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Mitochondrial DNA Diversity and Origins of South and Central American Goats
Mitochondrial DNA Diversity and Origins of South and Central American Goats
Summary We have analysed the genetic diversity of South and Central American (SCA) goats
by partially sequencing the mitochondrial control region of 93 individuals with a wide
geographical distribution. Nucleotide and haplotype diversities reached values of
0.020 ± 0.00081 and 0.963 ± 0.0012 respectively. We have also observed a rather weak
phylogeographic structure, with almost 69% of genetic variation included in the within-
breed variance component. The topology of a median-joining network analysis including 286
European, Iberian, Atlantic and SCA mitochondrial sequences was very complex, with most
of the haplotypes forming part of independent small clusters. SCA sequences showed a
scattered distribution throughout the network, and clustering with Spanish and Portuguese
sequences occurred only occasionally, not allowing the distinguishing of a clear Iberian
signature. Conversely, we found a prominent cluster including Canarian, Chilean, Argen-
tinian and Bolivian mitochondrial haplotypes. This result was independently confirmed by
constructing a Bayesian phylogenetic tree (posterior probability of 0.97). Sharing of mito-
chondrial haplotypes by SCA and Canarian goats suggests that goat populations from the
Atlantic archipelagos, where Spanish and Portuguese ships en route to the New World used to
stow food and supplies, participated in the foundation of SCA caprine breeds.
2009 The Authors, Journal compilation 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322 315
316 Amills et al.
migratory processes under which these SCA populations were analysis. The comparison of the genetic diversity of the
formed and evolved. Upon the conquest and colonization of American, Iberian and European goat breeds was achieved by
the New World by the Spanish and the Portuguese, goats and using the aforementioned dataset and a pool of 106 sequences
other livestock were massively transported through the extracted from the GenBank. This additional dataset included
Atlantic Ocean to be used as a food supply in exploratory and sequences from Swiss (Chamois, Verzaska, Saanen and
military expeditions (Rodero et al. 1992). There are abundant Toggenburg, n = 35), Portuguese (Serpentina, Serrana,
historical records demonstrating beyond any doubt the Algarvia and Charnequeira, n = 41), Italian (Girgentana,
essential role that Andalusian and Lusitanic breeds played in Maltese and Derivata di Siria, n = 21), Irish (Irish Island,
this process, with most of the transatlantic exploratory jour- n = 4), Canarian (n = 4) and Danish (n = 1) breeds (Luikart
neys in the 15th century departing from a coastal area that et al. 2001; Pereira et al. 2005; Sardina et al. 2006).
goes from the San Vicente Cape to the Bay of Cádiz (Rodero
et al. 1992). In contrast, the magnitude of the contribution of
Phylogenetic and genetic diversity analyses
the Atlantic archipelagos, which were invariably ports of call
for ships and galleys en route to SCA, to the formation of Phylogenetic and genetic diversity analyses were performed
American creole breeds has been scarcely documented and it using a 463 bp region shared by mitochondrial control
is still a matter of debate. sequences obtained by us and others. Nucleotide diversity
(p), Fu and Li statistics (F) and haplotype diversity were
computed with the DNASP 4.00 software (Rozas et al. 2003),
Materials and methods
whereas the significance of F was calculated with a coa-
lescent algorithm implemented in this program. The spatial
Sample collection and partial sequencing of the
analysis of the molecular variance was performed with the
goat mitochondrial control region
SAMOVA software (Dupanloup et al. 2002). The median-
Genomic DNA was extracted from either hair or blood joining network was constructed with the NETWORK 4.2
samples corresponding to 152 goats from the South of Spain program (Bandelt et al. 2000). Positions were weighted
(Malagueña, Murciano-Granadina breeds, n = 22), Portu- according to their mutational frequency and the relative
