Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland : comparison with contemporary sheep breeds

RESEARCH Open Access Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds Marianna Niemi 1 , Auli Bläuer 1,2 , Terhi Iso-Touru 1 , Veronica Nyström 3,5 , Janne Harjula 1,2 , Jussi-Pekka Taavitsainen 2 , Jan Storå 4 , Kerstin Lidén 4 and Juha Kantanen 1* Abstract Background: Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval periods by sequencing a partial mitochondrial DNA D-loop and the 5’-promoter region of the SRY gene. We compared the maternal (mitochondrial DNA haplotypes) and paternal (SNP oY1) genetic diversity of ancient sheep in Finland with modern domestic sheep populations in Europe and Asia to study temporal changes in genetic variation and affinities between ancient and modern populations. Results: A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY1, which is frequent in modern north-European sheep breeds. Conclusions: Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past. Our ancient DNA results fit well with the genetic context of domestic sheep as determined by analyses of modern north-European sheep breeds. * Correspondence: [email protected] 1 Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600, Jokioinen, Finland Full list of author information is available at the end of the article Genetics Selection Evolution © 2013 Niemi et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Niemi et al. Genetics Selection Evolution 2013, 45:2 http://www.gsejournal.org/content/45/1/2 Background Archaeological and molecular genetic evidence suggests that sheep’s(Ovis aries) wild ancestor was the Asiatic mouflon (O. orientalis) and that it was domesticated about 11 000 years ago in the Fertile Crescent region [1]. The genetic history of the domestication of sheep has been investigated by analysing maternally inherited mitochondrial DNA (mtDNA) in modern sheep breeds. To date, five phylogenetically divergent mtDNA haplogroups descending probably from several O. orientalis populations have been identified in domestic sheep [2] i.e. haplogroups A and B that are present in sheep in many parts of the world and haplogroups C, D and E that have a much more restricted geographic range [2,3]. Sheep spread across Europe in separate migration episodes over time from their domestication site in the Near East [4]. Chessa et al. [4] have provided evidence that contemporary sheep breeds and populations of north-western and northern Europe, e.g. the Finnish native sheep breeds, Finnsheep, Kainuu Grey and Åland still share genetic ancestry with the most primitive type of sheep in Europe descending from the first immigrant wave [4]. The earliest archeological record for burned sheep bone in Finland dated by radiocarbon is from the late Stone Age (3 679 ± 33 BP, cal 2150–1950 BC; [5]). However, such archaeological evidence of animal husbandry in Finland is scarce and domesticated animals may have arrived in Finland with the expansion of the Corded Ware culture from the south via the Baltics, but also from the west (Scandinavia) and east (Russia). Available archaeological data indicate that, in Finland, sheep husbandry developed first in fairly limited areas of the southern and south-western regions. The size of the sheep population was then probably quite small and the arrival of any new animals e.g. with immigrants would have had a significant effect on the population’s gene pool. During the Iron Age, agriculture developed in eastern and central Finland until reaching the northern limit of permanent cultivation (ca. 62°N latitude) [6]. Population size, demography and morphological characters of medieval sheep in Finland can be inferred from historical tax registers. For example, in 1620, there were at least 188 300 sheep in Finland [7]. Foreign “Spanish” sheep (i.e. ancestors of modern Merino sheep) with finer wool were imported into Finland at least from the 16th century onwards to serve the local wool industry [8]. Exotic breeding material was introduced mainly through imported rams, which means that the admixture may not have shaped the original mtDNA diversity in the Finnish native sheep. However, nuclear marker analysis of modern sheep breeds has shown that imported animals probably had a limited effect on the gene pool of the Finnish sheep population [9]. The Finnish Sheep Breeding Organization was established in 1918 and breeding of the main native breed, Finnsheep, depended essentially on animals from the eastern part of Finland [10]. In recent years, several molecular and population genetic studies have focused