Abstract Numerous studies have indicated that Morocco’s indigenous sheep breeds are genetically homogenous, posing a risk to their survival in the challenging harsh climate conditions where they ...predominantly inhabit. To understand the genetic behind genetic homogeneity through the lens of runs of homozygosity (ROH), we analyzed the whole genome sequences of five indigenous sheep breeds (Beni Guil, Ouled Djellal, D’man, Sardi, Timahdite and Admixed).The results from principal component, admixture, Fst, and neighbour joining tree analyses consistently showed a homogenous genetic structure. This structure was characterized by an average length of 1.83 Mb for runs of homozygosity (ROH) segments, with a limited number of long ROH segments (24–48 Mb and > 48 Mb). The most common ROH segments were those ranging from 1–6 Mb. The most significant regions of homozygosity (ROH Islands) were mostly observed in two chromosomes, namely Chr1 and Chr5. Specifically, ROH Islands were exclusively discovered in the Ouled Djellal breed on Chr1, whereas Chr5 exhibited ROH Islands in all breeds. The analysis of ROH Island and iHS technique was employed to detect signatures of selection on Chr1 and Chr5. The results indicate that Chr5 had a high level of homogeneity, with the same genes being discovered across all breeds. In contrast, Chr1 displays some genetic variances between breeds. Genes identified on Chr5 included SLC39A1, IL23A, CAST, IL5, IL13 , and IL4 which are responsible for immune response while genes identified on Chr1 include SOD1, SLAMF9, RTP4, CLDN1, and PRKAA2. ROH segment profile and effective population sizes patterns suggests that the genetic uniformity of studied breeds is the outcome of events that transpired between 250 and 300 generations ago. This research not only contributes to the understanding of ROH distribution across breeds but helps design and implement native sheep breeding and conservation strategies in Morocco. Future research, incorporating a broader sample size and utilizing the pangenome for reference, is recommended to further elucidate these breeds’ genomic landscapes and adaptive mechanisms.
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The common pheasant, a game species widely introduced throughout the world, can be considered as an ideal model to study the effects of introduction events on local adaptations, biogeographic ...patterns, and genetic divergence processes. We aimed to assess the origin, spatial patterns of genetic variation, and demographic history of the introduced populations in the contact zone of Central and Southeast Europe, using mitochondrial DNA control region sequences and microsatellite loci. Both types of molecular markers indicated relatively low to moderate levels of genetic variation. The mtDNA analyses revealed that common pheasants across the study area are divided into two distinct clades: B (mongolicus group) and F (colchicus group). Analyses of the microsatellite data consistently suggested a differentiation between Hungary and Serbia, with the pheasant population in Hungary being much more genetically homogeneous, while that of Serbia has much more genetic mixture and admixture. This cryptic differentiation was not detected using a non-spatial Bayesian clustering model. The analyses also provided strong evidence for a recent population expansion. This fundamental information is essential for adequate and effective conservation management of populations of a game species of great economic and ecological importance in the studied geographical region.
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Habitat loss and fragmentation are among the biggest threats to amphibian populations and anthropogenic climate change may exacerbate these. The response of Iran's amphibians to climate change is ...uncertain and yet making an accurate prediction of how the species will respond is critical for conservation. We assessed how expected future climate scenarios before the years 2050 and 2070 might influence the geographic distribution and habitat connectivity of the Lorestan Mountain Newt (Neurergus kaiseri). We examined presence data (2010–2018) of the species according to environmental and anthropogenic factors, and created an ensemble model of habitat suitability based on eight species distribution models (SDMs). Then, we used the concept of circuit theory to estimate potential linkages between the habitat patches. We applied the ensemble calibrated models and quantified spatial connectivity to assess the influence of climate change on the species range for the years 2050 and 2070 under four representative concentration pathways (RCPs) of three general circulation models (GCMs). Models using current climate predicted that 6.8% of the 267,609 km2 study area has suitable conditions for the species, but only about 7% of these climatically suitable landscapes are covered by conservation areas. Temperature and precipitation-related climatic variables made the largest contribution to the distribution model. Under projected climate conditions, we found a decline of 56–98% of the suitable habitat and predicted a potential for distributional shifts towards higher elevations by 2050 and 2070. Although there is relatively good connectivity between many habitat patches today, models predict that suitable areas available to the newt will become increasingly fragmented under projected climate change scenarios. Our findings support the hypothesis that projected climatic shifts will negatively influence suitable habitats of amphibians and likely cause upward shifts in elevation in range of some species. Identifying potentially suitable habitats and important linkages between habitat patches under different climate scenarios are crucial steps in conservation planning for the Lorestan Mountain Newt.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Abstract Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in ...current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval ( GI ) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders ( fa/fe ) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size ( Ne ) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.
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The focus of this review is to offer an overview of food and nutritional security, to identify associated constraints, and propose possible alternative solutions for improving the East African ...poultry sub-sector in the pursuit of food security, focusing on chicken breeding. To better understand the prospects of the poultry industry, we highlighted and combined confirming evidence of the phenotypic variability and genetic diversity of East African chicken genetic resources using both morphological and molecular tools, as well as performance traits. Furthermore, this work gives a detailed indication of what would be lost if indigenous chicken populations are left to suffer the ongoing massive genetic erosions due to various factors, not limited to indiscriminate crossbreeding. Previous and recent attempts to improve the productivity of indigenous chicken are highlighted, and possible future breeding plans and areas of immediate research are suggested as well. This review concludes that under the prevailing conditions, the village chicken production system appears to be the most imperious production system that needs to be extensively developed ; however, for the sustainability of the industry, the proposed improvement strategies should create a permanent balance between the competing needs of genetic improvement and the genetic diversity of the indigenous chicken genetic resource.
