Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected , with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures , principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars , whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of understanding levels of genetic diversity and connectivity to making informed management and conservation decisions with the goal to maintain functional connectivity across the region.Mesoamerican jaguars ( Panthera onca) have been extirpated from over 54% of their historic range , Costa Rica [n = 50], Guatemala [n = 24], Honduras [n = 34], Mexico [n = 40]). We identified 115 individual jaguars  and P(ID)sibs estimates were 3.36E-11 and 5.82E-05, which confirms high resolving power for identifying individual jaguars using this set of microsatellites. Overall nDNA PCR amplification success rate for microsatellites was 60.4%. Cumulative mean genotyping error rates were 4.9% for false alleles and 17.9% for allelic dropout.We genotyped a total of 445 jaguar scats collected across five Mesoamerican countries , rarified AR of 3.43 , HO of 0.59 , and HE of 0.59   with the exception of NA. The global inbreeding coefficient was 0.05 , ranging from -0.08 to 0.13 at different sampling localities  . Genetic.04, SD) , but didcalities . We dete jaguars . HoweverFCA075 in Belize, P = 0.001; FCA126 in Costa Rica, P = 0.003) after applying sequential Bonferroni correction (Departure from Hardy-Weinberg equilibrium was significant in two cases (rrection . LD was K = 3) with varying levels of genetic admixture  sampled across Mesoamerica and varied in levels of genetic admixture (Q > 0.7). Further hierarchical clustering analysis of jaguars sampled across the Selva Maya region  and Honduras showed evidence for genetic differentiation (K = 2): Selva Maya jaguars clustered separately from Honduran jaguars with overall high assignment membership values for all individuals (Q > 0.7) , we concluded that low genetic structuring (K = 1) was evident (K = 1) when Costa Rican jaguars were assessed separately  . For Hondmixture . Costa R evident . Furtherparately . Additioparately . In accoparately .F0 dispersers among sampling sites across Mesoamerica. One F0 disperser was detected in southern Mexico at Sierra Mixe in Oaxaca, indicating gene flow from the Guatemala sampling sites. The second F0 disperser sampled at the Río Plátano Biosphere Reserve in southeastern Honduras was genetically assigned to sampling sites in Costa Rica  indicated that most of the variance (V) was attributable to genetic variation among the lowest hierarchical level, individuals within sampling sites  (Population-based gene flow estimates using pairwise  to 0.21 . The hig= 0.001) . These rr = 0.375, P = 0.001)  , after which r decreased to become statistically indistinguishable from zero, as would be expected in the case of nonrandom genetic structure such that spatially proximal individuals are genetically more similar than spatially distant jaguars. The spatial autocorrelation analysis also revealed an x-intercept of r at ~ 340 km, indicating the extent of positive genetic structure  . Mantel = 0.001) . We did tructure .Habitat loss and fragmentation represent severe threats to jaguars since they exist at low densities, and have large spatial requirements and dispersal patterns mediated by the occurrence of habitat and prey e.g., , 8). Non. Non8]).Genetic diversity has important ecological consequences in natural populations, including the maintenance of evolutionary potential and individual fitness to respond to threats such as environmental change and disease e.g., , 70). Al. Al70]).Honduran jaguars exhibited the second lowest genetic diversity estimate  among alEffective conservation and management of threatened carnivore species occurring across complex, heterogeneous landscapes require an assessment of genetic connectivity in natural populations. Patterns of genetic structure in wide-ranging carnivores such as jaguars are shaped by a multitude of contemporary and historical factors, which are of ecological, environmental or anthropogenic nature e.g., , 77–79).–79.77–79Despite differences in the assumptions of analytical methodologies used here to assess genetic connectivity in Mesoamerican jaguars, individual- and population-based approaches yielded results that were broadly concordant, with the exception of AMOVA. AMOVA supported the inference that Mesoamerican jaguars are a single, admixed population with low genetic differentiation associated among geographic divisions of hypothesized a priori groupings  . Since AFST and Dest estimates . Based on these results we declare this region of high conservation concern and recognize the need to conduct further genetic sampling for jaguars across eastern, central, southern Guatemala and most of Honduras to genetically ground-truth functional connectivity of previously identified movement corridors.Genetic differentiation between Selva Maya and Honduran jaguars appeared to be more substantial than expected considering their close geographic proximity. Bayesian clustering Figs  and 4B aInterestingly, we detected a potential first-generation migrant (i.e. disperser) at the Río Plátano Biosphere Reserve in southern Honduras , which wFor Costa Rica, the Bayesian clustering analysis included DNA samples obtained across northern, central, and southern Costa Rica, suggested no genetic subdivision of Costa Rican jaguars Figs  and 4E. As recommended by previous empirical studies , we empAn accurate understanding of contemporary genetic connectivity is key to preserve genetic health of wild jaguar populations existing across fragmented landscapes. This study detected moderate to relatively high levels of genetic diversity and low to moderate genetic differentiation in Mesoamerican jaguars at different hierarchical levels. The results presented here have several important implications for conservation and management of wild jaguar populations across Mesoamerica, and elsewhere within their range. First, since jaguars are starting to exhibit genetic differentiation within Mesoamerica, attention should be given to keeping and restoring functional connectivity between core jaguar populations by increasing structural connectivity  and minimizing human disturbance. Our results suggested that genetic connectivity is less certain across central regions of Mesoamerica (Honduras and surrounding sites). More complete genetic sampling is needed to examine other regions of conservation concern . Second, since habitat loss and fragmentation have been identified as primary global threats to mammals, interdisciplinary research efforts combining large-scale genetic monitoring with landscape genetics methodologies need to be conducted to examine if and how different landscape features, as well as varying levels of structural connectivity, shape patterns of contemporary gene flow in wide-ranging carnivores such as jaguars. Third, while the landscape is of key importance with respect to functional connectivity, ex- and intrinsic factors potentially impacting jaguar movement, including population densities of jaguars, their prey, and other competing wildlife species, need to be examined simultaneously with the genetic monitoring effort. In conclusion, we recommend comprehensive regional conservation and management for threatened species such as jaguars, which integrate interdisciplinary research efforts, including conservation and landscape genetic studies at fine- and large spatial scales into their decision-making.S1 FigK) in Mesoamerican jaguars using STRUCTURE, version 2.3.4 [K), A) and delta K |)/SD(L(K)), D) for each K value. Bayesian clustering analysis was conducted for jaguars detected in (a) Guatemala, Belize, and Honduras (n = 72), (b) Honduras and Costa Rica (n = 43), (c) Guatemala and Belize (n = 65), and (d) Costa Rica (n = 36). SD, standard deviation; L’(K), mean rate of change of the likelihood distribution (B); |L”(K)|, absolute value of the 2nd order rate of change of the likelihood distribution (C).The optimal number of genetic clusters (on 2.3.4  was chos(DOCX)Click here for additional data file.S2 FigK = 2) using STRUCTURE, version 2.3.4 [n = 48), excluding closely related individuals. Individuals were collected at various sampling sites . (a) STRUCTURE barplot—vertical bars represent individuals and the color of each bar visualizes the % of membership (Q) the individual belongs to the genetic clusters (K) identified. (b) The optimal number of genetic clusters (K) in was chosen based on posterior probabilities (mean L(K), A) and delta K |)/SD(L(K)), D) for each K value. SD, standard deviation; L’(K), mean rate of change of the likelihood distribution (B); |L”(K)|, absolute value of the 2nd order rate of change of the likelihood distribution (C).Results were obtained from Bayesian clustering analysis (on 2.3.4  and geno(DOCX)Click here for additional data file.S1 Materials and Methods(DOCX)Click here for additional data file.S1 Tablen = 115) detected across five Mesoamerican countries , including number of alleles (NA), rarified allelic richness (AR), expected heterozygosity (HE), and inbreeding coefficient (FIS).n, number of individual felids; SD, standard deviation.Estimates of genetic diversity for jaguars ((DOCX)Click here for additional data file.S2 TableP-value for the Hardy-Weinberg equilibrium (HWE) test (PHW), and frequency of null alleles (FNull) at 12 microsatellite loci for 115 jaguar samples collected across five Mesoamerican countries . n, number of individuals.(DOCX)Click here for additional data file.