on the modern Finnish native sheep breeds with analyses of within-population diversity and population structure using mtDNA, Y-chromosome markers, autosomal microsatellites and whole-genome SNP [3,9,11-15]. It has been shown that the three native Finnish sheep breeds, Finnsheep, Kainuu Grey and Åland and several other North-European native sheep breeds belong to the Nordic group of short tailed sheep [13,14]. Two different mtDNA haplogroups, A and B, segregate in the Finnish native sheep and as in other European sheep breeds; haplogroup B is much more frequent than haplogroup A [3]. In addition, Meadows et al. [12] reported that the three different Y-chromosome haplotypes assigned to two different haplogroups were present in Finnsheep, Kainuu Grey and Åland breeds. In this study, we present a new approach to the molecular and population genetics of the Finnish native sheep breeds based on the analysis of ancient DNA (aDNA) from ancestral populations from the Late Iron Age (800–1200 AD), Medieval (1200–1550 AD) and Post-Medieval periods (1550–1800 AD). Comparing the genetic diversity of ancient populations with contemporary breeds can reveal temporal genetic changes and gene pool developments, as exemplified in a cattle Ychromosome study [16] and in a mtDNA analysis for inferring the domestication history of European pigs [17]. However, ancient DNA studies can also reveal relatively minor changes in population diversity patterns. For example, frequencies of the mtDNA haplogroups A and B detected in ancient Chinese sheep populations from theBronzeAgearesimilartothoseincontemporary Chinese sheep breeds [18,19]. We investigated the genetic diversity of ancient sheep remains in Finland by sequencing a 523-bp mtDNA Dloop sequence and a 130-bp segment in the 5’-promoter region of the ovine sex determining region Y (SRY) gene to detect a biallelic Y-chromosome SNP marker oY1. We compared mtDNA and Y-chromosome marker data from ancient and modern domestic sheep populations in Finland and other parts of Europe and Asia and studied temporal changes in maternal and paternal genetic diversity and mtDNA diversity patterns. For the mtDNA study, two modern datasets were used: (1) 10 modern European sheep breeds were sequenced and (2) additional mtDNA sequences were collected from GenBank that spanned the same mtDNA D-loop nucleotide sites as those present in the ancient mtDNA sequences. To our knowledge, this is the first time that mtDNA and Ychromosome genetic diversities of ancient sheep populations are investigated in the same study. Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 2 of 14 http://www.gsejournal.org/content/45/1/2 Materials and methods Ancient sheep bone material For the aDNA analysis, 36 sheep bones were selected from 14 different locations and 18 different archaeological excavations across Finland and one site in northern Norway (Table 1, Additional file 1: Figure S1). As a rule, unburned bone from time periods prior to the Late Iron Age is not preserved in the Finnish acid soil; thus earlier bone material consists of small burned fragments that are not useful for aDNA analyses [20]. The earliest unburned bones available for this study derive from the Late Iron Age (800–1200 AD). When possible, metacarpal or metatarsal bones were selected for two reasons: (1) these bones are easy to distinguish between sheep and goats and (2) they are often found in a complete or semi-complete state in the excavations because since they are nutritionally poor they were not usually butchered for cooking. However, other bone elements were also sampled, e.g. when metapodials were not present in the sample, or were badly preserved or fragmented, or if they did not form the highest Minimum Number of Individuals (MNI) within the excavation or phase. In some cases, only bones that are directly identifiable as from sheep or goat (e.g. teeth) were selected because it is possible to identify a species from analyses of the mtDNA Dloop region. Care was taken not to sample the same individual twice i.e. within one site and phase, elements located on the same side were selected for a given sample, otherwise age and size of the animal were used to separate different individuals. All samples that based on the archaeological context were assumed to originate from the Iron Age or Medieval period were radiocarbon-dated. In addition, Post-Medieval samples for which dating was uncertain from the archaeological context, were also radiocarbon-dated. Nineteen sheep bones or teeth were radiocarbon-dated in the Laboratory of Chronology of the Finnish Museum of