gal (Bravia breed, n = 9), Cape Verde (n = 28), Cuba weight of transversions vs. transitions was set to 3
(n = 25), México (n = 22), Brazil (n = 12), Venezuela according to Bandelt (2007). Bayesian phylogenetic trees
(n = 4), Argentina (n = 9), Chile (n = 10), United States were calculated with MRBAYES V3.1.2 (Ronquist & Huelsen-
(Spanish goat, a breed of Mexican ancestry, n = 6) and beck 2003). In this Bayesian analysis, we employed a
Bolivia (n = 5). Specimens were collected by local personnel Hasegawa, Kishino & Yano (1985) evolutionary model
with expertise in zootechny in order to ensure that they previously selected with MODELTEST (Posada & Crandall
correspond to indigenous populations without introgression 1998). Evolutionary parameters (proportion of invariant
with foreign commercial breeds. Hair DNA extraction was sites, a-value and transition to transversion rates) were
performed with the DNeasy Blood & Tissue Kit (Qiagen) estimated with both MODELTEST and MRBAYES. After 2.5 mil-
according to the manufacturerÕs instructions, with the lion iterations, the initial 5000 trees were discarded and the
exception of the lysis method, which instead involved an remaining 20 000 ones were employed to construct a
incubation in 350 ll lysis buffer (100 mM Tris–Cl pH 8, consensus tree that was visualized with TREEVIEW (Page
100 mM NaCl, 3 mM CaCl2, 2% SDS, 40 mM dithiothreitol 1996). A neighbour-joining tree and a multidimensional
and 250 lg/ml proteinase K) at 56 C for 3–4 h. The pro- scaling plot based on Da distances (number of net nucleotide
tocol for DNA isolation from peripheral blood mononuclear substitutions per site between populations) amongst popu-
cells has been previously reported (Amills et al. 2004). lations were constructed with MEGA 3.1 and XLSTAT softwares
Purified genomic DNA was used as a template to amplify respectively. Da distances were calculated with the DNASP 4.00
and sequence 653 bp of the mitochondrial control region software (Rozas et al. 2003) as follows:
with a previously described technique (Amills et al. 2004).
Da ¼ DXY ðDX þ DY Þ=2
Sequences corresponding to different mitochondrial haplo-
types were submitted to GenBank (GenBank accession where DXY is the average distance between populations X
numbers: EF372411–EF372515). The basic local alignment and Y, and DX and DY are the mean within-population
search tool (BLASTN, http://blast.ncbi.nlm.nih.gov/Blast.cgi) distances (Nei & Miller 1990).
with default parameters was employed to perform compar-
ative searches throughout the GenBank nucleotide collec-
Results
tion database. Other mitochondrial control region
sequences from Spanish (Malagueña, Murciano Granadina
Genetic diversity of SCA goats
and Guadarrama, n = 8) and Canarian (Palmera, Majorera
and Tinerfeña, n = 20) breeds characterized in a previous Sequencing of the mitochondrial control region of SCA
study (Amills et al. 2004) were also incorporated to our goats (n = 93) with a wide geographical distribution
2009 The Authors, Journal compilation 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322
Atlantic origin of American goats 317
Table 1 Genetic diversity at the mitochondrial control region (463 bp) Table 2 Spatial analysis of the molecular variance of the mitochondrial
of South and Central American (SCA), Atlantic, Iberian and European control region (463 bp) in South and Central American (SCA) goat
(non-Iberian) goats. breeds.
Haplotype No.
Population N1 p2 Nh3 diversity groups Populations r2WB r2AG r2ABWG
SCA 93 20.09 (0.81) 54 0.963 (0.012) 2 Argentina, Chile 68.85% 19.90% 11.25%
Atlantic 52 (24) 19.53 (1.07) 28 0.965 (0.011) Remaining SCA populations
Iberian 80 (49) 22.23 (0.73) 71 0.996 (0.003) 3 Argentina, Chile, Bolivia 73.54% 24.62% 1.84%
European4 61 (61) 19.02 (0.92) 53 0.994 (0.005) México
Remaining SCA populations
1
N: Number of sampled individuals (sequences extracted from GenBank
are shown between parentheses). r2WB, variance within breeds; r2AG, variance amongst groups; r2AGWB,
2
Nucleotide diversity · 103. variance amongst groups and within breeds.
3
Nh: Number of haplotypes.
