The Aberdeen Angus cattle genotyping has revealed 2.38 ± 0.31% AMC-cows and 1.67 ± 0.19 % AMC-bulls, 0.65 ± 0.07% DDC-cows and 0.90 ± 0.10% DDC-bulls. The single animals among the Hereford cattle were carriers of MSUD and CWH (on 0.27 ± 0.05%), ICM and HY (on 0.16 ± 0.03%). The Simmental cattle were free from OS. All Belgian Blue livestock were M1- and 0.84%-CMD1-carriers. The different ages Aberdeen Angus cattle genotyping has shown the tendency of the AMC- and DDC frequencies to increase in the later generations. The statistically significant increase of DDC of 1.17% in the cows’ population born in 2019 compared to those born in 2015 allows concluding the further development of the DNA analysis-based measures preventing the manifestation of the genetic anomalies in meat cattle herds is necessary.The article highlighted the problem of meat cattle genetic defects. The aim was the development of DNA tests for some genetic defects diagnostics, the determination of the animal carriers and their frequencies tracking in time. The 1490 DNA samples from the Aberdeen Angus ( The issue of providing people with food and food safety is relevant regardless of the time and geographical location of any state. One of the most important strategic objectives is to increase the consumption of meat products, in particular beef, as the main source of essential amino acids. In this regard, the efforts of specialists of the beef cattle industry are constantly directed at finding ways to increase the productivity of animals, and the use for this purpose of breeding material of specialized meat cattle breeds is very promising . Howeverwww.illumina.com (accessed date 11 March 2021)), which contains 777,609 single nucleotide polymorphisms (SNPs), have been used in the current time [Modern molecular biology over the world characters by the rapid development of genomic selection, allowing the selection of a decision based on genomic breeding values (GEBV) estimation with simultaneous parentage verification, imputation and genetic defects identification . For theent time .However, the use of the DNA chips is limited by the character of studied mutations and is appropriate for only SNP genotyping . In some cases, the farmer is faced with the need to identify animals exclusively that carry genetic defects, and the use of DNA chips for only this purpose is not cost-effective.Due to this fact, the use of genetic defects DNA-diagnostics based on the different polymerase chain reaction (PCR) modifications in addition to the genome sequencing methods is not losing actuality.https://omia.org/home/ (accessed date 11 March 2021), https://www.ncbi.nlm.nih.gov/ (accessed date 11 March 2021)), we have studied five genetic defects registered in Aberdeen Angus cattle , five defects of Hereford cattle , one defect of Simmental cattle (OS) and two defects of Belgian Blue cattle (M1 and CMD1). The short characteristics of the defects and caused mutations are presented in Disposing the knowledge about some gene mutations associated with the appearance of genetic diseases  from Aberdeen Angus (n = 701), Hereford (n = 385), Simmental (n = 286) and Belgian Blue (n = 118) cattle deposited in DNA collections of the L.K. Ernst Federal Research Center for Animal Husbandry were used as materials. The probes were obtained by sets of DNA extraction from the animal’s biomaterial , according to the manufacturer’s instructions . The descriptions of the animals from which the DNA samples have been obtained are presented in The DNA probes  and PCR-RFLP (for the defects caused by SNP) methods.Genotyping has been carried out by using oligonucleotide primers as earlier designed  ,21 as neThe PCR was carried out on the thermocycler Biorad T100  in volumes of 10–15 microliters under the next conditions: initial denaturation—3 min, 35 cycles of denaturation-annealing-elongation (45-30-40 s) and final elongation—4 min. The temperatures of denaturation and elongation were 95 °C and 72 °C, respectively; the annealing temperatures depended on the mutations .https://nc2.neb.com/NEBcutter2/ (accessed date 11 March 2021)). For the mutant allele associated with the defect, the restriction site for restriction endonuclease DraIII (restriction site CACNNN↑GTG) was found. The validation of PCR-RFLP for CMD1 and DD diagnostics earlier was conducted by Sanger sequencing  with the assessment of the results by UGENE Software.For SNP diagnostics, the PCR-RFLP method was chosen for CMD1 based on the further digestion of the PCR-fragment of the enzyme (restriction endonuclease). The choice of restriction sites was performed by the NEBcutter V2.0 Software :M is the average meaning of the frequencies of all populations, and N is the number of the populations.The average frequency was counted by formula (2):Due to the heterogeneity of population sizes, the average square deviation of the general population was also calculated by Formula (3):t = 1.972 (significance level 0.05).The statistical significance of the frequencies’ differences was evaluated by criterion t-student by an online service ,23 and chttps://www.statskingdom.com (accessed date 11 March 2021)).For the evaluation of the effect of the fixed factors, breed and gender, on the common frequencies of animal carriers in different age populations, we have used the analysis of variance (two-way ANOVA) by using the corresponding software , two populations of Aberdeen Angus bulls  and three populations of Hereford heifers (1a–c).In We observed increasing frequencies of the genotypes heterozygous on the mutant alleles associated with AM and DD genetic defects in cow and bull of Aberdeen Angus cattle populations. The frequency of AMC animal carriers among the cow population from 2013 to 2015 increased by 1.06%, and from 2015 to 2019, this figure was already 7.43%. For the DD genetic defect, these figures were 0.71% and 1.17%, respectively. In the bull population, the increase of AMC and DDC animal carriers from 2015 to 2019 was 3.33% and 1.80%, respectively.t = 2.21, α = 0.05). The observed differences of AMC animal carriers between 1b (born 2013) and 1c (born 2015) populations (1.06%), 2a (born 2015) and 2b (born 2019) (3.33%), have not shown statistical significance because the meanings of t-criterion were 1.00, 0.89 and 1.5, respectively. The differences in DDC animal carrier between 1b and 1c (0.71%), 2a and 2b (1.80%), were also insignificant (t = 1.00).The statistical analysis of the differences in AMC and DDC animal carrier frequencies showed a significant increase of the DDC animal carriers by 1.17% in the Aberdeen Angus cow population 1d (born 2015) compared with 1c (born 2019)  on the frequencies of animal carriers in the populations of Aberdeen Angus (AA), Hereford (HE), Simmental (SI) and Belgian Blue (BB) breeds. For this purpose, we counted the quantity of animals free from the mutations. The results have been presented in 0) proposes no differences in the means of variable A (or B) categories, i.e., the absence of the influence of the breed and gender of animals on the proportion of genetic carriers in the populations. The condition of the H0 confirmation was p-value > α (0.05). As for Factor A (breed) and B (Gender), the p-values consisted of 0.2586 and 0.1327, respectively, which do not reject H0 because the chances of a type I error, rejecting a correct H0, is too high (25.86% for factor A and 13.27% for factor B). Therefore, we can conclude the absence of significant influence of breed or gender of animals on the frequencies of genetic defect carriers in populations.The null hypothesis .In this study, we set a goal to comprehensively assess the state of the genetic defects problem in Russia by using already developed and newly created methods for identifying animals that carry hereditary anomalies. Along with analyzing the frequency of occurrence of mutant alleles in beef cattle populations, we also analyzed the dynamics of the spread of certain mutations over time.The conducted study has shown the frequency of animal carriers of genetic defects in most farms was relatively low. However, an investigation conducted earlier demonstrated the extremely high figure in a single farm: in 2019, we observed cows from a farm in the central region of Russia, and almost 40% of the animals were carrying the mutant allele associated with the DD genetic defect . In addiWe also observed in one farm in the Northern-West region of Russia trends of increasing animal carriers of genetic defects (AM and DD) in the next generations .The data obtained in the course of this work confirm the relevance of the problem being studied since multiple increases in animals carrying the genetic defect AM were found in two farms, and in some cases, the data was reliable. Relating to the DD genetic defect, we have also observed a non-significant increase in the DDC-carrying animals over the years .At the beginning of the study, we assumed that the Hereford breed was free from harmful mutations associated with congenital pathologies . HoweverThe cows of the Belgian Blue population have the presence of the allele  linked wThe Simmental cattle breed has a double purpose because its feature is the development of milk and meat dependently from the direction of selection and management . This brAs we have proposed, the fixed factors breed or gender did not influence the quantity of genetic defect carriers in the populations, which was confirmed by a two-way ANOVA.We are partly reassured by the absence of carrier animals in the Hereford and Simmental bull populations, but the situation may change if there is no control. We would like to emphasize the special importance of genetic testing breeding bulls because due to the widespread use of artificial insemination in cattle breeding, a bull with the seed that dozens of cows are inseminated with can be a significant factor in the spread of hereditary anomalies in the herd.Therefore, due to the study, we have revealed the animal carriers of the genetic defects and found the tendency to increase in the next generations that point to the danger of the inherited anomalies manifestation and the need to input control measures in the Russian Federation territory.It should be noted that the main feature of congenital-inherited diseases is the impossibility of their treatment. Despite the possible development of gene therapy measures, they are very expensive and unbeneficial for the beef cattle breeding. Therefore, currently most animals affected by type I genetic diseases die soon after birth, and those that survive with the manifestation of non-lethal genetic defects of type II require the costs of care and treatment. These are lost profits for the farmers. Additionally, today, the most effective prevention measure is the early identification of the animal carriers of the genetic pathologies and preventing further crossing with animals free from genetic defects. Moreover, genetic selection for improved animal health has the potential to complement genetic gains associated with selection for improved productivity traits. Unlike traditional prevention and treatment strategies for diseases, the genetic gain is cumulative and can persist over generations . TherefoKonovalova, E.N., Kostyunina, O.V. and Zinovieva, N.A: Diagnostic technique for the polymorphism of genes AGRN, ISG15 and HES4 causing lethal genetic defect of multiple arthrogryposis of cattle meat breeds. RU Patent 2703396C2. 2019.Konovalova, E.N., Kostyunina, O.V. and Zinovieva, N.A. Method of diagnosing polymorphism of NHLRC2 gene causing genetic defect of duplication of Aberdeen Angus breed cattle development. RU Patent 2715330C2. 2020.The test systems for the AM and DD diagnostics have been patented:


Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 – 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines . A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.Finger millet [ Eleusine coracana (L.)] is an important nutraceutical crop. It is highly adapted to the semiarid tropics and is grown as a staple food crop in Asia and Africa. Globally, it is the sixth most important crop among cereals in terms of production, and it contributes about 12% of the total millet area . To enhance the use of diversity in crop improvement, core and mini-core collections were established in finger millet , plana (48 accessions), elongata (31 accessions), compacta (28 accessions), and some unclassified (5 accessions). Each race was further grouped into subraces, except compacta that have no subrace. The diversity panel consists of both landraces (264 accessions) and breeding material (50 accessions) (A diversity panel of 314 finger millet accessions originating from 23 different countries was constituted for this study . These aessions) .www.diversityarrays.com); details regarding DArT genotyping methods and procedures can be found at http://www.diversityarrays.com/dart-application and in Kilian et al.  were used for genotyping. Eight seeds of each accession were randomly chosen to constitute a sample for DNA extraction and sequencing. The seed samples from the 2018 rainy season harvested material were cleaned properly to avoid contamination by dust particles. The seeds were then placed in each well of the PCR plate and tightly sealed to avoid contamination. DNA extraction and sequencing were done by DArT private limited , polymorphism information content  and gene diversity (He), were computed for regions, races, and biological status using R v.3.6.0 package “poppr” , eight accessions  were removed for having >50% missing data; so, all the downstream analyses were carried out only on 306 accessions. The call rate ranged from 80 to 100%, of which 30,869 markers displayed a >85% call rate. Reproducibility ranged from 95 to 100%, and 88.80% of SNP markers showed >97% reproducibility.vulgaris and elongata had higher gene diversity (0.144), followed by compacta (0.142), and the lowest gene diversity was in race plana (0.129). Likewise, landraces (0.144) showed greater gene diversity compared with breeding lines (0.117) , and plana had a low value (0.233). Similarly, landraces (0.273) had a higher Shannon Index than breeding lines (0.204)  with a mean value of 0.110. The gene diversity for all loci in the entire set of germplasms ranged from 0.001 to 0.50, with an average of 0.114 . The fre (0.117) . The Afr (0.204) .elongata had the highest genetic distance (0.326), followed by vulgaris (0.299) and compacta (0.280), and the lowest was in race plana (0.275). The average genetic diversity among landraces was 0.299, while breeding lines had a value of 0.267 (Table 4).Genetic distance was assessed by the modified Roger's distance (MRD) method. The genetic distance among individuals ranged from 0.040 to 0.450 with a mean value of 0.301. Among regions, the highest mean genetic distance was found in the Asian accessions (0.286), followed by the African accessions (0.276). The genetic distance of accessions from Europe and North America was 0.247 and 0.217, respectively; however, the sample size in these two regions was low (<10) and was, therefore, ignored for further discussion. Among races, Fst. Pairwise Fst estimates between Asia and Africa were significant (0.198), which indicates the presence of genetic differentiation between the geographical origin, and the genetic distance between the African and Asian was 0.327. Among races , while compacta and plana had the lowest (0.281). The distance between vulgaris and compacta (0.294) and vulgaris and plana (0.302) was low compared with that between elongata and compacta (0.308) and elongata and plana (0.310). Significant genetic divergence and Fst were observed between landraces and breeding lines (0.313 and 0.136), respectively  was measured by MRD and the pairwise estimates of ng races , pairwisectively .Considering the relatedness of the accessions, the most diverse individual accessions and pairs of accessions were identified . AccessiThe ward.D2 agglomerative hierarchical clustering method, representing the relationship based on MRD, showed that 306 finger millet accessions were split into two distinct clusters  based on geographical origin . ClusterFst) estimated from STRUCTURE results for each of the two subpopulations was 0.548 and 0.622, and the ancestry-inferred cluster proportion of the membership of the samples was 0.644 and 0.356. The gene diversity of the two subpopulations was 0.087 and 0.093  according to a geographical region of origin (K = 2) . The accnd 0.093 .In addition to population structure at K = 2, the STRUCTURE results showed two more peaks at K = 6 and K = 8 . Interesvulgaris was grouped into cluster I, while the remaining 42% was under cluster II . The majority of the accessions of race plana were grouped under cluster II (89%). Landraces were grouped in both clusters I and II . However, most of the breeding lines were grouped in cluster I (94%) since they were mainly developed from an Asian breeding program, particularly in India   for the For this study, we established a diversity panel of 314 finger millet accessions, representing all the four races and their sub-races, originating from 23 countries. This set purposefully included the entire mini-core collection (80 accessions)  based on inflorescence morphology. Among the races, elongata had the highest average genetic distance  compared with other races in the diversity panel and, also, in the entire germplasm of finger millet conserved at the ICRISAT Genebank. Although finger millet is classified into races and subraces, there are no studies on their impact on diversity and the relationship between races and geographical regions. Studies also have reported the lack of proper clustering among finger millet races  and can be used to detect quantitative trait loci (QTLs)/gene in the finger millet population. Insights into finger millet diversity and population structure from this study will help breeders plan their breeding strategy to develop high-yielding cultivars with a broad genetic base for food, nutrition, and environmental security.The original contributions presented in the study are included in the article/MV and VCRA contributed to the conception and the design of the study. This work is part of Ph.D. thesis research of CBac. CBab supported student research as chairman. CBac, VA, and MV performed the statistical analysis. CBac and MV wrote the first draft of the manuscript. SD and RG provided the financial and technical support for this study. All the authors contributed to the revision of the manuscript, read, and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Vitis vinifera and show that all analyses support a single domestication event that occurred in Western Asia and was followed by numerous and pervasive introgressions from European wild populations. This admixture generated the so-called international wine grapes that have diffused from Alpine countries worldwide. Across Europe, marked differences in genomic diversity are observed in local varieties that are traditionally cultivated in different wine producing countries, with Italy and France showing the largest diversity. Three genomic regions of reduced genetic diversity are observed, presumably as a consequence of artificial selection. In the lowest diversity region, two candidate genes that gained berry–specific expression in domesticated varieties may contribute to the change in berry size and morphology that makes the fruit attractive for human consumption and adapted for winemaking.In order to elucidate the still controversial processes that originated European wine grapes from its wild progenitor, here we analyse 204 genomes of  Reports on the origin of European wine grapes are controversial. Here, the authors perform population genetics analyses on a large set of representative wine-making varieties and reveal a single domestication event at the origin of the entire germplasm followed by repeated introgression from wild populations. Vitis vinifera L. subsp. sativa (DC.) Hegi, hereafter sativa, also known as subsp. vinifera1) is linked to the history of ancient populations that settled across the Caspian Sea Basin, the Near East and the Mediterranean Basin. Grape cultivation and winemaking began somewhere in the South Caucasus2, the northern Fertile Crescent, or the Levant3, following domestication from local forms of the wild ancestor Vitis vinifera L. subsp. sylvestris (C.C. Gmel.) Hegi (hereafter sylvestris) that has a broad geographic distribution consisting of small isolated populations that are scattered across Europe, northern Africa and Western Asia5. From the cradle of domestication6, grape cultivars followed a predominant westward pattern of dispersal, driven by human migration and maritime trades, paralleled by a differentiation in use for fresh consumption (table grapes) or winemaking (wine grapes)7. Table grapes were also introduced eastwards into Central Asia along land trade routes. The cultivation of domesticated grapes dates back four millennia in the eastern Mediterranean and two millennia in Western Europe, with vegetative propagation becoming more and more prevalent as a mode of reproduction to preserve the genetic identity of valuable accessions that may have arisen from spontaneous crosses. Paleogenomic evidence supports a very early adoption of vegetative propagation and an ancient origin of some of the currently cultivated varieties, with Savagnin Blanc being at least 900 years old8. Western European varieties are the foundation of the global wine industry, with ten varieties  accounting for 26% of the vineyards worldwide9.Phylogeography of cultivated grapes  or as sylvestris var. aberrans that today is rare or almost extinct in Azerbaijan and Turkmenistan but, in the past, was reported to thrive across the southern Caspian Sea Basin and to be distinguished by large and glabrous leaves10. Cultivated grapevines have been classified in three ecogeographical groups: orientalis, pontica, and occidentalis10. Orientalis is considered the ancestral group and is supposed to be morphologically more similar to the wild ancestor sylvestris var. aberrans. Pontica is more similar to eastern forms of sylvestris var. typica, today thriving in South Caucasus, eastern Anatolia and Armenian highlands. The botanist Negrul also proposed an ecogeographical divide between pontica georgica, which includes typical Caucasian wine grapes, and pontica balcanica that includes representative varieties of the eastern Mediterranean Basin. Hereafter, we refer to orientalis and pontica georgica as cultivated germplasm of eastern origin. Feral grapes are present in the cradle of domestication as relic populations of transitional forms from sylvestris to sativa, more similar to the sylvestris lineages that underwent domestication10, hereafter referred to as eastern feral grapes. According to Levadoux4, feral grapes are occasionally found also in Europe as hybrids between genuinely autochthonous sylvestris and