Oceanic islands are of particular importance for the conservation of global diversity. Rare island plants with small population sizes and unique genetic patterns resulting from prolonged evolutionary isolation are usually extremely fragile. Therefore, research dedicated to conservation of these plants should consider threat factors, population structure and genetic diversity to enable the development of scientifically supported management programs. For Lactuca watsoniana, Azorean lettuce, we performed a comprehensive population genetic study, unravelling genetic diversity patterns intrinsically related to geographical distances and barriers. Our study showed that genetic diversity levels in island plants can be relatively high even for rare plants. Lactuca watsoniana, is an endangered Asteraceae with small population sizes. Therefore, we expect to find a lower level of genetic diversity than in the other more common endemic Asteraceae. The intra- and interpopulation genetic structure and diversity of L. watsoniana was assessed using eight newly developed microsatellite markers. We included 135 individuals, from all 13 known populations in the study. Because our microsatellite results suggested that the species is tetraploid, we analysed the microsatellite data (i) in codominant format using PolySat  and SPAgedi (genetic diversity indexes) and (ii) in dominant format using Arlequin (AMOVA) and STRUCTURE . A total of 129 alleles were found for all L. watsoniana populations. In contrast to our expectations, we found a high level of intrapopulation genetic diversity . Our results show the existence of five well-defined genetic groups, one for each of the three islands São Miguel, Terceira and Faial, plus two groups for the East and West side of Pico Island (Fst = 0.45). The study revealed the existence of high levels of genetic diversity, which should be interpreted taking into consideration the ploidy level of this rare taxon.Island plants are frequently used as model systems in evolutionary biology to understand factors that might explain genetic diversity and population differentiation levels. Theory suggests that island plants should have lower levels of genetic diversity than their continental relatives, but this hypothesis has been rejected in several recent studies. In the Azores, the population level genetic diversity is generally low. However, like in most island systems, there are high levels of genetic differentiation between different islands. The Azores lettuce,  Oceanic islands have been important study systems for ecologists, evolutionary and conservation biologists and are widely recognized as natural laboratories, for studying evolution due to their discrete geographical nature and diversity of species and habitats . OceanicGeological, geographical and ecological conditions, such as island age and area, geographical isolation by oceanic barriers, climatic stability, environmental heterogeneity, high habitat diversity and the absence of competitors, have been pointed out as key determinants of the speciation patterns observed within volcanic archipelagos . These high levels of genetic diversity may have been the result of genetic drift  high genetic diversity but low population differentiation—Leontodon and Tolpis have already been studied and showed high population genetic diversity and a complex genetic structure, with clear geographical-linked patterns . It is probably extinct in São Jorge Island, from where two specimens exist in the Lisbon University herbarium (LISU), collected between the valleys of ‘Ribeira do Salto’ and ‘Ribeira de S. João’. Lactuca watsoniana is today restricted to the steep slopes of craters, ravines, and temperate juniper rain forest, between 600 and 800 m above sea level , Estimates for its total population size range from 500 to 2000 individuals , but recLactuca watsoniana propagules are dispersed by wind and water  markers. Based on the relative depauperation of the extant populations, we expected to find relatively low levels of genetic diversity.In the context of a holistic view, and considering that a previous germination study was already conducted for L. watsoniana; (2) to estimate intra and inter-population genetic variation patterns; (3) to identify populations with low genetic variability and inbreeding; and (4) to verify the occurrence of other putative operational taxonomic units.Our objectives were (1) to determine the population genetic structure of L. watsoniana, we also aim to use the results of the present study to better understand the evolution of island plants in the Azores as well as in other relatively remote and geologically young island systems.Beyond the conservation of 2. However, the islands reveal very uneven dimensions: the larger, São Miguel (745.8 km2), Pico (448.4 km2) and Terceira (403.4 km2), represent 70 % of the total surface; São Jorge (245.9 km2), Faial (173.8 km2) and Flores (141.6 km2) have an intermediate size; Santa Maria (97.1 km2), Graciosa (61.2 km2) and Corvo (17.2 km2) are the smallest of the archipelago. Santa Maria is the oldest island of the archipelago (6.3 M years) and Pico being the youngest island of the Azorean Archipelago . Samples from every single individual were taken in populations with up to 30 plants and in larger populations, 20 samples were collected in populations. Lactuca palmensis from La Palma Island (Canary Islands) and North American species—L. biennis, L. canadensis, L. floridana, L. graminifolia, L. hirsuta, L. ludoviciana and L. tenerrima—were obtained from herbarium specimens of the United States National Herbarium, Smithsonian Institute; L. tenerrima samples were also obtained from specimens at the BM herbarium of The Natural History Museum, London; and a L. sativa sample was obtained in the local market. Depending on leaf size, we collected one or two leaves per individual and immediately stored them in a plastic bag with silica gel. After drying, the leaves were vacuum sealed in plastic bags and stored in folders. The locations of all populations were geo-referenced and mapped using ArcMap® 10.2.2  where an Illumina paired-end (IPE) shotgun library was prepared for microsatellite sequencing  to enable the use of a third primer identical to the M13R, which allows for an inexpensive fluorescent labelling of the PCR product obtained . A GTTT L. watsoniana using a final volume of 25 μl, including 25 ng of DNA, 1× NH4 Buffer, 1.5 mM MgCl2, 0.4 μM of FAM-M13R, 0.08 μM of tagged primer, 0.36 μM of unlabelled tag primer, 200 μM of dNTPs, 1U of Polymerase  and using a Biometra TGradient thermocycler. Touchdown thermal cycling programmes  with digest code D-CPMIC-101.After optimization, all samples were amplified following L. watsoniana (manuscript in prep). This information was used to define the statistical analysis methods, since polyploid organisms raise analytical limitations, namely, problems associated with inferring allele frequencies and assumptions regarding inheritance , computed for all loci and individual inbreeding coefficient (Fi), computed as kinship coefficient between homologous gene copies within individuals. The total genetic diversity (HT) was determined using the unbiased estimate method of ® based on SPAGeDi allelic frequency data.Considering the tetraploid nature of  SPAGeDi , as a muK value ranging from 1 to 10. Estimation of best K value was conducted with STRUCTURE Harvester  equilibrium.Taking into consideration the ploidy level, we first analysed the population structure with a Principal Coordinate Analysis (PCoA), based on the matrix of Bruvo distances between individuals, using the R package PolySat . Then wearvester  followinon 1.1.2  using thon 1.1.2 . For Anaon 1.1.2  to (1) cTo determine the order of barriers to gene flow possibly occurring within the archipelago, the Nei’s genetic distance matrix corresponding to the Azorean populations was analysed with the Monmonier algorithm, using BARRIER version 2.2 , 1978 wahttp://www.r-project.org/). We also modelled Nei’s genetic distance as a function of geographical distance and of the presence of geographical barriers, using beta regression with the BETAREG package in R  and L. biennis (loci Lw-01.08037 and Lw-01.08435). A total of 129 alleles were found for L. watsoniana, with a total genetic diversity (HT) of 0.85, an overall excess of heterozygotes , and with a total multilocus average proportion of private alleles of 26.5 %. The total number of alleles per locus varied from 10 to 31  and the highest multilocus number of alleles (9), while the ‘Miradouro do Canário’ population in São Miguel Island and ‘Subida da Montanha’ in Pico Island did not show any private alleles . The meaL. sativa e L. biennis samples) from 13 populations, based on eight microsatellite loci, revealed the existence of a close relationship between the North American species and L. watsoniana populations and a clear separation from L. palmensis, as shown by PCoA  denoted a considerable overall differentiation among populations, with Fst values ranging from 0.13 between São Miguel populations (SMLC and SMMC) up to 0.99 between PICA and TERC populations  to the models including an increasing number of geographical barriers: (i) considering the existence of barriers between different populations clusters as determined with STRUCTURE ; (ii) considering the existence of barriers between populations as determined with BARRIER . The graphical representation of the best fitting model shows how the inclusion of barriers increases the fit of the geographical model (Regarding isolation by distance (IBD) models, el tests . Globallal model . Also, oal model .Figure L. watsoniana is tetraploid. To the best of our knowledge, only two of the nine endemic Azorean Asteraceae are polyploid, namely, Pericallis malvifolia  an allotetraploid colonizer from North America or (b) an ancestral diploid population leading to an autotetraploid form, with later extinction of the ancestral diploid. Considering the absence of other endemic or native Lactuca species in the Azores, and the existence of allotetraploid North American Lactuca species . Meanwhile, field and laboratory observations indicate that isolated L. watsoniana individuals flower regularly but mostly produce infertile seeds whereas in relatively large populations, such as those found in Pico Island, a very high number of viable seeds are produced, annually. In this sense, according to Cichorium and Lactuca. Further studies should be undertaken to enlighten this matter, namely experiments of forced self-pollination and cross-pollination  was higher than those found for many other plant species (Leontodon filii and L. rigens (Gst = 77.3 %) , Pico (5.88 %) and Terceira (3.64 %), indicating that some degree of differentiation occurred between those islands.Estimated gene flow values were always below 1, contrary to the much higher values obtained for releasei , and betLactuca watsoniana show a strong geographic structure. Isolation by distance (IBD) and the existence of effective barriers to gene flow, the Atlantic Ocean and Pico Mountain, were found to be related with genetic distance. Therefore, L. watsoniana seems to be an intermediate case between hierarchical island and stepping stone models . Moreover, during a preliminary analysis, we included island age and differences in island age between populations, in our models to explain genetic distance, but without significant improvement of the modelling results.On the other hand, besides geographical distance and the existence of barriers, population genetic structure might be the result of the populations sampled being relicts, resulting from geological events, such as volcanic eruptions, as hypothesized for  azorica a, b and L. watsoniana individuals, from almost complete consumption of above ground plant material (goats in São Miguel Island) to the removal of the developing synflorescence (cattle in Terceira Island). Damage caused by human intervention in the native vegetation is the most probable explanation for the possible extinction of L. watsoniana in São Jorge Island, where the native vegetation has been replaced by invasive plants in the site of the historical collection. Pico Island holds the highest number of individuals including many young plants, what could be a direct consequence of being one of the less altered islands in the archipelago. One justification would be that Pico represents a sample of a formerly wider genetic pool that was eroded in the remaining islands, which through possible genetic bottlenecks only kept part of that wider pool, similarly to what might have happened to Tolpis azorica populations in the central sub-archipelago of the Azores , ‘Caminho da Criação’ on São Miguel (SMCC) and Terceira (TEGA and TENR), should be considered priority for conservation.L. watsoniana populations in São Miguel island are severely threatened by herbivores , which in Terceira have already alarmingly obliterated most of the Serra do Galhardo population. These animals should be controlled or eradicated from these protected areas.The awareness of the threats by habitat loss and degradation resulting from changes in land use indicates that extreme care should be taken regarding the implementation of augmentation conservation strategies. Some measures have been implemented to locally control invasive species  and FEDER funds through the Operational Programme for Competitiveness Factors—COMPETE and by National Funds through FCT—Foundation for Science and Technology under the UID/BIA/50027/2013 and POCI-01-0145-FEDER-006821.This study was funded by E.F.D., participated in sampling, performed genetic analyses, and wrote the first draft; E.F.D and L.S. conceived the idea for the paper; L. S. was involved in the statistical analysis; M.M. was involved in the genetic analysis; H.S. participated in field work. All authors helped revise the manuscript.None declared.


