003). All
of the markers used here are located within a 10cM region of the X-chromosome and were
typed only in males. This allowed the unambiguous assignment of a haplotype to an
individual without pedigree information.
We found LD in this region of the X-chromosome in all of the cattle populations, and
between linked and unlinked markers in all of the populations except for the Near Eastern
hybrids. These results concur with Farnir et al. 2000 who surveyed 284 autosomal markers
and found that intra-chromosomal LD extends over several tens of centiMorgans and is
12
common between non-syntenic loci in dairy cattle populations. In that case, the high levels
of overall LD may have been a result of a small effective population size, (LONJOU et al.
1999) which could be as low as 50 for 1.2 million Holstein-Friesian females, or admixture
(FARNIR et al. 2000).
Recurrent introgression has been cited previously as the cause of higher than expected levels
of LD in African American human populations (LAUTENBERGER et al. 2000). Here, the very
high level in the West African hybrid population may partially be explained by recent and
continuous gene flow to this region (PFAFF et al. 2001). Pfaff and colleagues argue that
maintenance of LD over relatively large (~10 cM) chromosomal segments is a not typical of
a single admixture event, but is a characteristic of a continuous gene flow pattern of
admixture. While the initial introgression of B. indicus chromosomes into Africa is likely
ancient, zebu-taurine admixture in West Africa probably began only recently in many
populations where it had previously been constrained by the tsetse/trypanosomiasis
infestation zone; a barrier to introgression. Understanding the patterns of LD in the hybrid
populations from the surround of the West African tsetse zone will prove useful if these
populations are used to map genes which influence disease traits (LAAN and PAABO 1997).
In the absence of mutation, every portion of a chromosome in a hybrid individual should be
directly traceable to one of the individual’s ancestors. When two distinct gene pools meet, a
mosaic genome is produced (CHAPMAN and THOMPSON 2002), containing intact segments
from each contributing founder populations (NORDBORG and TAVARE 2002). Genomes that
have undergone recent hybridisation will have largely intact ancestral haplotypes, while
recombination will act to disrupt these haplotypes in subsequent generations (WIEHE et al.
2000). If admixture is ancient, reciprocal recombination, genetic drift and mutation will have
13
eroded the association between markers from parental populations and a greater density of
markers will be required to detect significant associations.
Here we employed a Bayesian method to assign probable ancestry to each allele in every X-
chromosome haplotype. The amount of fragmentation in haplotypes was assessed by the
posterior distribution of τ, and this was used as a measure for the age of admixture. The mean
values of τ (Table 1) for each of the cattle breeds are between 4.27 and 21.3 which is
substantially less the number of generations since admixture is believed to have first
occurred. However, as discussed earlier, in the case of cattle a single admixture event may
not accurately model the historical reality and τ only has expectation equal to the number of
generations since admixture in the case of a single admixture event. Furthermore, the prior
has the effect of favouring small values of τ.
The values obtained appear to show some geographical consistency, whereby most hybrid
populations from southern Africa and the Near East appear to have experienced older
admixture than those in the more northern part of the African continent. Furthermore there is
a decline in age of admixture from east to west in the latter. The differences between the east
and the west of the continent support a scenario of earlier introgression of B. indicus material
into the former populations, as the degree of recombination would be expected to accumulate
with time. This finding is supported by high levels of LD in West African hybrids, and
previous work which has shown that the major B. indicus introductions occurred in the East:
probably in the region of the Horn (HANOTTE et al. 2002).
The difference in τ values between the south and the north of Africa may be a signal of
different histories of cattle in the two regions. However, it is well established that the earliest
14
Our sample from Madagascar suggests that admixture here was older but this sample is very
small, n=4, and should not be over-interpreted. There is limited archaeological evidence for
early arrival of B. indicus cattle to Madagascar and zebu cattle occupy a place of prominence
Based on archaeological evidence the origins of B. indicus introgression in Africa are
controversial. Some authors have suggested that they were found as early as 3500-2000 BP
(HASSAN 2000; MARSHALL 2000; PARIS 2000), but these studies are inconclusive, and the
earliest verified archaeological date for their presence is in the Horn of Africa in the second
century AD (MARSHALL 2000). The archaeological record shows that B. taurus cattle were
present in northern Africa and the Sahara from approximately 6000 BP (HASSAN 2000), and
spread as far south as Kenya by 3000 BP (HASSAN 2000; MITCHELL 2005). Further
southward movement may have been hampered by ecological factors such as the many sub-
Saharan disease challenges to which domestic cattle would be maladapted (GIFFORD-
GONZALEZ 2000; MITCHELL 2005), and relatively few cattle were present in the south until
1000 AD (SMITH 2000). It is therefore possible that nomadic pastoralists in eastern Africa
were herding animals comprised of the two cattle lineages before the expansion of domestic
cattle to the south.