Natural History, University of Helsinki (Table 1). Iron age Eleven samples excavated at four different sites from the Iron Age were included in this study (Table 1, Additional file 1: Figure S1). The aDNA samples (sample ID: OaM1-5) belong to the Viking Age phase of the Mulli site (1090–930 BP, Table 1). The animal bone assemblage from this site is mainly composed of domestic animals, but also contains a variety of wild mammals. Eastern Finland Viking Age sites were sampled (OaSys1 and OaMik1) and samples from two Iron Age cemetery sites in south-west and southern Finland (OaLui1-2 and OaKir1) were collected. The sample from Brodtkorbneset, Pasvik (Norway) (OaPas1) derives from a rectangular hearth of Sami origin and also dates to the late Iron Age (984 ± 31 BP, Table 1). Medieval period Eleven samples from western and eastern Finland from the Medieval period were analysed (Table 1, Additional file 1: Figure S1) among which eight originated from the town of Turku (OaÅA3-6, OaVet1-4), the largest Medieval town in Finland that is situated on the southwest coast by the river Aura, one from Bridgettine Abbey of Naantali (OaNaa1) situated in south-west Finland ca. 18 km from Turku, one from Kökar monastery, a medieval Franciscan monastery situated in the Åland archipelago (OaKök1), and one from eastern Finnish Karelia i.e. a deserted Greek Orthodox village in Papinniemi in Uukuniemi (OaUuk2). Post-Medieval period Fourteen samples from the Post-Medieval period were analysed (Table 1, Additional file 1: Figure S1) among which six were collected from the shores of the Gulf of Bothnia, from Pietarsaari (OaPie1), Tornio (OaTor1-2) and Oulu (OaOul1-3), seven from south-west and southern Finland i.e. two from Kökar monastery (OaKök2-4), two from Turku (OaÅA1-2) and two from Helsinki (OaHel1-2), both in urban contexts and one from an inland region at Pihtipudas (OaPih1). Modern sheep The occurrence of ancient sheep mtDNA sequences in modern sheep breeds was investigated with two datasets: (1) our own dataset of 94 unrelated animals from 10 sheep breeds or local varieties [see Additional file 1: FigureS1]and(2)adatasetcomposedofGenBanksequence data of 50 European and Asian sheep breeds previously published. Our own dataset was also used for the comparison between ancient and modern DNA. Previously described in [3,14], breeds included in our own dataset are the following: the Finnish native sheep breeds Finnsheep, Kainuu Grey and Åland, the Viena sheep from Russian Karelia, Bozakh sheep from the Caucasus, Romanov and Oparino sheep from central Russia, Olkuska sheep from Poland, the morphological type of Vlashko Vitoroga–Pramenka sheep from Serbia and Oxford Down sheep from the UK. All sheep breeds were locally developed breeds except for Oxford Down, which is a synthetic commercial English breed [40]. Kainuu Grey, Åland, Oparino, Olkuska and Vlashko Vitoroga-Pramenka sheep have undergone a reduction in population size during the last 10 years and are rare or endangered breeds. Results from a Y-chromosome SNP oY1 analysis in ancient sheep were compared with those of a global sheep Y-chromosome study including Finnsheep, Kainuu Grey and Åland sheep [12]. Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 3 of 14 http://www.gsejournal.org/content/45/1/2 DNA extraction and laboratory methods Laboratory environment and DNA extraction of ancient sheep samples Bone samples were prepared by removing the outer layer of the bones and collecting 50 to 200 mg of bone powder with a drill. DNA extraction was carried out in an air-controlled sterile laboratory and in a laminar flow hood (EU-14 HEPA filtered air under positive air pressure isolation). Separate laboratories were used for sample preparation, DNA extraction and PCR amplification. Table 1 Summary of ancient samples studied in this article Sample Dating aDNA Sample ID Location Site Bone type *BP (± 1σ) **Period mtDNA SRY gene OaMik1 Mikkeli Moisio Latokartano [21] Mandible 865 ± 33 Iron Age No OaM1 Raisio Mulli [22] Metacarpal 965 ± 30 Iron Age Yes unreadable OaM2 Raisio Mulli [22] Metacarpal 1040 ± 31 Iron Age Yes No OaM3 Raisio Mulli [22] Metacarpal 955 ± 30 Iron Age Yes unreadable OaM4 Raisio Mulli [22] Metacarpal 995 ± 30 Iron Age Yes unreadable OaM5 Raisio Mulli [22] Metacarpal 1081 ± 32 Iron Age Yes unreadable OaSys1 Sysmä Ihananiemi [23] Tooth (Molar) 1093 ± 31 Iron Age No OaKir1 Turku Kirkkomäki [24] Tooth fragments NA Iron Age No OaLui1 Eura Luistari [25,26] Tooth fragments NA Iron Age No OaLui2 Eura Luistari [25,26] Tooth fragments NA Iron Age No OaPas1 Pasvik (Norway) Brodtkorbneset [27] Metatarsal 984 ± 31 Iron Age Partial No OaNaa1 Naantali Luostari [28] Metacarpal 452 ± 30 Medieval Yes Yes OaUuk2 Uukuniemi Papinniemi [29] Metatarsal 410 ± 30 Medieval Yes No OaÅA3 Turku Åbo Akademi [30] Metacarpal 506 ± 32 Medieval Yes No OaÅA4 Turku Åbo Akademi [30] Metacarpal 581 ± 31 Medieval Yes No OaÅA5 Turku Åbo Akademi [30] Metacarpal 722 ± 32 Medieval Yes No OaÅA6 Turku Åbo Akademi [30] Metacarpal 737 ± 32 Medieval Yes No OaVet1 Turku Aboa Vetus [28,31] Horncore 487 ± 30 Medieval No OaVet2 Turku Aboa Vetus [28,31] Maxilla DBC Medieval No OaVet3 Turku Aboa Vetus [28,31] Axis 550 ± 30 Medieval No OaVet4 Turku Aboa Vetus [28,31] Lower jaw DBC Medieval No OaKök1 Kökar Kloster [32] Metacarpal 489 ± 30 Medieval Yes No OaHel1 Helsinki Snellmaninkatu [33] Metatarsal DBC Post-Med Yes No OaHel2 Helsinki Snellmaninkatu [33] Metatarsal DBC Post-Med Yes No OaOul1 Oulu Kajaaninkatu [34] Radius DBC Post-Med Yes No OaOul2 Oulu Lyseo [35] Radius DBC Post-Med Yes No OaOul3 Oulu Pikisaari [36] Radius DBC Post-Med Yes No OaPie1 Pietarsaari Lassfolk [37] Metacarpal DBC Post-Med Yes No OaTor1 Tornio Keskikatu [38] Metacarpal DBC Post-Med Yes Yes OaTor2 Tornio Keskikatu [38] Metacarpal DBC Post-Med Yes No OaÅA1 Turku Åbo Akademi [30] Metacarpal DBC Post-Med Yes unreadable OaÅA2 Turku Åbo Akademi [30] Metacarpal DBC Post-Med Yes No OaPih1 Pihtipudas Hämeensaari [39] Tibia 342 ± 30 Post-Med Yes No OaKök2 Kökar Kloster [32] Metacarpal 305 ± 30 Post-Med Yes Yes OaKök3 Kökar Kloster [32] Metacarpal DBC Post-Med Yes No OaKök4 Kökar Kloster [32] Metacarpal DBC Post-Med Yes No Identity of samples include: sample ID, location i.e. town where samples were excavated, archaeological site, and type of bone (museums ID available upon request); dating of samples include radiocarbon-dates (*BP (± 1σ)) or dates estimated by the context (DBC) and corresponding historical **periods (Post-Med = Post-Medieval); results of mtDNA D-loop and Y-chromosomal SRY gene sequence analysis are indicated for each sample; only the samples yielding mtDNA were analysed for the SRY gene. Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 4 of 14 http://www.gsejournal.org/content/45/1/2 The laboratories and equipment were UV-treated and bleach was used to clean the laminar and laboratory regularly. Protective whole body suits, double gloves and masks were used inside the aDNA laboratory. Two aDNA laboratories participated in aDNA analyses (MTT Agrifood Research Finland and Stockholm University, Sweden). DNA extraction was carried out as described in [41]. The bone powder was digested in 900 μL 0.5 M EDTA, 100 μL 10 M urea and 5 μL proteinase K (20 mg/ml) with constant stirring at 55°C overnight. After centrifugation (2000 rpm for 5 min), the supernatant was concentrated and DNA was extracted with a QIAquick PCR Purification Kit (Qiagen, Sweden) according to the manufacturer’s instructions. DNA markers, primer design and PCR A 523-bp sequence of mtDNA encompassing part of the mtDNA D-loop from ancient sheep ([GenBank: NC001941] positions 15,978-16,501) was analysed. A 130-bp sequence in the 5’-promoter region of the SRY gene on ovine Y-chromosome ([GenBank:AY604734] positions 58–179) was analysed to detect the Ychromosome SNP marker (oY1) [GenBank:AY604734.2: g.67, A>G]. Primers [see Additional file 2: Table S1] for five overlapping fragments of mtDNA D-loop sequence and one Y-chromosome SRY gene fragment were designed with Primer3 [42] using mtDNA and SRY gene reference sequences [GenBank:NC001941] and [GenBank: AF026566.1], respectively. PCR for ancient DNA was performed in 25 μL mixture that contained 1× PCR buffer (Qiagen, Sweden), 0.2 μM of each primer, 0.4 mM dNTP, 2.5 mM MgCl 2 (Qiagen, Sweden), 0.25 units (U) of Uracil DNA Glycosylase (UNG, Sigma-Aldrich), 1.5 U of HotStarTaq DNA Polymerase (Qiagen, Sweden) and 5–10 μL of DNA extract. The PCR program consisted in initial steps at 37°C for 10 min and 95°C for 15 min followed by 55 three-step cycles at 94°C for 30 s, AT°C for 40s and 72°C for 1 min and a final step at 72°C for 10 min. AT stands for the annealing temperature specific to each primer set [see Additional file 2: Table S1]. Authenticity of ancient sheep DNA Common measures to prevent contamination were used [43,44], such as separated areas for sample preparation, ancient DNA analyses and pre-PCR, wearing protective clothing, using disposable tools and pipettes with aerosol resistant filter tips and treating equipment and working surfaces with bleach and ultra-violet irradiation frequently (see DNA extraction and laboratory methods). Overlapping primers