There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions. Some traits or genetic conditions are controlled by a single gene , while others are controlled by many genes (polygenic or quantitative traits). Eighty-seven percent of qualitative traits in cattle are recessively inherited . It is nGenome-wide association studies (GWASs) are possible due to the availability of technology that allows high-throughput genotyping of single-nucleotide polymorphisms (SNPs). These SNPs are variants, or alleles, in the DNA sequence that may be associated with the expression of a trait or characteristic in cattle. The technology allows deciphering the genetics behind the expression of economically important traits. Genomic regions associated with productive traits have been identified in dairy –4 and beHigh-throughput sequencing offers the opportunity to identify causative genetic variants, which was previously unavailable . AccessiMSTN) in beef cattle where different SNP and insertion/deletions are responsible for the condition . CD18 resides on chromosome 1 . Animals with this condition lack growth during embryonic development. Embryo mortality occurs approximately at 40 days of gestation . CarrierThis is a kidney condition characterized by interstitial fibrosis with inflammatory cell infiltration. This condition has been identified in the Wagyu, or Japanese Black Cattle. Animals with this condition have delayed growth and high levels of ureic nitrogen in blood . The genHorns may be a problem when handling cattle. It has been estimated that de-horning cattle, as well as loss of meat due to bruising from horns, represents a cost of approximately $25 million annually to the United States beef industry . Losses The locus of the gene responsible for horn development was detected on chromosome 1 and was termed POLL , 41. A lMSTN. Later, it was demonstrated that this was the same gene that caused double muscling in cattle   . This al (V180F) .Leptin is the hormone produced by the obesity gene (ob). It is secreted by adipocytes, and it has been associated with feed consumption and energy balance in mice and humans. The leptin gene is located on bovine chromosome 4. A genetic marker was identified in the sequence  and in tSCL4A2 gene has been associated with the condition in Red Angus. The gene resides on chromosome 4 . These proteins are coded by four genes on chromosome 6. The order of these genes on the chromosome is CSN1S1, CSN2, CSN1S2, and CSN3. The genomic region is referred to as the CN locus because these four genes are tightly linked  is located in bovine chromosome 7, and a genetic marker was identified within this gene. An association between meat tenderness and this genetic marker in the calpastatin gene has been observed in several studies  digestion to identify a restriction fragment length polymorphism of a fragment of the gene to identify carriers of the condition  and is now thought to represent the bovine ortholog of the most common form of genetic CJD (E200K) in humans  is a neurodegenerative fatal condition affecting cattle. This condition is a transmissible spongiform encephalopathy that is similar to scrapie in sheep, chronic wasting disease in deer, and Creutzfeld–Jacob disease (CJD) in humans. BSE is caused by an accumulation of an abnormally folded isoform of the prion protein in central nervous system tissues. While the vast majority of cases of BSE were the result of ingesting feed derived from animal origin protein products contaminated with infected central nervous system tissues, today there are recognized atypical BSE cases that are thought to arise spontaneously and are not attributed to a transmissible origin in feedstuffs . Definedical BSE . Althougical BSE , one H-tical BSE  was asson humans . Intracrn humans . A comprn humans . The locn humans , 100. Sen humans , besideswith BSE –104. Othwith BSE –107; thiTG1) resides on chromosome 14. The first association of genetic markers in this gene was reported by Thaller et al. . A mutation in the E1-alpha subunit, from a cytosine to a thymine, produces an incomplete enzyme (changes from a glutamine to a stop codon) in Hereford cattle. Animals with this condition have elevated levels of isocaproic acid which is the substrate of the enzyme . Littlejohn et al. (PRLR) on chromosome 20 and the prolactin gene (PRL) on chromosome 23, as responsible for the slick hair condition. Littlejohn et al. . For these genetic conditions, it would be possible to select for favorable alleles within the herd. This would increase productivity and make the production system more efficient. This is important where productivity is limited by hazardous environmental conditions.The producer may want to introduce genetic conditions in the herd, or completely avoid them . These genetic conditions need to be carefully assessed if they were to be introduced in the herd. It would increase productivity by increasing amount of muscle mass and salable meat. However, adequate management of the herd needs to take place to avoid detrimental effects that would result in economic losses to the producer. These losses would be in the form of expenses due to calving difficulty, or losses of the calf due to poor management.If the goal is to sell to international markets, there are genetic conditions that producers need to be aware . These conditions have only been identified in specific breeds, and they would not represent a problem in other breeds. However, if the producer decides to introduce these breeds for international trade, screening for genetic conditions needs to be undertaken before productivity is hindered.Deleterious genetic conditions need to be recognized . These genetic conditions will limit productivity of animals expressing the trait. Animals should be eliminated from the herd to benefit the production system. A point of caution is that in spite of current genetic testing being highly effective at accurately identifying carrier animals of particular traits, leukochimerism can result in erroneous test results if blood is used as a convenient DNA source; test results must always be confirmed with an independent tissue source not subject to mixed genotypes .As advances in molecular biology continue, the impact on our ability to more rapidly detect traits of economic importance will only improve. Use of haplotype reconstruction and haplotracking with a database of >1 million cattleMention of trade name, proprietary product, or specified equipment does not constitute a guarantee or warranty by the USDA and does not imply approval to the exclusion of other products that may be suitable.EC and MK wrote and reviewed the manuscript.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.


Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past , present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens) display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations) present lower values. Recent genetic signature of bottleneck was detected in few populations (8%). The molecular variation was higher within the populations (77%) and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently—more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of the sea daffodil especially during LGM because of strong variation in coastline caused by glaciations.The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil,  Pancratium maritimum L. (Amaryllidaceae), which is a perennial clonal geophyte of coastal sands (fixed/mobile sand dunes and beaches) of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments [The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities . All of ronments , 7, 8.P. maritimum offers greater advantages over short-lived organisms for exploring how much genetic variation is associated with current and/or past/future environmental conditions using statistical simulations [Asplenium fontanum (L.) Bernh. [Eucalyptus gomphocephala DC. [Taxus baccata L. [Because of the buffering effects of its life history traits  on changes in genetic structure, ulations , 10, as ) Bernh. , Eucalyphala DC.  and Taxuccata L. .P. maritimum is a bulbous species capable of vegetative reproduction by bulbils [Pancratium in nature are known; its haploid number is n = 11 [Briefly,  bulbils ; flowers bulbils ; seeds a bulbils , 17; no  bulbils , 21, 22,s n = 11 . Little In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past: the last interglacial , the last glacial maximum ; the present conditions ; and near-future } and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. As a side issue, a simulation analysis was performed correlating current genetic structure with past environmental data (LIG and LGM periods), to evaluate as past climatic changes may have influenced present-day genetic structure of this plant.P. maritimum on a large and representative sample of populations and individuals. This choice is motived by the nature of SSRs which are codominant, neutral, highly polymorphic and reproducible markers. To evaluate a distribution model for this plant, the World Climate Database was consulted, using the available climatic information for three historical periods .To this aim, we employed nuclear microsatellite markers  to investigate patterns of the diversity and genetic structure in Pancratium maritimum belongs to genus Pancratium L., which likely evolved during the Miocene [P. maritimum was found to be a self-compatible and autogamous species, in contrast to the data of Eisikowitch and Galil [Pancratium population from Israel, in which the plants were found to be self-incompatible and exclusively pollinated from hawk moths. Miocene . No info Miocene , and eac Miocene . The see Miocene , 17, 26. Miocene . Medrano Miocene  suggestend Galil , who stuThis plant is currently endangered along the Mediterranean coasts due to the loss of its natural habitat caused by human pressure  , 32, 33.http://www.iucnredlist.org/apps/redlist/search), leading to concerns regarding the future of this species [Nevertheless, this species has not yet been evaluated by the IUCN . No specific permissions were required for the sampling in all locations  and overlapped on the ortho-photo of Google Earth for successive analyses. To infer how the present human impact affects the 48 sampled P. maritimum populations, we calculated the Human Footprint Value (HFP) through the Global Human Footprint Database, v2 (1995 -2004) [P. maritimum populations (The sampled 5 -2004)  using a ulations . The Euculations . This chP. maritimum [By using the microsatellite library obtained from aritimum , after aaritimum  and Di Maritimum . Standararitimum .T), observed and expected heterozygosity (HO and HE), and inbreeding indexes (FIS) using GenAlEx version 6.5 software [ST) was computed with FreeNA software, which implements the ENA correction method to amend for the positive bias that is induced by the presence of possible null alleles in FST estimation and provides an accurate estimation of FST in the presence of null alleles [To achieve genotyping accuracy, we analysed SSR data with the Micro-Checker version 2.2.3 software  to detersoftware . The fix alleles . Deviati alleles , within  alleles  using th alleles .T), number of private alleles (S), average observed (HO), expected heterozygosity (HE), and unbiased heterozygosity (uHE), the latter representing the expected heterozygosity under HWE within populations, adjusted for sample size using GenAlEx version 6.5 software. The allelic richness (AR) was also calculated for each population using the FSTAT version 2.9.3.2 software [R is the number of alleles independent of sample-size as determined using the rarefaction method of El Mousadik and Petit [IS was calculated using the same previous software [For each population, we estimated genetic diversity across all loci using the percentage of polymorphic loci (P), observed number of alleles  and geographical distance  between populations using a Mantel test in Arlequin version 3.1 software [The pairwise genetic differentiation F alleles  using 10 alleles  genetic software  with 100An analysis of molecular variance (AMOVA) was used to partition the total genetic variation within and among population components using Arlequin version 3.5.1.3 software. The significance of the AMOVA was assessed with 1000 permutations of the data.K), the dataset was also analysed by Bayesian-model-based clustering methods, as implemented in the software STRUCTURE version 2.3.4 software [To estimate the distribution of individuals among natural genetic groups  using environmental predictors referring to the current time, and then projecting the models over past and future versions of these predictors. Occurrence data used for the training of SDMs were gathered from our database, literature, public databases and personal communication with experts . In particular, we used the climate change model output “HadGEM2” from the V assessment report [As an initial set of environmental predictors, we considered the 19 bioclimatic variables derived from the WORLDCLIM database at a spatial resolution of 30 arc-seconds (ca. 1 km)  and the t report , for thet report . For comt report . We const report ). The oct report  and the t report . To avoit report , 77. Fort report . Finallyt report . Such a t report , 84, 85.ST and environmental distance while controlling for geographic distance, as in Mayol et al. [ST and environmental distance (i.e. isolation by adaptation) due to strong patterns of IBD; thus, it is possible to discern the contribution of geographic and environmental distance in the obtained pattern.To determine the contribution of present environments on genetic differentiation, we tested for the relationship between the pairwise Fl et al. . This chP. maritimum populations that were included in the genetic analyses (ST). To investigate the correlation of past climate and pairwise FST, we retained only those populations in which a suitable environment existed for P. maritimum persistence during the LGM and LIG periods. Accordingly, we selected those occurrence points among the 48 populations occurring in cells that were predicted to be suitable by the SDMs during the LGM and LIG periods [We computed Euclidean distance matrices based on the values of the environmental variables that were used for the model training and measured at the locations of the 48 analyses , S1 File periods .AL = 8.3%), in Israel , and in a southern Italian population . The remaining populations presented a range of null alleles from 0.8%-2.9% , with a range of 0.29–0.98; the HE ranged from 0.42 to 0.65 with an average of 0.54 (± 0.05); the FIS value across all of the loci was -0.08 (± 0.14), ranging from -0.56 to 0.36; and the FST values ranged from 0.14–0.33 (mean 0.24 ± 0.03) and 0.14–0.32 (mean 0.23 ± 0.03) with ENA correction  , using sequential Holm-Bonferroni corrections. Of the 288 population-by-locus tests, 115 (39.9%) deviated significantly from HWE after sequential Holm-Bonferroni correction. However, these tests were not limited to a single locus or sampling site; thus, all six of the loci were retained for further analysis.P. maritimum populations are shown in PL) within populations ranged from 67 to 100%. Private alleles (S) were found in 17 out of 48 populations. For each population, the values for HO ranged from 0.38 to 0.87 (mean 0.6 ± 0.02), those of HE ranged from 0.39 to 0.7 (mean 0.54 ± 0.01), and similar values were obtained with sample size correction (uHE), as shown in R) ranged from 2.14 to 3.85 (mean 2.84 ± 0.06). The FIS values ranged from -0.55  to 0.28  with an average of -0.09 (± 0.03), and very low levels of inbreeding were detected in the majority of the analysed populations, except for ten populations with FIS values greater than 0.1, as shown in The genetic diversity parameters that were analysed for the 48 ST values were obtained when correcting or not for the presence of null alleles (ENA correction). The corrected values ranged from 0.046  to 0.53 , with an average of 0.23 .Similar pairwise F of 0.23 . AccordiThe assignment of accessions into groups or gene pools was further assessed based on the assignment tests that were carried out with STRUCTURE. These analyses identified a major peak at K = 2 and another peak at K = 4 . The higTPM = 0.008; PSSM = 0.023); Z, southern Italy–Le Cesine ; MB, Morocco–Bouknadel ; and J, Portugal–Fonte da Telha . Seven populations were discarded by the Wilcoxon sign-rank test due to a low number of individuals ; VN, Italy, Ca’ Roman (Venice); ER, Italy–Eraclea (Venice); MA, Morocco–Mehdya; KA, Spain–L’Ampolla; and KR, Turkey–Karasu.According to the changes in population size, the Wilcoxon sign-rank test revealed a recent demographic bottleneck in four populations under both the TPM and the SSM model : CS, Cor n < 10, : IV, CroSDMs reached high predictive performance, with a mean testing AUC of 0.987 (SD = 0.013) and a mean TSS of 0.952 SD = 0.040). Both AUC and TSS values are ranked as “excellent” according to the classifications proposed by Swets  and Land0. Both AP. maritimum was predicted to occupy the coastline of the entire Mediterranean basin, also including the southern and north-western coasts of the Black Sea  , whereas correlations with other predictors were not significant , south-eastern Corsica (CS), and southern and northern Spain (KA and W)}; in contrast, during the LGM, only AG  and D (south-eastern Sardinia) localities were present. Thus, we restricted the calculation of correlations with pairwise FST to only LIG predictions. LIG climates contributed similarly as did the current climates to genetic divergence, with a positive association between the pairwise FST and Precipitation of Coldest Quarter (BIO19)  and with all others predictors yielding non-significant relationships. Congruent results were also obtained using the pairwise FST not correcting for null alleles (data not shown).For the current time, Mantel partial correlations and MMRR revealed a significant positive association between the pairwise Fnificant . SDMs prP. maritimum in the course of time. According to our genetic data (E = 0.56 ± 0.013), although not uniformly distributed (FST = 0.23 ± 0.03); marginal populations (i.e. Atlantic Sea populations), in fact, present a lower genetic diversity, as already observed in literature [P. maritimum, as, for example, the presence of a bulb, which allows survival under difficult conditions. It is important to note in this respect that genetic diversity is not correlated with human pressure in any of the analysed populations (IS = 0.09 ± 0.03) and this is related to the different reproductive strategies used by P. maritimum according to different external pressures (i.e. vegetative reproduction and out/in-crossing pollinations). Molecular variation is higher within (77%) than among populations; genetic differentiation among populations  R.Br., which presents a similar biology  [P. maritimum [Cakile maritima Scop., Eryngium maritimum L., Salsola kali L., Halimione portulacoides (L.) Aellen, Crithmum maritimum L. in [Carex extensa Gooden. in [Our integrated analysis supports the hypothesis that the environmental variables and the sea currents as well as the Mediterranean coasts have played important roles in shaping the genetic structure of tic data , Fig 2, terature , 89. Theulations . Even ifspersal) . In the aritimum , 93, andum L. in ; Carex eoden. in  and refeP. maritimum increased, and a peak is foreseen in the near future thanks both to the fact that areas currently with more temperate climate should reach a climate more similar to that of the present-day Mediterranean coast and also to the good capacities of resistance, resilience and adaptability of P. maritimum [P. maritimum has recolonized the sand dune habitat in time, as indirectly documented by our current genetic data and modelling simulations.Comparing the different climatic simulations in time Figs –6, the garitimum , 33, 96.aritimum . This waaritimum . Indeed,aritimum , and thearitimum , 100. HoP. maritimum  living in a dry environment (e.g. savannah). According to Holdsworth [P. maritimum is influenced to a limited extent by the current climatic conditions, and even after the accumulation of the initial critical mass, flowering can occur almost every year. In this case, the presence of a rainy period must be one of the prerequisites for the improved fitness of the sea daffodil as supposed in Holdsworth [P. maritimum is directly proportional to winter rainfall [In addition, the species distribution models do not suggest that the distribution of the sea daffodil is linked to distinct climatic regimes, even if the bioclimatic variables have great importance for the life cycle of ldsworth  and Perrldsworth . Accordildsworth , rainfalldsworth , even ifldsworth . Dafni eldsworth  reportedldsworth  and Dafnldsworth . Considerainfall , with a rainfall , 101. ThWe refrain from speculations on the possible future scenarios emerging by our model; however, it is now certain that the increased temperature, as amply demonstrated in literature , 104, siP. maritimum genetic structure. Thanks to this multi-faceted approach, we highlight the importance of the inclusion of complementary, non-genetic data, for better interpreting genetic patterns, and in order to have a better understanding of the evolution of plants in space and time. This integrated approach may be used in other organisms to create a complete and informative database, providing new tools to explore the effect of climate factors on the patterns of genetic diversity in a wider context.Genetic data of the sea daffodil were combined with past and present climatic information to assess the role of the environment in the observed patterns of S1 FileST with ENA correction. Sheet 4: Pairwise distance matrix FST with no ENA correction. Sheet 5: Pairwise distance matrix FST/1-FST with ENA correction. Sheet 6: Pairwise distance matrix FST/1-FST with no ENA correction.Sheet 1: Pairwise geographic  distance. Sheet 2: Pairwise geographic  distance . Sheet 3: Pairwise distance matrix F(XLS)Click here for additional data file.S2 FilePancratium maritimum accessions that were used in both the Species Distribution Models (SDMs) and the genetic analyses. Sheet 2: Relative contribution to the models and related response curves of each environmental predictor.Sheet 1: Dataset of the (XLS)Click here for additional data file.S3 FilePancratium maritimum and genetic clusters (K) as obtained for the 48 P. maritimum populations  using STRUCTURE (K = 4).Graph of delta K values to determine the ideal number of groups that were present in the accessions of (DOCX)Click here for additional data file.


