MBE Advance Access originally published online on June 16, 2006
Molecular Biology and Evolution 2006 23(9):1776-1783; doi:10.1093/molbev/msl043
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Article |
Sheep Mitochondrial DNA Variation in European, Caucasian, and Central Asian Areas
inkulov
* Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland; All-Russian Research Institute of Animal Husbandry, Russian Academy of Agricultural Sciences, Dubrovitsy, Russia; Animal Science Department, University of Novi Sad, Novi Sad, Serbia and Montenegro; Siberian Branch of Russian Academy of Agricultural Science, Krasnoobsk, Russia; || All-Russian Research Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Sciences, St Petersburg-Pushkin, Russia; ¶ Department of Sheep and Goat Breeding, Agricultural University of Cracow, Cracow, Poland; and # Institute of Veterinary Medicine and Animal Sciences of the Estonian University of Life Sciences, Tartu, Estonia
E-mail: juha.kantanen{at}mtt.fi.
 |
Abstract |
|---|
 TOP Abstract IntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Three distinct mitochondrial maternal lineages (haplotype Groups A, B, and C) have been found in the domestic sheep. Group B has been observed primarily in European domestic sheep. The European mouflon carries this haplotype group. This could suggest that European mouflon was independently domesticated in Europe, although archaeological evidence supports sheep domestication in the central part of the Fertile Crescent. To investigate this question, we sequenced a highly variable segment of mitochondrial DNA (mtDNA) in 406 unrelated animals from 48 breeds or local varieties. They originated from a wide area spanning northern Europe and the Balkans to the Altay Mountains in south Siberia. The sample included a representative cross-section of sheep breeds from areas close to the postulated Near Eastern domestication center and breeds from more distant northern areas. Four (A, B, C, and D) highly diverged sheep lineages were observed in Caucasus, 3 (A, B and C) in Central Asia, and 2 (A and B) in the eastern fringe of Europe, which included the area north and west of the Black Sea and the Ural Mountains. Only one example of Group D was detected. The other haplotype groups demonstrated signs of population expansion. Sequence variation within the lineages implied Group A to have expanded first. This group was the most frequent type only in Caucasian and Central Asian breeds. Expansion of Group C appeared most recently. The expansion of Group B involving Caucasian sheep took place at nearly the same time as the expansion of Group A. Group B expansion for the eastern European area started approximately 3,000 years after the earliest inferred expansion. An independent European domestication of sheep is unlikely. The distribution of Group A variation as well as other results are compatible with the Near East being the domestication site. Groups C and D may have been introgressed later into a domestic stock, but larger samples are needed to infer their geographical origin. The results suggest that some mitochondrial lineages arrived in northern Europe from the Near East across Russia.
Key Words: Ovis aries • sheep • domestication • mtDNA
|
Introduction |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
In several species, mitochondrial DNA (mtDNA) has been used to study domestication history. The first surveys of mtDNA variation in the domestic sheep (Ovis aries) revealed 2 distinct lineages (A and B; Wood and Phua 1996
; Hiendleder, Mainz et al. 1998; Hiendleder et al. 2002), and recently, a third distinct haplotype group was reported (C; Guo et al. 2005; Pedrosa et al. 2005). The number of highly diverged lineages in other domestic ruminants is 4 for goat (Sultana et al. 2003), 2 for cattle (Loftus et al. 1994), and 2 for water buffalo (Tanaka et al. 1996), and separate domestication regions have been inferred. Similarly, the presence of several distinct lineages has been inferred as multiple sheep domestications (e.g., Pedrosa et al. 2005). The number of culturally and biologically independent domestication events may be lower than the number of distinct lineages because the original wild population may have been polymorphic, or new maternal lineages may have been introgressed from different wild populations into the domesticated population (Zeder et al. 2006).
The previous studies on sheep mtDNA sequence diversity (Wood and Phua 1996; Hiendleder, Mainz et al. 1998; Hiendleder et al. 2002; Guo et al. 2005) have been mainly based on European or Asian sheep distant from the postulated Near East domestication center (Smith 1998). A single haplotype group, Group B, predominates in European sheep populations, and it is the only group that has been observed in the European mouflon. This haplotype group is less common in the native eastern Eurasian breeds (Hiendleder, Mainz et al. 1998; Hiendleder et al. 2002, Guo et al. 2005, Meadows et al. 2005) with a notable exception for the Javanese thin tailed (Meadows et al. 2005), which may result from crossbreeding with breeds originating from Europe (reviewed by Davis et al. 2002). The predominance of Group B in Europe supports an independent European domestication of sheep, which has been suggested earlier (e.g., Ryder 1983, p 23–4). However, the most reliable archaeological data suggest that sheep domestication occurred in the central part of the Fertile Crescent in the Near East approximately 9,000 years ago (Smith 1998), and the European mouflon can represent a primitive feral sheep rather than a truly wild sheep (Poplin 1979). A recent study in Turkish sheep showed 3 distinct maternal lineages, and this was regarded as a support for the high importance of Turkey in sheep domestication (Pedrosa et al. 2005). However, the hypothesis of Near Easter sheep domestication has not been conclusively explored with comparisons of genetic variation between geographical areas. The aim of the present study was to assess the support for the European and Near Eastern domestication of sheep. This was based on extensive sampling in Caucasus area, which is located very close to the hypothesized Near East domestication center, and in a wide northern area spanning the North European countries and the Balkans to the Altay Mountains in south Siberia, which represents a geographical area clearly exterior to the postulated Near Eastern domestication sites (e.g., Pedrosa et al. 2005). The rich sheep diversity in the study area contains indigenous fat-tailed, fat-rumped, and thin-tailed fleece sheep (Ryder 1984), including both short- and long-tailed breeds.