specific to sheep DNA were designed to prevent possible annealing to human DNA and were checked by amplification (see DNA extraction and laboratory methods). The authenticity of the aDNA analysis was controlled at various steps of the laboratory work-flow. In general, when consistent sequences were obtained in three or more amplifications, the sequence was considered reproducible and accepted as authentic. In the aDNA extraction step, 13 of the samples (out of the 26 samples which were successfully amplified for the 523-bp mtDNA Dloop sequence) (Table 1) were extracted several times, and at least two PCR-reactions were performed for separate DNA extractions to amplify and sequence each overlapping mtDNA D-loop fragment at least twice. Applying these strict extraction and amplification steps aimed at confirming the reproducibility of our aDNA sequence protocol and no sequence anomalies were detected. Moreover, five samples (OaM1, OaNaa1, OaTor2, OaÅA5 and OaÅA6) were extracted, amplified and sequenced in two different aDNA laboratories (MTT Agrifood Research Finland and Stockholm University, Sweden) and the results were identical. At each step of the aDNA extraction and amplification procedure, negative controls were performed. In the first extraction of our aDNA trial, a mammoth sample was used as positive control, which constitutes a suitable control because a previous study [45] has shown that it does contain mammoth DNA, it does not contain modern DNA and its sequence clearly differs from that of sheep. Mitochondrial DNA amplification of modern sheep samples DNA from 94 modern sheep of 10 European and Asian breeds [3,14] were analysed. Additional file 2: Table S1 includes primers for the amplification of a 664-bp sequence of mtDNA [see Additional file 2: Table S1]. The same PCR reaction mix was used for these samples than for the aDNA samples except that UNG was not included. PCR conditions were as follows: 95°C for 15 min followed by 32 three-step cycles at 94°C for 30 s, 58°C for 40 s and 72° for 1 min and a final step at 72°C for 10 min. 500 ng of template DNA were used per reaction. Y-chromosome marker data were available from a previous study [12]. Sequencing of PCR products PCR products of modern and ancient DNA samples were purified using ExoSAP-IT enzyme (GE Healthcare Life sciences, UK). Sequencing reactions were performed using DYEnamic ET Terminator Kit (GE Healthcare Life sciences, UK). The sequencing products were purified by ethanol precipitation and separated on MegaBACE1000 ™ (Amersham Biosciences, UK). Both strands of each fragment were sequenced and the same primers were used for both sequencing and fragment amplification. Sequence data were base-called with Cimarron 3.12 Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 5 of 14 http://www.gsejournal.org/content/45/1/2 basecaller using a MegaBACE Sequence analyzer v. 3.0.0111.1603 (Amersham Biosciences, UK). Sequences were analysed with Sequencher 4.6 8 (Gene Codes, Ann Arbor, MI). Statistical analyses Mitochondrial DNA sequences from 94 modern sheep [GenBank: JX484017-JX484110] and 26 ancient sheep [GenBank: JX484111-JX484137] were aligned using CLUSTALW2 [46] (penalties for gap opening, gap extension, gap distances were 10, 0.20 and 5, respectively). When statistical analyses were performed for a subset of sequences, the CLUSTALW2 alignment was carried out separately for each cohort. The size of the aligned mtDNA sequence was 523-bp. One Iron Age sample (OaPas1), for which only 297-bp of the mtDNA D-loop was sequenced, was omitted from the statistical analyses (Table 1). A corresponding CLUSTALW2 alignment was done for the Y-chromosome 130-bp sequences [JX484138JX484140]. Alignment gaps were excluded from the statistical analyses. The appropriate DNA substitution model to analyse our mtDNA data was the Hasegawa-Kishino-Yano model ([47]; HKY85)+Гsupported both by FindModel [48] web server (http://www.hiv.lanl.gov/content/sequence/ findmodel/findmodel.html) and MEGA5.05 program [49] and selected on the basis of the Akaike information criterion (AIC) [48] for different models. The phylogenetic analysis of the 94 modern and 26 ancient sheep sequences and one outgroup sequence from urial sheep (Ovis vignei bochariensis [GenBank:AF039580.1]) was conducted using two approaches. MEGA5.05 was used to construct the Neighbor-joining (NJ) tree with 1000 bootstrap replicates. However, the Tamura-Nei substitution model [50] with a Г distribution parameter value α= 0.05 was used in the analysis because HKY is not implemented in the MEGA software and the Tamura-Nei model