Despite the increasing availability of direct-to-consumer (DTC) genetic testing, it is currently unclear how such services are regulated in Europe, due to the lack of EU or national legislation specifically addressing this issue. In this article, we provide an overview of laws that could potentially impact the regulation of DTC genetic testing in 26 European countries, namely Austria, Belgium, Cyprus, the Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Norway, Poland, Portugal, Romania, Slovakia, Slovenia, Spain, Sweden, the Netherlands and the United Kingdom. Emphasis is placed on provisions relating to medical supervision, genetic counselling and informed consent. Our results indicate that currently there is a wide spectrum of laws regarding genetic testing in Europe. There are countries (e.g. France and Germany) which essentially ban DTC genetic testing, while in others (e.g. Luxembourg and Poland) DTC genetic testing may only be restricted by general laws, usually regarding health care services and patients’ rights. Since the 1960s, genetic tests have been provided to patients for health-related reasons within a clinical setting  medical devices. For example, the Unfair Commercial Practices Directive 2005/29 EC , issued by the Council of Europe and its Additional Protocol on Genetic Testing for Health Purposes, which is the first international binding document (upon ratification) specifically addressing genetic testing Lwoff . The OviThe different above-mentioned regulatory approaches have resulted in a fragmented landscape when it comes to the regulation of DTC genetic testing. In this article, we provide an overview of the wide spectrum of national laws regulating genetic tests which could potentially impact DTC genetic testing in 26 European countries. Particular emphasis is placed on provisions relating to three specific issues: medical supervision, genetic counselling and informed consent. Furthermore, the desirability of adopting a harmonized regulatory framework across Europe with regard to these issues is discussed in the light of the recent adoption of the EU Regulation on IVD medical devices and the debate that preceded its adoption.Experts in health law and/or regulation of genetic testing from countries where the Regulation on IVD medical devices will apply  were contacted by LK, HCH and PB and invited to contribute to this study. Experts were asked to answer questions regarding national laws pertinent to the regulatory control of DTC genetic testing services in the country where they have an expertise on the legal framework. Particular emphasis was placed on whether medical supervision and genetic counselling are mandatory and whether there are specific requirements for informed consent in the context of genetic testing.Each collaborator’s answers constituted what we refer to, as a ‘national report’ which was returned to LK, who then analysed, summarized and grouped the legislations into categories based on similarities. Experts were then re-contacted in order for them to clarify any details regarding their initial answers, ensure the correct interpretation of their reports and the accuracy of the final text. All collaborators are co-authors of this study. One exception to this approach is the information included regarding Portugal; this information was largely based on the description of the Portuguese legal context in the article ‘Legislation on direct-to-consumer genetic testing in seven European countries’ .Slovenia, Norway and recently the Czech Republic have agreed to be bound by it. However, to date, none of these countries have put into force provisions rendering health-related genetic testing performed without medical supervision illegal.Medical supervision in the context of health-related genetic testing has been assigned particular importance, as it aims to assist patients in making informed healthcare choices and ensure that they have access to high-quality tests that are appropriate for them. In this regard, Article 7 of the Additional Protocol on genetic testing for health purposes prescribes that ‘A genetic test for health purposes may only be performed under individualized medical supervision’  and, more specifically, Article 12 on ‘Predictive genetic tests’. Article 12 of the Oviedo Convention prescribes thattests which are predictive of genetic diseases or which serve either to identify the subject as a carrier of a gene responsible for a disease or to detect a genetic predisposition or susceptibility to a disease may be performed only for health purposes or for scientific research linked to health purposes, and subject to appropriate genetic counselling /2001 article 12), appropriate genetic counselling is mandatory for predictive, carrier and predisposition genetic tests. In Norway  ratified international treaties are directly applicable. Therefore, the requirements regarding genetic counselling imposed by Article 12 of the Oviedo Convention are applicable even without being incorporated into national law  are Italy, the Parliament has authorized the ratification and has incorporated the Convention in the domestic system, but has not yet deposited the instruments of ratification. In this regard, in Italy, genetic counselling is mandatory. This should be the case not only for health-related genetic tests, but also for genetic tests informing on family relationships. This is because based on the General Authorisation No. 8/2014 for the Processing of Genetic Data by the Data Protection Authority: ‘With regard to processing operations carried out via genetic tests for healthcare and/or family reunion purposes, genetic counselling shall be provided to data subjects both before and after performing the tests’  makes the provision of genetic counselling mandatory for certain categories of tests and provides detailed and strict conditions for its provision , the physician who intends to undertake a genetic examination is under an obligation to provide prior information to the patient regarding the purpose, type, scope, and significance of the examination and the anticipated meaningfulness of the results  the characteristics of the sought disease, (2) the means of detecting it and (3) the possibilities of prevention and treatment. The information must be summarised in a written document which could be used to inform the family members. Only the prescribing medical doctor can deliver the information on the results to the patient who has the right not to know. This information must be included in the medical record.In Spain, the conditions for informed consent are regulated for all genetic tests performed in a health context. According to Act 14/2007 , as well as genetic tests for prenatal diagnosis, are only allowed to be performed upon written consent of the person to be tested within the context of the genetic counselling as described above. The informed consent form should indicate that the patient has been informed in advance about the genetic test’s nature, consequences and significance. The information should be provided by a medical specialist with an education in human genetics/medical genetics or a medical specialist competent for the respective specialty  genetic testing, the general obligation to provide due care applies and so do the provisions in the Danish Act on Health regarding patients’ right to information, consent and privacy. Although these rules are not specifically targeting genetic testing, they have an impact on, for example, the right to information both before and after the test, the right not to know as well as protection of genetic information and regulation of access to and disclosure of information both within the healthcare services and to third parties. The Act on Health also contains special provisions regarding young patients’ right to self-determination and proxy consent in regard to children and non-autonomous adults, which are of importance for genetic testing.For example, in Dutch ‘Medical Treatment Contracts Act’,  healthcare providers should provide information about the indication, the proposed treatment, alternatives, prognoses have, risks and possible side effects before starting a medical intervention. Furthermore, a healthcare worker always needs informed consent of the patient in order to perform any test, including a genetic test. The patient can also decide that he/she wishes to be spared certain information or the results.On the same line, according to the France, which essentially bans DTC genetic testing, by limiting the use of genetic testing to specific health-related tests, mandating the involvement of healthcare professionals and penalizing users of tests that do not fulfil these conditions. Similarly, Germany has legislation that has been considered by some as targeting DTC genetic testing and limiting the access German consumers may have to this type of testing , and, as a result, the only restrictions in place are those based on more general laws, usually regarding healthcare services and patients’ rights.Based on the above information, it is evident that European countries follow different approaches when it comes to regulation of genetic testing and impose various levels of restrictions. On the one end of the spectrum is Sweden and Ireland), despite genetic counselling not being specifically addressed, its necessity may be implied by provisions relevant to informed consent. This is because it may be argued that, in the context of genetic testing, unless genetic counselling takes place, consent cannot really be informed.It is worth noticing that the aspects of genetic testing that this article particularly addresses, namely medical supervision, genetic counselling and informed consent, are closely connected and often overlap in practice. For example, it is often the case that informed consent is obtained from the patient during a genetic consultation performed by a healthcare professional who may have also prescribed the test. When it comes to health-related genetic testing, medical supervision, genetic counselling and informed consent have some fundamentally similar goals, namely to guide users to make decisions about their health based on genetic tests that are appropriate for them, after understanding their benefits, limitations and possible implications. The close connection of these notions can be noticed in some national laws that do not address these aspects separately. In many jurisdictions  even if the laws do not explicitly refer to the commercial context, it seems to be evident that the law restricts the provision of DTC genetic tests. In Hungary, the Genetic Act of 2008 has a broad scope, originally tailored to the public healthcare system, but it also applies to private companies operating in Hungary in that it explicitly regulates the type of tests that are allowed. In other countries, however, it is not clear whether the law only regulates the genetic testing process within the clinic or whether relevant provision could be the basis for banning or limiting DTC companies from marketing their products in specific European countries  is currently not prohibited in the country. A number of companies are selling DTC services to UK consumers and 23andMe is currently selling its kits both through its website and through the pharmaceutical chain Superdrug  still fall outside the national jurisdiction. For example, in the Netherlands, the Dutch Act on Population Screening   ban DTC genetic testing, while others do not appear to have much regulatory framework for this model of provision. With a steadily increasing number of companies and different tests sold, such an overview provides a rich resource that can be used to further understand the legal landscape in Europe and to potentially identify different legislative tools that may be useful in helping guide DTC genetic testing companies to act responsibly.