escapees from the vineyards (lambrusques métisses) or naturalized seedling populations of sativa growing outside the agricultural land , hereafter collectively referred to as western feral grapes, that may explain the morphological similarity observed between western sylvestris and some local varieties, e.g. varieties of the Lambrusco family11. The origin of western European wine grapes is debated12. According to one hypothesis1, a reciprocal gene flow between introduced varieties and local wild populations  occurred after the westward dispersal of domesticated forms, when the area of grape cultivation overlapped with the European range of distribution of sylvestris13. According to another hypothesis12, cultivated grapes have at least two origins, one in the East and the other in the West, and western wine grapes may have had their origin in an independent event of domestication from western sylvestris.Botanical classification of wild and cultivated grapes is all but simple. Wild forms have been classified either as occidentalis wine grapes remain unaddressed questions. To provide answers, we analysed whole-genome sequencing (WGS) data of 204 V. vinifera accessions and ten outgroup species, 124 of which were generated in this study. Prior to this study, the analysis of DNA sequence variation in V. vinifera has been partially addressed using genotypic data obtained either with SNP chips from hundreds of accessions16 or with WGS from a few individuals17, which allowed the detection of a network of pedigree relationships. WGS of large diversity panels provides several orders of magnitude more information that is not affected by any type of ascertainment bias. Unlike a recent WGS study of Liang and coworkers18 that focused on Vitis species, interspecific hybrids and recently bred V. vinifera varieties, here we present a WGS–based analysis of a panel of V. vinifera varieties that well represent the cultivated genetic diversity.Exactly which domesticated types were initially introduced for winemaking into the Mediterranean Basin and what has led to the formation of the In this work, we provide several lines of evidence that support that processes that lead to the creation of the European wine grapes are dominated by introductions of table grapes from the East followed by extensive and frequent gene flow from local wild forms. We also show that genome-wide levels of diversity in cultivated and wild forms are similar, revealing that the domestication bottleneck has had limited effects on the crop germplasm. We identify, in a region of the genome on chromosome 17 that has undergone a selective sweep, a gain-of-function mutation that led to gene expression changes in two genes that may be related to the domestication process. We finally show that current patterns of genetic variation in wine grapes are associated with geographic and climatic variation.V. vinifera  and two Vitis species at a genome coverage ranging from 8-fold to 90-fold (average 26) and obtained archived sequence reads for another 82 vinifera accessions and 8 other grape species . Validation of SNP calls showed low error rates in genotyping for homozygous and heterozygous sites , suggesting a largely incomplete lineage sorting in the genus Vitis  using whole genome sequence data of 203 accessions of vinifera  to infer their genetic ancestry and a statistical model developed by Pickrell and Pritchard23 (implemented in the software TreeMix) to infer splits and gene flow between cultivated and wild grapes . The rest of the cultivated germplasm, represented by varieties that today are grown in Alpine countries, appears to be the result of admixture. The statistics to estimate the number of ancestral populations suggested that eastern and western ancestry is the main divide, according to the Evanno’s test , which is dominant in western sylvestris, and one  that is dominant in eastern sylvestris  are predicted, with one  predominantly found with the W2 component in table grapes, and the other  almost exclusively found in wine grapes. These two components, which are detectable in some eastern feral grapes but not in wild grape samples, could be derived from extinct forms of sylvestris  and deserve special attention to better understand the structure of genetic diversity in the cultivated compartment. The C2 component is detectable in cultivated varieties of the Muscat family as well as in European wine grapes. The C1 component is most frequently associated with table and wine grapes from around the Mediterranean Basin.When we applied the model-based clustering to the species germplasm WGS data , from Southern Italy and from the Iberian Peninsula, representing 13.0% of all accessions. Only K = 4 generated a divide between table grapes and Caucasian wine grapes into two ancestral populations that correspond to Negrul’s orientalis and pontica georgica, respectively. The other two ancestral populations with K = 4 were represented by wine grapes from the Alpine countries  and by varieties from the Balkans, Greece and Southern Italy, largely corresponding to Negrul’s pontica balcanica. The adoption of K = 4  and widely accepted in grapevine taxonomy.In order to test which scenario of ancestral populations is more consistent with the taxonomic treatment of the cultivated compartment, we applied the model-based clustering to the cultivated germplasm alone  than to pontica georgica ancestors (Caucasian wine grapes), in partial disagreement with Negrul’s hypothesis  as primitive European varieties, which represented the ninth group included in Fig. 17 and with our demographic model that predicts the nadir of effective population size 2 K years before the present  shows a similar genetic constitution—resulting from a possible cross between an escapee from the vineyards and a genuine autochthonous sylvestris, as suggested by18—but an opposite case of classification (lambrusque métis) presumably because the accession was found outside of a vineyard. There is no evidence of parent–offspring relationships between KE–06 and cultivated varieties of the WGS panel, but we detected the highest level of haplotype sharing with Savagnin Blanc and Pinot Noir . The pairs Pinot/B00ERBY, Savagnin Blanc/Petit Manseng, Savagnin Blanc/Riesling Bleu (collection Oberlin), and Petit Manseng/Gros Manseng share a parent–offspring relationship . Our analysis of both the WGS panel and the diversity panel did not reveal any instance of cultivated varieties carrying pure Western sylvestris ancestry that would be expected in the scenario of an independent domestication event.A principal component and coordinate analysis . For each cultivated variety and the corresponding geographical location, we associated the genetic ancestry coefficients with 29 bioclimatic variables  and extended hitchhiking  controlling a series of berry traits in wine as well as in table grapes have been found overlapping with the sweep region on chromosome 1734.The sweep on chromosome 17 has been proposed by Myles and coworkersasm Fig. , we idenasm Fig. . In addiasm Fig. . The pheVIT_217s0000g05570 and VIT_217s0000g05580, corresponding to gene numbers 6 and 7 in the diagram of Fig. 36, and Gordin Verde, a wine grape from Moldova, unrelated to Berzamino  and resumption of berry growth38. This second phase of increase in berry size, unlike the first one, occurs exclusively by cell expansion40. A genome-wide association study  and QTLs for extreme variation in berry size and seed content colocalize42 on chromosome 18 with a seed morphogenesis regulator MADS-Box gene43. Doligez and coworkers34 showed, additionally, that the QTL overlapping with the sweep region on chromosome 17 explains the residual variation in berry weight not explained by seed content and it is therefore possible that factors in this region promote pericarp growth at a rate that is more than proportional to the increase in SFW, which is reflected by lower seed-to-berry ratio. The selected haplotypes are associated with a change in berry morphology towards a larger pericarp per unit of SFW. This leads to an increase in size of the fleshy and edible part of the berry, making it more attractive for fresh consumption. It also decreases more than proportionally the seed content released from crushed berries into the must, which greatly improves tannin chemistry and textural sensory attributes in wines. This effect is due to a reduction of the leakage during maceration of astringent and bitter condensed tannins with low degree of polymerization from seeds in favor of the extraction of more palatable condensed tannins with higher degree of polymerization from skins. The kinase gene encodes a LRR–RLK that is orthologous to a kinase in Arabidopsis (At5G62710) that is expressed in ovaries and in vascular tissues44 and that shows high homology with the FEI2 kinase. RLKs play a pivotal role in sensing external stimuli, activating downstream signaling pathways and regulating cell behavior involved in response to pathogens, growth, and developmental processes in plants. The FEI2 kinase has been shown in Arabidopsis45 to promote anisotropic cell expansion through a modulation of cell wall function, a role that FEI2 fulfils by interacting directly with 1-aminocyclopropane-1-carboxylic acid (ACC) synthase, a key enzyme for ethylene biosynthesis. The grape berry is considered a non-climateric fruit, lacking a concomitant increase in respiration rate and ethylene biosynthesis at the onset of ripening, but the rise in endogenous ethylene production that is consistently observed a few days before the inception of the second phase of berry growth regulates several aspects of ripening46, including an increase of berry diameter that can be further augmented by the application of exogenous ethylene at véraison47. In light of the specific function of the LRR–receptor kinase ortholog in other plants, it is possible that the haplotypes selected during grape domestication may have provided cultivated varieties with new opportunities for ethylene-related cell expansion during berry ripening thanks to the greatly increased expression of the LRR–receptor kinase gene.Two nearby genes in the sweep region captured our attention because they show the lowest level of diversity Fig.  and becaDetails of sequenced accessions are reported in Supplementary Data Two-bud cuttings of 15 cultivated varieties (replicated twice) were forced to rooting in potted soil. A single shoot per cutting was raised until the stage of 10–12 leaves in a common garden experiment. At that stage, the fourth distal (fully expanded) leaf was sampled from each replicate and variety at the same time and frozen immediately for RNA extraction. Berries of an expanded set of 90 accessions were sampled at same developmental stage on different dates according to their curve of berry growth, from two replicated field plots. From each plot two batches of asynchronous berries were collected over the same bunches, one composed of hard berries , the other composed of soft berries , both sorted by firmness to the touch. The accuracy of berry sorting was validated by subsampling from each batch random subsets of berries for destructive measurements, e.g., soluble solids concentration Fig. . The res48. Raw variants were called using the UnifiedGenotyper tool in GATK49 version 3.3-0 with 0.01 heterozygosity parameter. Variant sites in each variety were retained if they matched the following parameters: Phred-scaled quality score >50; five reads of minimum