Lens species are considered to be more resistant against major biotic and abiotic stresses than that of the cultivated species. In the present study, we assessed the comparative agronomic performance of lentil (Lens culinaris subsp. culinaris) inter-sub-specific  and interspecific (L. ervoides) derivatives, also discussed its probable basis of occurrence. The F3, F4, and F5 inter sub-specific and interspecific populations of ILL8006 × ILWL62 and ILL10829 × ILWL30, respectively revealed a substantial range of variation for majority of agro-morphological traits as reflected by the range, mean and coefficient of variation. A high level of fruitful heterosis was also observed in F3 and F4 progeny for important traits of interest. Phenotypic coefficient of variation (PCV) was higher in magnitude than genotypic coefficient of variation (GCV) in all generations for several quantitative characters. The results showed high heritability estimates for majority of traits in conjunction with low to high genetic advance in F3 and F4 generations. Further, F5 progeny of ILL10829 × ILWL30, manifested resistant disease reaction for fifteen recombinant inbred lines (RILs) against (Fusarium oxysporum f. sp. lentis (Vasd. Srin.) Gord.). The multilocation agronomic evaluation of both crosses showed better results for earliness, desirable seed yield and Fusarium wilt resistance under two agro-ecological regions of north-western India. These better performing recombinants of ILL8006 × ILWL62 and ILL10829 × ILWL30 can be advanced for further genetic improvement and developing high yielding disease resistant cultivars of lentil.The development of transgressive phenotype in the segregating populations has been speculated to contribute to niche divergence of hybrid lineages, which occurs most frequently at larger genetic distances. Wild  Lens culinaris Medikus subsp. culinaris) is a rich in protein (22–35%), minerals  and vitamins for human nutrition  to measure the nature and magnitude of useful heterosis and other genetic variability parameters in F3 and F4 progeny for important characters and (3) to study the comparative agronomic performance of F5 derivatives of both wide crosses including resistance against Fusarium wilt.The Lentil , Pusa, New Delhi, India  and summer Himalayan nursery Experimental Farm at CSK, Himachal Pradesh Agricultural University Research Station, Sangla, India . The F1 hybrids were developed manually and the true hybridity of all F1 seeds were also confirmed by Inter Simple Sequence Repeats (ISSR) markers  method of breeding. In F3 and F4 generations, data were recorded on various quantitative traits viz; days to flowering, days to maturity, plant height (cm), number of branches plant−1, number of pods plant−1, 100-seed weight (g), seed yield plant−1 (g), biological yield plant−1 (g), and harvest index (%). The experiments on F3, F4, and F5 progenies were conducted in Augmented Block Design  = √A/VP × 100 as per Lush ; VG is genotypic variance and VP is phenotypic variance. The numerical data were also subjected to biometrical analysis using SAS software  coined by Koseoglu et al. (3 and F4 generations as: HF (%) = [(F3 and F4-BP)/BP] × 100%, where, BP is the mean value of the better parent of a particular cross.The means were adjusted using online software package for augmented block design developed by Rathore et al. . Before per Lush . Expecten et al. . Here, ku et al.  were als5 interspecific plant populations of cross ILL10829 × ILWL30 were screened against Fusarium wilt (Fusarium oxysporum f. sp. lentis (Vasd. Srin.) Gord.) reaction in the wilt sick plot at Pulse Research Farm of Rafi Ahmad Kidwai, College of Agriculture, Sehore Madhya Pradesh, India . The wilt sick plot was maintained following methods given by Bayaa and Erskine (5 interspecific derivatives were sown under Complete Randomized Block Design (CRBD) in two replications of 2.0 m row length and 30 cm apart. The plants were spaced in 10 cm of each row. However, resistant (PL639) and susceptible (L-9-12) checks were repeated every after 15 lines of each replication. The sickness of the soil was tested by raising seedlings of susceptible cultivars, which were wilted completely in 30 days after germination. Data were recorded for all the F5 plant populations on alternate days after 15 days. The scale was used to score the disease reaction for Fusarium wilt as suggested by Bayaa and Erskine  varieties taken as female parents (ILL8006 and ILL10829) hybridized with wild species used as male parents, ILWL62  and ILWL30 (L. ervoides). Overall pod and seed set percentage was calculated as 10.20 and 11.50%, respectively. The results revealed sufficient variability among genetic materials as evident from the analysis of variance (ANOVA) for various traits (significant at p = 0.05) studied and it was further reflected by the range, mean and coefficient of variation for majority of characters  to 45.77% (number of pods plant−1). Likewise, cross-combination of ILL8006 × ILWL62, heterosis mean ranged from −88.64% (Seed yield plant−1) to 38.15% (Days to maturity). However, in F4 generation of cross ILL10829 × ILWL30, the heterosis mean varied from −98.20% (seed yield plant−1) to 39.94% (days to maturity). The cross-combination of ILL8006 × ILWL62, heterosis ranged from −97.80% (seed yield plant−1) to 44.65% (days to maturity). Although, there were wide range of variation for majority of traits with respect to heterosis values in F3 and F4 generations. As far as other genetic parameters are concerned, in general, the extent of phenotypic coefficient of variation (PCV) was higher in magnitude than genotypic coefficient of variation (GCV) for all characters  and vector loadings for important agro-morphological traits in different generations are given in Table 3 generation of cross ILL8006 × ILWL62, PC1 accounted for 56.21% of variation, was loaded on plant height, number of branches plant−1, number of pods plant−1, seed yield plant−1 and biological yield plant−1, while PC2 accounted for 16.17% of variation, was loaded on 100-seed weight  were died. There were significant differences among the average percentage of died/wilted plants for 15 recombinant inbred lines (RILs), in which disease incidence was <10%. The mean wilt disease incidence score ranged from 1 to 9 scales with an overall mean of 6.18 and a coefficient of variation of 29.49%. However, the distribution of test entries in incidence against the pathogen showed that only two recombinant inbred lines namely RIL18 and RIL86 performed lowest wilted symptoms (<5%) and were rated as highly resistant  Gord.) as measured by the range, mean, and coefficient of variation including some other important genetic variability parameters in F3,F4 and F5 generations. The results revealed sufficient variability and differences in range of F3 and F4 generations for days to flowering and maturity of both crosses was due to early and late flowering segregants and the appearance of late flowering and maturity recombinants in all generations, suggesting fixation of late maturing wild alleles in the background of cultivated varieties  breeding methods and were used to compare the relative efficiency of these methods for maintaining genetic variability and desirable selection opportunities. They suggested that SSD method maintained more genetic variability than BP for most of the characters studied. As far as screening of F5 generation of cross ILL10829 × ILWL30 against Fusarium wilt is concern, all plant population of susceptible check variety died indicating that the disease incidence was sufficient for effective screening and selection of resistant genetic materials, and inoculums was homogeneously distributed in the wilt sick plot (Nene and Haware, 5 interspecific population derived from interspecific hybridization with L. ervoides can be a useful gene source for breeding Fusarium wilt resistant cultivars. This can be easily hybridized with other susceptible but productive lentil varieties by intraspecific or intravarietal hybridization programme (Bayaa and Erskine, L. ervoides is highly desirable, because they possess genes for adaptive variation and Fusarium wilt resistance and may further produce other higher yielding derivatives upon hybridization with cultigens, other than we already achieved in the current study. Furthermore, the common better performing F5 recombinant lines selected from Delhi and Shimla centers reveals their wider adaptation and potential for developing high yielding cultivars of lentil and these lines can also be utilized as donors for further cross- breeding purposes in lentil genetic improvement (Singh et al., Lens species against anthracnose (Fiala, L. ervoides and subspecies L. culinaris subsp. orientalis is quite relevant for diversification of cultivated gene pool. The following results were concluded as wild Lens taxa are invaluable source of useful genes and alleles for important agro-morphological traits and resistant against Fusarium wilt. We also found considerable fruitful heterosis for important characters both in F3 and F4 wide cross populations including highly resistant derivatives against Fusarium wilt. Further, multilocation evaluation of these crosses manifested consistent desirable expression against earliness and seed yield under two locations, suggesting their wider adaptation. The useful genetic materials are being advanced for further breeding and desirable selection.Pattern analysis demonstrates that the most important characters with greater weight contributing to total variation are plant height, number of branches planthlbaurer , in whice Fiala, , ascochye Fiala, , Stemphye Fiala,  and yiele Fiala,  have beeMS: conceived the study and draft research paper. JR, BS, SK, DS, ASax, and AH: Helped in data recording and analysis. ASar: provided wild species from ICARDA and supported this research in India.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.


Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation  were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060) and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) of 1800 km Knowledge of the genetic structure and gene flow in wild animal populations is crucial for making decisions to improve their sustainability. Factors known to influence the genetic structure and gene flow in animals include behavioral traits such as dispersal, social behavior and mating systems , 2, landCanis simensis) [Puma concolor) [Lynx lynx) [Ursus arctos) [Panthera onca) [Canis lupus) [Panthera tigris). In addition, knowledge of the patterns of gene flow is crucial for developing conservation plans by identifying population units and source populations that require management [Large carnivores have the ability to go across long distances and endure in diverse environmental conditions , 12. Howimensis) , pumas (oncolor) , Eurasianx lynx) , brown b arctos) , jaguarsra onca) , and Isls lupus)  has beennagement .Panthera tigris tigris) is found in six tiger landscape complexes in India [2, one of the 42 global source sites of tigers [2) than the national average in India (300 people/km2) [The tiger is an iconic species for the conservation initiatives because of its role as an apex predator in various ecosystems. All 13 tiger range countries have been experiencing profound economic growth over the last two decades , and as in India . Of thesf tigers , is a unf tigers , 35. TALple/km2) , hence mThe tiger is found in patchy habitats with forests, agricultural land, and human habitations in the TAL region of India . The wesSeveral ecological studies have emphasized the need to reduce anthropogenic pressure and restore corridors to provide a better opportunity for large mammals to move between the protected areas in WTAL , 38, 39.Reduction of anthropogenic pressure has been shown to be effective in tiger management in this region. For example, the Gujjars, a pastoralist community in WTAL, were relocated from the eastern part of RTR, facilitating the recolonization of this habitat by tigers from the source population of CTR , 38. RedIn the absence of ecological and biological details on movements of tigers, genetic characteristics can be used to understand the responses of species to the landscape and anthropogenic features. However, most genetic studies conducted on the Bengal tiger have been either in some way focused on the global status , 42 or wTherefore, we sampled tigers across most of the WTAL region and assessed the level of genetic connectivity and the population’s genetic structure in this globally significant tiger landscape. Given the previous ecological knowledge and the lack of genetic information, the present study focused on the following objectives: (1) genetic characterization and determination of population structure; (2) determination of the effect of anthropogenic pressure and recent developmental activity on genetic structure; (3) tracing the demographic history of the Bengal tiger in WTAL.All the blood, tissue and skin samples used in the present study were from tigers that had died naturally or in conflicts, and were provided by the Forest Department, Uttarakhand, to the national wildlife reference sample repository at the Wildlife Institute of India. Tiger scat samples were collected noninvasively without animal capture or handling. Therefore, sample collection did not require any handling of the animals. All necessary permissions to collect and store the samples at the national wildlife reference sample repository were obtained from the Ministry of Forest, Environment and Climate Change, Government of India and Forest Department, Uttarakhand (letter No. 1/29/2003-PT).2, including RTR (Rajaji Tiger Reserve), CTR (Corbett Tiger Reserve) and the adjoining forest areas, falling within the Bijnore, Lansdown, Ramnagar, Terai West, Central and Terai East forest divisions (FD) of TAL. There are several identified corridors  connecting tiger reserves and FDs in WTAL  were used previously in a study by Singh et al. [A total of 71 tiger samples  available at the Wildlife Institute of India were used. All tissue, blood and scat samples were collected between 2005 and 2014 across WTAL  by the Forest Department of Uttarakhand. Scat samples  of the field-collected tissue and 60% (7 of 12) scat samples from WTAL were used to address genotyping error. Each sample was genotyped three times, and the maximum likelihood of allele dropout (ADO) and false allele (FA) error rates were quantified using PEDANT version 1.0 with 10,000 search steps for enumerating each error rate . The scoHE), observed heterozygosity (HO), mean number of alleles, and allelic richness (AR) were estimated using FSTAT [HWE) was checked with the null hypothesis of random union of gametes at each locus within and across sampling locations at each study area using the exact test [LD) among all the locus pairs was also calculated using GENEPOP [FIS) was estimated for the whole WTAL and for the two sampling sites (RTR and CTR) according to the method of Weir and Cockerham [Genetic diversity measures, expected heterozygosity (ng FSTAT . The Haract test  in GENEPact test . Bonferr GENEPOP . Wright’ockerham  using GEockerham .NE) was calculated using an approach based on the LD as performed in LDNe 1.31 [Pcrit was set to 0.02, which provides a balance between precision and bias from rare alleles [The effective population size , while others used both multilocus genotype and geo-referenced information (e.g. TESS and GENELAND). Multivariate ordination analyses, such as the discriminant analysis of principle component (DAPC) and spatial principle component analysis (sPCA) were also used, as these can provide a useful validation of Bayesian clustering output , 64 not LOCPRIOR = 1) and without prior (LOCPRIOR = 0) knowledge of sampling locations. A series of 20 independent runs was conducted for each value of K between 1 and 10, with a burn-in period of 50,000 iterations and data were collected for 500,000 iterations. STRUCTURE was run using a data set comprising samples from (1) WTAL, including RTR, CTR and the adjoining FDs and (2) CTR and the adjoining FDs. Using the posterior probabilities of the data for a given K (ln P (K)) and the second-order rate of change of the log probability of the data between consecutive values of ΔK [q) above 0.7 as a realistic cut-off value to assign an individual to a population.STRUCTURE  uses a Bes of ΔK , calculaes of ΔK , the mosTESS v.2.3  was run The presence of null alleles may bias the results obtained with the Bayesian approach because of deviations from the HWE. Multivariate analyses constitute an alternative approach and can be used to validate individual Bayesian clustering. Discriminant analysis of principal components (DAPC), a non-model-based method that has been developed recently and implemented in the adegenet R package , provideFST was used as an indirect measure to examine the historical gene flow. It was calculated using Arlequin 3.5.2.1  [The pairwise ization) . This paization)  was also−7 iterations, of which 1×10−7 was discarded as a burn-in. Multiple runs were carried out with different seed numbers and delta values to ascertain the final parameter that would accept 40–60% of changes in the total chain length and to examine convergence and consistency among runs.Further, three more analyses, i.e. the likelihood-based estimator, posterior probability distribution, and sibship analysis, were used to identify migrants between RTR and the source population (CTR) and residents. We categorized as a migrant an individual that does not originate from the sampled population and a resident (non-migrant) as an individual that originates from the sampled population. The recent migration (over the last 5–6 generations) was calculated using a Bayesian MCMC method implemented in BAYESASSv.1.3 . The metLh or Lh/Lmax) beyond which individuals could be assumed to be migrants [A likelihood-based estimator was also used to identify migrant, admixed and resident individuals. Exclusion probabilities were calculated using the Monte Carlo method of Paetkau et al. , becausemigrants . An alphmigrants .Sibship analysis is a novel approach in detecting migrants, admixed individuals and residents in a population and has been successfully used previously, for example for wolves . Waples http://www.ngdc.noaa.gov/dmsp/sensors/ols.html; accessed 23 August 2011) and analyzed it in ArcGIS 10.0 (ESRI 2011) software.The distribution and movements of tigers are largely governed by the availability of prey , the levWe did not observe any allelic dropout or false alleles in the tested tissue samples, which comprised 20% (n = 12) of all tissue samples. Within the scat samples, genotyping error rate varied among loci, however, ADO rate ranged from 0% to 17% and FA between 0 to 5% . The meaMNA) and allelic richness (AR), were 6.69 and 6.57, respectively. The observed and expected heterozygosity in WTAL were 0.50 and 0.64, respectively. Deviations from HWE were inferred for five loci  in CTR and in six loci  in the RTR tiger populations. When the data were tested globally, it was found that only three loci  were consistently showing deviations across the sampling sites. These three loci also showed the high frequency of the null allele  was significantly different from zero and was positive for both populations (0.18 for CTR and 0.31 for RTR) and the overall value was 0.23 (All the markers (n = 13) were polymorphic, with 4–10 alleles . The baswas 0.23 .G-W index lower than 0.68 is evidence of a bottleneck, whereas values greater than 0.68 would denote no bottleneck history. In the present data set, the G-W values were between 0.73 and 0.77 (The effective population size was estimated to be 81.2 (95% CI: 47.7–195.9) for the CTR and 46.8 (13.6 to infinite) for RTR populations . The resand 0.77 .The Bayesian cluster analysis with STRUCTURE indicated two as the most probable number of genetic clusters (K = 2), by the mean likelihood (mean ln P (k) = -1267)  and DeltPopulation clustering analysis with spatial information implemented in