|
Materials and Methods |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Sampling and DNA Extraction
Samples of 406 unrelated animals from 48 breeds or local varieties were studied. Sampling was done in large collective or institute farm flocks of recognized breeds or in several smallholder flocks of local varieties. Sheep were grouped into 16 regional groups (fig. 1; Supplementary Table 1, Supplementary Material online) representing 3 wider areas (Caucasian area, Central Asian area, and the remaining eastern fringe of Europe). Four of these regional groups are located in the Caucasian area: south Caucasus (Azerbaijan Mountain Merino, Bozakh, Gala, Karabakh, Mazekh, Tushin), north Caucasus (Andi, Dagestan local, Dagestan Mountain Merino, Karachai, Lezgian), Stavropol (Caucasian, North Caucasus Mutton-Wool, Stavropol), and the Caspian Depression (Aksaraisk sheep type, Grozny, Soviet Merino, Volgograd). Two of the groups are located in Central Asia: east of Caspian Sea (Edilbai, Karakul) and Altay (Gorno-Altay local, Kulunda). The remaining 10 regional groups are located in the area west of the Ural Mountains and cover the eastern fringe of Europe (fig. 1): the Middle Volga region (Kuibyshev, Mordovian local), the Volga-Kama region at the intersection of the Volga and Kama Rivers (Komi local, Mari local, Oparin, Udmurtian local), west Russia (Kuchugur, Romanov, Russian Romney Marsh), Russian Karelia (Vepsia sheep, Viena sheep), Ukraina (Carpathian Mountain, Sokolsk), east of Baltic Sea (Finnsheep, Finnish Grey Landrace, Estonian Blackhead, Estonian Whitehead, Saaremaa local, and Ruhnu local), Poland (Olkuska, Swiniarka, Wrzosowka), southeast Europe (the original place of Tsigai breeds: Serbian Tsigai, Russian Tsigai), Norway (Spael Sheep, Old Spael Sheep, Norwegian Feral Sheep), and Britain (Oxford Down). DNA samples were extracted from blood as described previously (Tapio et al. 2003
) or using the PickPen/QuickPick gDNA method (Bio-Nobile, Finland) according to the manufacturer's instructions.
|
Sequence Data
The DNA region analyzed was a highly variable 721-nt long segment of the mtDNA control region, running from base 15,541 to base 16,261 in relation to the full mitochondrial sequence (accession number NC001941; Hiendleder, Lewalski et al. 1998
). Based on this complete genome sequence, 4 primers were designed. The primers were named to indicate the locations and whether they hybridized with the heavy (H) or the light (L) strand. OarCR15389-15410L and OarCR29-48H were used to produce sequencing template using polymerase chain reaction (PCR), and OarCR15412-15436L and OarCR16368-16391H were used to sequence both complementary strands. In PCR, 0.05 µg of total DNA was used in 50 µl volume of standard DyNAZyme II (Finnzymes, Finland) PCR reaction mix. The template production conditions were as follows: 2 min 94°C; 10 times 1 min 94°C, 1 min 56°C, 2 min 70°C; 10 times 45 s 90°C, 1 min 54°C, 2 min 70°C; 20 times 45 s 88°C, 1 min 52°C, 2 min 70°C; 5 min 70°C. PCR products were purified using ExoSAP-IT (Amersham Biosciences, United Kingdom). Sequencing reactions were performed with DYEnamic ET Terminator Kit (Amersham Biosciences) using 10 µl of purified template. The sequencing reaction had 29 cycles of the following temperatures: 20 s 95°C, 15 s 50°C, and 1 min 60°C. The sequencing products were purified using Amersham Biosciences Autoseq 96 plates and analyzed using MegaBACE 500 (Amersham Biosciences). Fluorogram analysis was performed using Cimarron 3.12 base-caller implemented in MegaBACE Sequence Analyser (Amersham Biosciences). The complementary sequence reads were combined using Phred/Phrap software (Ewing et al. 1998). This combining utilized Phred-estimated base-calling confidences. The combination of complementary reads was done also with fixed, equal confidence for each base-call. If this implied that there were major differences between the sequence reads, the reads were considered unreliable and were excluded in an early phase of the analysis. The ends of the sequences were trimmed to exclude problematic segments after a manual check.