coverage; read coverage comprised between 0.5 and 1.5-fold the modal coverage of the variety, maximum coverage relaxed to 2.5 if the SNP passed the filters in other five varieties, minimum coverage relaxed to 0.25 fold the modal coverage in case of homozygous calls; reference/alternate allele coverage ratio between 0.25 and 0.75 for calling heterozygous genotypes, normalized Phred-scaled likelihoods (PL) of the homozygous genotype = 0 and PL value of non-zero PL values > 10 for homozygous assignment; ratio between allelic depth and depth passing quality filters (AD/DP) > 0.05; minimum number of varieties carrying the variant = 1. Variant sites were retained in the dataset if genotype calls passed the filters in >50% of the varieties. Variants sites in repetitive DNA were removed from subsequent analyses. Repetitive DNA included high copy number sequences reconstructed by ReAS50, transposable elements annotated in Repbase51, and microsatellites ±10 bp identified using the software Sputnik.Filtered DNA reads . Type-I errors were controlled using a max(T) permutation procedure with 1000 permutations and plotted in Supplementary Fig. GWAS was performed using 88 accessions with fully developed seeds (Supplementary Data Vitis vinifera 12Xv0 genome assembly of the strain PN40024 (GCA_000003745.2) with the exception of the upper arm of chromosome 15. We constructed two genetic maps using S1 families derived from Pinot Noir and Schiava Grossa that incorporated 16,358 and 10,179 SNPs, respectively , IMIDRA Finca El Encin, Madrid and ICVV, Logroño (Spain) and JKI Geilweilerhof, Siebeldingen (Germany). The accession TA–6264, previously assigned to sylvestris by Liang and coworkers18, was reclassified as sativa Listan Negro. The accession Aramon sequenced by Zhou and coworkers17 was reclassified as Touriga National. The accessions Turkmenistan2, Azerbajian1, Azerbajian2, Pakistan1 and Pakistan3, previously assigned to sylvestris17, were reclassified as eastern feral based on ancestry component proportions. The accessions Turkmenistan1 and Pakistan2 from the same set17 were reclassified as interspecific backcrosses and therefore excluded from all analyses. Eastern feral accessions from this study showed parent–offspring  or second-degree  relationships with cultivated varieties. The pairs K2 and TA–6263, K26 and K27 showed identical SNP profiles. The pairs K22 and TA–6245, KE–23 and TA–6253, KE–23 and TA–6246, Pakistan1 and Pakistan3 showed PO relationships.Gene models refer to the V2.1 gene annotationsylvestris based on proportional membership ≥0.99 or to western feral otherwise. SNPs in the large sweep region on chromosome 2 were excluded from ADMIXTURE analyses. For TreeMix analysis only, eastern feral grapes were considered as such only if they did not share first-degree or second-degree relationships with cultivated varieties. The ML trees shown in the main text figures were built using blocks of 300 SNPs for the WGS dataset with correction for sample size effects and blocks of ten SNPs for the SNP-chip based dataset. Validation with other combinations of window sizes and number of migration events are shown in Supplementary Fig. Vitis sp., recipient = Table grapes, donor = western sylvestris, generating = Alpine wine grapes. Excess of shared derived alleles between sylvestris and Alpine wine grapes was expressed by a modified version of Patterson’s D statistics (fd), adjusted to purge signals of introgression from ancestral population structure25. Haplotypes in the selective sweep of chr17 were first inferred from heterozygous accessions carrying a reference haplotype. This initial set of haplotypes was used to infer additional haplotypes from other heterozygous accession. Haplotypes could be inferred from 196 out of 204 accession, including 121 out of 123 cultivated varieties. Gene phylogeny reported in Fig. 58 curated by Gblocks. Trees were drawn with TreeDyn. Geographical maps of spatial population genetic structure were drawn using tess3r59.Cultivated varieties were assigned to one of the ADMIXTURE K groups based on ≥0.85 genetic ancestry. The other cultivated varieties with proportional membership <0.85 were assigned to admixed populations. Feral or wild western Europe grapes were assigned to western 1 in Supplementary Method 2 in Supplementary Method 3 . Data was sourced from 30 arc-second rasters corresponding to a spatial resolution of 1 km2 at the equator and represent the average of the temporal range 1970–2000. Seasonal potential evapotranspiration (PET) was calculated using the Thornthwaite equation60 as a sum of the monthly PET from April through September. Seasonal climatic water deficit (cwd) was calculated as the sum of monthly deficit between precipitation and PET form April through September. To avoid the biases due to data multicollinearity among independent variables in the GLM for correlating climate variables with genetic variation, we first identified correlation among climate variables  were downloaded from WorldClim (Further information on research design is available in the Supplementary InformationPeer Review FileDescription of Additional Supplementary FilesSupplementary Data 1Supplementary Data 2Supplementary Data 3Reporting Summary


Signal transducer and activator of transcription 3 (Stat3) is a cytoplasmic transcription factor that participates in various biologic processes. Loss of Stat3 causes hyperimmunoglobulin E syndrome, presenting with skeletal disorders including osteoporosis, recurrent fractures, scoliosis, and craniosynostosis. The objective of this study is to explore the effect and mechanism of Stat3 on osteogenesis of mesenchymal progenitors.Stat3 was conditionally knockout (CKO) in mesenchymal progenitors by crossing the pair-related homeobox gene 1-cre (Prx1-Cre) with Stat3-floxed strain mice. Whole-mount-skeletal staining, histology, and micro-CT were used to assess the differences between Stat3 CKO and control mice. Further, in vitro experiments were conducted to evaluate the osteogenesis potential of primary isolated bone marrow mesenchymal stem cells (BMSCs) from both control and Stat3 CKO mice. After osteogenic induction for 14d, alizarin red staining was used to show the calcium deposit, while the western blotting was applied to detect the expression of osteogenic markers.Compared with the control, Stat3 CKO mice were present with shortened limbs, multiple fractures of long bone, and open calvarial fontanels. The abnormal growth plate structure and reduced collagen fiber were found in Stat3 CKO limbs. According to micro-CT analysis, the reduced cortical bone thickness and bone volume were found on Stat3 CKO mice. The in vitro osteogenic differentiation of BMSCs was inhibited in Stat3 CKO samples. After osteogenic induction for 14d, the significantly diminished calcium deposits were found in Stat3 CKO BMSCs. The decreased expression of osteogenic markers (OPN and COL1A1) was observed in Stat3 CKO BMSCs, compared with the control.Stat3 played a critical role in bone development and osteogenesis. Loss of Stat3 impaired the osteogenesis of mesenchymal progenitors in vivo and in vitro.The online version contains supplementary material available at 10.1186/s13578-021-00685-3. The skeleton development is a complex process involving cell migration, proliferation, and differentiation . The difSignal transducer and activator of transcription 3 (Stat3) is a cytoplasmic transcription factor and extensively participates in cell proliferation and differentiation .Heterozygous Stat3 mutation in humans leads to Job syndrome , which is characterized by recurrent multiple organ infection along with skeletal, dental abnormalities –7. The sIn the current study, Stat3 was conditional knockout (CKO) in mesenchymal progenitors in vivo by using the pair-related homeobox gene 1-Cre (Prx1-Cre) crossed with Stat3-floxed strain mice –14. The f/f, stock no.016923 [f/f were crossed with the Prx1-Cre mice to generate Prx1-Cre; Stat3f/+ mice. Next, Prx1-Cre; Stat3f/+ mice were crossed with Stat3f/f mice to generate Prx1-Cre; Stat3f/f conditional knockout (CKO) mutant mice. The Cre-negative littermates were taken as the control of Stat3 CKO mutants. Mouse tail genotyping was performed by polymerase chain reaction (PCR) and the primer sequences for PCR were listed in Table The animal work was carried out according to federal guidelines, with the approval by the Animal Ethical and Welfare Committee of Sun Yat-sen University . Mice were purchased from the Jackson Laboratory . To genSkeletons from neonatal (P0) mice were processed for Alizarin Red S (sigma A5533) and Alcian Blue (sigma A5268) staining to demonstrate bone and cartilage. The protocol was same as previously described . PictureFor histology, limbs were fixed in 10% formalin  for 24 h. For 8-week-old samples, 4-weeks’ decalcification by 10% tetrasodium EDTA were conducted. After dehydrated by graded ethanol and cleared in xylene, limbs were embedded in paraffin and sectioned at 4 μm thickness along the long axis. Sections were stained with safranin O/fast green, masson, hematoxylin and eosin (H&E) . Sections were mounted in neutral resins and then scanned by AperioAT2 scanner (Leica Microsystems). The quantification of safranin O/fast green and the Masson staining was carried out by ImageJ. Specifically, in safranin O/fast green stained sections, the area of proliferative zone and hypertrophic zone was measured respectively, which was then divided by the total area of the growth plate to obtain the relative surface area of the region of interest. In the Masson-stained sections, the blue-stained collagen fiber area was divided by total tissue area to calculate the collagen fraction. For histomorphometric, three samples per group were used. For each sample, three sections were selected. The mean value of the three slides was considered as the result of one sample.For IHF staining, the antigen retrieval was performed in a citrate buffer . Sections were blocked in normal goat serum (NGS) for 1 h before incubation with primary antibodies overnight at 4 °C. The next day, sections were incubated with Alexafluor-594 conjugated secondary antibody  for 1 h at room temperature. Sections were mounted in mounting medium with DAPI from Vector Laboratories. The images were captured by an inversion fluorescence microscope . The antibodies used for IHF were listed in Table The skeletons were scanned and analyzed using a μCT 50 system  with a spatial resolution of 10 μm. For trabecular bone morphometric analysis of distal femur, the starting slice was taken where the growth plates were fully merged and extended for 100 slices proximally. The morphometric analysis was performed for bone mineral density (BMD), bone volume per tissue volume , and cortical bone thickness by μCT 50 system. The 3D reconstruction of the skeletons and cross-section images were performed by Dataviewer and CTvox .