4
Pool of Italian, French, Swiss, Irish and Danish breeds.
components are shown in Table 2). When the number of
groups was set to three, we observed the following groups:
revealed the existence of 54 different haplotypes, all of them (i) Chile, Argentina and Bolivia, (ii) México and (iii)
belonging to the A lineage, which is the most frequent all remaining SCA populations.
over the world (Table 1). Measurement of nucleotide and
haplotype diversities in our SCA continental population
Relationships between SCA goats and other Iberian,
yielded values of 0.020 ± 0.00081 and 0.963 ± 0.012
Atlantic and European populations
respectively (Table 1). The sample size employed (almost
100 individuals) and the wide geographical distribution of A median-joining network-based phylogenetic analysis
the populations studied make this analysis fairly represen- involving 286 American, Iberian, Atlantic and European
tative of the existing genetic variation at a continental level. goat mitochondrial sequences is shown in Fig. 1. In general,
These levels of nucleotide diversity are notably similar to the SCA sequences showed a scattered distribution throughout
ones observed in the Atlantic, Iberian and European popu- the network, with a few clusters encompassing individuals
lations (Table 1). However, if we consider the ratio between with the same geographic origin. This diffuse topology,
the number of different haplotypes and the total number of which is rather complex because a significant amount
analysed sequences (54/93 = 0.58 for SCA; 28/52 = 0.54 of haplotypes are unique or are shared by a small number of
for Atlantic; 71/80 = 0.89 for Iberian; 53/61 = 0.87 for individuals, has been observed in previous works dealing
European population), it is clear that SCA and Atlantic with Portuguese (Pereira et al. 2005) and Chinese (Chen
populations have a relatively smaller proportion of different et al. 2005) goats. Occasional clustering between SCA
haplotypes than Iberian and European populations. A sequences and their European, Iberian and Cape Verdean
regional analysis of genetic variability is presented in counterparts was observed, but it was difficult to identify a
Table S1. These results should be taken with caution given clear relationship between these three populations and SCA
the small sample size of several of the analysed populations, goats because of their scattered distribution. The only
but they suggest that genetic diversity is particularly exception to this general trend was a cluster of considerable
reduced in Argentinian and Chilean goats. size that included Canarian, Chilean, Argentinian and
Bolivian mitochondrial haplotypes (Fig. 1 and Fig. S1). The
existence of this cluster, which was also closely connected to
Population structure
Cuban, Mexican and Cape Verdean haplotypes (Fig. S1),
The Fu and Li F-statistic corresponding to the analysis might suggest that Canarian goats contributed to the
of SCA mitochondrial sequences yielded a negative and foundation of the genetic pool of SCA breeds.
non-significant value of )1.578 (P = 0.071). Analysis of With the aim of confirming the results obtained with the
geographical structure using SAMOVA 1.0 (Dupanloup et al. median-joining network approach and inferring their
2002), a software based on a simulated annealing algo- statistical significance, we performed an independent phy-
rithm that maximizes the proportion of total genetic vari- logenetic analysis. The 286 sequences employed in the
ance due to differences between groups of populations, network analysis corresponded to 195 different haplotypes
demonstrated that most of genetic variation occurs within that were subsequently analysed by means of a Bayesian
breeds (Table 2). When the number of groups was set to tree (Fig. 2). This phylogenetic tree reliably recovered the
two, the spatial analysis of the molecular variance (SAMOVA) aforementioned Canarian cluster with a highly significant
defined the existence of two groups, 1 (Argentina and Chile) posterior probability (97%). Moreover, and as previously
and 2 (remaining populations) with almost 69% of the observed, clustering of SCA sequences with their Iberian,
genetic variation occurring within breeds (variance Cape Verdean and European counterparts was occasional
2009 The Authors, Journal compilation 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322
318 Amills et al.
South American
Cape Verde
Canary Islands
Iberian
European pool
Figure 1 Median-joining network analysis of 286 American, Iberian, Atlantic (Canarian and Cape Verdean) and European goat mitochondrial control
region sequences. The size of the circles is proportional to haplotype frequencies. Transversions were weighted three times as high as transitions
according to Bandelt (2007), and sites were weighted according to their mutational frequencies. The MP option was employed to delete all superfluous
median vectors and links that were not contained in the shortest trees of the network. This figure is in colour in the online version of the paper.
and, with a few exceptions, individuals with the same that all the SCA mitochondrial control region sequences
geographical origin did not group together, confirming the belonged to lineage A. Our inability to detect mitochondrial
lack of a well-defined phylogeographic structure. A third lineages B, C, D, F and G in SCA goats is not surprising given
analysis exploring genetic relationships amongst goat pop- that these lineages are also very rare, or even absent, in
ulations was carried out by constructing a multidimen- Europe (Luikart et al. 2001; Joshi et al. 2003; Naderi et al.