The following previously published wild and domestic sheep data were used for comparison: Ovis aries musimon (AY091487
[GenBank]
; Hiendleder et al. 2002), Ovis ammon collium (AY091492
[GenBank]
; Hiendleder et al. 2002), Ovis ammon nigrimontana (AY091494
[GenBank]
; Hiendleder et al. 2002), Ovis vignei bochariensis (AF039580
[GenBank]
, AY091491
[GenBank]
, and AY091490
[GenBank]
; Hiendleder, Mainz et al. 1998; Hiendleder et al. 2002), Ovis vignei arkal (AY091489
[GenBank]
; Hiendleder et al. 2002), and O. aries (Mongolian) (AY829402
[GenBank]
; Guo et al. 2005). Novel domestic sheep sequences were submitted to GenBank (accession numbers DQ242050–DQ242455). The sequences were aligned using MAP2 software (Ye and Huang 2005) with the default parameters but setting alignment gaps larger than 75 nt not to be penalized more than a 75-nt gap.
Data Analysis
MEGA 3.1 (Kumar et al. 2004) was used to construct a Neighbor-Joining tree and to measure differences within and between the observed distinct haplotype groups. Network 4.1.0.9
[EC]
(Bandelt et al. 1999; available from: http://www.fluxus-engineering.com/) was used to construct median-joining networks separately for the sequences within each haplotype group in order to estimate short-scale evolutionary relationships. If the network indicated that the maximum number of mutations at a site exceeded 4, the site was excluded and the network was rebuilt. Groups A and B had 5 common excluded sites (15,956, 15,957, 16,008, 16,048, and 16,133). In Group A, the sites 15,939 and 15,971 were also excluded. In Group B, 28 other sites were not considered (15,566, 15,592, 15,601, 15,621, 15,639, 15,645_15,646insT, 15,933, 15,934, 15,943, 15,948, 15,955, 15,958, 15,959, 15,961, 15,963, 15,977, 15,982, 15,993, 16,003, 16,019, 16,036, 16,042, 16,044, 16,096, 16,097, 16,101, 16,218, and 16,245). Site numbering is given in relation to the full mitochondrial sequence (accession number NC001941).
The distribution of the sequence types represented by nodes in the median-joining network was tested using a simplified phylogeographic test. This test was a permutational contingency test, where the geographic sampling area (Caucasus, Central Asia, and the remaining eastern fringe of Europe) was treated as a categorical variable (Templeton et al. 1995). In each network for the 3 haplotype groups, the sequence types were grouped into 3 classes: 1) rare types occurring once or twice, 2) the phylogenetically central common root type, and 3) other types. The null distribution (the sampling area is unrelated to the observation, e.g., rare sequence types are equally likely to be found in any area) was created by 106 permutations using Geodis 2.2 (Posada et al. 2000).
Signs of population expansion were explored using Arlequin 2.001 (Schneider et al. 1999) with the following steps. First, Fu's Fs test of selective neutrality (Fu 1997), which compares the observed haplotype number to the observed number of pairwise differences, was used to establish the presence of population expansion. Second, based on the observed distribution of pairwise differences between sequences (i.e., mismatch distribution), the model parameters for the sudden population expansion model (Rogers 1995) were estimated, and the fit of the data to the inferred model was tested (Schneider and Excoffier 1999). Deletion polymorphisms were ignored in the analysis.
R8s 1.70 software (Sanderson 2003) was used to estimate the time to the most recent common ancestor for each distinct domestic sheep lineage (i.e., time in which all the within-group variation emerged). This analysis required a phylogenetic tree with branch lengths. To construct this, the appropriate mutation model was determined first. This was done using a hierarchical likelihood ratio test in Modeltest 3.06 (Posada and Crandall 1998). Second, similarity of substitution rate in the evolutionary paths from an ancestral sequence type into pairs of present-day domestic sheep mtDNA haplotypes was studied using a model-based relative rate test implemented in HY-PHY (Pond et al. 2005). This test compares the evolutionary distance from an outgroup to 2 different "ingroup" haplotypes. The hypothesis testing is based on the difference between the likelihood of data with and without the assumption of equivalent substitution rate. In this relative rate test, Ovis ammon nigrimontana (AY091494; Hiendleder et al. 2002) was the outgroup. Haplotypes were excluded from the phylogenetic dating analysis based on a testwise P value 0.05. Third, the remaining unique domestic sheep haplotypes were used to construct a Bayesian phylogeny using MrBayes 3.1.2 (Ronquist and Huelsenbeck 2003). In construction of the phylogeny, the default priors of MrBayes were utilized, and simple uniform molecular clock was assumed. MrBayes was run for 6 million iterations. This was performed using 4 parallel chains with temperature setting 0.03 in order to make the analysis explore possible trees and parameters more efficiently. The first million iterations were excluded as "burn-in." From the remaining 5 million iterations, 12,500 trees were sampled to construct a consensus tree that included all groupings that occurred in the majority of the trees. Fourth, this Bayesian tree was given as input to r8s software. One substitution rate across the entire tree was assumed, and a so-called truncated Newton algorithm was used to estimate times (see r8s documentation for details).