−1 penicillin, and 100 μg·mL−1 streptomycin , 2 mmol·L−1 l-glutamine , 55 μmol·L−1 2-mercaptoethanol . Cells at passage 2 were employed for the following in vitro experiments  PBS. Single-cell suspensions from long bone marrow were obtained through 70-μm cell mesh and seeded on 100-mm dishes . Non-adherent cells were removed after 3-days’ culture in alpha-MEM  supplemented with 20% FBS , 100 U·mLThe mesenchymal stem cell characterization was performed, including (a) the flow cytometry were conducted to show that these cells were positive for CD29, CD44 and were negative for CD34 and CD45 , (b) osteoblastic and (c) adipogenic differentiation were applied to show the multi-lineage differentiation capacity of the primary isolated cells. The antibodies used for flow cytometry were listed in Table −7 M dexamethasone . After 7 days’ induction, alkaline phosphatase (ALP) expressions were detected by Alkaline Phosphatase Stain kit  according to the manufacturer’s instructions. Images were taken by Leica Microsystems and ImageJ was applied to quantify the stained areas. After 14-days’ osteogenic induction, the calcium deposit was evaluated by Alizarin Red S staining . Images were taken by Leica Microsystems, followed by quantification using 10% cetylpyridinium chloride (CPC)  to dissolve the stained calcium deposit. The absorbance value of the dissolved solution at 562 nm was measured by microplate spectrophotometer .For osteogenic differentiation, the BMSCs were plated in 6-well plates and cultured in osteogenic induction medium containing 10 mM β-glycerol phosphate , and 50 μM ascorbic acid  10Adipogenic induction medium was provided by Cyagen Biosciences, Inc. . After 12-days’ induction according to manufacture instruction, the cultured cells were stained with oil red O solution , and were observed under light microscope (Leica Microsystems).Total protein of mouse hindlimbs and BMSCs was extracted using the RIPA lysis buffer  containing proteinase and phosphatase inhibitors , and then quantified by the BCA method . The proteins were separated by SDS-PAGE gel electrophoresis  and transferred to a polyvinylidene fluoride (PVDF) membrane . After 1 h blocking by 5% BSA, membranes were incubated at 4 °C overnight with relevant primary antibodies. The PVDF membranes were incubated in HRP conjugated secondary antibody for 1 h at room temperature. Immunoreactivities were detected by a chemiluminescence kit . Data were normalized to GAPDH and quantified by ImageJ. The antibodies used in this study were listed in Table P < 0.05.The data were presented as means ± standard deviation (SD). Student's t-tests were used to compare the difference between Stat3 CKO and the control. The GraphPad Prism 7.0 software were applied for statistical analysis. The significance level was set at f/f (Stat3 CKO) and Cre negative littermate control. The deletion of Stat3 was further confirmed by western blot and IHF staining. . The abnormalities were found in both proximal long bones (the humerus and femur) and distal long bones . Multiple fractures were observed in the forelimbs and hindlimbs of Stat3 CKO mice . Masson’s trichrome staining showed that plenty of collagen fiber (stained in blue by Masson) existed in the trabecular bone area and endosteal surface of cortical bone on control mice, meanwhile much less collagen was observed on the Stat3 CKO mice . IHF staining showed less COL1A1 and OPN expression at ulna proximal epiphysis and endosteal surface of cortical bone , while the difference in BMD was not significant     staining intensity, compared with the control (05) Fig. A. Accord05) Fig. B. Quantiopn and col1a1 genes, indicating that there were putative binding sites of Stat3 on these genes  of both In the present study, the severe bone abnormality was observed in Stat3 CKO mice, including shortened limbs, multiple fractures, and reduced bone volume. In vitro study showed that the osteogenic differentiation was reduced in Stat3-deficient BMSCs when compared with the control.Skeletal development is an orchestrated process comprising intramembranous and endochondral ossification, which both begin with condensation of mesenchymal progenitors . During −/− mice, which was highly consistent with our findings in the proximal ulna of Stat3 CKO mice [c/c mice) [Stats family has various functions in mammalian development , 23. AmoCKO mice . This si/c mice) . As expe/c mice) . Taken topn and col1a1, but the exact interaction between OPN, COL1A1, and Stat3 needs to be further explored. Nevertheless, in our study, Stat3 deficiency resulted in decreased expression of both collagenous (COL1A1) and non-collagenous (OPN) protein in vitro, which in turn, impaired the osteogenic differentiation of BMSCs and less mineralization of the cells was found.The in vitro expression of osteogenic markers (OPN and COL1A1) was found diminished in response to Stat3-dificiency. OPN is one of the major non-collagenous proteins that plays key roles in determining bone morphology . BioinfoBesides OPN and COL1A1, there were some other genes that could interact with Stat3 according to literatures. Studies have discovered that activated Stat3 could bind to the promoter of several osteogenesis related genes, such as Runx2  and OCN In conclusion, Stat3 was essential for osteogenesis of mesenchymal progenitors in vivo and in vitro. Stat3 CKO mice showed severe skeletal abnormality and Stat3-deficient BMSCs was presented with reduced osteogenic differentiation ability, likely in part by regulating the expression of OPN and COL1A1.Additional file 1: .Additional file 2:Fig. S1. Decreased expression of COL1A1 and OPN in P0 Stat3 CKO mice (P0) compared with the control.Additional file 3:Fig. S2. Stat3 could activate the transcription of mouse col1a1 and opn genes.


With climate change bound to affect food and feed production, emphasis will shift to resilient and adapted indigenous livestock to sustain animal production. However, indigenous livestock comprise several varieties, strains and ecotypes whose genomes are poorly characterized. Here, we investigated genomic variation in an African thin-tailed Desert Sheep sampled in Sudan, using 600K genotype data generated from 92 individuals representing five ecotypes. We included data from 18 fat-tailed and 45 thin-tailed sheep from China, to investigate shared ancestry and perform comparative genomic analysis. We observed a clear genomic differentiation between the African thin-tailed Desert Sheep and the Chinese thin-tailed and fat-tailed sheep, suggesting a broad genetic structure between the fat-tailed and thin-tailed sheep in general, and that at least two autosomal gene pools comprise the genome profile of the thin-tailed sheep. Further analysis detected two distinct genetic clusters in both the African thin-tailed Desert Sheep and the Chinese thin-tailed sheep, suggesting a fine-scale and complex genome architecture in thin-tailed sheep. Selection signature analysis suggested differences in adaptation, production, reproduction and morphology likely underly the fine-scale genetic structure in the African thin-tailed Desert Sheep. This may need to be considered in designing breeding programs and genome-wide association studies. A common research thread that links population and quantitative genomics is the elucidation of patterns and processes underlying population genetic structure. Whether such structure is stable in time and space is increasingly addressed for its utility in determining how many genetically distinct populations exist and their inter-relationships . InsightOvis aries) are central to national economies as a source of cash, meat, milk, fiber, etc., and to traditional societies as repositories of socio-cultural values. Sheep are also essential components of diverse production systems due partly to their versatility to adapt to local biophysical and production environments. Domestic sheep comprise three broad types: thin-tailed, fat-tailed, and fat-rumped sheep  and the phenol-chloroform method were used to extract DNA from the Sudanese and Chinese samples, respectively. The samples were genotyped with the Ovine Infinium 600K BeadChip at GeneSeek Inc. (Sudanese samples) and Compass Biotechnology (Chinese samples). Of the 606,006 SNPs present in the BeadChip, 577,401 are autosomal, 27,314 are on the X-chromosome and 1,291 remain unmapped.Whole blood was collected through jugular venipuncture from 121 animals representing five ecotypes of thin-tailed Desert Sheep in Sudan , 2. Bloor2 threshold, respectively, resulting in 390,243 SNPs that were used for population structure and phylogenetic analysis.The genotypes from both sets of samples were merged and the data were screened for quality with PLINK . SamplesO) and expected (HE) heterozygosity, inbreeding coefficient F and Pi-HAT statistics. The “detectRUNS” package (FROH) was computed as the ratio of the total length of ROH to the length of autosomes (2.45 Gb)  .r2) between alleles at two SNP loci using the “indep” option in PLINK. Following E) was estimated with the equation NEt = (1/4c) (1/r2 - 1), where NEt represents the effective population size t generations ago, t = 1/2c, r2 is the LD between pairwise SNPs and c is the genetic distance in Morgan between a pair of SNPs  phylogeny, principal component analysis (PCA) and ADMIXTURE modeling. The NJ tree was generated to visualize relationships using pairwise s. MEGA7  was useds. MEGA7 . Genomics. MEGA7 . The patg CLUMPP  and visuThe NJ tree, PCA and ADMIXTURE revealed evidence of broad- and fine-scale genetic structures in the datasets. To detect genomic regions showing divergence between the observed genetic structures, we analyzed the dataset for signatures of divergent selection.Using the detectRUNS package, we implemented the frequency-based threshold approach to define genome-wide ROH islands in each genetic cluster that was revealed by the NJ tree, PCA and ADMIXTURE. This approach set a percentage of animals within a genetic cluster or a population having a SNP in an ROH region as the threshold. The threshold used in our analysis to select the genomic regions with a high frequency of ROH islands was 50%. Private ROH islands were determined by filtering out homozygous variants in ROHs in a specific genetic cluster, but which could not be found in ROHs of the other genetic clusters. This allowed the detection of either whole or segments of ROHs that were either shared or were private to a genetic cluster. The frequency of ROHs were plotted against their physical genomic positions and visualized with a Manhattan plot.FST  derived from all the windows tested for a given comparison. FST values. We set the top 0.1% positive values of ZFST as the threshold to identify the candidate regions under selection.where μWe also investigated signatures of selection using XP-EHH . It assep-values were estimated from the standard normal distribution  was used to annotate the candidate regions using the BioMart Tool in Ensembl and NCBI databases. The functional annotation tool in DAVID v6.8  and HE (0.343 ± 0.000) while the highest values were observed in Shanbali (SH) (HO = 0.355 ± 0.008) and Kabashi (KA) (HE = 0.357 ± 0.000). Among the Chinese breeds, the Black Tibetan (HZ) had the lowest values of HO (0.336 ± 0.045) and HE (0.332 ± 0.0001), whereas the highest values were present in Zeku (ZK) (HO = 0.348 ± 0.005) and Tan Sheep (HE = 0.360 ± 0.000). The average Pi-HAT value for the Sudan thin-tailed Desert Sheep was 0.056 ± 0.016, ranging between 0.081 and 0.112 (FROH = 0.014 and F = 0.009). This validated our sampling strategy which targeted only mature unrelated animals. The Sudanese thin-tailed Desert Sheep had on average longer lengths of ROH, higher FROH but lower F compared to the Chinese breeds.The average values of Hed 0.300 . Among tnd 0.112 . This suE over generation time  with both HA and SH. Among the Chinese breeds, the lowest values of FST occurred between the thin-tailed Oula (QOL) and Zeku (ZK).Genetic differentiation was assessed by calculating pairwise d breeds . The oveFST genetic distance