sional scaling plot (Fig. 3a) and a neighbour-joining tree 2007). More specifically, in the Iberian Peninsula, lineage C
(Fig. 3b), where the number of net nucleotide substitutions has a very low frequency (<5%) and lineages B, D, F and G
per site between populations (Da) was used as a distance seem to be completely absent (Amills et al. 2004; Azor et al.
measurement. This analysis highlighted the existence 2005; Pereira et al. 2005; Naderi et al. 2007). According to
of three main groups: one including Canarian, Bolivian, our data, in the Atlantic archipelagos, the situation is rather
Argentinian and Chilean goats; a second involving Euro- similar, with an absolute predominance of lineage
pean, Iberian and Mexican goats; and a third encompassing A. Nucleotide diversities in Atlantic and SCA goats were
the remaining populations (Fig. 3a,b). similar to the ones characterized in Iberian and European
breeds, but haplotype diversities were somewhat lower and
the ratios between the number of different haplotypes and
Discussion
the total number of sequences were much lower. Although
The current gene pool of SCA goats was founded in the last data presented in Table S1 should be interpreted with
five centuries as a result of the introduction of this species to caution, because sample size for several populations is quite
America by the Spanish and Portuguese colonizers. Our limited, this regional analysis of genetic diversity suggests
main goal was to acquire a general perspective of the final that nucleotide and haplotype diversities are particularly
consequences of this process by exploring mitochondrial reduced in two Andean populations located in Chile and
genetic variation of caprine breeds with a large geographi- Argentina. Our interpretation is that these two populations
cal distribution in SCA. We can conclude from this survey descended from Canarian goats, which show a decreased
2009 The Authors, Journal compilation 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322
Atlantic origin of American goats 319
FALCO1
100
95
97
92
93
98
91
96
100
100
100
100
96
100
South American 96
100 100
97
Cape Verde
100
96
Figure 2 Bayesian phylogenetic tree displaying Canary Islands
the genetic relationships between 195
American, European, Atlantic (Canarian and Iberian 100
97
probability: 97) is indicated with a red arrow.
98
This figure is in colour in the online version of
100
the paper.
genetic diversity when compared, for instance, to Cape component (Luikart et al. 2001). Naderi et al. (2007), in an
Verdean goats. The most likely explanation for this low analysis involving 2430 individuals from all over the world,
genetic variability of Canarian goats is that an important also reported that 77% of mitochondrial DNA variation is
founder effect took place 2200 years ago, when the first distributed within breeds. Similarly, in Indian goats, 83% of
inhabitants of the Canary Islands settled the archipelago, the total molecular variance was included in the within-
carrying with them a small number of domestic animals breed component (Joshi et al. 2003). As a reference, in cattle,
(Capote et al. 2004). the within-breed and amongst-group components include
The SAMOVA analysis of SCA sequences showed that 45% and 51% of the total variation respectively (Luikart
around 69% of the genetic variation corresponds to the et al. 2001). The weak structuring of goat breeds is one of
within-population component, meaning that creole breeds the main pieces of evidence supporting the utilization of this
are poorly differentiated at the genetic level. This low phy- domestic species as a portable food resource accompanying
logeographic structure observed in SCA breeds is a recurring human migratory movements from time immemorial.
theme when analysing mitochondrial variation of caprine There is compelling and abundant historical evidence
populations. The AMOVA analysis of 406 European, African supporting the idea that Iberian livestock was extensively
and Asian goat sequences revealed that 78.7% of transported from the South of Spain and Portugal to
mitochondrial variation corresponded to the within-breed America (Rodero et al. 1992). In Spain, Sevilla, Cádiz, San-
2009 The Authors, Journal compilation 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322
320 Amills et al.
2009 The Authors, Journal compilation 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322
Atlantic origin of American goats 321
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Acknowledgements PLoS ONE 2, e1012.
Nei M. & Miller J.C. (1990) A simple method for estimating average
We are grateful to Jean-Marie Luginbuhl, Liliana Allegretti,
number of nucleotide substitutions within and between popula-
Alfredo Teixeira, Vladimir Ribera, Norge Fonseca, José A.
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Emilio Cabrera, Felipe Trujillo and René Garcés for provid- Biosciences 12, 357–8.
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Supporting information
Additional supporting information may be found in the
online version of this article.
2009 The Authors, Journal compilation 2009 International Society for Animal Genetics, Animal Genetics, 40, 315–322