domesticated cattle of Africa were found in the north of the continent and were B. taurus in
nature, and that introgression of B. indicus into the continent via the Horn of Africa was
secondary. Our results suggest that these earliest hybrids may have been the animals that
later gave rise to southern populations. This scenario implies that B. indicus introgression
occurred before pastoralism spread extensively southwards and indeed, despite extensive
sampling, there is no evidence for the presence of pure African B. taurus in the south of the
continent (HANOTTE et al. 2002).
15
16
in Malagasy ritual and culture, which is compatible with an extensive history on the island
(HEMMER 1990; VAN DER ZWAN and EVERS 1998).
The employment of haplotypic mosaicism as an indicator of the antiquity of admixture
receives some confirmation from the Near Eastern results. The region between the primary
centres of B. indicus and B. taurus domestication is an area of ancient interaction between the
two lineages. As such, the sample from Iraq yields one of the highest values of τ within the
haplotypes.
Acknowledgements
This material is based on works supported by Science Foundation Ireland under grant no. 02-
IN.1-B256. AR Freeman was funded by a Wellcome Studentship in Biodiversity number
054275/Z/98/Z. We would like to thank David Lynn, Colm O’hUigin, Paul McKeigue and
Mark Shriver for helpful discussions and Claude Gaillard for provision of samples.
17
LITERATURE CITED
AMARAL, M. E., S. R. KATA and J. E. WOMACK, 2002 A radiation hybrid map of bovine X chromosome (BTAX). Mamm Genome 13: 268-271.
BISHOP, M. D., S. M. KAPPES, J. W. KEELE, R. T. STONE, S. L. SUNDEN, G. A. HAWKINS, S. S.
TOLDO, R. FRIES, M. D. GROSZ, J. YOO and ET AL., 1994 A genetic linkage map for cattle. Genetics 136: 619-639.
BRADLEY, D. G., D. E. MACHUGH, P. CUNNINGHAM and R. T. LOFTUS, 1996 Mitochondrial
diversity and the origins of African and European cattle. Proc Natl Acad Sci U S A 93: 5131-5135.
BRADLEY, D. G., D. E. MACHUGH, R. T. LOFTUS, R. S. SOW, C. H. HOSTE and E. P.
CUNNINGHAM, 1994 Zebu-taurine variation in Y chromosomal DNA: a sensitive assay for genetic introgression in west African trypanotolerant cattle populations. Anim Genet 25: 7-12.
CHAPMAN, N. H., and E. A. THOMPSON, 2002 The effect of population history on the lengths
of ancestral chromosome segments. Genetics 162: 449-458. DEEKS, J., D. ALTMAN and M. BRADBURN, 2001 Statistical methods for examining
heterogeneity and combining results from several studies in meta-analysis., pp. 285-372 in Systematic reviews in health care. Meta-analysis in context., edited by M. EGGER, G. DAVEY SMITH and D. ALTMAN. BMJ Books, London.
FALUSH, D., M. STEPHENS and J. K. PRITCHARD, 2003 Inference of population structure using
multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
FARNIR, F., W. COPPIETERS, J. J. ARRANZ, P. BERZI, N. CAMBISANO, B. GRISART, L. KARIM,
F. MARCQ, L. MOREAU, M. MNI, C. NEZER, P. SIMON, P. VANMANSHOVEN, D. WAGENAAR and M. GEORGES, 2000 Extensive genome-wide linkage disequilibrium in cattle. Genome Res 10: 220-227.