matrix  and SD_G2 . We also classify the Chinese breeds into three genetic clusters, i.e., CN_G1 (Tan Sheep), CN_G2 (ZK and QOL), and CN_G3 (HZ).We used the ADMIXTURE tool to investigate genome architecture and complement the NJ phylogeny and PCA. Running ADMIXTURE using all the study individuals resulted in the lowest CV error at K = 3 . At thisobserved . The fird  and OAR3  spanning seven and two genes  and/or two comparative analyses (SD_G1 verses SD_G2/CN_G1/CN_G2)  . Among tanalyses . Among tFST) identified a total of 697 and 765 putative genes that overlapped with candidate regions identified in SD_G1   and resilience. Here, we present findings of the analysis of genomic variation in the indigenous African long-legged thin-tailed Desert Sheep from Sudan. The overall average Hki sheep , an indiki sheep , but falki sheep  and in Nki sheep . The levhinhorn) . The chiThe lack of stringent artificial selection coupled with random mating in the Sudanese thin-tailed Desert Sheep may explain their high levels of genetic diversity but low levels of genetic differentiation and inbreeding. The former may be enhancing their fitness and could be responsible for their adaptive resilience to the desert environments where they are raised.E over the past 1,000 generations. All the samples analysed showed a rapid decay in LD within the first 300 kb. From around 0.1 Mb, the Chinese breeds had higher r2 values, which most likely reflected an attempt at their standardization as distinct breeds compared to the Sudanese thin-tailed Desert Sheep, where such efforts are lacking. However, for both subsets, the r2 values averaged below 0.15, suggesting very limited extension of high LD blocks across their genomes. This r2 value ranked below the minimum threshold range of 0.33 ≤ r2 ≤ 0.80 that is meaningful for GWAS  a separation of African sheep from the Chinese breeds, (ii) a separation of fat-tailed sheep (Tan breed) from both African and Chinese thin-tailed sheep, and (iii) different genetic backgrounds in both the African and the Chinese thin-tailed sheep. While the first result suggest genetic divergence that has most likely arisen due to reproductive isolation between sheep in different continents coupled with genetic drift, the second result confirm the existence of differences in genetic makeup of fat-tailed and thin-tailed sheep. A similar result based on the analysis of microsatellites was reported previously between African fat-tailed and thin-tailed sheep  results also revealed what we hypothesized to be a fine-scale genetic structure among the individuals analyzed. The analyses revealed at least two distinct genetic clusters in the Sudanese thin-tailed Desert Sheep; one which was specific to AL and another to the four remaining ecotypes. The analyses also identified two genetic clusters in the Sudanese thin-tailed sheep from China: one cluster was exclusive to HZ and another occurred in QOL and ZK and at low frequency in HZ. Given that the five ecotypes of thin-tailed Desert Sheep are all derived from a low altitude hot arid environment while the Chinese thin-tailed breeds are adapted to an alpine/sub-alpine high-altitude rangeland, this fine-scale genetic structure was unexpected. It may hint at a complex genome architecture in the thin-tailed sheep because it cannot be explained by differential selection for adaptation. It is, however, likely that artificial selection may be driving the divergence in the Chinese thin-tailed sheep. With a common genomic background observed in QOL and ZK and the same occurring at a low frequency in HZ, it suggests that HZ has been gradually diverging from QOL and ZK. HZ has a predominantly black coat while QOL and ZK have mainly white coats with some black to brown patches around heads and legs. QOL and ZK also occur in close geographic proximity and can thus cross mate while HZ is isolated and farmers keeping this breed avoid mating it with other breeds, so as to maintain its distinct black coat, genetic purity and recognition.A combination of NJ phylogeny, PCA and ADMIXTURE , a candidate gene for gastrointestinal nematode resistance in sheep , 10, 13, 18 (two regions), and 26 (one region) . Within in sheep . The PDG on OAR6 , 8. It h on OAR6 . PDGFRA  the pig . Nazari-ed sheep  while CAin sheep . These rFAM120B, PSMB1, and PDCD2. FAM120B has been suggested to be a potential candidate for twinning rate in humans   . The prohamsters . These rNR6A1, NR5A1, ADGRD2, PSMB7, and NEK6) and the top-most significant position was close to NR5A1. The expression of NR5A1 drives Leydig cell differentiation from progenitor cells  differentiated both SD_G1  and SD_Gor cells , thus inor cells . In micel glands . Anotherlificacy . Whethertic pigs  and the tic pigs . From a tic pigs , while ttic pigs .TLR2), TLR4 or both in macrophages and dendritic cells. Thus, the HA metabolic process may be facilitating the adaptation to desert environments in African long-legged thin tailed sheep.The African long-legged thin-tailed sheep is raised in desert environments where they are exposed year-round, to complex interacting biophysical stressors, including high temperatures, physical exhaustion, direct solar radiation, feed and water scarcity. In this context, the revelation of the GO biological term “hyaluronan metabolic process (GO:0030212)” in four out of the six comparisons involving SD_G1 and SD_G2 is relevant. Hyaluronan (HA) comprises a major component of the extracellular matrix (ECM) in vertebrates and is a straight chain glycosaminoglycan which mediates diverse functions depending on molecular size and tissue concentration, both of which are regulated by the balance between its biosynthesis and catabolism . HA occuIn this study, we analyzed the genetic diversity, structure and signatures of selection in the African thin-tailed Desert Sheep sampled from Sudan. We included one breed of fat-tailed and three breeds of thin-tailed sheep from China for comparative genomic analysis. We found high levels of genetic diversity but low levels of genetic differentiation among the five ecotypes of Sudanese thin-tailed Desert Sheep. The analysis also revealed a broad- and fine-scale genetic structures in the sheep analyzed, suggesting that these would need to be accounted for in genome-wide association analysis in the discovery of the genetic basis of important traits and in breeding program design. Selection signature analysis identified candidate regions that could potentially differentiate the two genetic clusters observed in the African thin-tailed Desert Sheep from the two genetic clusters observed in the Chinese thin-tailed sheep. These regions spanned a set of potential candidate genes associated with traits of adaptive, production and reproduction significance as well as morphological differentiation. While our study provides a foundation for understanding the genome structure and dynamics of African indigenous sheep, it reveals findings that could form the basis of studies that combine genomic and phenomic approaches in the quest to understand the genome architecture of indigenous livestock.10.6084/m9.figshare.14785278.v1.The data presented in the study are deposited in the figshare repository, accession number doi: The blood samples from the Sudanese thin-tailed Desert Sheep were collected after consent was granted by flock owners and local administration officials in Sudan. No further permissions were required from the ethics committee of the Organization of Veterinary Service, Government of Sudan. All animal experiments in this study were fully approved by the Animal Care and Use Committee of the Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (IAS-CAAS) with the following reference number: IASCAAS-AE-03, on September 1, 2014.QZ, YM, and JM conceived, designed, and supervised the study and genotyped the Chinese breeds. JM, MR, and AH genotyped the Sudanese thin-tailed Desert Sheep. FE organised the sampling in Sudan. AAh and AAb analyzed the data with support from HB, RI and LX. AAb, AAh, J-LH, and JM wrote and revised the manuscript. All authors read and approved the final version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the evolution and genetic basis of quantitative traits. We have expanded the resource with new lines and new populations, and here report the genotype and haplotype composition of CeMEE version 2, including a large set of putative de novo mutations, and updated additive and epistatic mapping simulations. Additive quantitative trait loci explaining 4% of trait variance are detected with >80% power, and the median detection interval approaches single-gene resolution on the highly recombinant chromosome arms. Although CeMEE populations are derived from a long-term evolution experiment, genetic structure is dominated by variation present in the ancestral population.The  Evolutionary biologists and complex-trait geneticists share the goal of dissecting heritable phenotypic variation down to the level of causal molecular genes and variants . MultipaC. elegans multiparental experimental evolution (CeMEE) panel as the first MP panel for this model organism , a powerful metazoan MP resource . In the de novo mutation appearing during lab evolution. Our findings show some similarity to those found in mutation accumulation experiments, where selection is minimized .de novo mutations by jointly calling all 957 RIL samples with any sequencing data with the 16 founders against the WS220 N2 reference , as in Heterozygous calls were elevated among CA100 RILs, mostly for population replicate CA3100 . Minor allelic proportions were generally low, however (11% of these 135 lines had mean proportions >20%). We removed extreme cases as part of our quality control .C. elegans natural diversity resource [CeNDR] isotypes in soft-filtered release 20180527) as likely false negatives . This filtering biases detection to mutations that arose early in evolution and were selected, directly or indirectly; we exclude rare mutations, such as those arising during RIL construction, as they are more likely to be false positives. We also excluded all sites where the founders vary in an independent data set (n  =  2) and, based on segregating sites covered by at least 3 reads, a maximum of 20% where both reference and alternate alleles were seen with mean minor allele frequency > 20% (n  = 24). After sequence and genotype filtering, outlier lines with haplotype reconstruction posterior log likelihoods (see below) beyond the 0.1 percentile in deviation from the population median for more than three chromosomes were also excluded (n  = 13). Haplotype reconstruction outliers showed no significant population bias; they were consistently associated with a high minor allele proportion at heterozygous sites, though not always a high frequency of heterozygous sites genome-wide.Quality control considered homozygosity, sequencing depth, and haplotype reconstruction likelihood, and we additionally filtered on relatedness to remove very closely related lines. From 957 sequenced lines, identity at segregating sites was thresholded to a maximum of 90% , minimum expected sequencing depth of at least 0.1× .Ra) by Brent search (depModel) for each line  in Mathematica 11.0.1  or selection of the unique founder haplotypes .Haplotype representation and diversity in A) constructed from segregating SNVs (excluding ambiguous imputations) were decomposed with the base R function prcomp . For each heritability scenario, defined by focal marker