TESS gave results similar to that of STRUCTURE with locprior information and suggested that there are two clusters in WTAL, with a few individuals migrating between these see . GENELANTaken as a whole, the different Bayesian clustering methods converged in identifying two distinct genetic clusters, i.e. RTR and CTR including adjoining FDs. The third cluster detected by GENELAND supports the subdivision of CTR and its adjoining FDs also identified by STRUCTURE . The mulFST value  between RTR and CTR tiger populations in WTAL suggested moderate historical gene flow among the populations. The level of genetic differentiation in CTR and adjoining forest divisions suggested high gene flow between these populations  also suggests significant differentiation between the populations , habitat quality characteristics , and the extent of anthropogenic factors  showed that WTAL had no large scale differences in the habitat quality and abundance of prey species but protected areas are relatively better in these aspects than other FDs . HoweverHO = 0.50, HE = 0.64; AR = 6.5) in tiger populations from WTAL. However, all of these estimates are lower than those reported in Bengal tiger populations from other regions  in India [HE = 0.502±0.027) in comparison with stable, viable populations (HE = 0.677±0.012) [FIS) has probably already affected the population. Philopatric felids that are threatened by poaching are known to have high FIS value as have been reported by other studies in viz tiger (Panthera tigris tigris) [Panthera pardus pardus) [Panthera leo) [Puma concolor) [Leopardus pardalis) [This study revealed the existence of a moderate level of allelic diversity and genetic variation  . However tigris) , 46, Afr pardus) , Africanera leo) , puma (Poncolor) , and oceardalis) . Recent ardalis) , 46, 97.ardalis) , which mardalis) . Howeverardalis) . Still, FST = 0.060) between CTR and RTR provide evidence that the Rajaji–Corbett corridor is more affected by anthropogenic disturbance in comparison to Kosi River and Nihal Bhakra corridors. The significant differentiation and high gene flow between CTR and Ramnagar FD (i.e. FST = 0.04) suggest that the corridor between these populations is functional. There is no differentiation (FST = 0.01) between CTR and the Terai East, Central and West FDs, indicating that there is sufficient migration and gene flow. Most of the eastern parts of CTR experience relatively low disturbance compared to the western part of CTR  might be due to the presence of a weak population structure . The priDetection of first-generation migrants (GENECLASS 2) and asymmetric migration in the last three to five generations (BAYESASS) between CTR and RTR provides evidence of migration between the populations even with this level of disturbance. Two migrants and one admixed individual were detected between RTR and CTR, which suggests that the Rajaji–Corbett corridor is functional but at a low scale. BAYESASS identified contemporary migration and suggested that there is asymmetric migration from CTR to RTR, with a rate of more than 5% m = 0.089). This asymmetric gene flow is characteristic for source–sink population dynamics, with individuals moving from more stable, higher density populations (CTR) into a neighboring low-density population (RTR). Emigrant tigers from CTR to eastern RTR are probably exploring areas of low disturbance in order to settle there. Harihar et al.  reported. This asIn Asia, the TAL region is one of the most threatened and fragmented landscapes , and theEucalyptus spp., Ailanthus excelsa, Populus ciliate) to meet industrial needs. Johnsingh and Negi [2) in 2000, the authors recorded only three pugmarks of tigers and emphasized the seriousness of the anthropogenic pressure in some parts of this landscape. Joshi et al. [The increasing human population and its demands and various development-related infrastructure projects have broken the connectivity of the forest in this tiger landscape, as evidenced in night light intensity . Variousand Negi  reportedi et al.  also repi et al. . Recent i et al. , 39 alsoSeveral ecological studies carried out in this landscape , 3839 hOur results have important implications for the management of the tigers in the WTAL region.Our data suggest the presence of low to moderate gene flow among different populations in WTAL. Therefore, we suggest immediate conservation strategies to minimize anthropogenic factors especially in the two identified corridors, i.e., C1 and C2 . MovemenThe GLSI, GENELAND and allele sorting analyses towards the east in Corbett between Ramnagar and Terai east FDs  around cAs tiger are philopatric, related individual are expected in a stable population. However the observed distinct genetic clusters (both Bayesian and non-Bayesian), significant genetic differentiation, and low sibship relationship between CTR and RTR reveal the absence of a viable stable population in the eastern RTR (Chilla). This may also be supported by the presence of high turnover of the individuals observed during camera trapping, though the area could sustain between 11 and 15 tigers . This maBesides habitat fragmentation, poaching has been a major threat in this landscape because there are large numbers of villages in the plains of southern TAL. In a habitat that follows a “stepping-stone” pattern, emigrants have higher probability of coming in contact with human habitation while dispersing. Therefore, the observed genetic diversity and viability of this source population in CTR may be maintained through high reproductive success and by providing adequate protection in the adjoining areas so that floater males are able to contribute to the gene pool, which will reduce inbreeding.To maintain connectivity and avoid human–wildlife conflicts in this landscape, the measures that have been suggested previously , 47, 48 Monitoring of genetic characteristics across this landscape at least once every five years is suggested so the appropriate corrective measures could be taken in case the level of genetic structuring increases.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S1 Fig(DOCX)Click here for additional data file.S2 FigK = 2.Individual assignment probabilities of Bengal tiger to genetic clusters using the model-based program TESS run of (DOCX)Click here for additional data file.S3 Fig(a) Results with RTR, CTR and adjoining forest divisions; (b) results with CTR and adjoining forest divisions. In the bar plots of both figures each individual is represented by a single vertical colored line and lengths of colored line is proportional to each of the inferred clusters.(DOCX)Click here for additional data file.S4 FigContours are component scores representing similarity across the landscape.(DOCX)Click here for additional data file.


Potato has a narrow genetic base which is due to its development, as it takes its genetic root from a few genotypes originated from South America.Solanum tuberosum L.) genotypes originated from different geographical regions.The objective of this study was to assess the genetic relationships among potato (This study has rendered 25 useful SSRs and EST-SSRs that were located in pre-existing genetic maps, fingerprinted in a collection of the 47 potato genotypes from America, Europe and Iran.The number of alleles per locus ranged from 2 to 9 with an average of 6.22 alleles per locus. UPGMA dendrogram, constructed from microsatellite data based on Jaccard similarity coefficient slightly clustered the American and European potatoes according to their geographical distribution. Iranian genotype, "Istanbuli", joined to a group with American genotype. The results indicated that American genotypes show the highest expected heterozygosity compared to the European genotype. This result was expected due to the narrow genetic base of European potatoes considering their origin from a limited number of introductions.It could be concluded that SSR is an appropriate marker for evaluating genetic diversity within and among potatoes from different geographical regions. Solanum tuberosum L., Solanaceae family) is currently the subject of the highest production rate in the most developing countries. Potato is spread in most countries in Europe as an agricultural crop and consumed as a food product. The most important cause of its distribution was providing food, preservation, and eradication of the poverty  and genetic characteristics (such as protection against many devastating pests and pathogens). Together, these attributes present a significant barrier to the potato improvement using classical breeding approaches. Little is known about the genetic diversity of the improved esources . Identifesources . Severalesources -7.S. tuberosum cultivars  have identified about 112 potato microsatellites which were located on all 12 chromosomes of the genome (Simple sequence repeat (SSR) or microsatellite markers are highly polymorphic, abundant in the genome, and co-dominant. The first potato SSR study was based on DNA sequences from public databases . SSR marultivars -10. MilbSubsequently, SSRs has been used for studying the genetic relationship and distances between wild and cultivated potato cultivars -16. SSR Although Iran is definitely one of the potato producers in the Middle East, reliable information on the relationships among the cultivated potatoes in Iran, also in addition to the origin, and characteristics of an Iranian potato “Istanbuli” is limited. Furthermore, approximately all varieties which are cultivated for the commercial purposes and used in the evaluation of the breeding programs were introduced from European countries, especially from Netherlands and Germany, nd recently from the United States. Therefore, as the main goal, the focus of the present study was an investigation of the genetic diversity and phylogenetic relationships among European, American, and an Iranian (Istanbuli) potato genotypes using SSR and EST-SSR markers. In addition, there were some colorful potato tubers that have been introduced to Iran which we didn’t have any information about their phylogenetic relationship with the other potatoes that have been