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Frequencies of mtDNA clades of wild boar populations based on D-loop (upper panel) and mitogenomic analyses (lower panel). The maps were created with the ArcGIS software 10.3.1. based on source map from ESRI https:// www. esri. com/ en-us/ home.
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The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern Europe are not well recognized. We analysed 101 newly obtained sequences of complete mtDNA genomes and 548 D-loop sequences of the species and combined them with previously published...
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... compared the frequencies of different mtDNA clades and the indices of genetic diversity among 9 (mitogenomes) and 15 local (D-loop) populations (Fig. 5, Tables S2, S3). The frequency of clade 1 was highest in the South-West Poland (42-67%) and it declined to 20-0% towards south and east (Fig. 5). Clade 2 were found exclusively in Poland, with the exception of one individual recorded in Eastern Belarus. The share of clade 3 was highest in north-eastern, eastern and south eastern parts ...
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... compared the frequencies of different mtDNA clades and the indices of genetic diversity among 9 (mitogenomes) and 15 local (D-loop) populations (Fig. 5, Tables S2, S3). The frequency of clade 1 was highest in the South-West Poland (42-67%) and it declined to 20-0% towards south and east (Fig. 5). Clade 2 were found exclusively in Poland, with the exception of one individual recorded in Eastern Belarus. The share of clade 3 was highest in north-eastern, eastern and south eastern parts of Central and Eastern Europe (up to 80-100% in Russia, Belarus, Ukraine and Hungary) and it declined towards west (20-33% in Western ...
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... indices of haplotype diversity (Hd and B) revealed that the most diverse populations of wild boar in our studied region inhabited southern, central and northern Poland and north-eastern Belarus (Tables S2, S3, comp. Figure 5). The nucleotide diversity of the D-loop populations increased significantly with latitude (r = 0.712, p = 0.003), but we did not find such statistically significant correlations for haplotype diversity indices. ...
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... Nonetheless, the genetic diversity of animal populations from more recently recolonized areas may be even larger than that of populations from southern, previous Last Glacial Maximum refugia (e.g. Markova et al. 2020, Niedziałkowska et al. 2021Plis et al. 2022). In addition, species may respond to climate oscillations in species-specific ways (Pedreschi et al. 2019) leading to a complex web of subspecific and ecotypic differentiation even within refugia (Ancillotto et al. 2023). ...
The history of human colonisation in the Mediterranean has long been recognised as a crucial factor influencing biodiversity patterns in southern Europe. Nonetheless, our understanding of how anthropogenic and natural dispersal events interacted in shaping wildlife distributions, particularly in small mammals, remains limited. The edible dormouse Glis glis, a widespread European species, whose distribution includes several islands in the Mediterranean, present an opportunity to investigate these interactions. In this work, we used the edible dormouse to test hypotheses regarding the interplay between natural and anthropogenic dispersal in shaping species' distributions in Mediterranean archipelagos. We compared genetic sequences from samples collected on Mediterranean islands (Elba Island, Corsica, Sardinia, Sicily and Salina Island) and the mainland. Twenty-one samples were analysed by amplifying and sequencing a fragment of the cytochrome oxidase subunit I gene. Results indicated that samples from Sardinia and Elba Island belong to the same clade of mainland Italy, specifically to the subspecies G. g. italicus. This finding does not support the existence of an endemic Sardinian subspe-cies and suggests recent introduction events. In contrast, Salina Island only included individuals belonging to the Sicilian subspecies, whereas Sicily hosts a mixed population of G. g. italicus and G. g. insularis. The Corsican population likely originated from a different stock than Sardinia, possibly originating from Northern Italy or southern France. Overall, our findings underscore the significant role of anthropogenic dispersal in shaping the current distribution of the edible dormouse on islands.
... * Nikolay I. Markov nimarkov@mail.ru The genetics of wild and domestic S. scrofa has been extensively investigated (Groenen et al. 2012;Frantz et al. 2013;Kostyunina et al. 2022;de Jong et al. 2023), and most studies on wild populations come from Europe (e.g., Alexandri et al. 2012;Kusza et al. 2014;Vilaça et al. 2014;Veličković et al. 2015;Iacolina et al. 2016;Niedziałkowska et al. 2021;de Jong et al. 2023), Far East (e.g., Watanobe et al. 2003;Wu et al. 2007;Cho et al. 2009;Ramayo et al. 2011;Choi et al. 2020) and a few areas of Eastern and Southeastern Asia (Choi et al. 2020). Subspecies of wild S. scrofa are categorized into European, Asian, and South-Asian groups (Genov 1999). ...
