Diatraea saccharalis, is widespread throughout the Western Hemisphere, and is considered an introduced species in the southern United States. Although this moth has a wide distribution and is a pest of many crop plants including sugarcane, corn, sorghum and rice, it is considered one species. The objective was to investigate whether more than one introduction of D. saccharalis had occurred in the southern United States and whether any cryptic species were present. We field collected D. saccharalis in Texas, Louisiana and Florida in the southern United States. Two molecular markers, AFLPs and mitochondrial COI, were used to examine genetic variation among these regional populations and to compare the sequences with those available in GenBank and BOLD. We found geographic population structure in the southern United States which suggests two introductions and the presence of a previously unknown cryptic species. Management of D. saccharalis would likely benefit from further investigation of population genetics throughout the range of this species.The sugarcane borer moth,  Diatraea saccharalis (Fabricius) (Lepidoptera: Crambidae), is widely distributed in the Western Hemisphere throughout much of South America, Central America, the Caribbean, and the southern United States D. saccharalis are numerous D. saccharalis include crops such as sugarcane (Saccharum spp), corn (Zea mays L.), sorghum (Sorghum bicolor L.) and rice (Oryza sativa L.) D. saccharalis is considered an introduced insect pest Diatraea saccharalis was first reported as a pest in Louisiana around 1854 D. saccharalis larvae feeding in its cultivated host plants includes a decrease in plant sugar content and crop yields, reduction of plant biomass, and increased susceptibility to plant pathogens by providing points of pathogen entry The sugarcane borer, D. saccharalis has a broad geographic distribution in addition to a wide host plant range D. saccharalis may have been introduced into the southern United States. Genetically distinct populations of insects can vary in their susceptibility to natural enemies and other control tactics Although Diatraea species relies on morphological identification as there have been few genetic or molecular studies focusing on D. saccharalisD. saccharalis populations from Louisiana, Mexico, and Brazil found a Nei's genetic distance of 0.23 between the Brazilian population and those from Texas and Louisiana, while the genetic distance between the Mexico and Louisiana populations was only 0.02 D. saccharalis populations throughout its range found that a population from Valle del Cauca, Colombia, averaged 2.7% distance from other populations including those from Brazil; however, relationships between other D. saccharalis populations were difficult to resolve, perhaps due to the small sample sizes for many populations D. saccharalis from Central America, the Caribbean and the southern United States could contribute to a more comprehensive analysis of geographic population structure, to explore if D. saccharalis consists of a species complex or is indeed one widespread polyphagous species.Identification of D. saccharalis may have been introduced from different areas of this species range. The insect became a pest in Texas, Louisiana and Florida during different decades over the course of nearly a century. Classical biological control programs which released exotic natural enemies for control of D. saccharalis were conducted in the southern US and different parasitoid species established in Texas, Louisiana, and Florida Lixophaga diatraea Townsend (Diptera: Tachinidae), established in Louisiana but not in Texas or Florida. While the parasitoid wasp, Cotesia flavipes Cameron (Hymenoptera: Braconidae) failed to establish in Louisiana, it took hold in Texas and Florida In the southern United States, more than one genotype of D. saccharalis in the southern United States, to determine whether these regional populations of D. saccharalis are genetically distinct, possibly representing independent introductions and/or cryptic species. We investigated this question by collecting D. saccharalis in Texas, Louisiana and Florida and by examining their population structure using amplified fragment length polymorphisms (AFLPs). In addition, a 658 base pair region of the mitochondrial DNA COI gene was sequenced from several individuals from each southern United States population. The mitochondrial COI sequences were compared to publicly available COI sequences for D. saccharalis, to investigate potential source populations for those established in the southern US, as well as to estimate the number of potential cryptic species which may exist within this species.The objective of this study was to investigate the geographic population structure of Diatraea saccharalis from Texas, Louisiana and Florida were field collected as larvae or adults during 2009–2010. No specific permissions were required for collecting