was supported by AIC. The maximum likelihood (ML) analysis was performed using PhyML v. 3.0 program [51] and the HKY85+Г(lnL = −1271.48434, Гdistribution parameter value α= 0.047). Bootstrap support for a ML tree was calculated using 1000 bootstrap replicates and the tree was drawn with the TreeView program v. [52]. In addition, a median-joining network (with ε= 0 to be most conservative) between the haplotypes was constructed and mismatch distribution was performed using NETWORK 4.6.0.0 [53]. The following parameters were calculated to estimate the genetic diversity of the mtDNA data in the different cohorts (i.e., in the ancient populations and modern breeds): number of haplotypes (h), number of segregating sites (S), haplotype diversity (Hd = probability that two mtDNA sequences chosen randomly from the sample are different), nucleotide diversity (π= number of nucleotide differences between randomly chosen pairs of sequences), and average number of nucleotide differences (K) (DnaSP v.5 [54]). Theta-estimates (‘theta’θ=N e μ, where N e is the effective population size in the case of a haploid locus and μis the overall mutation rate at the haplotype level) were computed using ARLEQUIN v. 3.5 [55]: the expected level of diversity, θ S, was derived from the observed number of segregating sites S and θ π from the observed mean number of pairwise nucleotide differences π. Furthermore, Tajima’s D test statistic was computed using DnaSP. We investigated the distribution of the ancient mtDNA sequences present among the 94 sequences of the modern sheep samples sequenced here and searched for shared identical sequences in the GenBank DNA database (NCBI/BLAST, http://blast.ncbi.nlm.nih.gov/ Blast.cgi). The haplotypes were determined using DnaSP [see Additional file 3: Table S2]. The ancient Y-chromosome SNP oY1 data were compared with modern data [9,12] and geographic frequency distributions of oY1 alleles. The modern Y-chromosome SNP data [9,12] on the frequencies of oY1 alleles are presented in Additional file 4: Table S3. Results Radiocarbon dating Nineteen samples were successfully radiocarbon-dated, while for three samples, the quantity of collagen in the enamel was not sufficient for this technique (Table 1). The radiocarbon dating indicated that two samples, (OaPih1, OaKök2), were younger and one (OaUuk2) was older than inferred from the archaeological records from the same sites (Table 1). The dating results indicated that the oldest samples successfully analyzed for mtDNA were approximately 1000 years old. Success rate of aDNA analyses Mitochondrial DNA analysis was carried out on 36 ancient sheep samples and mtDNA amplification was successful for 27 samples, including the partial mtDNA sequence of the OaPas1 sample (Table 1). Most of these 27 samples required several amplifications per fragment in order to obtain at least three good-quality sequences from at least two PCR reactions. Excluding the samples for which no mtDNA amplification was obtained and considering all separate amplifications for the five mtDNA D-loop fragments, the amplification success rate was 46%, 56% and 68% for sheep samples from the Iron Age, Medieval and Post-Medieval periods, respectively. Average amplification success rates and fragment lengths for the mtDNA D-loop sequence are summarised in [Additional file 2: Table S1]. As expected, with aDNA samples, the highest success rate was obtained when the amplified fragments of mtDNA D-loop were shortest. In addition, among the aDNA samples from different periods, those from the Post-Medieval period had the highest success Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 6 of 14 http://www.gsejournal.org/content/45/1/2 rate, which is explained by the fact that Post-Medieval material is abundant allowing a more critical prior-selection of bones than for older materials. Reproducible sequences were obtained for seven of the 11 Medieval samples and for five (plus one partial) of the 11 Iron Age samples (Table 1). Amplification of a 130-bp sequence of Y-chromosome 5’promoter region in the SRY gene was tested in aDNA samples that were successfully amplified for mtDNA and three contained the SRY gene sequence. As expected, among the different aDNA analyses, amplification success rate was lowest (12%) for the fragment containing the SRY gene. Mitochondrial DNA haplotypes Alignment between the 94 modern and 26 ancient DNA sequences (OaPas1 containing a partial mtDNA sequence was excluded) revealed 47 SNP (46 transitions and one transversion) and three insertion-deletions [see Additional file 5: Figure S2]. When