classified by several molecular markers . Therefoin vitro propagated cultivars, washed three times in distilled water, were frozen in liquid nitrogen, and kept at - 80°C. Genomic DNA was extracted using the CTAB method described by Murray and Thompson, 1980  with the length of 18 to 20 oligonucleotides, Tm between 50 and 60°C and amplification product length between 100 -250 bp.Forty-seven potato genotypes were analyzed using 25 microsatellite primer pairs . Six ESTTaq DNA polymerase (CinnaGen Co.) and approximately 10-20 ng of genomic DNA.All reactions were performed in a Mastercycler gradient 96 thermocycler . PCR cycling conditions consisted of an initial denaturation step at 95°C for 3 min, followed by 30 cycles of 95°C denaturation for 1 min, 30 s at optimal annealing temperature , 0.2 mM dNTPs, 0.3 μM of each forward and reverse primers, 1.5 mM MgCL2 1 unit of perature  and 72°CPCR products were discriminated on 12% non-denaturing polyacrylamide gel electrophoresis in 1X TBE buffer along with 100bp DNA ladder (Fermentase) and visualized by silver staining .2, where gi is the frequency of the ith genotype , expected heterozygosity (He), Shannon’s Information index (I), and the gene flow (Nm).POPGENE 1.32 software  was usedhttp://pritch.bsd.uchicago.edu/structure.html) by two independent runs of K = 1-2 using the admixture model with 10,000 repetitions of MCMC.The program STRUCTURE 2.3.3 was applied to classify individuals into their origin and identification of the genetic relationship as well as ancestral source populations of the potato’s genotypes   of the polymorphic loci revealed that most loci, except STI033, STM0031, STM2022, ST21/22, F < 0.01) . ConsideThe number of alleles detected per SSR locus ranged from 2 (STM1049) to 9 (STM1104), respectively . A totalPIC values for 25 microsatellites and EST markers varied from 0.12 to 0.70. The high number of polymorphic bands, considerable discriminatory power, and reliable pattern of productivity recommended SSRs as reliable tools in evaluating genetic diversity among various potato variants. In this research, the amplification efficiency of EST-SSR markers was much higher than that of genomic SSRs.The genetic relationships among 47 potato genotypes were investigated by cluster analysis using Jaccard’s similarity coefficients and UPGMA algorithm (cophenetic correlation coefficient of 0.821).UPGMA dendrogram was clustered for American and European potatoes according to their geographical origin . AlthougPrinciple component analysis (PCA) based on genetic similarity matrix has revealed that the first three principle components (PCs) account for 30.14% of the total molecular variation, showing SSR and EST-SSR markers are distributed through the genome.Therefore, genetic relationships assessment among accessions should be established based on cluster analysis or more numbers of PCs .He) and Shannon’s information index (I), as the two useful intra-region gene diversity indices, ranged from 0.4710 to 0.4879 and from 0.8306 to 0.7404, respectively. Among the groups, the highest expected heterozygosity was observed in American group.Forty-seven potato genotypes were grouped into two groups; European and American. We waived the Iranian sample, Istanbuli, in this grouping since it was merely one genotype. All the used loci were polymorphic within and among each geographical group. The mean value of expected heterozygosity      , Ashkena. 2001) , Ghislai. (2004) , and Fei01 , Ghis98 , Ashk. 2005) -32. Besi. (2005) -34.The  -32. Beset al. (2005)  (The polymorphic information content (PIC) and the polymorphism rate (P) were used to estimate the genetic diversity. High polymorphism results were observed in the primer pairs with PIC > 0.5. The mean PIC value obtained in this study was 0.42, indicating that SSR markers could discriminate medium loci polymorphism which is useful for genetic variation of the potato genotypes in this research as well as being in agreement with the results of Feingold et al. 05 (20) a. (2009) .et al. (2002)    that hav. (2009)  that havThe lack of clear discrimination for Iranian genotype from that of American in the present clusteranalysis reflects low genetic differentiation between them. This result is in controversy with the study which showed a genetic similarity of the Iranian genotype, Istanbuli, with the European potatoes . Some poNm = 3.8668) among American and European potatoes may be explained in part by the clonal propagation and existence of a common ancestor (The high relative gene flow (ancestor . The genancestor  when it ancestor -15.In conclusion, the SSR and EST-SSR markers with sufficient polymorphism can be successfully used for assessment of genetic diversity and population structure of the potato germplasm. The close genetic relationship between American and European potatoes could show the existence of common ancestors that might be due to an inherent narrow genetic base from which the potato gene pool was domesticated, combined with the historical migration of germplasm, and potato’s propagation manner.


O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing  and for chloroplast variation using Sanger sequencing (25 polymorphic sites).Understanding population structure of the wild progenitor of Asian cultivated rice  with traditional species designations, O. rufipogon  and O. nivara , differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies.Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.Our results suggest that the cultivated The online version of this article (doi:10.1186/s12284-016-0119-0) contains supplementary material, which is available to authorized users. Oryza rufipogon species complex (ORSC) is the wild progenitor of Asian cultivated rice, O. sativa  or annual (O. nivara), based on morphology, life/mating habit, and the ecological habitat in which they are found. The perennial form, O. rufipogon, is reportedly photoperiod sensitive and cross-pollinated; it is aquatic and found in areas with year-round standing water, such as swamps, river beds, and marshes. In contrast, O. nivara is considered to be annual, upright, photoperiod insensitive, and predominantly self-fertilized; it is found in seasonally wet habitats such as lake shores and river banks, which undergo periodic flooding with the monsoon rains  and indel analysis for nuclear DNA, and Sanger sequencing for chloroplast DNA to: 1) characterize the population structure of the ORSC, 2) determine the relationship between the subpopulations of the ORSC and O. sativa, 3) elucidate the relationship between ORSC population structure, geographical distribution, annual-perennial life habit , and archaeo-botanical history, and 4) select a subset of diverse accessions as the basis for developing an immortal wild diversity panel for future genetic studies.Previous studies have sought to interpret the genetic and geographical relationships among accessions in the ORSC . W2 accessions were also widely distributed across South and SE Asia, but were the predominant group in southern India and Sri Lanka. W3 accessions were found only in the geographically isolated Papua New Guinea region and were not found on the mainland. W4 accessions were widely distributed across SE Asia, extending west into northern India and east into southern China and Taiwan. W5 accessions were mainly from Nepal and western India, and were closely related to W2. W6 accessions were the predominant group in eastern Asia, found mostly in China and Taiwan. Interestingly, of the 16 W1/W6 admixed accessions in our collection, seven were from China or northern Vietnam, and nine were collected in Myanmar, NE India or Bangladesh  , and contrasted sharply with test results in W1, W4 and W6 accessions, the most widely distributed and most highly admixed subpopulations of the ORSC    accessions, the W4 population with aus (orange) accessions, and the W6 population with japonica (blue) accessions . In contrast, W2, W3 and W5 did not cluster with any of the cultivated groups. These data support the hypothesis that the aus, the indica and the japonica subpopulations of O. sativa evolved from genetically distinct ORSC lineages. Further, they underscore the finding that the aus subpopulation is distinct from both indica and japonica and represents one of three domestication foci for rice in Asia  and Fst values to determine the degree of genome-wide divergence between wild and cultivated groups. These comparisons supported the close relationship between W1 and the indica subpopulation, W4 and aus, and W6 and japonica, while W2, W3 and W5 were maximally differentiated from the O. sativa subpopulations  accessions were nested within one of the W1 clusters, aus accessions (yellow) emerged from one branch of the W4 cluster corresponding to samples from Bangladesh and India, the temperate japonica, tropical japonica and aromatic subpopulations (shades of blue and pink) emerged from the W6 group with long branch-lengths, and the three independent groups, W2, W3 and W5, were highly divergent based on long branch lengths with strong bootstrap support in the rooted NJ tree. W1 was found at the root position, and clustered with the O. officinalis (CC) outgroup, suggesting that the root position is among the W1 lineages. This interpretation was supported by the NJ dendrogram   and W6 (japonica-like) groups  were found to carry one or both domestication traits  and the RC gene (for pericarp color). Both genes had been previously cloned and the functional polymorphisms associated with the loss of color in O. sativa were determined to be a 22 bp deletion in BH4  allele at RC carried an O. sativa extended haplotype around the RC locus while accessions carrying the wild type allele carried an ORSC-specific haplotype around RC. , consistent with the evidence that these two ORSC groups were most frequently admixed with O. sativa.It is noteworthy that ORSC. When the six wild subpopulations identified in this study were analyzed in relation to the two primary species designations, O. rufipogon  and O. nivara , we observed a significant correlation  , W4 (64 %), and W5 (83 %) accessions were classified as