FELIUS, M., 1995 Cattle breeds - an Encyclopedia. Misset, Doetinchem, Netherlands. FREEMAN, A. R., C. M. MEGHAN, D. E. MACHUGH, R. T. LOFTUS, M. D. ACHUKWI, A. BADO,
B. SAUVEROCHE and D. G. BRADLEY, 2004 Admixture and diversity in West African cattle populations. Molecular Ecology 13: 3477.
GIFFORD-GONZALEZ, D., 2000 Animal Disease Challenges to the Emergence of Pastoralism
in Sub-Saharan Africa. African Archaeological Review 17: 95-139. HANOTTE, O., D. G. BRADLEY, J. W. OCHIENG, Y. VERJEE, E. W. HILL and J. E. REGE, 2002
African pastoralism: genetic imprints of origins and migrations. Science 296: 336-339.
18
HANOTTE, O., C. L. TAWAH, D. G. BRADLEY, M. OKOMO, Y. VERJEE, J. OCHIENG and J. E. REGE, 2000 Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub-saharan African cattle breeds. Mol Ecol 9: 387-396.
HASSAN, F. A., 2000 Climate and cattle in North Africa: a first approximation., pp. 61-86 in
The Origins and Development of African Livestock: archaeology, genetics, linguistics and ethnography., edited by R. M. BLENCH and K. C. MACDONALD. UCL Press, London.
HEMMER, H., 1990 Domestication : The Decline of Environmental Appreciation, pp. 11,
edited by H. HEMMER. Cambridge University Press. HOGGART, C. J., E. J. PARRA, M. D. SHRIVER, C. BONILLA, R. A. KITTLES, D. G. CLAYTON
and P. M. MCKEIGUE, 2003 Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72: 1492-1504.
HOGGART, C. J., M. D. SHRIVER, R. A. KITTLES, D. G. CLAYTON and P. M. MCKEIGUE, 2004
Design and analysis of admixture mapping studies. Am J Hum Genet 74: 965-978. IHARA, N., A. TAKASUGA, K. MIZOSHITA, H. TAKEDA, M. SUGIMOTO, Y. MIZOGUCHI, T.
HIRANO, T. ITOH, T. WATANABE, K. M. REED, W. M. SNELLING, S. M. KAPPES, C. W. BEATTIE, G. L. BENNETT and Y. SUGIMOTO, 2004 A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Res 14: 1987-1998.
KAPPES, S. M., J. W. KEELE, R. T. STONE, R. A. MCGRAW, T. S. SONSTEGARD, T. P. SMITH,
N. L. LOPEZ-CORRALES and C. W. BEATTIE, 1997 A second-generation linkage map of the bovine genome. Genome Res 7: 235-249.
KUMAR, P., A. R. FREEMAN, R. T. LOFTUS, C. GAILLARD, D. Q. FULLER and D. G. BRADLEY,
2003 Admixture analysis of South Asian cattle. Heredity 91: 43-50. LAAN, M., and S. PAABO, 1997 Demographic history and linkage disequilibrium in human
populations. Nat Genet 17: 435-438. LAUTENBERGER, J. A., J. C. STEPHENS, S. J. O'BRIEN and M. W. SMITH, 2000 Significant
admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet 66: 969-978.
LOFTUS, R. T., O. ERTUGRUL, A. H. HARBA, M. A. EL-BARODY, D. E. MACHUGH, S. D. PARK
and D. G. BRADLEY, 1999 A microsatellite survey of cattle from a centre of origin: the Near East. Mol Ecol 8: 2015-2022.
LOFTUS, R. T., D. E. MACHUGH, D. G. BRADLEY, P. M. SHARP and P. CUNNINGHAM, 1994
Evidence for two independent domestications of cattle. Proc Natl Acad Sci U S A 91: 2757-2761.
LONJOU, C., A. COLLINS and N. E. MORTON, 1999 Allelic association between marker loci.
Proc Natl Acad Sci U S A 96: 1621-1626.
19
MACHUGH, D. E., M. D. SHRIVER, R. T. LOFTUS, P. CUNNINGHAM and D. G. BRADLEY, 1997 Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146: 1071-1086.
MARSHALL, F., 2000 The origins and spread of domestic animals in East Africa, pp. 191-221
in The Origins and Development of African Livestock: archaeology, genetics, linguistics and ethnography., edited by R. M. BLENCH and K. C. MACDONALD. UCL Press, London.