Meanwhile the bivariate twin models estimated shared environmental contributions to the variance and covariance in fasting blood glucose in Danish twins, and in systolic and diastolic blood pressure, low and high density lipoprotein cholesterol in Chinese twins. Overall, our longitudinal twin study on long-term stability of metabolic phenotypes in Danish and Chinese twins identified a common pattern of high genetic control over phenotype conservation, and at the same time revealed population-specific patterns of genetic and common environmental regulation on the variance as well as covariance of glucose and blood pressure.Longitudinal twin studies on long term conservation of individual metabolic phenotypes can help to explore the genetic and environmental basis in maintaining metabolic homeostasis and metabolic health. We performed a longitudinal twin study on 12 metabolic phenotypes from Danish twins followed up for 12 years and Chinese twins traced for 7 years. The study covered a relatively large sample of 502 pairs of Danish adult twins with a mean age at intake of 38 years and a total of 181 Chinese adult twin pairs with a mean baseline age of 39.5 years. Bivariate twin models were fitted to the longitudinal measurements taken at two time points (at baseline and follow-up) to estimate the genetic and environmental contributions to phenotype variation and correlation at and between the two time points. High genetic components in the regulation of intra-individual phenotype correlation or stability over time were estimated in both Danish (h Similar to most complex traits, metabolic phenotypes are regulated by both genetic and environmental factors with the interaction between them as central to the development of metabolic abnormality and diseases , 2. AsseThe longitudinal pattern of metabolic traits can reflect both long-term stability and change in phenotype over time. Although the progression of metabolic phenotypes over life course can be more indicative of disorder-related modifications and disease onset , studyinThis paper reports results from two longitudinal studies on multiple metabolic phenotypes covering body mass, lipids, glucose and blood pressure conducted in Danish (followed up for 12 years) and Chinese (traced for 7 years) twins representing two ethnically distinct populations living in different social-cultural and geographic circumstances. The aim of the study is two-fold: firstly, to perform the first longitudinal twin study to assess the genetic and environmental contributions in maintaining metabolic homeostasis of different phenotypes in each of the two samples respectively; secondly, to identify and compare the different patterns of genetic regulation on the long-term stability of metabolic phenotypes between the two samples representing eastern (Chinese) and western (Danish) populations.Participants for the Danish study were recruited from the nationwide, population-based Danish Twin Registry during 1997–2000 to examine the genetic and environmental backgrounds in the development of insulin resistance, abdominal obesity and cardiovascular risk factors, i.e. the GEMINAKAR study as described previously . Twins wZygosity of twins was determined using microsatellite markers . The Danish part of the study was approved by the local scientific committee of the Region of Southern Denmark  and by the Danish Data protection Board . Written informed consent was obtained from all participants in the study.The sampling of the Chinese twins was based on the Qingdao Twin Registry at the Qingdao Center for Disease Control and Prevention (Qingdao CDC). At baseline, twins were recruited randomly through residence registry and the local disease control network of Qingdao CDC in 2006–2007. The exclusion criterion included pregnancy, breastfeeding, known diabetes and/or cardiovascular disease and use of weight-reducing medicaments within one month . Only co2). SBP and DBP measurements (mmHg) were taken after at least 5 minutes of rest following a standard procedure using a conventional mercurial sphygmomanometer. Three measurements were taken from each subject, with at least 1 minute between each measurement and the mean hereof was calculated and used in subsequent analyses. GLU concentration was analyzed by the glucose dehydrogenase oxidation method both for Danish and Chinese blood samples [The 12 metabolic phenotypes included total cholesterol (TC), triglycerides (TG), high density lipoprotein cholesterol (HDL), low density lipoprotein cholesterol (LDL), fasting blood glucose (GLU), body weight (WT), body mass index (BMI), waist (WAIST), hip (HIP) circumference, waist-hip- ratio (WHR), systolic (SBP), and diastolic (DBP) blood pressure. All metabolic phenotypes were measured according to standard procedures as described elsewhere for both samples . In brie samples , 14. Blo samples , 14.h2) can be calculated as the proportion of genetic variance among the total variance, i.e. The classical twin method was applied to analyze the longitudinal data by fitting bivariate twin models  to the mFor each parameter estimated, a 95% confidence interval (CI) was computed using the likelihood-based method . As deschttp://www.vcu.edu/mx) was used for fitting bivariate models.Before fitting the twin models, each phenotype value was log transformed to minimize possible skewed phenotype distribution. The free Mx package  with its 95% confidence interval between the two waves for both Danish and Chinese twins. The overall mean of individual phenotypes varied with waves, meanwhile we also found significant intra-individual phenotype correlation between the two time points for each of the 12 phenotypes and in each of the two samples providing the basis for exploring the genetic and environmental components in the maintaining phenotypic stability.We next fitted full bivariate twin models to the phenotype measurements at the two times. As described in the method section, nested model were also fitted by dropping the additive genetic and shared environmental components in the phenotypic variances at time 1 (baseline) and time 2 (follow-up) and in the phenotypic covariance between them. After comparison in performances of all nested models with corresponding full model of each phenotype, the best fitting model was selected Tables  which alThe Chinese data were analyzed in the same way as Danish twins. Based on longitudinal data from Danish and Chinese twins, we were able to assess the genetic and environmental basis in maintaining intra-individual stability of 12 metabolic phenotypes. Although the samples were taken from two populations of distinct ethnic and environmental background, we found consistent patterns of high genetic and low environmental controls over stability of nearly all metabolic phenotypes. Our results emphasize the high importance of genetic factors in the conservation of metabolic phenotypes.In a recent study, Yousri et al.  analyzedwave1) instead of stability of metabolic phenotypes [g = 1) was estimated for TG, HDL and high genetic correlation (rg>0.9) for 3 out of the 5 body mass traits. In the Chinese twins (g>0.9) and complete genetic correlations were estimated for LDL, GLU, all body mass traits and blood pressure. It is interesting to see that, while there was a persistent genetic control over glucose metabolism in the Chinese twins, the best fitting model for GLU estimated no genetic correlation in the Danish twins (c = 1). Moreover, the genetic contributions to GLU level at the two time points were all lower in Danish than in Chinese twins (at time 1: 0.14 versus 0.68 and time 2: 0.25 versus 0.72)  was estimated for SBP and DBP respectively, but corresponding proportion of genetic covariance was only moderate . In Danish twins, however, the genetic correlation (rg) was only 0.67 for SBP and 0.55 for DBP but the corresponding proportion of genetic covariance was high for both SBP  and DBP . Based on the higher genetic correlation but lower proportion of genetic covariance in Chinese twins as compared with the lower genetic correlation but higher proportion of genetic covariance in the Danish twins, we assume that the genetic components are lasting/persistent over time but with limited/moderate contribution to blood pressure conservation in Chinese twins. In Danish twins, the high genetic covariance but low genetic correlation between the two times as compared to the Chinese twins lead to the assumption of a low degree of overlap in genes affecting blood pressure at each time point in the Danish twins although genetic factor plays an important role in maintaining long-term blood pressure stability. Moreover, apart from the complete genetic correlation, the Chinese twins also had very high shared environmental correlation on SBP  and on DBP  which was in striking difference with the Danish twins who had no estimates on common environment. In brief, both genetic and family environmental factors persistently contributed in maintaining the stability of SBP and of DBP in Chinese twins; the Danish twins displayed high genetic regulation over the levels of blood pressure, a pattern consistent with Li et al. [In the Chinese twins, complete genetic correlation (ri et al. .In summary, our longitudinal twin study on long-term stability of metabolic phenotypes in Danish and Chinese twins identified a common pattern of high genetic control over metabolic phenotype conservation, and meanwhile revealed population-specific patterns of genetic and common environmental regulation over the variance as well as covariance of fasting blood glucose and blood pressure.