... Pan-Eurasian phylogeny (e.g., in Larson et al. 2005Larson et al. , 2007Choi et al. 2020) has shown that the European and Near Eastern clades cluster together in what could be called "the Western clade" and is distinct from haplotypes originating from Eastern Asia. A number of clusters have been identified within the European group (Niedziałkowska et al. 2021;de Jong et al. 2023), while no clear divergence has been detected within the Pan-Asian clade, denoted as clade D2 by Larson et al. (2005) and as clade C3 by Choi et al. (2020). ...
... Thus, the sampling map covers almost the entire Asian part of the wild boar range from the Pacific to the Caspian Sea ( Fig. 1), with the exception of India. We also used sequences of the complete mtDNA genome of the European wild boar published by Niedziałkowska et al. (2021) to assess broad-scale phylogenetic relationships of Central Asian animals (Supplementary Information 1, Tables S1 and S2). ...
The widespread occurrence of the wild boar Sus scrofa, its controversial role in natural communities, and its close relationship with humans make this animal an important and convenient subject for studying the history and evolution of natural communities. The territory of Central Asia has been poorly represented in mammalian phylogeographic studies, namely in the case of wild boars and domestic pigs. In this study, we provide new information on wild boar genetic diversity in Central Asia in terms of mitochondrial and Y-chromosome markers and compare the set of haplotypes observed in Uzbekistan and Kazakhstan with those from other parts of the species’ range. The wild boar population in Central Asia is characterized by high uniqueness of mitochondrial and Y-chromosome markers and high haplotype diversity (as compared to other Asian regions). A maternal lineage marker (mitochondrial-DNA control region) clearly places this species in the Asian clade, whereas a paternal lineage markers (AMELY + USP9) positions it closer to wild boars from the western clade. Thus, the molecular genetic data supported the existence of a regionally specific subspecies of the wild boar: S. s. nigripes Blanford, 1875. Median-joining network analysis showed that Central Asia may be a center of dispersal and formation of S. scrofa genetic lineages in North Asia.
... European Roe Deer probably survived the LGM in a large range covering an area from the Iberian Peninsula to the Caucasus Mountains and in 2 northern regions-one in the proximity of the Carpathian Mountains, and one in eastern Europe (present-day Belarussian-Russian border area; Plis et al. 2022a). The presence of contact (suture) zones of different genetic lineages and clades in central and eastern Europe, increasing the genetic diversity in these regions, has also been revealed in the Bank Vole (Clethrionomys glareolus) (Wójcik et al. 2010;Tarnowska et al. 2016Tarnowska et al. , 2019Marková et al. 2020), Moose (Niedziałkowska et al. , 2016a, and Wild Boar (Sus scrofa; Niedziałkowska et al. 2021b)-as well as in other rodent, ungulate, and carnivore species (Stojak and Tarnowska 2019). ...
... The western roe deer (sites 8 and 9) have a large proportion of alleles commonly found in the fennoscandian population, and were indicated as a distinct genetic cluster or population by STRUCTURE, DAPC, and Geneland. Such patterns indicate that in postglacial times Fennoscandia was recolonized by roe deer originating from western Europe, which is in agreement with the distribution of The lower genetic diversity and endemicity of southern European Roe Deer may be a consequence of their continued isolation in former LGM refugia, as has been demonstrated for several mammalian species such as the Bank Vole (Marková et al. 2020), Grey Wolf (Canis lupus; Stronen et al. 2013), Wild Boar (Niedziałkowska et al. 2021b), and Red Deer (Zachos et al. 2016;Doan et al. 2017;Doan et al. 2022). Low genetic diversity and/or genetic distinctiveness of the southern European Roe Deer have earlier been documented by studies on populations in Spain, Italy, and Greece (Mucci et al. 2012;Tsaparis et al. 2019;Barros et al. 2020;Plis et al. 2022aPlis et al. , 2022b. ...