|
Results |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
General Observations
The sequenced segment spanned 721 nt in relation to the full sheep mitochondrial sequence (NC001941). The analyses were based on the region that corresponds to the sites from 15,541 to 15,643 and from 15,933 to 16,261. A central region, which consisted mainly of long tandem repeats, was excluded. The exact boundaries of the discarded part were set by the MAP2 software, which aligns only significantly similar blocks (Ye and Huang 2005
). The alignment was 432 nt long. In the obtained 406 domestic mtDNA sequences, 210 haplotypes were identified. They were defined by 124 polymorphic sites, including 3 sites where the polymorphism was only a presence/absence of an alignment gap. Among the 210 haplotypes in the 48 populations, 159 were observed once, whereas the most common haplotype occurred 61 times (Supplementary Table 2, Supplementary Material online).
The haplotypes divided into 4 distinct haplotype groups (fig. 2): Groups A, B, (Wood and Phua 1996), C (Pedrosa et al. 2005), and a new Group D. This division was confirmed by split decomposition analysis (Bandelt and Dress 1992; unpublished data). The average proportion of different nucleotides between unique haplotypes was 2.8%. Within Groups A, B, and C, this proportion was 0.9%, 0.7%, and 0.4%, respectively. The average proportion of dissimilar nucleotides in pairs of haplotypes from different haplotype groups was 5.5%. Between pairs of haplotype groups, this proportion varied from 5.0% (between Groups B and D) to 6.1% (between Groups A and C). Groups A and B were the most common and occurred in 22% and 71% of the studied sheep, respectively. Frequencies of the 2 other groups were low; the frequency of Group C was 7%, and Group D was detected in only one Karachai sheep from north Caucasus.
|
Analysis of Haplotype Group Expansions
The median-joining networks showed a star-shaped pattern (fig. 3). This phylogenetic pattern is commonly understood to be indicative of a population expansion. Two statistical approaches supported this inference. First, the Fs (Fu 1997
) statistic, which is particularly sensitive to population growth, showed a significant (P < 0.001) departure from neutrality in all 3 haplotype groups with multiple haplotypes (A: –26.0; B: –26.1; and C: –7.1). Second, the observed mismatch distributions were fitted to the sudden expansion model (Rogers 1995), and the analysis supported population expansion in each haplotype group. The observed mismatch distributions did not deviate from the expectations of the fitted models (P > 0.36; table 1) according to the sum of squared deviation statistic (Schneider and Excoffier 1999). The estimated initial and postexpansion scaled effective population sizes (i.e., 2Mu, twice the mitochondrial effective population size multiplied with the mutation rate) were as follows: Group A: 0.0 and 230.2; Group B: 0.174 and 137.1; and Group C: 0.0 and 2.6 (table 1). This result indicated that the mtDNA variation within the 3 haplotype groups originated from a very small ewe population. The results of the separate mismatch analysis for each studied area are presented in table 1.
|
|
The analysis described above also included estimation of the scaled numbers of generations after the expansion (i.e., 2tu, twice the number of generations after the expansion multiplied with the mutation rate; table 1). These were transformed to time estimates by setting the time estimate of the earliest expansion (Group A: 2tu = 4.01; table 1) to equal 9,000 years before present. The time estimates for Group B and Group C corresponded to expansions 6,400 and 7,000 years ago, respectively. The separate analyses for the 3 geographical areas resulted in wider confidence intervals for the estimate of 2tu than for the combined sample. The only exception was Group B. For this haplotype group, the estimate of 2tu for Caucasus differed considerably from that for the eastern fringe of Europe, and the confidence intervals remained relatively narrow. The expansion of Group B involving Caucasian sheep was estimated to have begun approximately at the same time as expansion of Group A. The estimate based on whole data was affected by the data from eastern European sheep, for which a later demographic expansion commencing 4,000–6,400 years ago was inferred.