Elevated Myc expression has been noted in basal breast cancer but therapies targeting Myc directly are lacking. It is therefore critical to characterize the interaction of Myc with other genes and pathways to uncover future potential therapeutic strategies. In this study, we bioinformatically predicted a role for Stat3 in Myc induced mammary tumors and tested it using mouse models. During normal mammary function, loss of Stat3 in Myc transgenic dams resulted in lethality of pups due to lactation deficiencies. We also observed that deletion of Stat3 in the mammary glands of MMTV-Myc mice unexpectedly resulted in increased and earlier hyperplasia and expedited tumorigenesis. However, despite arising earlier, Myc tumors lacking Stat3 grew more slowly with alterations in the resulting histological subtypes, including a dramatic increase in EMT-like tumors. We also observed that these tumors had impaired angiogenesis and a slight decrease in lung metastases. This metastatic finding is distinct from previously published findings in both MMTV-Neu and MMTV-PyMT mouse models. Together, the literature and our current research demonstrate that Stat3 can function as an oncogene or as a tumor repressor depending on the oncogenic driver and developmental context. Elevaferation , 7. Whilferation . Expressferation .Stat3 is constitutively activated in breast cancer  and actiin vivo. To test the hypothesis that Stat3 alters Myc tumorigenesis, we interbred MMTV-Myc mice with a conditional knockout of Stat3. This revealed unexpected roles for Stat3 in tumor development but not metastasis.Given the functions of Stat3 and widespread effects of Myc in breast cancer, it is therefore essential to examine the interaction of these two genes To investigate the role of Stat3 in different oncogene-driven tumors, we compared gene expression profiles of MMTV-Myc and MMTV-Neu tumors. First, significant up-regulated and down-regulated genes from the Stat3 pathway  were ideFl/Fl mice to generate Stat3 conditional knockout mice in the MMTV-Myc background (Myc Stat3 CKO). We noticed that pups from the Myc Stat3 CKO dams were runted or died before weaning age. These pups were fully rescued with foster dams, demonstrating that vitality was due to defects in the Myc Stat3 CKO dams. To study the effects of Stat3 in normal developmental functions with Myc overexpression, we monitored the first litters of Myc Stat3 CKO, Stat3 CKO, and Myc dams. Litter size was normalized to 6 at postnatal day 1 and pup weight was tracked . Median tumor onset was 294 days in Myc Stat3 CKO mice and 360 days in Myc mice with Stat3. Interestingly, we noted that once tumors were palpable in the Myc Stat3 CKO mice, the majority of tumors grew relatively slowly compared to the Myc control tumors Figure . Measuriy Figure . Consisty Figure , p=0.04.While the delay in growth rate was substantial with loss of Stat3, we noted that several tumors that appeared to grow at the same rate as the Myc control tumors. Given the previous observation that tumors with MMTV-Cre directed excision could select against tumor progenitor cells with Cre expression , we examGiven the alterations to growth rate of the tumor and the selective pressure to maintain Stat3 expression, we hypothesized that loss of Stat3 may result in alterations to the morphology of the tumors. After a histological examination we noted changes in subtypes of these tumors Figure . Notably3  was from Abcam . F4/80 antibody (Q61549) was from Serotec . CD31 antibody (DIA-310) was from HistoBioTec . Stat3 (#9139), phospho-Stat3 , and beta-tubulin (#2128) antibodies were purchased from Cell Signaling Technology . Secondary goat anti-mouse and secondary goat anti-rabbit antibodies were from Abcam. Positive signals were quantified using Image J software.WT/Fl(1): 5′-GCTGCCAACAGCCACTGCCCCAG-3′;Stat3WT/Fl (2): 5′ GAAGGCAGGTCTCTCTGGTGCTTC-3′;Stat3 ko: 5′-CAGAACCAGGCGGCTCGTGGCG-3′.The primer sequences used in determining Stat3 excision were; Stat3Analysis was completed with Graphpad prism.


In the past decade, the ability to generate whole-genome sequences has provided geneticists with a view of the astonishing breadth of genetic variation. This, in theory, means we should be able to identify the specific differences in DNA sequence that lead to an inherited phenotype, including disease states. But this wealth of new information has revealed perhaps the most fundamental challenge for geneticists since Mendel. While we understand that phenotypes are influenced by genetic variation, we do not yet know how to interpret individual genome sequences and, therefore, we cannot predict which genetic variants are linked to which phenotypes. Indeed, the term “missing heritability” was coined to highlight the fact that in natural populations the genes or genetic elements associated with complex traits explain only a small proportion of the phenotypic variation in these traits.In stark contrast, controlled crosses of model organisms have generated a wealth of information about the genetic basis of phenotypes. From broad associations of genomic regions with traits to individual polymorphisms that act by well understood mechanisms, geneticists have been remarkably successful in revealing the impact of genetic variation on phenotype. Applications as diverse as targeted drug therapy and dramatic improvements in agricultural output have been enabled by our understanding of genetics. But it remains a significant challenge to transfer this understanding to natural populations. To bridge the gap between natural populations and experimental systems, experimental systems need to incorporate more of the complexity of natural populations. This has given rise to a burst of creativity in the design of genetic reference populations. The basic idea is simple: combine the strength of the experimental system, where the genetic composition can be replicated, with the genetic diversity of the target population. Rather than choose two inbred lines or two phenotypically divergent individuals as founders of a genetic reference panel (recombinant inbreds), choose eight, or 25. Using multiple lines as founders of a set of inbred lines whose haplotypes can be replicated has been referred to as Interconnected populations multiparent, advanced-generation intercross design, Complex Cross, and multiparental RIL. We are choosing to refer to this broad set of genetic reference panels as multiparent populations (MPP).GENETICS and G3 in 2012 . Systematic monitoring of progress with the mouse collaborative cross has provided a window into the impact of drift on the genomes . The first set of papers describing these strains was published in Arabidopsis . These issues of GENETICS and G3 feature MPPs of Sorghum  rely on data sharing. One of the benefits to working with a reference panel is the ability to leverage data collected in different ways, for different purposes. Our journals have long had policies for reagent and data sharing that reflect the values of our community, and this is evident in these articles on MPPs. Each MPP paper in these issues has the Data availability section that is standard for all GSA publications, as well as a one-page guide to the data that makes it easier to browse the data behind the papers. G3 and GENETICS have designed a special web resource for MPPs. Papers are organized in a special collections page with subheaders that help navigate the growing literature. Our journals have long partnered with model organism databases FlyBase, SGD, WormBase, and others, and we now incorporate news, blogs, tips, and protocols directly on our webpage to help geneticists interested in MPPs get a handle on this topic. Tweet your insights to #MPP #GSAjournals, and use MPP as a keyword of your MPP papers to enable text search engines to collate this literature. The GSA journals are committed to creating a community platform that spans species and disciplines yet remains focused on common research questions. We thank the authors, referees, and editors for making this resource a reality!In recognition of the ongoing importance of MPPs for understanding fundamental questions in genetics,


Oedaleus decorus, a steppic Southwestern‐Palearctic species. We applied a recently developed hybridization capture (hyRAD) protocol that allows retrieving orthologous sequences even from degraded DNA characteristic of museum specimens. We identified single nucleotide polymorphisms in 68 historical and 51 modern samples in order to (i) unravel the spatial genetic structure across part of the species distribution and (ii) assess the loss of genetic diversity over the past century in Swiss populations. Our results revealed (i) the presence of three potential glacial refugia spread across the European continent and converging spatially in the Alpine area. In addition, and despite a limited population sample size, our results indicate (ii) a loss of allelic richness in contemporary Swiss populations compared to historical populations, whereas levels of expected heterozygosities were not significantly different. This observation is compatible with an increase in the bottleneck magnitude experienced by central European populations of O. decorus following human‐mediated land‐use change impacting steppic habitats. Our results confirm that application of hyRAD to museum samples produces valuable information to study genetic processes across time and space.Analyzing genetic variation through time and space is important to identify key evolutionary and ecological processes in populations. However, using contemporary genetic data to infer the dynamics of genetic diversity may be at risk of a bias, as inferences are performed from a set of extant populations, setting aside unavailable, rare, or now extinct lineages. Here, we took advantage of new developments in next‐generation sequencing to analyze the spatial and temporal genetic dynamics of the grasshopper  The species is characterized by a large South‐Palearctic distribution, ranging from Macaronesian Islands through the Mediterranean Basin to central Asia —a recently developed technique using fragments generated by RAD as baits to capture homologous sequences generated by shotgun and easily applicable to any nonmodel species . We eluted the resulting product a second time to increase the amount of isolated DNA. Additionally, muscle tissue from the hind‐legs of 65 fresh specimens collected between 2005 and 2009 and 27 museum specimens  were individually assembled using SOAPdenovo V2.04 with a Appendix . We asseAppendix .2.3.3Before mapping, we processed reads with Trimmomatic V0.3  with BWA V0.7.12 . We realigned the subsequent bam files with GenomeAnalysisTK V2.8  not all sequences nonhomologous to the probes are filtered out during the enrichment step of hyRAD, it becomes possible to retrieve genes present in multiple copies, which are found at high coverage in the DNA samples. This is notably the case of the mitochondrial genome, which we partly retrieved in 40 specimens with the highest number of reads and spanning the species distribution Table . We mapp2.4O. decorus for reconstructing continent‐level phylogeographic patterns.We used a combination of fresh samples and samples collected during the past decades for the spatial analysis. Thus, we assumed that local genetic differences accumulated over the last century are negligible in comparison with the spatial genetic variations accumulated over the Quaternary evolutionary history of 2.4.1k numbers of groups ranging from 1 to 10 and a simple prior , which is appropriate to study populations isolated from each other  to detect deviation from Hardy–Weinberg expectations (HWE). Thus, we performed exact tests for deviation from HWE only within the two extant populations using 1,000 permutations with the Monte Carlo procedure implemented in the R‐package pegas  were excluded from further analyses.Sample size in each historical population was too small  was calculated for each individual using the R‐package hierfstat , expected heterozygosity  were calculated using hierfstat  to control for difference in population size using adegenet . The Eastern cluster was composed of specimens originating from the Eastern part of the species range  as well as individuals coming from the Aosta Valley in northern Italy. Finally, specimens originating from northeastern and northwestern Italy were assigned to both southern and central European/Iberian lineages. Introgression of the southern lineage was also found in half of the individuals assigned to the Eastern lineage. The maximum‐likelihood phylogeny based on mitochondrial DNA was congruent with the structure of those four clusters  and Lower Hérens Valley 1940 (n = 4) showed three private alleles with low frequency in Lower Hérens Valley 2005 and 144 private alleles in Lower Hérens Valley 1940  and Lower Hérens Valley 2005 (n = 15), we detected 15 private alleles in Gampel 2005 and 71 private alleles in Lower Hérens Valley 2005  SNP data and highlighted four lineages, which produced spatial genetic clustering at the scale of the western Palearctic that were generally consistent between both approaches. At the temporal level, we identified a decrease in allelic richness in contemporary populations. Our study demonstrates the utility of DNA isolated from museum specimens when associated with hybridization capture methods, to investigate genetic changes related to population decline and to achieve a wide geographical coverage of samples to establish the spatial genetic structure of nonmodel organisms.The aim of this study was to combine genetic data generated from museum specimens and modern samples to reconstruct the spatial genetic structure of 4.1O. decorus was consistent. Four geographically structured groups were recognized . However, two hypotheses can account for the postglacial expansion of the Southwestern‐Palearctic lineage: (i) recolonization of Europe from southern Italy or (ii) from northern Africa. Italy is generally considered as a major refugium in southern Europe  and Lower Hérens Valley , by an increase in the bottleneck magnitude over time. Although we could not identify a clear‐cut demographic scenario for the Finges population—the population with the largest number of collected samples in our study  and environmental effects  are known to greatly influence species extinction risk .Raw reads, mitochondrial DNA alignment as well as the VCF datasets used for the analyses are available in ZENODO ( Click here for additional data file.


Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data  from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris (20) and P. dumosus (35). Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans-Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Contrasting with previous studies, we did not find evidence of recent gene flow between wild and cultivated populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods. Our results contribute to the understanding of the domestication history of P. coccineus, and highlight how the genetic signatures of domestication can be substantially different between closely related species.The runner bean is a legume species from Mesoamerica closely related to common bean ( Phaseolus coccineus L.) is one of the five Phaseolus species that were domesticated in Mesoamerica, and it is the third-most economically important, after P. vulgaris L. and P. lunatus L. The domestication process of this species continues today both in the Americas and Europe, where it was introduced by the Spaniards. One of its main characteristics is its ability to tolerate cooler climates than other Phaseolus and up to date it is an important food source for smallholders and indigenous groups in Mexico , from northern Mexico (Chihuahua) to Panama (P. coccineus subsp. coccineus (mostly with red flowers), including 11 wild varieties and the domesticated form, and P. coccineus subsp. striatus (purple or mauve flowers), conformed by eight wild varieties. No genetic evidence supports these subspecies and varieties, but given the environmental and cultural heterogeneous landscape where P. coccineus occurs, it is expected that the species should be genetically structured.Wild o Panama . It has o Panama : P. coccP. coccineus is currently grown in Mexico, Guatemala, Honduras and Costa Rica, and in lesser degree in South America. In Europe, it is mostly cultivated in the United Kingdom, Netherlands, Italy, and Spain  examine the extent of the domestication bottleneck in this species by comparing the levels of genetic diversity and geographic patterns of the wild, feral and domesticated Mexican populations; and (3) identify candidate loci under natural and artificial selection in P. coccineus genome.Here, we aim to deal with the previous knowledge gaps by using genomic data to (1) provide information about the domestication history of Phaseolus coccineus individuals from 10 wild, three feral and 11 cultivated Mexican populations and one cultivar from Spain were analyzed, as well as plants from the breeding line Blanco Tlaxcala. Taxonomic and wild/feral/domesticated categories were assigned based on morphology and habitat observations. Only one of the wild populations that were sampled corresponds to subsp. striatus, the rest belong to subsp. coccineus. A population was classified as feral if it was growing out of cultivation and presented intermediate traits between wild and domesticated forms. The Mexican samples cover the species distribution and main cultivation areas at the national level. As outgroups, samples from the closely related species P. vulgaris (three wild and one cultivated) and P. dumosus (seven cultivated) were included . DNA samples were genotyped at the Institute for Genomic Diversity at Cornell University . SequencP. vulgaris reference genome v1.0 (Phytozome) DOE-JGI and USDA-NIFA, http://phytozome.jgi.doe.gov/ , which are the domesticated species of the Vulgaris clade . Specifically we examined if the cultivated samples was recovered as a monophylogenetic group. For the phylogenetic analysis, wild and cultivated samples of P. coccineus, P. vulgaris, and P. dumosus were analyzed under three schemes:We inferred the population structure of ure v1.3  was usedP. coccineus solely. We used the program SNAPP 1.3.0  from our runs by examining log files with the program Tracer 1.5 . Specifically, we used the Hierfstat package  to obtain confidence intervals. To test the hypothesis that ni = nj  we used a pairwise χ2 tests with Bonferroni correction to avoid false positive results (FIS at the sampling location (P. coccineus dataset) and at the species level (VDC dataset) applying the same test.To evaluate the existence and degree of the domestication bottleneck on  package  in R  in which the position of the Wild-Sierra Madre Occidental (Wild-SMOCC) clade was evaluated  considering the Wild-SMOCC population fixed as sister clade of the Wild-Trans-Mexican Volcanic Belt (Wild-TMVB) populations (see section Results). The number of domestication events was tested as follows: multiple events . A subsample from the SNAPP dataset (279 SNPs) and the scheme of eight clusters were used to set populations in DIYABC . Priors were set as follow: log-uniform distributions across all parameters, Ne ranging from 100 to 100,000 individuals, mutation rate set to 10-8–10-6 across SNPs, and divergence times among populations set to 10–100,000 generations ago (Table 1).In order to confirm the hypothesis of a single domestication event in Mexico suggested by our phylogenetic analyses (see section Results) we applied the Approximate Bayesian computation ABC;  method iWe compared the fit of the single vs. multiple domestication events scenarios by estimating their posterior probabilities: with the obtained reference tables from each scenario, we ranked the simulated datasets in order of increasing distance to the observed data considering direct and logistic approaches . DistancP. coccineus to identify candidate loci related to domestication, to cultivar diversification, and to natural selection. Before the candidate SNPs analysis, an additional filter based on linkage disequilibrium (LD) was applied. To determine the threshold distance at which there is no LD, we estimate the inter-variant allele correlations (r2) using PLINK 1.9 . Also, an additional SNPs filter was made and MAF were adjusted to consider SNPs present in at least five individuals. For this dataset, that is MAF = 0.023. For Bayescan no additional filter was made. Second, to identify loci related to diversification in the context of domestication, only cultivated samples were analyzed. In the pcadapt analyses, the first six components were assessed because they explain the genetic structure of populations, and MAF threshold was set to 0.038 to excluded alleles present in less than five individuals. Notice that in this case, diversification refers to the phase that follows initial domestication and involves the spread and adaptation to different agro-ecological and socio-cultural environments . For each annotated loci we looked for homologous proteins with the highest similarity in other plants, and examined if the homolog genes in Glycine max (soybean) were among the domestication-related loci associated with flowering time and seed size in this species . After assembly and SNP discovery, the VDC group dataset contains 241 individuals of P. coccineus, 20 of P. vulgaris and 35 of P. dumosus, 50 273 SNPs, 2.24% mean missing data per individual, and a mean depth per site of 58.63. The P. coccineus dataset includes 242 individuals , 42,548 SNPs, 3.97% mean missing data per individual, and a mean depth per site of 50.41.A total of 296 individuals representing four ecoregions of Mexico . The genetic clusters seem to be related to geographic distances , except the population Wild-striatus, which is geographically close to populations of P. coccineus subsp. coccineus but seems genetically isolated. Samples from the Spanish population  were assigned to the Cult-TMVB genetic group, but unlike the individuals of this cluster, samples from Spain do not present a mixed ancestry. Regarding samples of the breeding line Blanco Tlaxcala , they are grouped with landraces from Cult-SMOCC cluster.The Figures 2A,C) are consistent with the Admixture genetic groups . Nevertheless, both analysis suggested the Wild-TMVB group as a paraphyletic clade. ML topology revealed a finer-scale structure, identifying three paraphyletic clades within this genetic cluster, and Wild-striatus cluster is a nested clade differentiated from the rest of the Wild-TMVB group . Remarkably, the domesticated populations integrate a monophyletic clade statistically well supported, suggesting a unique domestication event for the Mexican populations. Nevertheless, these phylogenetic hypotheses do not allow to distinguish the genetic pool from which domestication took place, although the Wild-SUR-CH genetic cluster can be discarded.The phylogenetic hypotheses constructed with FastTree and SplitsTree . However, the SplitsTree method indicated a basal reticulate pattern among P. dumosus, P. coccineus, and P. vulgaris , suggesting ancestral gene flow, but not recent. Furthermore, there is no evidence of recent gene flow between wild and cultivated groups, but only within genetic clusters .The ML and Neighbor-Net topologies in which Figures 3B,C), 53 single topologies summarize the 95% HPD consensus tree, indicating a different divergence pattern in which Wild-TMVB populations are the closest clade to the domesticated group. Nevertheless, the complex assignment of individuals within Wild-TMVB and Wild-striatus are shown in a non-solved pattern within the cloudgram as well as in low values of nodal support in the consensus topology . Despite these main inconsistencies between ML and Neighbor-Net vs. SNAPP topologies, all hypotheses favor the occurrence of a single domestication event.Regarding SNAPP cloudgram , which is congruent with the results of SNAPP phylogenetic analyses. Evaluation of the posterior predictions via PCA indicated that parameter values and summary statistics from the simulated datasets based on Scenario 1 closely matched the empirical data . At the genetic cluster level, the Wild-TMVB group presented the highest diversity and the Cult-OV group the lowest. No clear pattern in the amount of diversity was