Although the European Roe Deer (Capreolus capreolus) is one of the most common and widespread ungulate species in Europe and inhabiting a variety of habitats, few studies have addressed its population structure at a large spatial scale using nuclear genetic data. The aims of our study were to: (i) investigate genetic diversity, level of admixture, and genetic structure across European Roe Deer populations; (ii) identify barriers to gene flow; and (iii) reveal factors that have impacted the observed pattern of population genetic structure. Using 12 microsatellite loci, we analyzed 920 European Roe Deer samples from 16 study sites from northern, southern, central, and eastern Europe. The highest genetic diversity was found in central and eastern sites, and lowest in the northern and southern sites. There were 2 main groups of genetically related populations in the study area—one inhabiting mainly Fennoscandia, and the second in the continental part of Europe. This second population was further divided into 3 to 5 spatially distributed genetic clusters. European Roe Deer belonging to the Siberian mitochondrial DNA clade, inhabiting large parts of eastern Europe, were not identified as a separate population in the analysis of microsatellite loci. No isolation by distance (IBD) was detected between roe deer from the fennoscandian and the continental study sites, but the Baltic Sea was inferred to be the main barrier to gene flow. Only weak IBD was revealed within the continental population. Three lower-level genetic barriers were detected in the western, southern, and eastern parts of the study area. The main factors inferred as shaping the observed genetic diversity and population structure of European Roe Deer were postglacial recolonization, admixture of different populations of the species originating from several Last Glacial Maximum refugial areas, and isolation of several study sites.
... These animals were common and widespread from France to Belarus from the early Holocene onwards, varying in body size according to Bergman's rule, with northern individuals from north-eastern Germany being larger than southern ones from Spain and Italy (Albarella et al., 2009). Despite the recent intensification or reintroduction and introgression with domestic pigs on the genetic make-up of wild boar populations in Europe (Goedbloed et al., 2013), their deep genetic structure across Europe remains mainly determined by the post glacial dispersal from southern refuges located in Spain, Italy for Western Europe, and the Balkans for Central Europe (de Jong et al., 2023;Niedziałkowska et al., 2021), with a loss of genetic diversity towards the northern range of the species (Vilaça et al., 2014). ...
Evolutionary biologists have recently solicited archaeologists to help document and understand the morphological evolution of animals in response to human activities and, more generally, to help reconstruct the history and significance of the anthropogenic impact on worldwide ecosystems. Artificial selection associated with domestication is the best-known example of a major anthropogenic morphological evolution preserved in the archaeological record. However, the impact of the domesti-cation process and dispersal on the morphological evolution of animals has been far less explored. To fill this gap, we focused on 4500 years of evolution in Western Europe Sus scrofa, covering the Neolithic transition-a major anthropogenic ecological disturbance involving landscape modification and the translocation of domestic mammals. Using geometric morphometrics on key phenotypic markers preserved in the archaeological record, associated with isotopic studies, we explored how, and in response to which cultural drivers, the Neolithic niche construction has influenced the morphological evolution of Western European wild boars (Sus scrofa scrofa). The decoupling of size and shape components from bone morphological variation has facilitated the identification of several processes of phenotypic diversification of Sus s. scrofa in response to human behaviour during the Neolithic transition in Western Europe.
... In central and northern parts of the continent, there are contact zones of different mtDNA lineages of several mammal species such as rodents, ungulates and large carnivores originating from separate LGM refugia (Taberlet et al. 1998;Stojak and Tarnowska 2019;Niedziałkowska et al. 2021a). One of those species is the bank vole Myodes (Clethrionomys) glareolus-a common forest rodent inhabiting almost the whole of Europe and large areas of the Western Asia up to the Lake Baikal (Hutterer et al. 2021). ...
... Owing to the admixture of different recolonisation waves of migrants from several distinct bank vole populations, the mtDNA genetic diversity of populations of various mammal species inhabiting central Europe is higher than that in other areas of the continent (e.g., Niedziałkowska et al. 2014), including the past LGM refugia (Veličković et al. 2016;Marková et al. 2020;Niedziałkowska et al. 2021a). In addition, the genetic diversity parameters (P, π) calculated for bank vole populations and SNP clusters in NE Poland were higher than such values obtained for populations inhabiting southern LGM refugia (compare Marková et al. 2020). ...