To complement the above time estimates, a phylogenetic molecular dating method was used to estimate the time to the most recent common ancestor of each polymorphic haplotype group. The Hasegawa et al. (1985) model with invariable sites and gamma-distributed mutation rate variation between sites was found to fit into the data. The model-based relative rate test did not indicate variation in mutation rates between the evolutionary paths to present-day haplotypes. Only 2.3% of the tests between the pairs had P values below 0.05. As a precautious measure, this testwise P value of 0.05 was used as a criterion to exclude haplotypes from dating of the most recent common ancestors. In total, 39 haplotypes were removed. The phylogenetic tree in figure 2 presents this data with 171 domestic sheep haplotypes. Using the constructed Bayesian phylogeny with branch lengths (unpublished data), the times to the most recent common ancestors were 9,000, 8,850, and 5,900 years for Groups A, B, and C, respectively.
Differences between Geographical Areas
The haplotype group distribution had 2 distinctive geographical patterns (fig. 1). First, Group C was present in the Caucasian and Central Asian areas but absent in the eastern fringe of Europe (north and west of the Black Sea and the Ural Mountains). On the regions east of the Black Sea, the frequency of Group C varied from 8.1% (the Caspian Depression) to 22% (east of the Caspian Sea; fig. 1). A second recorded pattern was the absence of Group A in the 4 studied populations from southeastern Europe (the Tsigai breeds and the Ukrainian breeds; fig. 1; Supplementary Table 1, Supplementary Material online). The region dominated by Group B reached north of the Black Sea and included Russian Karelia and the Volga-Kama region (fig. 1), whereas Group A was found as a minor group in the area. Further east, the frequency of Group B decreases while Group A becomes more important. The transition is gradual, and only 7.8% of the mitochondrial variation was due to differentiation between the 3 wide areas (unpublished data).
Identification of the ancestral sequence type in the median-joining networks (fig. 3) was unambiguous in Groups B and C but more complicated in Group A. The phylogenetically central and most numerous type can be assumed to be the most ancient (root) node in the network, whereas the haplotypes at the periphery of the network are the most recently arisen variants (Crandall and Templeton 1993). Unlike Groups B and C, Group A had a few common types that were relatively central in the network (i.e., linked to several other nodes). However, the most frequent central type was the probable ancient type for Group A as well. This was supported by 2 additional observations. First, the most common type was observed in 18 breeds, whereas the second most common sequence type was observed in only 5 breeds (unpublished data). Another supporting observation was based on the argument by Templeton et al. (1995) that during slow gradual range expansion, new haplotypes emerging in the periphery of population range may subsequently spread over a larger area, increase in frequency, and even replace the ancient types in these new areas. Presently, all the Central Asian Group A sequence types were directly connected either to the most common type (not occurring in Central Asia) or to another Central Asian type. Thus, a single direction of gene flow (out of the Near East) was sufficient to explain the Group A types in Central Asia, if the root was set at the most common type. Other places for the root would require a more complicated hypothesis.
The geographical distribution of Group A diversity suggested that this group existed in the Caucasus area earlier than in the 2 other areas. First, there was a significant difference in ancestral type frequency between Central Asia and the other 2 areas (2-tailed contingency test P < 0.025); the ancestral type was observed in Caucasus and the European area but not observed in Central Asia at all. As described above, the diversity pattern suggested slow gradual spread of domesticated sheep to Central Asia involving haplotype frequency changes caused by a chain of founding events. Second, Group A was rare in eastern Europe (fig. 1), and the distribution of sequence types suggested gradual expansion over this region as well; the region had fewer rare nonroot sequence types than the other areas (2-tailed contingency test P < 0.026). These rare types were replaced by nonroot types reaching moderately high frequencies (fig. 3). More precisely, there were 3 nonroot Group A sequence types that were detected in the 2 breeds of the Middle Volga region. They were also detected in the old native breeds in Nordic Countries and in Russian Karelia. In addition, the most common Group A sequence type in Finland seems to be descendant of one of these haplotypes (fig. 3). This suggests a previously unrecognized migration of sheep to northern Europe through Russia. This pattern caused by spatial expansion came close to deviate significantly (P = 0.10, table 1) from the pattern expected from fitted model assuming only demographic expansion. Therefore, the estimated model parameters for Group A in the eastern Europe might reflect the history inaccurately.