MITCHELL, P., 2005 African connections pp. 33-63. AltaMira, Walnut Creek, CA. NORDBORG, M., and S. TAVARE, 2002 Linkage disequilibrium: what history has to tell us.
Trends Genet 18: 83-90. PARIS, F., 2000 African livestock remains from Saharan mortuary context in The Origins and
Development of African Livestock: archaeology, genetics, linguistics and ethnography., edited by R. M. BLENCH and K. C. MACDONALD. UCL Press, London.
PFAFF, C. L., E. J. PARRA, C. BONILLA, K. HIESTER, P. M. MCKEIGUE, M. I. KAMBOH, R. G.
HUTCHINSON, R. E. FERRELL, E. BOERWINKLE and M. D. SHRIVER, 2001 Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. Am J Hum Genet 68: 198-207.
RAYMOND, M., and F. ROUSSET, 1995 GENEPOP (version 1.2): population genetics software
for exact tests and ecumenicism. J. Heredity 86: 248-249. RITZ, L. R., M. L. GLOWATZKI-MULLIS, D. E. MACHUGH and C. GAILLARD, 2000
Phylogenetic analysis of the tribe Bovini using microsatellites. Anim Genet 31: 178-185.
SMITH, A. B., 2000 The origins of the domesticated animals of southern Africa in The origins
and development of African livestock: archaeology, genetics, linguistics and ethnography, edited by R. M. BLENCH and K. C. MACDONALD. UCL Press, London.
SØNSTEGARD, T. S., W. BARENDSE, G. L. BENNETT, G. A. BROCKMANN, S. DAVIS, C.
DROEGEMULLER, E. KALM, S. M. KAPPES, C. KUHN, Y. LI, M. SCHWERIN, J. TAYLOR, H. THOMSEN, C. P. VAN TASSELL and C. C. YEH, 2001 Consensus and comprehensive linkage maps of the bovine sex chromosomes. Anim Genet 32: 115-117.
SØNSTEGARD, T. S., N. L. LOPEZ-CORRALES, S. M. KAPPES, R. T. STONE, S. AMBADY, F. A.
PONCE DE LEON and C. W. BEATTIE, 1997 An integrated genetic and physical map of the bovine X chromosome. Mamm Genome 8: 16-20.
SUN, H. S., M. R. DENTINE, W. BARENDSE and B. W. KIRKPATRICK, 1994 UWCA19 and
UWCA20: polymorphic bovine microsatellites. Anim. Genet 25: 121. VAN DER ZWAN, N., and S. EVERS, 1998 Madagascar: The Zebu as Guide Through Past and
Present. Berg en Dal, The Netherlands.
20
WIEHE, T., J. MOUNTAIN, P. PARHAM and M. SLATKIN, 2000 Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns. Genet Res 75: 61-73.
WILLIAMS, J. L., A. EGGEN, L. FERRETTI, C. J. FARR, M. GAUTIER, G. AMATI, G. BALL, T.
CARAMORR, R. CRITCHER, S. COSTA, P. HEXTALL, D. HILLS, A. JEULIN, S. L. KIGUWA, O. ROSS, A. L. SMITH, K. SAUNIER, B. URQUHART and D. WADDINGTON, 2002 A bovine whole-genome radiation hybrid panel and outline map. Mamm Genome 13: 469-474.
21
Table 1 Cattle breeds included in the present study. N is the number of individuals in each
sample, E(τ) and SD(τ) are the posterior mean and standard deviation of τ respectively and τ
is a measure of the age of admixture. The asterisks mark those breeds that were genotyped
using radioactively labelled PCR products.