Previous studies indicated that in some species phylogeographic patterns obtained in the analysis of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check whether there was any discordance between mtDNA and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in the analysis of other genetic markers and functional genes. However, genome-wide SNP analyses revealed the more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as recognised previously in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for insufficient amount of time to develop significant genetic differentiation.
... Molecular systematics confirms these clades [51] but also includes the Near Eastern (NE) clade, which in turn consists of two subclades (NE1 and NE2) [52]. The genetics of wild and domestic S. scrofa have been extensively investigated [53][54][55] and references therein), and most studies on wild populations come from Western Europe (e.g., [55][56][57][58][59]), the Far East [60][61][62][63], and a few areas of Southern and Central Asia [64]. The information on genetic diversity in recently introduced populations of the wild boar is scarce and represented by a few studies from New Zealand [65] and the South [45] and North [66,67] Americas. ...
... We addressed these questions by analyzing the diversity of haplotypes of the mtDNA control region. This genetic marker is widely used in the research on wild boar phylogeography and intraspecies taxonomy [55][56][57][58][59]61,64,[81][82][83][84] and for investigation into S. scrofa domestication [51,85]. We examined haplotypic [49,73]. ...
... We addressed these questions by analyzing the diversity of haplotypes of the mtDNA control region. This genetic marker is widely used in the research on wild boar phylogeography and intraspecies taxonomy [55][56][57][58][59]61,64,[81][82][83][84] and for investigation into S. scrofa domestication [51,85]. We examined haplotypic variation in the wild boar population from the eastern part of the Urals and compared it with the data from the founder populations. ...
Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of the establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from the proportions (%) of European and Asian animals in the founder populations. This is the first study on the genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.
... To limit the spread of ASF, control measures such as sanitary culling induced mortality that could contribute to the wild boar population decline [11]. Many research studies have focused on genetic analysis to understand the phylogeographic [12][13][14][15][16] and population genetic structure of the European wild boar [17][18][19][20][21][22][23][24][25]. Although various studies of the wild boar's genetic structure have been conducted, most of them have focused on the demographic history and investigations of the natural and artificial barriers. ...
... The contrasting findings in the present study compared with previous studies may be related to the geographic scale of the study, the use of different markers and the sample size. Furthermore, a study that analysed mtDNA D-loop sequences of wild boar in central and eastern Europe identified three mtDNA clades [16]. A possible explanation for the existence of three genetic groups may be associated with various factors such as multiple climatic fluctuations and past demographic and migratory events, and human-mediated translocations can affect the current patterns of the wild boar population's genetic structure [20,23,50,51]. ...
The emergence of African swine fever (ASF) in Lithuania and its subsequent persistence has led to a decline in the population of wild boar (Sus scrofa). ASF has been spreading in Lithuania since its introduction, therefore it is important to understand any genetic impact of ASF outbreaks on wild boar populations. The aim of this study was to assess how the propensity for an outbreak has shaped genetic variation in the wild boar population. A total of 491 wild boar samples were collected and genotyped using 16 STR markers. Allele richness varied between 15 and 51, and all SSR loci revealed a significant deviation from the Hardy–Weinberg equilibrium. Fixation indices indicated a significant reduction in heterozygosity within and between subpopulations. PCoA and STRUCTURE analysis demonstrated genetic differences between the western region which had had no outbreaks (restricted zone I) and the region with ASF infection (restricted zones II and III). It is concluded that environmental factors may play a particular role in shaping the regional gene flow and influence the genetic structure of the wild boar population in the region with ASF outbreaks.
... We addressed these questions by analyzing the diversity of haplotypes of the mtDNA control region. This genetic marker is widely used in the research on wild-boar phylogeography and intraspecies taxonomy [25][26][27][28][29][30][31][32][33][34][35] and for investigation into Sus scrofa domestication 18,36 . We examined haplotypic variation in the wild boar population from the eastern part of the Urals and compared it with the data from the founder populations. ...
Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar ( Sus scrofa L.) has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far-Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from proportions (%) of European and Asian animals in the founder populations. This is the first study on genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.
... Thus, the clades from Italy and Dagestan are representatives of the old evolutionary branch. The Italian clade is a sister haplogroup to the boar clade from Europe and North Africa [13]. Since the representatives of subspecies (Sus scrofa) are wild ancestors (Sus scrofa domesticus). ...