variance explained  and the number of markers in the polygenic component, we ran 1000 simulations sampling loci with minor allele frequency (MAF) > 5% from the LD pruned genotypes. Significance was set at effM) given observed linkage disequilibrium (LD). We used MultiTrans to estimate effM, which varies with LD, genetic relatedness and trait heritability , which differs slightly from simulated h2 due to sampling, yielding at least 800 simulations for each heritability scenario. Additive QTL simulation code is in Supplementary File S3.Additive QTL were simulated varying the variance explained by a single focal marker (0.01–0.12) and a background polygenic component  with total heritability set to 0.5 and effect sizes drawn from the standard normal distribution. We fit single marker linear mixed-effects models  test: The power to map interactions was tested by sampling marker pairs and simulating phenotypes with a given epistatic heritability—the proportion of variance explained by interaction of the focal markers—with effects drawn from the standard normal distribution . Markers were pruned of strong local LD  , defined here for this smaller set as the number of eigenvalues of the marker correlation matrix R that explain at least 99% of the variance. Covariance matrices sampled from an unobserved population are typically biased in the distribution of eigenvalues when the number of variables (markers) p is much larger than the number of observations n  and a conservative adjusted significance threshold  of h2 (linear regression adjusted r2).Genome-wide significance was declared at ositives . Meff waations n . FollowiPRJNA557613. Sequencing and other metadata are available from lukemn.github.io/cemee. Supplemental files and code are available at FigShare. They are also available from the CeMEE github, with genotypes in WS220 and WS245 reference genome coordinates, and input files for the R packages qtl and qtl2.All raw read data are available from the NCBI SRA under BioProject P-values, Supplementary File S6 contains marker positions in genetic distance, Supplementary File S7 contains an additive genetic relationship matrix, Supplementary File S8 contains recombination rate domain boundaries. See the Data Document for more details. All lines  are cryopreserved in replicated 96-vial plates and are freely available for noncommercial purposes.Supplementary Files S1 and S2 contain processed genotypes, Supplementary File S3 contains R  code forhttps://doi.org/10.25387/g3.12293138.Supplementary material is available at figshare: Through derivation of inbred lines from new experimentally evolved populations and (re)sequencing of RILs from existing populations, we expanded the CeMEE panel by more than 50% over the version 1 release .Ne, we continue to see 0 fixed SNV differences between any pair of replicate populations derived from A6140, consistent with an absence of bottlenecks and a highly polygenic architecture for fitness.The aims of a long-term evolution experiment and those of QTL mapping are not fully aligned. Drift and selection acting on standing genetic variation will lead to differentiation of populations, and potentially to loss of genetic diversity until mutation-selection-drift equilibrium. We showed previously extensive divergence from the founders during the initial MP funnel and domestication phases leading to A6140, with more than 32,000 SNVs fixing. Few large-scale hard sweeps were observed, however, with the loss of founder singletons accounting for around 80% of these cases, and over 97% of the autosomal genome remaining genetically variable . Although the new CA100 populations are more homogeneous than their CA50 progenitors , suggestRa) estimated during joint haplotype reconstruction shows continued gains in recombination in the CA[1-3]100 , we expect gains in resolution, subject to the maintenance of recombinant diversity within and among population replicates. Potential gain (or loss) of power due to atomization of linked quantitative trait nucleotides of antagonistic (or similar) effect is an empirical question . We refer to these here for brevity as ’new mutations’ and compare them with standing genetic variation . Most detected new mutations arose before sampling of the A6140, during the initial phase of lab adaptation We examined 12,826 filtered diallelic SNVs present in CeMEE RILs, but not founders, as potential X vs. autosomes, ratio of new mutations to SGV on the X = 0.57, with the next lowest value at 0.77 for chromosome IV). Second, although new mutations are found at similar frequencies to SGV across recombination rate domains, on average, they are less uniformly distributed across autosomes , and many more variants fall within introns  and effective population size  panel, a growing collection of wild isolates and genotype-phenotype associations (Another venue for improvement is integration between CeMEE and the ciations , particuciations , whereas


Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (The online version contains supplementary material available at 10.1007/s10592-022-01429-7. The need for conservation actions are rapidly increasing as biodiversity declines with the onset of the sixth mass extinction, which has already caused severe population declines in 30–50% of vertebrates worldwide  to track ancestry and recommend future breeding pairs   and the Mt. Washington colony in the Strathcona metapopulation (n = 4)  Fig. . Followihttps://github.com/jazjanes/VI-marmots). Genotypes were scored manually by visualizing the typical microsatellite stutter profile using unique sequence length and the number of copies of each sequence per individual . In determining individual genotypes, the minimum count required for a primary allele was 80 amplicons with a stutter peak within four base-pairs. For a genotype to be heterozygous the secondary allele needed a minimum of 20 amplicons with stutter peaks within four base-pairs, and the shortest allele needed to have the higher amplicon count of the two alleles. In the case of heterozygotes with two different sequences of the same length, the peak representing the second allele had to be greater than 80% of the first allele peak. Sequences with identical lengths were compared in BioEdit  was compared between captive vs. wild populations using a Mann–Whitney U test and between HTAS vs. length-based genotypes using both a Mann–Whitney and a Wilcoxon Signed-Rank test.Independent Shapiro–Wilk tests revealed that three separate estimates of allelic richness  all devMolecular estimates of individual inbreeding coefficients Ritland  and pairape 5.0 package  to avoid the recognized biased with ΔK  and Mt. Washington in the Strathcona metapopulation (n = 3). Of the 11 successful loci and 82 individuals genotyped, we sequenced an average of 9,854 ± 3,937 reads per individual, per locus, with all loci having a minimum of 3,508 average number of reads per individual. All loci were in linkage equilibrium and although eight of 11 loci deviated from Hardy–Weinberg equilibrium, they were retained in the analysis as specified in the methods , and another seven loci were removed because they were monomorphic  leaving 11 loci for analysis . Six of the 11 loci were in common with the loci used by Kruckenhauser et al. (P(one-tail) = 0.08, Table P < 0.001) but this difference was not supported by an independent Mann–Whitney test .Allelic richness from length-based and HTAS genotypes across 11 polymorphic loci revealed one to four alleles per locus  and a Mantel test .Molecular estimates of inbreeding (0.119 ± 0.247) were poorly, but positively, correlated with studbook estimates , and we did not discover any private alleles among wild colonies . However, molecular inbreeding coefficients were greater in the wild (0.41 ± 0.14) than the captive (0.15 ± 0.04) population , although this was partially driven by three outliers  with values outside of the theoretical limits of the estimate (− 1 to + 1). With these three outliers removed inbreeding coefficients became normally distributed and the wild population was only marginally greater than the captive population  = 1.99, P = 0.051). Pairwise relatedness estimates among wild marmots (0.14 ± 0.18) were not different from the captive (0.15 ± 0.19) population .Mean allelic richness of the captive population 2.3 ± 0.6) was not statistically different than the wild population across all 11 loci  across all runs . However, there was no obvious geographic pattern of cluster separation between the wild and captive populations or across wild colonies as both clusters were represented equally in wild and captive populations . Expanding our dataset to ten loci, including the same six polymorphic loci in common between the two studies plus Bibl18 .Using only the six loci in common with Kruckenhauser et al. , allelicWe compared the genetic diversity of VIM using both length-based microsatellite genotyping and next-generation sequencing to assess the ability of the HTAS approach to detect greater genetic variation in a species with low genetic diversity. Additionally, we used HTAS to compare molecular and studbook-derived estimates of relatedness and inbreeding. We determined that the HTAS approach did not detect significantly more genetic diversity compared to traditional fragment length analysis. However, the field behavioural observations used to establish the studbook created a reliable and effective way of minimizing inbreeding. Wild and captive populations were similar in all aspects except that the wild population had marginally higher molecular estimates of inbreeding. Genetic variation in VIM appears to have remained constant since the previous estimates, although some population structure may have degraded.Pan troglodytes) had a 61% increase in mean allelic richness using HTAS  saw a 79% increase , the only other species endemic to Vancouver Island that we are aware of , also exhibits low genetic variation . In all, despite the reduced cost and increased accessibility of the HTAS approach, this technique may have limited applications in the conservation and management of endangered species with reduced diversity as there are also fewer alleles hidden by homoplasy.Despite our expectations, the HTAS approach did not lead to a significant increase in allelic richness compared to traditional length-based genotyping. Only two additional alleles were identified across 11 loci. In contrast, chimpanzees  alleles which artificially increase similarity among individuals Taylor . In contGiven the low allelic richness in VIM, our molecular data are challenged to calculate relatedness and inbreeding with a high degree of confidence, which likely contributes in part to the unexplained variance Taylor . HoweverThe loss of genetic diversity as a result of captive breeding is a known concern, one that is often followed by the recommendation that molecular markers be incorporated into studbook data , including one cluster for Mt. Washington and two clusters split across the Nanaimo Lakes metapopulation. Our study also shows two clusters split across the Nanaimo Lakes metapopulation but fails to separate Mt. Washington as a unique cluster. Although only three samples from Mt. Washington were genotyped in the current study, these individuals did not have any private alleles which is in contrast to Kruckenhauser et al. .Supplementary file1 (DOCX 548 kb)Supplementary file2 (XLSX 81 kb)Below is the link to the electronic supplementary material.