O. nivara  in India, Bangladesh and SE Asia, as well as between W1 and W6  across SE Asia and into southern China. In this study, ORSC samples collected from Guangdong and Guangxi in southern China were related to both indica and japonica, while samples collected north of the Nanling mountains, in the central sub-tropical zone, were most closely related to japonica. The admixed nature of the ancestral W1 subpopulation is parallel to the scenario recently reported for barley    more recent gene flow continue to dilute the once-distinctive gene pools .To further examine the extent and direction of gene flows among and between O. officinalis (CC) and O. australiensis (EE)) were very distinct from those of the ORSC. The outgroup haplotypes joined the network at cpGroup V, a haplotype found almost exclusively in W1 and admixed individuals, further supporting the ancestral nature of the W1 group. The network had several loops; given the historically non-recombining nature of the chloroplast genome, loops are interpreted as being due to substitutional parallelisms and reversals rather than to recombination. This reticulate structure complicates interpretation of the network; however, outgroup rooting clearly split the network into two large groups strongly associated with the two major O. sativa varietal groups, JAPONICA  and INDICA , referred to as cpGroup I (or the JAPONICA-cpGroup) and cpGroup VIII (or the INDICA-cpGroup), respectively. cpGroup I haplotypes were found in 87.5 % of cultivated japonica cultivars and 58.8 % of W6 accessions, the most closely related ancestral group, while cpGroup VIII haplotypes were found in 77.8 % of cultivated indica, 80 % of cultivated aus cultivars, and only 47.6 and 48.4 % of the related W1 and W4 accessions, respectively. The divergence between these two chloroplast groups is not as obvious in the ORSC accessions as it is in the O. sativa groups. This is consistent with the results of the Mantel test suggesting that geographical dispersion of ORSC populations and admixture with O. sativa  has eroded the genetic composition of the ancestral populations from which O. sativa was originally domesticated.Haplotypes of outgroups , whereas haplotypes of the latter group were found only in W1 accessions  which is widely used to differentiate japonica  from indica/aus  in phylogenetic studies , while the ancestral SNP (“A”) was exclusively found in all out-groups and other AA genome species  and W5  both harbored the “G” SNP within the non-deletion allele , while the rest of the wild subpopulations collected across South and SE Asia and southern China, contained a mixture of all three chloroplast genotypes: the 69 bp non-deletion type with SNP-A, 69 bp non-deletion type with SNP-G, and the 69 bp deletion type.We next examined specific chloroplast sequence polymorphisms that were shared between ORSC and O. sativa, where deep coalescence (incomplete lineage sorting) and recent hybridization (admixture) both play a role. Because these two processes produce the same signature of incongruence, it is difficult to disentangle them or to accurately interpret the timing of events that contribute to the patterns of diversity among and between populations.The fact that chloroplast haplotype patterns are not identical to the nuclear genome groups in either wild or cultivated rice is not unexpected; rather it underscores the complex population dynamics in both the ORSC accessions were selected to represent the major subpopulation groups as part of the Wild Rice Diversity Panel 1 (W-RDP1)  seed stocks represent a valuable genetic resource as the basis for future genetic studies in this crop wild ancestor.Based on these studies of nuclear and chloroplast variation, 95 O. rufipogon using the traditional annual-perennial nomenclature system, and has relatively rapid LD decay, consistent with the out-crossing nature that is characteristic of most perennials, while W5  has >80 % of individuals classified as O. nivara and maintains LD over larger distances than any other subpopulation, in keeping with its predicted inbreeding habit.To gain further insight into the evolutionary history and population dynamics of the wild subpopulations, we compared levels of nucleotide diversity (π) and linkage disequilibrium (LD) decay among groups. Of the wild accessions not closely related to any cultivars, W3 and W5 behave as expected for small isolated populations: their within-population diversity is low,  is high,  represent an underappreciated genetic resource.The W4 subgroup is also characterized by high estimate of π (similar to that of W2), but has rapid LD decay. It has a distinctive relationship with the ia Khush . Its deeORSC accessions collected in China and Taiwan, the presumed center of domestication for the japonica subspecies of O. sativa  to southeast (W3) axis, with the subpopulations most closely affiliated with O. sativa  bracketed by those extremes. , W5  and two outgroups, O. officinalis (CC-genome) and O. australiensis (EE-genome), suggesting the possibility that the geographically isolated W5 and W3 subpopulations may have radiated from a common ancestor at about the same time. Isolated populations such as these that survive in natural refugia are of great interest for genetic studies and pre-breeding applications in rice improvement because they are likely to harbor variation rarely seen in cultivated rice. They also warrant special conservation efforts because they are increasingly threatened by habitat destruction.Geographically isolated Oryza species, particularly those native to Australia and New Guinea, is of interest to expand our understanding of both the AA genome and more distantly related Oryza relatives that exist in isolated populations in that part of the world  along with cultivated O. sativa in the form of mixed/contaminated seed lots through commercial trade and human migration. This, along with back-introgression from O. sativa to ORSC in farmer's fields, could explain the presence of such geographically unexpected admixed subpopulations. The fact that W1/W6 admixed accessions are found in eastern China and as far west as NE India is consistent with dissemination by humans and with genetic and archeological evidence documenting hybridization between japonica rice from Southern China and proto-indica rice in North India  and O. nivara , classified based on morphology, mating habit, and ecological habitat, suggest that the cultivated japonica subpopulation derives from a perennial ancestor, the aus subpopulation from an annual wild relative, and that indica is the result of admixture between divergent annual and perennial wild ancestors. Our findings are consistent with the hypothesis that the annual habit likely arose multiple times in response to diverse climatic factors across a broad geographical range. Understanding the relationship between subpopulation structure, ecology and geography is crucial for breeding programs seeking to harness the wealth of natural variation that resides in crop wild relatives. As part of this study, we also developed a wild diversity panel consisting of 95 purified (inbred) accessions representing the range of variation in the ORSC complex as the basis for future genetic studies.Six wild subpopulations were identified in a collection of 286 diverse ORSC accessions were imported from the International Rice Germplasm Collection  at the International Rice Research Institute in the Philippines and from the National Institute of Genetics (n = 3) in Japan   and one Australian O. rufipogon , and two O. australiensis ,   between the first and last SNP.Pairwise model Li . Geneticmodel Li . For estRC locus on chromosome 7 were constructed on 81 ORSC accessions from the Wild Rice Diversity Panel (W-RDP1)  were used. The final set of SNPs used to construct the haplotype map in Fig. Extended haplotypes (EHs) spanning a 580 kb region flanking the r2 between SNPs) within populations was calculated in 10 Megabase windows using Plink v1.9  and two O. australiensis (EE) . Ancestral and derived states were defined for all 25 polymorphic chloroplast loci based on allele frequencies estimated across 18 Oryza species Additional file 2: Figure S1.Analysis of model complexity (K). (PDF 174 kb)Additional file 3: Figure S2.ORSC and with O. sativa. (PDF 362 kb)Population structure in the Additional file 4: Figure S3.ORSC based on SNP data. (PDF 232 kb)Neighbor Joining (NJ) tree from the Additional file 5: Figure S4.ORSC. (PDF 892 kb)The relationship between geographical and genetic distance of the Additional file 6: Table S2.ORSC and five O. sativa subpopulations based on GBS-SNP data. (XLSX 12 kb)Pairwise Fst and genetic distance among six Additional file 7: Table S3.ORSC accessions grouped by subpopulation (at K = 6). Number of ORSC accessions with hull color and pericarp color phenotypes, grouped by subpopulation. (XLSX 11 kb)Pericarp and hull color of 157 Additional file 8: Table S4RC extended haplotype analysis  (XLSX 11 kb)Number of accessions included in Additional file 9: Figure S5.RC Haplotype Groups. (PDF 253 kb)Pericarp Color Associated with Additional file 10: Table S5.O. rufipogon and O. niva.ra.Figure S6.  Distribution of nuclear subpopulations within traditional species groups in the ORSC; rufipogon , O. nivara , and O. spontanea. (PDF 1329 kb)Chi-square statistic between genetic subgroups and two major traditional species groups, Additional file 11: Figure S7.Geographical distribution of samples based on traditional species nomenclature. (PDF 261 kb)Additional file 12: Figure S8.Chloroplast haplotype network including admixed samples. (PDF 598 kb)Additional file 13: Table S6AORSC chloroplast sequence polymorphisms. Table S6B. Oryza accessions from Genbank used to define ancestral vs derived mutations across the 25 chloroplast variable sites. (XLSX 18 kb)Additional file 14: Figure S9.ORSC subpopulation. (PDF 359 kb)Average DNA sequence diversity (π) within each Additional file 15: Table S7.Numeric LD Decay. (XLSX 14 kb)Additional file 16:Supplemental Text. Extended Materials and Methods SNP Information for Additional file 18: Figure S10.Distribution of GBS SNPs along the twelve chromosomes of rice. (PDF 119 kb)