A separate European sheep domestication appeared unlikely based on Group B variation, even if this hypothesis was supported by the high frequency of Group B haplotypes in Europe. There was a significant difference between the frequency of Group B root in Europe (0.66) and in Caucasus and Central Asia (0.50 and 0.44, respectively; 2-tailed contingency test P < 0.03). However, the mismatch distribution analysis (table 1) suggested that the expansion of Group B lineages began later in eastern Europe than in Caucasus. The observation can be explained by a strong maternal bottleneck at the time when the European population was founded from an earlier Near Eastern domesticated stock.
|
Discussion |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Four highly diverged sheep lineages (Groups A, B, C, and D) were observed in Caucasus, 3 (A, B, and C) in Central Asia, and 2 (A and B) in the eastern fringe of Europe, which included the area north and west from the Black Sea and the Ural Mountains. Only one sheep had a Group D haplotype. The other haplotype groups demonstrated signs of population expansion. Sequence variation within the lineages implied that the earliest demographic expansion for the common groups (A and B) initiated approximately at the same time, even though the data from the eastern fringe of Europe suggest that Group B expansion was more recent. Expansion of Group C seems most recent, but wide confidence interval prevents firm dating.
Domestic sheep are likely to have ancestry from at least 4 different geographical populations of wild mouflon. The differentiation between the 4 mtDNA haplotype groups was similar to that observed between distinct lineages in the goat (unpublished data based on publicly available goat sequences) and equals to that between recognized argali sheep subspecies (fig. 2, Hiendleder et al. 2002). The presence of such divergence in a single population of constant size has been estimated to be highly unlikely (Luikart et al. 2001). However, both European mouflons (King and Brooks 2003) and primitive feral Soay sheep (Coltman et al. 2003) exhibit a fine-scale genetic structure. The ewes stay in the population and in the geographical region they were born in, whereas the males are more prone to migrate. The distinct maternal lineages may have been maintained within a single ancestral mouflon subspecies, where the female population was subdivided. Maintaining very distinct lineages within a single narrow geographical region with a single female population is less likely.
All the presented results are compatible with the hypothesis of a Near East domestication center for sheep (Smith 1998). First, the Caucasus area located closest to the hypothesized Near East domestication center displays high mtDNA diversity and has all 4 haplotype groups. Second, estimated times to the initiation of expansion of each haplotype group are similar between the areas except in Group B. For this haplotype group, Caucasus shows evidence for the earliest expansion. Third, for Group A, the evidence of range expansion into other areas except the Caucasus area suggests that the other regions received this haplotype group more recently. In conclusion, our data suggest that both main haplotype groups were derived from wild populations approximately at the same time in the Near East. This makes their fully independent derivation from wild sheep unlikely.
Group C may have been derived from wild sheep later than Groups A and B. Group C exists mainly in the semidesert and steppe regions around the Caspian Sea, Central Asia, and China (fig. 1). This distribution overlays the distribution of fat-tailed sheep, while Group C is absent in the region spanning western Europe to the Ural Mountains, where only thin-tailed fleece sheep exist as indigenous breeds (Ryder 1984). The limited distribution supports a hypothesis of a more recent emergence of Group C in domestic sheep because gene flow has not had time to make the haplotype group even modestly frequent in Europe. The time estimates suggest that derivation of Group C from wild sheep took place 2,000 (table 1) or 3,100 (a phylogenetic estimate) years after the domestication of sheep. The confidence interval for the time (table 1) is much wider than for the other haplotype groups, and it is compatible with the initiation of expansion between 1,800 and 14,000 years ago. The practice of mating domestic ewes with wild rams in the regions close to the Caspian Sea has been documented even for the 20th century (Carruthers 1949). This is not directly applicable for maternally inherited variation but demonstrates long-lasting interest in deriving material from the wild sheep into domesticated stock. This may have included wild ewes or lambs, which brought the new type into the domestic stock. Further sampling in Asia is required to reliably infer the original distribution of Group C.
The Group D was observed in a single Caucasian sheep. There were 3 different kinds of further evidence confirming that this sequence represents a real fourth mitochondrial haplotype group rather than a sequencing artefact originating from a nuclear pseudogene. First, we confirmed the sequence data for this individual. In this, we used a different primer (the sequencing primer) to produce the template for the sequencing reaction. This should have led to a different sequence than the originally obtained, if our initial observation would have represented a nuclear pseudogene. This was not observed. Second, Guo et al. (2005) detected an individual carrying this haplotype group, although they distinguished the haplotype only as a highly differentiated variant within their C lineage, which mainly corresponds to our Group C. Considering the mtDNA sites used in the present statistical analyses, the sheep "M1516" (accession number AY829402) of Guo et al. (2005) had only 2 nucleotide differences (equals to 0.5%) to our Group D haplotype. This is well within the range of internal variation of the other 3 haplotype groups, and the mean difference of Group D to other 3 groups is similar to the average difference between the more common haplotype groups (fig. 2). The M1516 is the only previously reported "lineage C" individual (Guo et al. 2005; Pedrosa et al. 2005) that clusters to Group D (unpublished data). Finally, the test of relative substitution rate indicated that the rate for the evolutionary branch leading to the Group D haplotype is the same as for the branches leading to other haplotypes. If Group D represented an artefact originating from an ancient nuclear pseudogene, a lower mutation rate would be expected (e.g., Perna and Kocher 1996).