insects in any of these locations, and the field studies did not involve any endangered or protected species. In Louisiana, D. saccharalis larvae were collected on sugarcane plants. We first identified sugarcane plants with larval feeding damage  and then removed larvae from plants, placed them on artificial diet  in 60 ml plastic cups, and transported them to the laboratory to rear them into adults. Field collections in Louisiana were made in June and September 2009 at field sites within 200 km of the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) Sugarcane Research laboratory in Houma, Louisiana  throughout the growing season in 2009 and were similarly fed artificial diet until they became adults. In southern Texas, D. saccharalis larvae were rare on sugarcane plants. For this reason, live adult female D. saccharalis were used as lures to attract and trap adult males in July, August and September 2010 near a sugarcane mill in Santa Rosa, Texas  to ensure that any genetic differences we observed were not due to genetic differences which might exist between males and females. In addition, we used males rather than females since only males were attracted to the females in traps at the southern Texas and Florida sampling sites. The thorax of each male moth was removed and used for DNA extraction, while the abdomens were saved as vouchers and later used to prepare slides of the moth genitalia for species confirmation Moths were identified as male or female D. saccharalis collected from the regions described above in Texas, Louisiana, and Florida Amplified fragment length polymorphisms (AFLPs) were developed to compare the GeneMapper version 4.0  was used to determine presence or absence of fragments. Peaks were examined by eye to ensure the peak detection threshold was at least 1.5 times higher than the mean background level. The peak detection threshold was set for each primer combination, and was typically 100 luminescent units. Each AFLP marker was considered a locus and assumed to have two possible alleles . Bands not present in more than one individual were eliminated  prior to further analyses, as they were not considered informative. The SESim method D. saccharalis available in GenBank and the Bar Code of Life Data System (BOLD) databases D. saccharalis included in those databases, and to determine the number of genetically divergent lineages for the sequences available for D. saccharalis. The DNA used for sequencing COI was extracted from male D. saccharalis as described above using the Qiagen DNeasy Blood and Tissue kit (see DNA extraction).A 658 base pair region (the ‘bar code’) of the mitochondrial COI gene region was sequenced from two individuals from each of the four geographic regions sampled in this study from the southern US. The purpose was to compare the COI sequences of our samples with those available for 5_-ATTCAACCAATCATAAAGATATTGG-3 and the reverse primer sequence of LepR was 5_-TAAACTTCTGGATGTCCAAAAAATCA-3 . The touchdown PCR program consisted of an initial 2 minutes at 95°C, then 12 cycles of 95°C for 10 sec, 58–46°C for 10 sec with a lowering of 1°C temperature each cycle, and 72°C for 60 seconds. Following PCR, samples were cleaned up using a USB Exo-sap-it  PCR cleanup kit. Sequencing was carried out using the Big Dye Terminator v3.1 Cycle Sequencing Kit  followed by fractionation on an ABI 3730XL Genetic Analyzer.The barcode region of the COI gene was amplified using primers for the mitochondrial DNA ‘bar code’ of Lepidoptera described in Hajibabaei et al. D. saccharalis collected in the southern United States with 26 other D. saccharalis obtained from GenBank and BOLD . The forward and reverse sequences for each individual were assembled into a consensus sequence. We aligned our consensus sequences from and BOLD . AlignmeDiatraea saccharalis, based on the morphology of the male genitalia All the adult male moths from the four geographic areas sampled  were identified to D. saccharalis male adults  and two primer combinations  were used to obtain 96 AFLP markers. This number of individuals and markers were found to be sufficient in order to adequately represent population genetic structure of this insect in the sampled regions D. saccharalis present in the southern United States  in 1751. However, D. saccharalis was not recorded as a pest in Louisiana until 1855. In the early 1800s, additional sugarcane varieties were introduced into Louisiana D. saccharalis introduced into Louisiana.We used two molecular markers (AFLP and COI sequences) to examine variation in the population structure of D. saccharalis in Colombia is suggested by Palacio-Cortes et al. D. saccharalis from the Caribbean could comprise an additional lineage or could group together with the Florida cluster. Genetic distances among the three lineages of D. saccharalis depicted in D. saccharalis from Louisiana and Texas are genetically divergent from those in Brazil The mitochondrial COI