Traditionally, the mitochondrial genome is characterized as a “molecular clock” for tracking the history of phylogeny along the maternal line. Particular attention is paid to the distribution of mitochondrial DNA haplotypes among commercial pigs (Large White × Landrace) × Maxgro from RPE “Globinsky Pig Farm”, Globyno town, Poltava region, Ukraine. For the study of the genetic structure of the pigs’ hybrid markers of mitochondrial DNA — a maternal type of inheritance was used. DNA markers are a convenient tool for investigating the origin of pro-maternal pig breeds. Application of multiplex analysis PCR-RFLP (Polymerase chain reaction-restriction fragment length polymorphism) when examining the variable area of the D-loop between sites 15558–15917 mitochondrial genome of hybrid pigs made it possible to determine the pro-maternal haplotypes of the experimental sample (n=20). Thus, according to the multisite system developed by Pochernyaev K. F., determination of mitochondrial haplotypes of pigs, which are denoted by Latin letters from A to P allowed to determine the true pro-maternal haplotypes of the experimental sample of pigs (n=20), as evidenced by the presence of the Tas I website in the above-mentioned provisions what actually determine the haplotypes of mitochondrial DNA. According to the results of the study defined haplotypes characterize different breeds, namely 4 animals with haplotype C — Landrace (Ukraine, Poland). 6 pigs have mitochondrial haplotype N — Large White (Asian type) and 7 pigs with mitochondrial haplotype O — Landrace. 1 animal with haplotype G — wild pig and cross-border breed Wales (Italy). 2 representatives of haplotype D — not found among the breeds of domestic pigs. According to the established pro-maternal haplotypes of hybrid pigs, animals-carriers of haplotype O are representatives of Scandinavian female pigs F1 as used in uterine herds in Sweden and Ireland with the participation of the Maxgro terminal parent line in the hybridization system. Identified mitochondrial haplotypes were found to be breed-specific to hybrid pigs of Irish breeding, this is confirmed by the established polymorphism of the mitochondrial genome which is an objective marker even in complex hybridization schemes. The work was done with the support of the National Academy of Agrarian Sciences of Ukraine 31.01.00.07.F. “Investigate the pleiotropic effect gens that the SNP use in marker-associated pig breeding”. DR no. 0121U109838. Following the example of the developed systematization of the combination of restricted fragments by Pochernyaev K. F. in the future, I propose to create a database of reference haplotypes of mitochondrial DNA of pigs’ final hybrid. In the future, it will be used in further research to reconstruct the demographic history of commercial pigs of cross-border breeds.
... During glaciations, the ranges of cold sensitive species were limited to refugial areas located in the Balkan, the Iberian and the Apennine Peninsulas (Hewitt, 2004;Taberlet et al., 1998) and south-eastern part of the continent (the Black Sea region and the Caucasus Mts.; Markova & Puzachenko, 2019). Contribution of a given refugium into postglacial recolonization processes varied a lot among species such as, for example, red deer Cervus elaphus (Niedziałkowska, Doan, et al., 2021), wild boar Sus scrofa (Niedziałkowska, Tarnowska, et al., 2021), or common vole Microtus arvalis (Stojak et al., 2015). Cold-adapted species such as, for example, reindeer Rangifer tarandus (Sommer et al., 2014), saiga antelope Saiga tatarica (Nadachowski et al., 2016), or arctic fox Alopex lagopus (Dalén et al., 2007), thrived in the glacial stages, expanded their ranges southward, and during the onset of interglacial they underwent massive, large-scale extinctions. ...
... In addition to the earlier described Italian haplogroup, denoted as C7 in this paper, that occurred in the Apennine Peninsula only (Lorenzini et al., 2002;Mucci et al., 2012;Randi et al., 2004), we found three other haplogroups, each with a very restricted range: C5 recorded over the northern side of the Black Sea, C6 found mainly in Interestingly, the pan-European study on molecular biogeography of wild boar S. scrofa (Niedziałkowska, Tarnowska, et al., 2021) discovered a rare, ancient clade of the species in the Russian part of the range of roe deer haplogroup E1. Also, the Europe-wide study of wolf Canis lupus population by SNP analysis (Stronen et al., 2013) found that the western and northern Belarus wolves showed the most divergent genotypes within north-central Europe. ...
To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia.