Zearaja chilensis and Dipturus trachyderma) are the main component of the elasmobranch fisheries in the south-east Pacific Ocean. Both species are considered to be a single stock by the fishery management in Chile however, little is known about the level of demographic connectivity within the fishery. In this study, we used a genetic variation  to explore population connectivity at five locations along the Chilean coast. Analysis of Z. chilensis populations revealed significant genetic structure among off-shore locations , two locations in the Chiloé Interior Sea (Puerto Montt and Aysén) and Punta Arenas in southern Chile. For example, mtDNA haplotype diversity was similar across off-shore locations and Punta Arenas (h = 0.46–0.50), it was significantly different to those in the Chiloé Interior Sea (h = 0.08). These results raise concerns about the long-term survival of the species within the interior sea, as population resilience will rely almost exclusively on self-recruitment. In contrast, little evidence of genetic structure was found for D. trachyderma. Our results provide evidence for three management units for Z. chilensis, and we recommend that separate management arrangements are required for each of these units. However, there is no evidence to discriminate the extant population of Dipturus trachyderma as separate management units. The lack of genetic population subdivision for D. trachyderma appears to correspond with their higher dispersal ability and more offshore habitat preference.The longnose skates ( Dipturus batis (L. 1758), smooth skate D. innominatus (Garrick & Paul 1974), barndoor skate D. laevis (Mitchill 1818), longnosed skate D. oxyrinchus (L. 1758), white skate Rostroraja alba (Lacepède 1803), and the thornback ray Raja clavata L. 1758; where local extinctions have occurred as a result of continuous, unregulated fisheries  and geographic distance was also significant , supporting the hypothesis of isolation by distance of gene flow . One main cluster was identified using DAPC  . Howeverene flow . Populating DAPC  and, a sZch_MS13, Zch_MS10 and Zch_MS29 as monomorphic in this species and was thus excluded from further analysis. Evidence of scoring error was detected due to an excess of homozygotes at two loci (Zch_MS16 in SA and Zch_MS15 in VA). Deviation from HWE (P < 0.05) was observed at these loci and at locus Zch_MS19 in PM. However, no evidence of linkage disequilibrium was detected at any loci.Microsatellites alleles were analysed for 10 microsatellite loci for 95 individuals. Initial scoring identified three loci, D. trachyderma was lower than in Z. chilensis for the same loci ranging from two (Zch_MS6 and Zch_MS15) to six alleles (Zch_MS31 and Dtr_MS8) across all sampled locations  and pairwise FST test indicated no significant genetic differentiation among sampling locations (-0.035 to 0.041). However, significant differences were found between VA and PM    . DAPC ann waters .Zearaja chilensis and Dipturus trachyderma, two economically important elasmobranch fishes in South America. Mitochondrial and nuclear markers were used to provide insight into connectivity, genetic diversity and population structure along the Chilean coast from San Antonio in the north to Punta Arenas in the south.This study provides a genetic analysis of populations of The microsatellite loci (nDNA) analysis was not informative enough as expected for a nuclear marker to assess the stock structure of longnose skates. However, it is interesting that mitochondrial genome (mtDNA) provides resolution on population structure, even though mtDNA variation in elasmobranchs is notoriously low  and relaZ. chilensis might comprise three potential management units, whereas a single-unit harvest management strategy is currently employed in this fishery. For Z. chilensis, there were significant differences among all locations with the exception of Puerto Montt and Aysén. The latter two are located in the Chiloé Interior Sea and hence, might be expected to be a single, relatively isolated population. The pattern of mtDNA haplotype diversity among localities emphasises the likely susceptibility of longnose skates to local overexploitation. At Aysén, only mtCR haplotype Zch_CR2 was found in 100% of the individuals and at Puerto Montt it was found in 96%, emphasising the potential isolation of the Chiloé Interior Sea due to oceanographic features, such as cold subsurface currents, high freshwater contribution from precipitation and river discharges, and high depth profile (50 to 400 m) [Z. chilensis into the Chiloé Interior Sea and, as such, population resilience will rely almost exclusively on reproduction and self-recruiting by within- Chiloé Interior Sea adults.Our data revealed that populations of o 400 m) . Given tFuentealba & Leible , reporteD. trachyderma. The main disruption is detected between San Antonio and Valdivia in the north of the sampling area. Interestingly, 13% of specimens from Valdivia possessed a highly divergent haplotype. However, no significant population structure was found with mtDNA or microsatellite markers. Unfortunately, the low sample sizes for the Chiloé Interior Sea and Punta Arenas impeded resolution of population structure, and further research is required to assess the dispersal and connectivity of D. trachyderma along the Chilean coast.On the other hand, there were fewer mtDNA breaks in gene flow for Z. chilensis may suggest a lack of power in the microsatellite analysis. The power analysis conducted for this species shows that FST down to 0.01 could be detected with the sample sizes used here (n = 50 or less). Indeed, three population pairs were separated by significant FST of this magnitude, but FST lower than 0.01 measured in this study were not significant.The finding of genetic breaks between populations with mtDNA, but not with microsatellites for 2 area) [Z. chilensis, although we cannot confirm whether these migrations reflect small-scale movements due to preference and selection of particular habitats (e.g. nursery sites) or to natal philopatry.Aspects of the biology of chondrichthyan fishes may have the potential to influence the genetic findings such as the possibility of female regional philopatry to inshore egg-laying grounds. The mtDNA subdivision among locations may have been the result of such movements, with our samples comprising mostly juveniles that result directly from this reproductive behaviour. Natal philopatry is well-recognised among various marine vertebrates including elasmobranch fishes, but while it has been shown definitively for sharks , 73–76, 2 area) –81. ThesZ. chilensis and D. trachyderma are among the largest in marine fishes [Longnose skates are oviparous, producing egg capsules that contain a single embryo which spends weeks in the environment before hatching , 83. Alse fishes , 86 and,e fishes , 28. Thee fishes , 86. GivD. trachyderma inhabit deeper waters than Z. chilensis [D. trachyderma was described from the only mature female observed in Valdivia over a 10-year period of sampling . The smaller skate species (Z. chilensis) may have lower dispersal, with corresponding smaller home ranges and without extensive migrations; in contrast, the much larger D. trachyderma might be expected to have a greater dispersal potential. This proposed size of the home ranges is correlated with the pronounced genetic isolation by distance signature for Z. chilensis inferred from the microsatellite data. This relationship occurs when random mating does not occur within the entire population. Instead, there is an increased likelihood of mating among individuals in a local region as a consequence of the constrained dispersal potential of the species.The genotypes from microsatellite loci were not particularly informative regarding the spatial extent of stocks. We believe this is due to mating during the dispersal stage (non-egg-laying), where both sexes move into deeper water away from the coast as well as alongshore to seek suitable feeding habitats. Adult hilensis  and haveZ. chilensis in the past [The set of microsatellite loci used was carefully designed to detect any hybrids between the species, and discard this plausible hypothesis (hybridisation) as individuals of cryptic morphotypes have been reported for the past . The usethe past , 50.The synergy between genetic results and our understanding of biological features of longnose skates significantly increases the validity of our findings. For example, the addition of new genetic data has confirmed previous inferences about the reproductive and dispersal biology of longnose skates. The population dynamics uncovered represent an initial step towards an integrated stock and potential population connectivity assessment between South American countries. Our results elucidate new information for the sustainable management of the Chilean skate resources; however, appropriate management and enforcement actions from the Chilean government are needed to safeguard the species.Z. chilensis should be considered constrained and separate management arrangements are required for each of the management units detected. Currently, both longnose skates are caught by one single fishery widespread along the Chilean coast but only management measurements are enforced for Zearaja chilensis. There are no grounds to discriminate the extant population of Dipturus trachyderma as separate management units. However, as the fishery cannot positively separate any of the target species [Z. chilensis to be considered for D. trachyderma following the precautionary principle. The actual fishery management strategy and the low genetic diversity for D. trachyderma, raise concern over the conservation status of this species. The lack of genetic evidence for population subdivision appears to correspond with their higher dispersal ability and more offshore habitat preference.Our results provide evidence for three management units , and the spatial stock status for  species , we suggS1 TableMultiplex numbers are indicated in brackets.(DOCX)Click here for additional data file.