In Europe, protecting the genetic diversity of Apis mellifera is usually perceived in the context of limiting the spread of the evolutionary C-lineage within the original range of the M-lineage. ...However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees from the African A-lineage could represent another threat. This issue has not yet been investigated in detail, although A-mitotypes occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mtDNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35 %) had A-mitotypes. It is unlikely that their presence in the area resulted from natural migration but instead human driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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 data. We identified five phylogenetic clades in Europe with clear phylogeographic pattern. Two of them occurred mainly in western and central part of the continent, while the range of the third clade covered North-Eastern, Central and South-Eastern Europe. The two other clades had rather restricted distribution. In Central Europe, we identified a contact zone of three mtDNA clades. Population genetic structure reflected clear phylogeographic pattern of wild boar in this part of Europe. The contribution of lineages originating from the southern (Dinaric-Balkan) and eastern (northern cost of the Black Sea) areas to the observed phylogeographic pattern of the species in Central and Eastern Europe was larger than those from the regions located in southern France, Iberian, and Italian Peninsulas. The present work was the first mitogenomic analysis conducted in Central and Eastern Europe to study genetic diversity and structure of wild boar population.
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To improve sheep breeding and conservation of genetic resources, the mitochondrial DNA control region (mtDNA CR) of 399 sequences of African indigenous sheep breeds from previously published research ...articles were meta-analyzed to elucidate their phylogenetic relationship, diversity, and demographic history. A total of 272 haplotypes were found, of which 207 were unique and a high level of mtDNA CR variability was observed. Generally, the number of polymorphic sites, nucleotide and haplotype diversity were high (284, 0.254 ± 0.012 and 0.993 ± 0.002, respectively). The median-joining (MJ) network of haplotypes produced three major haplogroups (A, B and C), with haplogroup B being dominant. A mixture of populations suggests a common matrilineal origin and lack of and/or a weak phylogeographic structure. Mismatch analysis showed recent expansion of North African breeds, whereas East African and continental populations exhibited selection pressures for adaptation. A slight historical genetic difference was also observed between the fat tail and thin tail sheep breeds. However, further investigations are required using more samples and long sequence segments to achieve deeper levels of conclusions on the African sheep phylogenetic relationship. The present meta-analysis results contribute to the general understanding of African native sheep populations for improved management of sheep genetic resources.
Goat breeding has become an important sector in Eastern Europe, with Romania and Hungary being among the major producer countries. Given the limited number of research done up-to-date concerning ...genetic studies of indigenous goat breeds reared in Romania and Hungary, the current preliminary study aimed to analyze the variability of genes related to mastitis and gastrointestinal parasitism by using Kompetitive Allele Specific PCR (KASP™). We studied 52 single nucleotide polymorphisms (SNPs) belonging to 19 genes in indigenous breeds from both countries, namely Banat's White (n = 36), Carpatina (n = 35) from Romania and Hungarian Milking (n = 79) and identified 16 polymorphic SNPs among 10 genes (PTX3, IL6, CLEC4E, IL8, IL1RN, IL15RA, TNFSF13, SOCS3, TNF and TLR3) in 150 animals. Furthermore, the diversity of the studied breeds was investigated. The PIC values ranged from 0.042 to 0.691. The mean values of observed and expected heterozygosity were 0.235 and 0.246 respectively. The highest observed heterozygosity was obtained for IL15RA g.10343904C>T in Banat's White (0.464), IL15RA g.10354813C>T in Carpatina (0.577) and SOCS3 g.52626440T>G in Hungarian Milking (0.588). Pairwise FST values between the Romanian breeds and Romanian and Hungarian breeds were small (0.009 and 0.015), indicating the close relationship among the studied goat populations. From all the polymorphic SNPs identified, the Hungarian Milking breed showed the highest proportion of polymorphisms (100%), whereas the Carpatina breed had the lowest percentage (87.5%). The highest value of MAF was obtained for SOCS3 g.52626440T>G (0.46), IL15RA g.10343904C>T (0.47), IL15RA g.10344025C>T (0.45), and IL15RA g.10354813C>T (0.42). The 16 polymorphic SNPs identified in a panel of 150 unrelated individuals belonging to three Romanian and Hungarian indigenous goat breeds could be used in future genomic based breeding schemes as markers for genetic resistance to mastitis and gastrointestinal parasitism in goat breeds found in Eastern and Central Europe.
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The Eurasian Collared Dove (Streptopelia decaocto) is one of the most successful biological invaders among terrestrial vertebrates. However, little information is available on the genetic diversity ...of the species. A total of 134 Eurasian Collared Doves from Europe, Asia and the Caribbean (n = 20) were studied by sequencing a 658-bp length of mitochondrial DNA (mtDNA) cytochrome oxidase I (COI). Fifty-two different haplotypes and relatively high haplotype and nucleotide diversities (Hd±SD = 0.843±0.037 and π±SD = 0.026±0.013) were detected. Haplotype Ht1 was particularly dominant: it included 44.03% of the studied individuals, and contained sequences from 75% of the studied countries. Various analyses (FST, AMOVA, STRUCTURE) distinguished 2 groups on the genetic level, designated 'A' and 'B'. Two groups were also separated in the median-joining network and the maximum likelihood tree. The results of the neutrality tests were negative (Fu FS = -25.914; Tajima D = -2.606) and significantly different from zero (P≤0.001) for group A, whereas both values for group B were positive (Fu FS = 1.811; Tajima D = 0.674) and not significant (P>0.05). Statistically significant positive autocorrelation was revealed among individuals located up to 2000 km apart (r = 0.124; P = 0.001). The present results provide the first information on the genetic diversity and structure of the Eurasian Collared Dove, and can thereby serve as a factual and comparative basis for similar studies in the future.
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