Genetic variation, evolution, and conservation are three strictly interconnected words, but none of them exist without the others, unless wanting to waive a complete and operational sense. These terms are considered the key concepts in evolutionary biology and represent the essence of life on our planet. It must be taken into consideration that, while evolution and genetic variation are variants linked to purely natural aspects, conservation is instead—strictly speaking—an activity undertaken by mankind to balance other impacting human activities that strongly interfere, especially in the past three centuries, with the natural evolution and genetic variability of several animal and vegetal species . Genetic diversity is imperative for populations to adapt to environmental changes. From an evolutionary viewpoint, genetic diversity manifests itself through differences in several of the phenotypic characters of organisms, such as the color of eyes, hair and skin in humans, the color and type of banding in the shell of snails, as well as the color of flowers in plants. At a deeper level, proteins, amino acids, and DNA sequences, which are present in every biological entity , represent the first traits involved in variation. Looking at the origin of this molecular variability, nucleotide mutation is the primary source of genetic variation representing the raw material based on which natural selection operates and the development of evolutionary principles is based . According to the neutral theory of molecular evolution, stochastic fixation of a genetic mutation is the most important driving force behind nucleotide substitutions. Indeed, the majority of substitutions are attributed to a random fixation of neutral or nearly neutral mutations. According to the neutral theory, only a small minority of mutations become fixed by positive selections . As the Conservation genetics derives from population and evolutionary genetics as well as from the theories of quantitative genetics that are at the basis of domestic controlled reproduction. These theories generally deal with large populations whose genetic constitution is controlled by deterministic factors . At present, conservation genetics represent a distinct discipline that focuses on the consequences resulting from the reduction in populations , not only (and not anymore) for the mere appreciation of biodiversity, but also to provide a support for the management and conservation of endangered species or species deemed potentially dangerous to the human health. Therefore, this Special Issue aimed to combine the contributions of researchers working globally in the field of evolutionary genetics/biology, population genetics, molecular taxonomy, and conservation genetics, in order to obtain a bulk of papers that underscore the importance of studying genetic variability in organisms for safeguarding biodiversity, in all ways it can be understood ,9,10,11.Pinna nobilis—a Mediterranean endemic marine bivalve—that is now experiencing dreadful mass mortality. This Mediterranean flagship species, which is included in a protection regime under the Annex II of the Barcelona Convention (SPA/BD Protocol 1995), the Annex IV of the EU Habitats Directive (European Council Directive 92/43/EEC), and, more recently, in Italy, the Legislative Decree 190/2010, Art. 11 for the Marine Strategy Monitoring Program, has represented the focus of a few molecular surveys in the recent times. This species, after undergoing a severe conservation crisis in the 1980s because of a large decline in most populations due to different anthropogenic activities, is currently facing a new dramatic threat, and its conservation status is heavily compromised, since 2016, when a mass mortality event (MME) began to be observed in almost all the Mediterranean areas. So far, numerous epidemiological studies have been performed [P. nobilis to their minimum. The case study of P. nobilis is a virtuous example of how evolutionary and conservation genetics are strictly interconnected and have required (and will continue to require) studies based on integrated molecular approaches including the endangered host, its presumptive pathogens, and also sentinel species  [P. nobilis converged in evidencing a past good health for its populations in the entire Mediterranean region [P. nobilis can recover from MME both naturally and through targeted restocking programs. Regarding this latter point, there are several supporting examples in which the studies devoted to the appraisal of the genetic variability of a species and its distribution, on a small and large geographic spatial scale, have served to design appropriate conservation plans. As a matter of fact, these plans cannot ignore the correct assessment of the genetic variability of the species to be preserved with the aim to, whenever possible, not interfere with the evolutionary processes that, in time and space, have shaped the variability. An interesting study case that involved the research group of the authors of the present Editorial is represented by the endangered species Patella ferruginea which is an endemic gastropod of the Western Mediterranean, listed in Annex II of the Barcelona Convention (SPA/BD Protocol 1995) and Bern Convention (Directive 82/72/EEC), in Annex IV of the EU Habitats Directive (European Council Directive 92/43/EEC), and more recently, in Italy, in the Legislative Decree 190/2010, Art. 11 for the Marine Strategy Monitoring Program. This species started declining during prehistoric times mostly because of anthropogenic pressure. Presently, its geographic distribution is restricted to the north African shoreline, Spain, Sardinia, Corsica, and a few scattered sites in the Tuscan Archipelago and Sicily [Usually, the conservation status of endangered or threatened species is investigated through the means of genetic tools. It is important to note that in this context a striking case that is unfolding dramatically before our very eyes and could end with a quick extinction of a species if it fails to reverse the present trend. We are referring to the fan mussel erformed ,19,20,21species) . Furthern region ,24, in td Sicily . Despited Sicily ,27,28,29P. ferruginea in the Ligurian Sea (Western Mediterranean Sea) starting from offspring reproduced in vitro by donors from the Sardinian Marine Protected Area of Tavolara-Punta Coda Cavallo (Western Mediterranean Sea). Therefore, previous data on the genetic variability of P. ferruginea, both globally and in the geographic areas involved in this project, enabled the avoidance of both the introduction of non-native genotypes into wild indigenous populations, and “human-mediated” founder effects . Based on this background, in 2017 it was possible to implement a European conservation project (LIFE15 NAT/IT/000771), which, at the end of its execution, successfully led to the restocking of the population of When talking about evolution, genetics, and host adaptation, we cannot avoid discussing about viruses, which are biological entities capable of complex strategies modeled by the Darwinian natural selection. Viruses represent the best model to investigate such types of processes, because they are cosmopolitan and constantly mutate, thereby presenting a particularly high evolutionary rate that allows for the appreciation of adaptive variations within very few times/generations. Accordingly, the viruses currently present on earth are very well adapted to circumstances, because only the fittest have survived so far, and also because the process of natural selection favors viruses with little pathogenic power. In such a context, it should be pointed that, during the last two years of the global spread of the SARS-CoV-2 pandemic, the entire world has witnessed how evolution and genetics dynamics can become extremely dangerous. Indeed, when evolution and natural selection work on wild populations, favoring speciation and producing new evolutionary species sensu Wiley, 1978 , they appear to be a good mechanism in promoting the increase in biodiversity. On the contrary, when these forces work on potential etiological agents such as viruses, they produce new variants  that can cause epidemics, undoubtedly making evolution appear to be a “bad” entity.The Nobel prize winner, Sir Peter Medawar, during his speech at the award ceremony said, “no virus is known to do good. It has been well said that a virus is a piece of bad news wrapped up in protein”. The fact remains that evolution is neither good nor bad, simply unexpected. In addition, changes are random, and almost always result in bad combinations for the virus, which tends to weaken over time. However, random changes produce variations, variations facilitate the exploration of new possibilities, and new possibilities can be dire. Viruses are peculiar entities, being acellular microorganisms living as obligate endocellular parasites. They are capable of passing through filters that retain bacteria and represent the best expression of efficacy due to evolutionary mechanisms as they exhibit high-performing capabilities. Indeed, a virus needs to be able to pass from one host to another, to enter into the host cells, to take control of the host cells in order to replicate, as well as to leave from the cell and the host. In such a context, considering that both wild and domestic animals can potentially act as a reservoir for many viruses, the occurrence of spillover represents one of the most dangerous events that can happen for humans. One of the most serious problems created by viruses is the possibility of causing zoonoses . Zoonotic infections, originating in wildlife, can pose a significant threat to the human health . The mosIn such a context, among the family Coronaviridae, there is a further recently discovered threat belonging to the genus Alphacoronavirus, named SADS-CoV (Swine Acute Diarrhea Syndrome Coronavirus), also known as PEAV (Porcine Enteric Alpha-coronavirus) or SeA-CoV (Swine Enteric Alphacoronavirus). Although it is not a zoonosis, SADS-CoV possesses all characteristics to become a threat for human health, thus requiring constant monitoring . So far,In conclusion, irrespective of the biological entities being considered  and regardless of the fact they cause extinction, promote biodiversity, or evolve under selective pressure, evolution and genetics involve all levels of the expression of life across our planet.