The prognostic value of signal transducer and activator of transcription 3 (STAT3) and phospho-STAT3 in breast cancer remains controversial in heterogeneous. The objective of this meta-analysis was to evaluate STAT3 and phospho-STAT3 expression on the prognosis of breast cancer patients.PubMed, Cochrane Central Register of Controlled Trials, Embase, Web of Science, Chinese CNKI, and Wan Fang were searched up to 19th June 2017. Studies which investigated the STAT3 or phospho-STAT3 expression of patients with breast cancer on the basis of patient survival data or survival curve were eligible.p > 0.05). p-STAT3 expression is unrelated to disease-free survival . Notably, the pooled effect predicts better breast cancer-specific survival with p-STAT3 overexpression . Results of subgroup analyses show that STAT3 overexpression indicates shorter OS  when excluding the heterogeneity test. Meanwhile, p-STAT3-positive patients have a significantly higher OS than their counterparts .This meta-analysis involves 12 studies and 4513 female patients with breast cancer. No clear relationship exists between overall survival (OS) and high expression of STAT3 and p-STAT3 (hazard ratio [HR] = 0.95, 95% confidence interval [CI]: 0.62–1.46, Positive STAT3 expression may indicate poor OS. However, p-STAT3, as a potential molecular biomarker for predicting chemotherapeutic effect, appears to have better prognostic value than STAT3. Signal transducer and activator of transcription 3 (STAT3), one of the seven-member STAT family of transcription factors, can be activated by tyrosine kinase signals and dimerized to phospho-STAT3 (p-STAT3) . STAT3 aTo gain insight into the correlation of breast tumor with STAT3/p-STAT3, Li CY et al. 2016) conducted a quantitative meta-analysis of seven studies published up to April 2016. They found that high expression of STAT3 and p-STAT3 predicts poor prognosis in East Asians, while a positive outcome was found in non-East Asians 016 condu. AccordiPubMed, Cochrane Central Register of Controlled Trials, EMBASE, Web of Science, Chinese CNKI, and Wan Fang were searched using the following keywords: “signal transducer and activator of transcription 3” or “STAT3”; “phosphorylated signal transducer and activator of transcription 3” or “p-STAT3” or “phospho-STAT3,” and “breast cancer” or “breast carcinoma” or “breast neoplasms” or “mammary cancer” up to 19th June 2017.Included studies were those that (1) recruited patients with the histologic type of breast cancer; (2) measured the expression of STAT3 and p-STAT3 in tumor tissue by immunohistochemistry (IHC); (3) provided data concerning the correlation between STAT3/p-STAT3 expression and survival outcome or clinicopathological information, including tumor differentiation, TNM stages, lymph node metastasis, hazard ratio (HR), and their 95% confidence intervals (CI) or sufficient survival data; (4) used overlapping samples, from which the most complete ones were selected.Exclusion criteria were (1) duplicate reports, ongoing studies, literature published as abstracts, letters, editorials, theoretical papers, reviews, and case reports; (2) studies on breast cancer cell lines and animal models but not based on human patients; (3) studies that assessed the effect of medication without reporting STAT3/p-STAT3 expression and breast cancer; (4) studies without sufficient survival data to obtain HR and 95% CI; (5) studies whose research methods and experimental design were apparently dissimilar from those of the selected studies.http://digitizer.sourceforge.net/) was used to read the graphical survival plot [Two investigators  independently examined all literature searches to recognize eligible studies, abstracted data from all studies, and crosschecked data. Controversial problems were resolved by discussions between the two examiners. For each included study, we recorded baseline characteristics, histology, stage, grade, estrogen receptor (ER) and progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) status, cut-off value of positive expression, antibodies used for IHC, survival curves, and HRs and their 95% CIs and OS, DFS, or cancer-specific survival (CSS) rate. If the only obtainable data of HR and 95% CI were in the form of the survival curve, then Engauge Digitizer version 4.1 , we adopted the random-effects model to estimate the pooled outcome. The pooled HR and 95% CI of the OS for all 10 studies showed no clear relationship to STAT3 and p-STAT3 overexpression  . Interestingly, pSTAT3-positive patients indicate better breast cancer-specific survival than pSTAT3-negative patients in the random-effects model .Considering the significant heterogeneity  Figure . MeanwhiI2 = 39.1% and p value of Q test for heterogeneity test = 0.131, we tested p-STAT3 again in the fixed-effects model  . Accordingly, we performed heterogeneity test and sensitivity analysis. Dolled F. (2003) performed a heterogeneity test by applying the Galbraith plot  when the result of the heterogeneity test is excluded   predicted good OS.Subgroup analyses of HR for the OS of STAT3 and p-STAT3 expression were performed. First, subgroup analysis was performed to estimate whether biomarkers (STAT3 and p-STAT3) of breast cancer are different from the analysis above Figure . Results) Figure . Howevert Figure . Subsequ3) Table . In all p value of Egger’s test (p = 0.791) did not indicate publication bias.The p < 0.0001) [p = 0.557) is unrelated to OS, Li CY et al. (2016) conducted a subgroup analysis and found that the pooled HRs of OS differ with the origin change of population [STAT3 is a vital cytoplasmic transcription factor, and activated STAT3 (p-STAT3) is upregulated by aberrant upstream tyrosine kinases; p-STAT3 transports information to the nucleus and controls gene expression, which is essential for cancer cell growth and survival . Xu YH e 0.0001) . Li MX e 0.0001) . ConsideY et al. 016 condup > 0.05). Thus, we reviewed the enrolled literature searches again and found that both Sheen C. (2008) and Li SJ. (2011) reported that STAT3 is related to poor clinicopathological parameters and poor OS [I2 = 49.10%, p < 0.001) in the fixed-effects model when the results of the heterogeneity test involving patients with node-negative breast cancer are excluded. Chen YJ. et al. (2013) reported that positive p-STAT3 expression possibly indicates poor OS in breast cancer because it is significantly associated with tumor formation, migration, and invasion. By contrast, our meta-analysis found that pooled positive p-STAT3 expression indicates significantly better OS  in the fixed-effects model. Prior studies on other types of cancer have reported a similar observation. Monnien F et al. (2010) detected the nuclear expression of p-STAT3 in 104 cases of advanced rectal cancer (T3–T4) by IHC [p = 0.001). Similarly, Sonnenblick A. et al. (2013) claims that high p-STAT3 expression is connected with improved OS only among breast cancer patients who received adjuvant chemotherapy [p < 0.001). Nevertheless, trials associated with breast cancer CSS and DFS were relatively rare. We expect an updated pooled effect about both CSS and DFS through further validation using a large cohort of patients and prospective randomized data in breast cancer.This meta-analysis involves 12 studies and 4513 female patients with breast cancer. This study found no clear relationship between OS and high STAT3 and p-STAT3 expression  by IHC . They ar) by IHC . They footherapy . These rAdditionally, STAT3 is phosphorylated by various upstream genes. Tell RW et al. (2014) demonstrated that p70S6K phosphorylation and JNK signaling could induce pSTAT3 formation in basal-like cancers, SRC Y527 and EGFR Y1068 phosphorylation prompt STAT3 phosphorylation in luminal A, and PKC α S657 and YB-1 S102 stimulate STAT3 phosphorylation in luminal B-type breast cancers . Meanwhip > 0.1), we could not prevent potential bias among these studies. Despite our significant efforts to gather additional relevant information, publication bias was still inevitable. Small-sample or negative studies are unlikely to be accepted and published. Furthermore, some reports did not offer sufficient data for HRs and 95% CIs. We obtained data by reading the survival rates presented on the graphical survival plot. Nevertheless, this method cannot completely eliminate inaccuracy. Authentic conclusions cannot be drawn in the absence of all relevant information. Thus, large-scale RCT studies with long-term follow up and a full description of survival events are indispensable.Although the present meta-analysis suggests the absence of publication bias (In conclusion, positive STAT3 expression may indicate poor OS. However, p-STAT3, as a potential molecular biomarker for predicting chemotherapeutic effect, appears to have better prognostic value than STAT3.Positive STAT3 expression may indicate poor OS. However, p-STAT3, as a potential molecular biomarker for predicting chemotherapeutic effect, appears to have better prognostic value than STAT3.