Breed name N E(τ ) SD(τ) Regional designation Aberdeen Angus* 29 n/a n/a European Bos taurus
Charolais* 33 n/a n/a European Bos taurus
N’Dama (Guinea)* 36 n/a n/a West African Bos taurus
N’Dama (Guinea Bissau)* 22 n/a n/a West African Bos taurus
Somba* 10 n/a n/a West African Bos taurus
Gobra* 32 6.67 2.70 West African hybrids
Sokoto Gudali* 13 9.90 4.62 West African hybrids
Mbororo* 9 4.27 3.24 West African hybrids
Kuri* 13 13.00 5.01 West African hybrids
Arashie 16 10.71 4.79 East African hybrids
Ogaden 18 10.23 4.76 East African hybrids
Ankole 14 7.99 4.92 East African hybrids
Watusi 3 15.45 7.23 East African hybrids
Barotse 16 18.90 5.04 Southern African hybrids
Kavango 12 21.30 4.78 Southern African hybrids
Nguni 9 15.27 5.87 Southern African hybrids
Afrikaner 14 8.87 4.28 Southern African hybrids
Zebu Malagasy 4 17.92 6.65 Madagascar
Anatolian Black* 12 13.13 5.05 Near Eastern hybrids
Iraqi* 16 17.76 4.98 Near Eastern hybrids
Nellore* 12 n/a n/a Bos indicus, of Indian descent
Ongole* 3 n/a n/a Indian Bos indicus
22
Table 2. Primer sequences and Optimal PCR conditions for ten X chromosome microsatellites. Magnesium Chloride concentration is shown
by [MgCl2] and annealing temperature is denoted by TA
Locus name
Approximate chromosome position (Mb)
Accession number UniSTS Primers (5’-3’) Amplicon
size PCR
[MgCl2] TA PCR
BMS1616 7 G18677 27189 CAGTGTGTATAGCATGATTCCG AGTTGGTCTGCATTCATACATTAA 92-116 1.25 54-55ºC
BL1045
9.2 251338 TGCCAGAACAAGTCACAAGC CTCCAAGGGTGTCTCTATCCC 92-100 1.5 59ºC
UWCA19 9.4 U01794 251002 CTGTGATAACCTATATGGGAAAGGA GAGGACAGCAAAGTGATTCAGT 97-105 1.5 58ºC
BL1098 10 251324 CCACAACTTCCAGAAGCCTC CAGAAACCACCCAAACTAACC 203-235 1.25 56ºC
BMS960 11 G18760 74452 TGTAAATAGCTCCCCTCCTGC CTAGCAATTTGTTGTTCATGGC 106-128 1.75 57ºC
XBM701 11.7 251432 TTCCCCTTGAAATCATCTGG TCCAAGTTACCAAAATTGACCC 148-168 2.0 58ºC
BMS2713 12.2 G18462 69721 TGAATACCTGTTTCCAGCCC CTCCTAAGTCCAGGAAGCCC 143-155 1.5 56ºC
XBM7 251010 CTGTATTAGAGTTCCCTGGAGAAA GCCAACATGCCCTGTAGAAT 180-202 1.5 57ºC
XBM361 14.8 251341 ACACACTGAGAATTAAACTACAAAAACCACACAACTGAAGCCACTTTAAGC 150-162 1.25 58-59ºC
BMS649 16.3 G18728 37262 CTCGGACTCATAACGCACAT CGAGCAACAAGAGTGAAGGT 116-134 1.75 59ºC
23
FIGURE LEGENDS
Figure 1. Map showing approximate sampling sites for cattle populations included in the current
study. The areas of the pie charts are proportional to the number of animals in the population.
The pie charts represent a previously calculated mR value for each breed which is a measure of
Bos taurus/Bos indicus admixture which has been calculated using European B. taurus and
Indian B. indicus breeds as parental populations. The Nellore breed was sampled in Brazil, but is
comprised of Ongole individuals that were brought to South America (FELIUS 1995; RITZ et al.
2000).
Figure 2. Linkage disequilibrium plots showing LD assessed by the significance of allelic
associations at pairs of loci. The lightest grey shaded areas represent untyped markers. Grey
and black squares mark locus pairs with alleles associating with p-values of <0.01 and <0.05
respectively. The matrix plots facilitate comparison of LD levels among the different regional
groups. Additionally, the differences between LD among the sets of linked markers and
unlinked markers are also evident. To further clarify the differences both between regional
groups and between sets of linked and unlinked markers, the percentages of significant
associations (at the two designated levels) are also shown in two histograms. The cattle
populations are grouped according to Table 1.
Figure 3. Map showing values of τ. τ is the number of generations since a single admixture
event admixture. In these cattle populations admixture probably occurred in a continuous
manner, therefore τ is interpreted as a relative measure of the age of admixture among the
populations studied (see Materials and Methods). Higher values of τ are shaded with darker
shades of grey and suggest older admixture in those areas.