considering the alignment of the aDNA samples only, 27 transitions and no transversion were found. Fifty-six haplotypes (18 in the ancient and 46 in the modern DNA sequences) were identified among the 121 modern and ancient sheep samples (Figure 1, Tables 2 and 3). More than half of these haplotypes (30 of 56) were private to one individual and thus to one modern sheep breed or ancient sheep population indicating high variation in the analysed D-loop region. The NJ and ML analyses gave similar phylogenetic topologies thus only the ML tree is presented in Figure 1. Two highly divergent domestic sheep lineages, ovine mtDNA haplogroups A and B, were detected with relatively high statistical support. As expected, comparisons with reference sequences [GenBank: AF039577.1] and [GenBank: AF039578.1], haplogroups B and A were respectively the major and minor haplogroups. Frequencies of haplogroups A and B were 0% and 100% for the Iron Age, 28.6% and 71.4% for the Medieval and 14.3% and 85.7% for the Post-Medieval sheep cohorts, respectively and 21.9% and 78.1% for the Finnish modern sheep breeds. In addition, the Network analysis and mismatch distribution supported the existence of these two divergent haplogroups in the modern sheep breed data presented in Figures S3 and S4 [see Additional file 6: Figures S3 and S4]. These analyses reproduced the wellestablished observations with a star-shaped pattern in the ovine mtDNA haplotype network and a smooth shape of mismatch distribution indicating a population expansion in the history of the species. Similar patterns were observed in the Medieval-Iron Age and Post-Medieval cohorts when analysed separately (results not shown). We analysed the distribution of the 18 ancient Finnish sheep mtDNA haplotypes in the modern sheep breeds by sequencing samples of 10 Eurasian sheep breeds and by searching for shared sequences in the GenBank DNA database. The shared haplotype analysis showed that 14 of the 18 ancient haplotypes were present in the modern sheep breeds and in the GenBank DNA database (Figure 1) and [Additional file 3: Table S2]. In the modern sheep populations, frequencies of ancient haplotypes were highest in the native Finnish sheep breeds, Finnsheep (0.38) and Kainuu Grey (0.53) with six ancient haplotypes i.e. H11 in haplogroup A and H22, H32, H40, H42, H44 in haplogroup B. The two ancient haplotypes, H05 in haplogroup A and H32 in haplogroup B are common haplotypes while other rarer ancient haplotypes exist e.g. in contemporary native breeds from the Caucasus, Russia and Serbia [see Additional file 3: Table S2]. The four ancient haplotypes H06, H30, H43 and H50 were absent both in our own modern dataset and in the GenBank DNA database [see Additional file 3: Table S2]. Analysis of population diversity The statistics summarising the level of mtDNA variation in the Finnish ancient populations and modern sheep breeds and in seven other modern Eurasian breeds are presented in Tables 2 and 3, respectively. Additional file 1: Figure S1 shows the sites from which the Finnish archaeological samples were collected and for which mtDNA was successfully amplified. The Iron Age cohort comprising only five samples and excavated at a single archaeological site on the prehistorical farm Mulli displayed the lowest values for all diversity estimates (s, h, Hd, K, and π). Haplotype diversity was higher in ancient sheep samples from the Medieval and Post-Medieval periods (Hd = 1.0 and 0.98, respectively) than in any of the modern populations. The Post-Medieval samples originated from several archaeological sites, while the Medieval samples were excavated mainly in Turku. Among the modern sheep breeds analysed, Bozakh, Finnsheep and Pramenka showed the highest haplotype diversity (Hd > 0.90; Tables 2 and 3) while Olkuska and Åland had the lowest haplotype diversity (Hd = 0.75; Tables 2 and 3). The Finnsheep samples were collected in several sheep flocks from different parts of Finland. The measures taking in account the molecular nature of the data showed highest variation in the populations and breeds in which both haplogroups A and B were segregating. Nucleotide diversity varied among cohorts and was highest (π=15.51 * 10 -3 ) in Pramenka sheep, originating from the Balkan region, which was one of the main dispersal routes for Near Eastern domesticated sheep entering Europe. The diversity estimate θs is influenced by genetic bottlenecks, whereas θπ is relatively insensitive. Consequently, θπ-θs will be negative in stable populations under an infinite-sites model of mutation-drift equilibrium and Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 7 of 14 http://www.gsejournal.org/content/45/1/2 Figure 1 Maximum Likelihood tree of mtDNA haplotype sequences found within modern (black) and ancient (red) sheep. Branch topography supported by bootstrap values greater than 50% is indicated; the number of samples sharing haplotypes is given in brackets; breed names are abbreviated as Oxford Down (Oxf), Olkuska (OL), Pramenka (Pra), Bozakh (Boz), Oparino (Opa), Romanov (Ro), Viena (Vie), Kainuu Grey Sheep (Kai), Åland (ALD) and Finnsheep (Fin); ancient Finnish sheep samples are divided into three periods: Iron Age (Iron), Medieval (Med) and Post-Medieval (Post) according to radiocarbon or context dating (see Table 1); the tree is rooted with a sequence from urial sheep (Ovis vignei bochariensis) [GenBank: AF039580.1]. Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 8 of 14 http://www.gsejournal.org/content/45/1/2 positive as a result of a reduction in the number of segregating sites. In our data, θπ-θs estimates were negative i.e. -1.465 and −1.563 for Post Medieval and modern Finnsheep, respectively (Table 2), whereas they were positive for Åland, Kainuu Grey, Olkuska, and Pramenka sheep, and slightly positive for the Pramenka breed and the Medieval population (Tables 2 and 3). Statistically significant Tajima’sD-valueswerepositiveforKainuuGreyand Olkuska sheep, indicating a reduction of mtDNA diversity. Y-chromosome analysis For three of the 27 ancient sheep samples, Y-chromosome SRY sequences were amplified and were thus genetically identified as rams (Table 1) with one ram sample from the Medieval period and two from the Post-Medieval period (Table 1). All three ancient Finnish sheep had SNP G-oY1 in the SRY gene. In the modern Finnish breeds, the frequency of G-oY1 was 77%, 57%, and 60% in Finnsheep, Kainuu Grey, and Åland, respectively [see Additional file 4: Table S3], indicating that SNP G-oY1 is frequent in the modern north-European breeds (Figure 2). Discussion We successfully analysed mtDNA and Y-chromosome diversity in ancient sheep remains from Finland and found that Finnish sheep genetic diversity has been quite constant over the last 1000 years. Our aDNA results fit well with the genetic context of the modern northEuropean domestic sheep breeds analysed either previously [3,12] or in the present study. Both ovine haplogroups A and B have been present in the Finnish sheep population for at least more than 700 years and no remarkable temporal changes in their frequencies have occurred. Four of the 26 ancient mtDNA sequences Table 3 Summary statistics of modern Polish, Russian and UK breeds Statistics Modern sheep breeds Bozakh Olkuska Oparino Oxford Down Pramenka Romanov Viena N9999989 S 21 14 16 9 19 16 11 h8455756 Hd 0.97 0.75 0.86 0.81 0.94 0.89 0.89 K 7.44 7.39 5.89 2.83 8.11 6.96 4.39 π14.23 14.13 11.26 5.42 15.51 13.32 8.39 D−0.180 2.085* 0.002 −0.664 0.786 0.661 0.397 θs 7.727 5.151 5.887 3.311 6.991 6.171 4.047 θπ 7.667 7.389 5.889 2.833 8.333 6.964 4.389 θπ-θs−0.06 2.238 0.002 −0.478 1.342 0.793 0.342 N, number of individuals sampled; S, number of segregating sites (excluding indels); h, number of haplotypes; Hd, haplotype diversity; K, average number of differences; π, nucleotide diversity*10 -3 ; D, Tajima´s D statistic value where statistically significances P < 0.05 are marked with *; θs, ‘Theta’derived from the observed number of segregating sites S and θ π from the observed mean number of pairwise nucleotide differences π. Table 2 Summary statistics of ancient Finnish sheep populations from three periods and modern Finnish sheep breeds Statistics Ancient Finnish sheep Modern Finnish sheep breeds Post-Medieval Medieval Iron Age Åland Finnsheep Kainuu Grey N 14 7 5 9 15 8 S 25 18 2 17 14 15 h 12 7 2 4 10 4 Hd 0.98 1.00 0.40 0.75 0.93 0.82 K 6.13 7.81 0.80 7.94 2.61 8.11 π11.72 14.93 1.53 15.19 4.99 15.50 D−0.934 0.352 −0.973 1.315 −1.562 2.054* θs 7.861 7.347 0.960 6.255 4.306 5.785 θπ 6.396 8.095 0.800 7.944 2.743 8.107 θπ-θs−1.465 0.748 −0.16 1.689 −1.563 2.322 N, number of sampled individuals; S, number of segregating sites (excluding indels); h, number of haplotypes; Hd, haplotype diversity; K, average number of differences; π, nucleotide diversity*10 -3 ; D, Tajima´s D statistic value where statistically significances P < 0.05 are marked with *; θs, ‘Theta’derived from the observed number of segregating sites (S) and θ π from the observed mean number of pairwise nucleotide differences (π). Niemi et al. Genetics Selection Evolution 2013, 45:2 Page 9 of 14 http://www.gsejournal.org/content/45/1/2