All the presented molecular dates should be interpreted cautiously. They should not be strongly affected by the recently observed nonlinearity of apparent mutation rates, which suggests that mutation rates seem much higher in the recent rather than ancient phylogenetic history (Ho and Larson 2006), because the calibration point is very close to estimated times. However, we timed the first expansion (Group A) equal to the archaeologically estimated time of sheep domestication (9,000 year ago). Throughout the study, times were estimated in relation to this date. It should also be noted that the phylogenetic time estimate does not necessarily reflect the domestication date because it can be affected by the extent of diversity sampled in the domestication. Timing the domestication based on the timing of population expansion is a more reliable approach because it incorporates the sampling to the model as the initial population size. Presently, the 2 methods suggested the same order for the 3 haplotype group expansions.
Group B has been observed in the European mouflon, and it predominates in European breeds being at the same time a minority type in eastern Asia (Hiendleder, Mainz et al. 1998; Hiendleder et al. 2002, Guo et al. 2005). This pattern could have been caused by an independent domestication in Europe and subsequent gene flow to Asia. However, the expansion of Group B in Europe appears to have begun later than in the Caucasus. The frequency pattern can be explained by a genetic bottleneck when the European stock was founded from an earlier domestic stock, and there is no need to invoke an independent European domestication of sheep. The present study suggests an approximately 3,000 year time period between the domestication of sheep in the Near East and the arrival of sheep to temperate Europe. Although the confidence intervals around the point estimates are wide, this time difference is similar to the 2,000–3,000 year period that archaeological evidence has suggested as a separation of the initial sheep domestication event in the Near East and the later spread of agriculture to the temperate Europe (Smith 1998).
Our data suggest that the derivation of Groups A and B from the wild sheep took place approximately at the same time in the Near East, although sheep mtDNA variation in the uncharacterized regions of the Near East and its neighboring areas should be studied to strengthen this conclusion. The results imply an additional, previously unrecognized route of sheep from the Near East to northern Europe directly through Russia. Analysis of mtDNA variation in western European sheep will shed light on whether the Russian route has influenced European sheep diversity outside northern Europe.
|
Supplementary Material |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Supplementary Tables 1 and 2 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).
|
Acknowledgements |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
We thank Anneli Virta for technical assistance and Professor Asko Mäki-Tanila and anonymous referees for helpful comments on the manuscript. We acknowledge the following persons for assistance in sample collection in the Middle Volga and the Volga-Kama regions: Paula Kokkonen, Galina Mi
arina, Esa-Jussi Salminen, Konstantin Zamjatin, Vasili Petrov, Lidija Matrosova, Jouni Kortesharju, and Natalia Devjatkina. Dr Alexandr Ivanovich Kostenko from Ukrainian Academy of Agrarian Sciences, Kiev, aided in sampling of Ukrainian sheep. We thank the Nordic Gene Bank for Farm Animals (NGH) and Dr Ingrid Olsaker for the Norwegian sheep samples. This work was financially supported by the Academy of Finland and the Finnish Ministry of Agriculture and Forestry (SUNARE-program and Russia In Flux-program). M.T. was supported by the Department of Education in Finland (Finnish Graduate School in Population Genetics coordinated by Oulu University). |
Footnotes |
|---|
Anne Stone, Associate Editor
|
References |
|---|
|
TOPAbstractIntroductionMaterials and MethodsResultsDiscussionSupplementary MaterialAcknowledgementsReferences |
|---|
Bandelt H.-J, Dress AWM. 1992. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1:242–52.[CrossRef][Medline]
Bandelt H.-J, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48.[Abstract]
Carruthers D. 1949. Beyond the Caspian: a naturalist in Central Asia. Edinburgh, United Kingdom: Oliver and Boyd.
Coltman DW, Pilkington JG, Pemberton JM. 2003. Fine-scale genetic structure in a free-living ungulate population. Mol Ecol 12:733–42.[CrossRef][Medline]
Crandall KA, Templeton AR. 1993. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134:959–69.[Abstract]
Davis GH, Galloway SM, Ross IK, et al. (19 co-authors). 2002. DNA tests in prolific sheep from eight countries provide new evidence on origin of the Booroola (FecB) mutation. Biol Reprod 66:1869–74.
Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–85.