observed between wild and cultivated clusters. There were cultivated groups with high genetic variance (Cult-SUR-CH and Cult-TMVB), and wild clusters that presented lower diversity than cultivated populations (Wild-SMOCC). At the location level (Supplementary Table HE = 0.134) and Oaxaca Valley (HE = 0.148) presented the lowest diversity, and the highest was found in wild population located in Tlalpan, Mexico City (HE = 0.208). Regarding species, P. coccineus showed the highest diversity and P. dumosus the lowest.High levels of genetic diversity were found in wild and cultivated populations . On the contrary, at the species level P. vulgaris showed a deficit of heterozygotes, showing a high FIS. The inbreeding coefficient is positive when estimated taking into account all P. coccineus samples. This is caused by the Wahlund effect, which is the reduction of heterozygosity due to subpopulation structure. Regarding pairwise differentiation index, FST values ranged from 0.022 (Cult-TMVB vs. Cult-SMOCC) to 0.178 . As expected, the pair FST values are greater between wild genetic groups than between cultivated genetic clusters .Outstandingly, P. coccineus show smaller effective population sizes than wild populations. In some cases, like in Cult-TMVB and Cult-SMOCC, Ne was one order of magnitude smaller than in the rest of the populations. On the contrary, the genetic cluster Wild-SUR-CH had the biggest Ne (Table 1). The most recent split was estimated to happen 3.9 × 103 generations ago, and occurred between the Cult-SMOCC and the Cult-TMVB clusters. On the contrary, the oldest split event was dated in 4.95 × 105 generations ago between the Wild-SUR-CH and the rest of P. coccineus clade. The split event that separates wild and domesticated samples was dated about 2.1 × 104 generations ago . Since P. coccineus is usually treated as an annual when cultivated, that represents 21,000 years ago. In the case of wild, perennial plants, one generation could be more than a year.Cultivated populations of r2 value among SNPs located in the same chromosome separated by a maximum distance of 10,000 bp was 0.151. After eliminating SNPs closer than 3,000 bp, the mean r2 was 0.063 . Notably, the genetic and geographic structure of wild and cultivated groups can be recovered by these few candidate SNPs  and a clear separation of wild and domesticated populations is observed .Twenty four SNPs related to domestication, 13 to cultivar diversification and eight to natural selection were detected by both approaches and considered as candidate loci for further analyses . This includes Chiapas populations (Cult-SUR-CH), which are geographically and culturally closer to Guatemala than to Central and Northern Mexico. However, no samples from Guatemala and Honduras were included, therefore a second domestication event in this area cannot be discarded with the present data. Nonetheless, based on the results from SNAPP and DIYABC analyses, we were able to identify Wild-TMVB as the genetic pool from which domestication started in Mexico .Figure 4, t1). Assuming one generation per year in cultivated populations, this represents 3,950 years. But divergence between the cultivated and wild clades was dated in 21,000 generations . This date is out of range of any plant domestication event and it seems unlikely. There are evolutionary processes that may affect these estimations. Processes like selection, population subdivision and incomplete lineage sorting may result in an overestimations of divergence times because increase the time to coalescence, that is, the time it takes for the two sequences to find their common ancestor ; tasukhu in Hidalgo and Puebla (Otomi); ayocote in central states of Mexico (Nahuatl); shaushana or xaxana in Veracruz (Totonaco); ma-má-ja (Mazateco) in Oaxaca; and botil or shbotil chenec in Chiapas   . Associaes e.g., .Figure 2A), suggesting that they are escaped cultivars. This questions the hypothesis of an hybrid origin between wild and cultivated populations . Since little evidence of gene flow was found in SplitsTree , probably the mixed ancestry is due to shared polymorphisms or ancestral gene flow, rather than recent introgression events.The individuals identified as feral clustered in the domesticated clade . Probably the genetic bottleneck that originated European populations and the isolation from wild relatives and American landraces, have decreased the amount of shared ancestral polymorphisms between cultivars from TMVB and Spain.Contrary to what was reported by P. coccineus evolution, both in cultivated and wild populations . The Wild-TMVB cluster presented the highest genetic variation, followed by the Cult-TMVB and Cult-SUR-CH groups. On the contrary, the Cult-OV and Wild-SMOCC clusters showed the lowest HE. Regarding effective population sizes, these were greater in wild than in cultivated genetic clusters, which is expected due to the genetic bottlenecks associated to domestication process. Nevertheless, Ne estimations of domesticated groups are in the order of 103–104. Taking together all results, these suggest that the genetic bottleneck during domestication was not severe. Other factors that may favor the maintenance of genetic diversity in P. coccineus are its high outcrossing rate  suggests that it has been genetically isolated from the other genetic clusters.Analyzing the genetic variance at the location level, Spanish samples presented the lowest diversity . This population was previously studied by P. coccineus subsp. striatus to know if this is a common pattern and to explore the ecological and genetic causes and consequences of it.Regarding the inbreeding coefficient, the wild and cultivated genetic clusters presented negative d weight . Also, ad weight . OppositPhaseolus, both cultivated and wild, involves an interaction with a wide range of different cultures, and isolated populations are exposed to diverse environmental conditions. For example, compared to P. vulgaris, P. coccineus grows in more humid environments, at cooler temperatures and at higher altitudes. Nevertheless, there are few studies that aim to elucidate the genetic basis of adaptation, especially for the wild populations of Phaseolus crop species (P. coccineus genome is not fully saturated, and likely there are loci under selection that we did not sample. Nevertheless, this set of outliers are a first approximation to identify candidate loci to domestication and natural selection in runner bean.Mexico is an environmentally and culturally heterogeneous country, which favored crop genetic diversity. The distribution of  species . Our out species . Our stuThe fact that no loci overlapped between domestication, diversification and natural selection categories shows that different selective processes were detected. This is to be expected because, in general, loci under natural selection and artificial selection related to domestication and diversification are expected to differ across the genome .The loci involved in domestication are expected to be specially related to the phenotypic changes of the domestication syndrome , that isP. coccineus. Results suggest one domestication event for Mexico, which started from the wild genetic pool from TMVB. Furthermore, wild and domesticated populations are highly diverse and presented high values of Ne, suggesting that the demographic bottleneck due to domestication was not severe. These genomic analyses allow to highlight how the genetic signatures of domestication can be substantially different even between species of the same genus domesticated in the same geographic area. Common bean and scarlet runner bean are closely related species, nevertheless their reproductive strategies and domestication histories seem to be different: P. vulgaris tends to self-crossing, which theoretically facilities the domestication process, and it also suffered a severe domestication bottleneck. On the contrary, P. coccineus is an open pollinated species that presents high levels of genetic diversity and population structure, and its domestication did not result in a strong demographic bottleneck.The SNPs generated in this work provided high resolution data to understand the domestication of P. coccineus are highly structured. Most of the genetic clusters presented an heterozygotes excess, showing evidence of inbreeding depression. Interestingly, the population identified as P. coccineus subsp. striatus shows the greatest excess of heterozygotes and seems to be genetically isolated from other wild and cultivated populations. Contrasting with previous studies, our data shows that gene flow within and between wild and cultivated populations is not a common process. Fully testing this represents an area where further research is needed.Our findings also show that both wild and domesticated populations of P. coccineus wild and cultivated forms there is still a need of more sampling, specially including Central American populations. Complete and annotated genomes of Phaseolus and other legume crops will facilitate not only comparative genomics, but will give a better knowledge of the evolution and domestication of this group of plants that has been independently domesticated by several human groups across its distribution.The levels of diversity and population differentiation found here support that the runner bean is a potential source of variability for several traits for plant breeding . The datAG-G, DP, and AD-S designed the study. AG-G made the molecular procedures. AG-G, AM-Y, and MS-A conducted the analyses. All authors revised the results and wrote the manuscript.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. The handling Editor declared a shared affiliation and past co-authorship, though no other collaboration, with the authors and states that the process nevertheless met the standards of a fair and objective review.