Fu Y.-X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915–25.[Abstract]
Guo J, Du L.-X, Ma Y.-H, Guan W.-J, Li H.-B, Zhao Q.-J, Li X, Rao S.-Q. 2005. A novel maternal lineage revealed in sheep (Ovis aries). Anim Genet 36:331–6.[CrossRef][ISI][Medline]
Hasegawa M, Kishino H, Yano T. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–74.[CrossRef][ISI][Medline]
Hiendleder S, Kaupe B, Wassmuth R, Janke A. 2002. Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies. Proc R Soc Lond B Biol Sci 269:893–904.[Medline]
Hiendleder S, Lewalski H, Wassmuth R, Janke A. 1998. The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major ovine haplotype. J Mol Evol 47:441–8.[CrossRef][ISI][Medline]
Hiendleder S, Mainz K, Plante Y, Lewalski H. 1998. Analysis of mitochondrial DNA indicates that domestic sheep are derived from two different ancestral maternal sources: no evidence for contributions from urial and argali sheep. J Hered 89:113–20.
Ho SYW, Larson G. 2006. Molecular clocks: when times are a-changin'. Trends Genet 22:79–83.[CrossRef][ISI][Medline]
King R, Brooks SP. 2003. Survival and spatial fidelity of mouflons: the effect of location, age and sex. J Agric Biol Environ Stat 8:486–513.[CrossRef]
Kumar S, Tamura K, Nei M. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–63.
Loftus RT, MacHugh DE, Bradley DG, Sharp PM, Cunningham P. 1994. Evidence for two independent domestications of cattle. Proc Natl Acad Sci USA 91:2757–61.
Luikart G, Gielly L, Excoffier L, Vigne J-D, Bouvet J, Taberlet P. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc Natl Acad Sci USA 98:5927–32.
Meadows JRS, Li K, Kantanen J, et al. (11 co-authors). 2005. Mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe. J Hered 96:494–501.
Pedrosa S, Uzun M, Arranz JJ, Gutiérrez-Gil B, San Primitivo F, Bayón Y. 2005. Evidence of three maternal lineages in Near Eastern sheep supporting multiple domestication events. Proc R Soc Lond B Biol Sci 272:2211–7.[CrossRef]
Perna NT, Kocher TD. 1996. Mitochondrial DNA: molecular fossils in the nucleus. Curr Biol 6:128–9.[CrossRef][ISI][Medline]
Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676–9.
Poplin F. 1979. Origine du mouflon de Corse dans une nouvelle perspective paleontologique, par marronnage. Ann Génét Sél Anim 11:133–43.
Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–8.
Posada D, Crandall KA, Templeton AR. 2000. GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol Ecol 9:487–8.[CrossRef][Medline]
Rogers AR. 1995. Genetic evidence for a Pleistocene population explosion. Evolution 49:608–15.
Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–4.
Ryder ML. 1983. Sheep and man. London: Duckworth.
Ryder ML. 1984. Sheep. In: Mason IL, editor. Evolution of domesticated animals. London: Longman. p 63–85.
Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301–2.
Schneider S, Excoffier L. 1999. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152:1079–89.
Schneider S, Roessli D, Excoffier L. 1999. Arlequin version 2.0: a software for population genetic data analysis. University of Geneva, Switzerland: Genetics and Biometry Lab, Department of Anthropology. Available from: http://anthro.unige.ch/arlequin/. Accessed on 2001 Jan 2.
Smith BD. 1998. The emergence of agriculture. New York: Scientific American Library.
Sultana S, Mannen H, Tsuji S. 2003. Mitochondrial DNA diversity of Pakistani goats. Anim Genet 34:417–21.[CrossRef][ISI][Medline]
Tanaka K, Solis CD, Masangkay JS, Maeda K, Kawamoto Y, Namikawa T. 1996. Phylogenetic relationship among all living species of the genus Bubalus based on DNA sequences of the cytochrome b gene. Biochem Genet 34:443–52.[CrossRef][ISI][Medline]
Tapio M, Miceikiené I, Vilkki J, Kantanen J. 2003. Comparison of microsatellite and blood protein diversity in sheep: inconsistencies in fragmented breeds. Mol Ecol 12:2045–56.[CrossRef][Medline]
Templeton AR, Routman E, Phillips CA. 1995. Separating population structure from population history: a cladistic analysis of geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140:767–82.[Abstract]
Wood NJ, Phua SH. 1996. Variation in the control region sequence of the sheep mitochondrial genome. Anim Genet 27:25–33.[ISI][Medline]
Ye L, Huang X. 2005. MAP2: multiple alignment of syntenic genomic sequences. Nucleic Acids Res. 33:162–70.
Zeder MA, Emshwiller E, Smith BD, Bradley DG. 2006. Documenting domestication: the intersection of genetics and archaeology. Trends Genet 22:139–55.[CrossRef][ISI][Medline]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. R. S. Meadows, I. Cemal, O. Karaca, E. Gootwine, and J. W. Kijas Five Ovine Mitochondrial Lineages Identified From Sheep Breeds of the Near East Genetics, March 1, 2007; 175(3): 1371 - 1379. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||