data provide evidence for at least three distinct lineages in the Western Hemisphere: A Florida lineage, a lineage including Texas, Louisiana and Mexico, and a third lineage from South America that includes Brazil, Argentina, and Bolivia. A fourth divergent group of Plutella xylostella (L.), the diamond back moth, averaged ∼1%, which fell within the range of expected intraspecific variation Choristoneura (Lepidoptera: Tortricidae) species ranged from 1–2% Astraptes fulgerator (Lepidoptera: Hesperiidae) A. fulgerator from all the studied populations had identical genitalia and adults provided little indication of divergent lineages until genetic variation was explored within the group. The 2–3% divergence we have found among the D. saccharalis lineages we have identified suggests they are distinct species. The three lineages we have identified are geographically structured . To be robust, defining species limits should include multiple lines of evidence. Such an approach is referred to as integrative taxonomy D. saccharalis cryptic species complex, further lines of evidence would provide additional support of this assertion.In the last decade, DNA barcoding has provided a method to assess genetic diversity within and among species. Intraspecific genetic diversity of mitochondrial COI in D. saccharalis in the southern US due to the differential success of natural enemies which had been introduced into the region. We suspected Louisiana D. saccharalis populations would be divergent from Texas and/or Florida populations. However, our data show that Louisiana and Texas belong to the same genetic cluster while Florida constitutes a divergent genotype. Our data suggest that the difference in establishment of parasitoids of D. saccharalis in Texas or Louisiana is unlikely to be due to difference in D. saccharalis genotypes, but could be influenced by climatic differences or cultural practices which vary through the southern US. For example, in Louisiana, sugarcane fields are harvested in the fall, leaving little vegetation for parasitoids to overwinter, which could reduce parasitoid establishment. In contrast, sugarcane is grown year round in Texas and Florida We originally suspected the existence of more than one genotype of D. saccharalis from Louisiana as a lure to attract and trap Florida D. saccharalis male moths, yet we found that Louisiana moths are genetically divergent from the Florida moths. Moths from Louisiana and Florida are genetically distinct, yet the pheromones from Louisiana females were effective at attracting Florida males. Although we observed genetic diversity in D. saccharalis collections between the two genetically distinct clusters, trapping adults does not allow us to associate the individuals we collected with particular host plants. In order to determine if host plant associated strains exist for D. saccharalis, one would need to collect larvae from multiple host plants and examine the genetic differences among the host plant associated populations. Pheromones can cross-attract between species, especially if populations evolved in allopatry, where there is no selective pressure for signal divergence D. saccharalis have been investigated, and variation exists among populations; unfortunately, relative attraction of these blends to different D. saccharalis populations has not yet been tested We used live female D. saccharalis we have identified in this study deserve further attention. This insect is considered a major pest throughout the Western Hemisphere and has been easily confused with other species of Diatraea based on morphology. Genetically distinct lineages may differ in their damage potential and/or in their vulnerability to pest control strategies such as biological control. The ability to characterize and identify genotypes of D. saccharalis and related species or as of yet undiscovered species will improve pest management efforts against this pest and improve area-wide control efforts across its geographic distribution. Additional research on the population genetics of D. saccharalis in Central America and the Caribbean will further our understanding of its geographic population structure and clarify the composition of this potential cryptic species complex.The potential cryptic lineages of


Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement.Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie ( •Boehmeria nivea) were assessed by SCoT markers.Genetic diversity and population structure of ramie (•Boehmeria nivea.SCoT markers revealed high polymorphism and resolving ability in •The wild ramie showed moderate heterozygosity and gene flow with high genetic variation, suggesting unidirectional gene flow.•The domesticated population exhibited highest heterozygosity and close association with introduced population. Boehmeria nivea L. Gaudich., Urticaceae) is an industrially important crop. The principal end product is textile grade fiber, which is considered to be the longest and strongest in the plant kingdom  were selected for the present study. The Indian populations were collected from the Upper Assam region, Lower Assam region and Meghalaya  based protocol of 2 (1–3 mM) and dNTPs (0.1–0.4 mM). The final PCR cocktail (25 μl) contained 50 ng of template DNA, 1 × PCR buffer, 2.5 mM MgCl2, 0.2 mM dNTPS, 0.4 μM of primer and 1.5 U of Taq polymerase. The PCR programs were pre-run in a thermal cycler  at 94 °C for 4 min, followed by 43 cycles of 1 min at 94 °C, 1 min at annealing temperature (48–52 °C) and 2 min at 72 °C, with a final extension at 72 °C for 8 min. The PCR products were separated in 1.4% agarose gel in 1 × TAE buffer at 80 V for 1.5–2 h and visualized using a gel documentation system. To check the reliability of the amplification the experiments were repeated with random samples (30 no.).A total of 20 SCoT primers developed by i = 2fi(1 − fi), where fi is the frequency of amplified fragments at ith locus (p = ΣIb), according to bI = 1 − (2 × |0.5 − p|); p being the proportion of genotypes containing a band. Mean resolving power  or absent (0) following th locus . The disPp), number of observed (aN) and effective alleles (eN), Shanon's information index (I), total genetic diversity (Ht), population genetic diversity (Hs), Nei's expected heterozygosity (h), genetic identity (I) and genetic distance (D) were determined using POPGENE version 1.31 (Nm) among the populations was obtained following Nm = 0.25 × (1 − STG)/STG. Analysis of molecular variance (AMOVA) was performed in GenAlEx v.6.1  were polymorphic. Percent polymorphism varied from 20% to 100%, with 3–10 polymorphic bands per primer. The primers S13 and S31 exhibited the highest number of polymorphic bands (8). Polymorphism information content ranged from 0.25 (S12) to 0.93 (S6) with an average of 0.69. Only two primers, S7 and S12 showed low polymorphism (PIC < 0.5). The resolving power of the primers ranged from 1.24 (S19) to 5.00 (S13) with a mean value of 3.22. Mean resolving power over loci varied from 0.29 (S12) to 0.75 (S16), with an average of 0.50.Na), effective number of alleles (Ne), Shannon's information index (I) and Nei's genetic diversity (h) in the Indian ramie populations were 1.52, 1.35, 0.32 and 0.21, respectively (I (0.29) and h (0.21) than the other two populations. The population of Upper Assam exhibited lower genetic polymorphism (40.8%) than the other two populations. The average SCoT polymorphism in Indian population was over 50%. Total genetic diversity (Ht) and population diversity (Hs) were estimated to be 0.36 and 0.18, respectively. Relative genetic differentiation was high (STG = 0.27), revealing high gene flow (Nm = 1.34) among the three populations. Results from AMOVA identified significant variability among populations , along with 60.3% within-population genetic variability. Nei's unbiased genetic distance between the three populations varied from 0.076 (Upper Assam and Lower Assam) to 0.099   .Na, Ne, I and h values of introduced ramie genotypes were observed as 1.84, 1.46, 0.43 and 0.28, respectively. The percentage of SCoT polymorphism was higher in domesticated population (88.5%) than in natural ramie populations (Na (1.94) and Ne (1.44) values for the domesticated population were high, being similar to that of introduced population. The group exhibited high percentage of polymorphic loci (95.4%) and heterozygosity (h = 0.42). The domesticated populations were genetically closer to introduced population, with a genetic identity of 0.953. Overall AMOVA revealed significant differences between the three groups   (The ulations . The Na < 0.001) . The genThe weighted neighbor joining based cluster clearly distinguished the Indian populations from the introduced ramie populations, showing distinct sub-clusters of the populations from the Upper Assam, Lower Assam and Meghalaya . The popDendrobium nobile (Dendrobium. Since ramie is a cross-pollinated species, genetic variability is expected to be higher in ramie than in potato, which is a self-pollinated crop. Dendrobium, on the other hand might have a more complex genetic structure due to self-incompatibility and chimeric polyploidy (The SCoT markers are expected to be linked to functional genes and corresponding traits, thus the amplicons can be converted to gene targeted marker systems . Besidesm nobile . The resm nobile  and similyploidy . Informalyploidy , whereaslyploidy . High poThe genetic polymorphism generated by SCoT markers can also be used for tracing and reconstruction of breeding history of the domesticated genotypes. The introduced ramie accessions exhibited close genetic association with the domesticated genotypes, but not with the Indian natural ramie populations. Our results show that initiation of ramie breeding in India relied primarily on the introduction of new cultivars from other countries. The Indian native ramie has higher adaptability; thus this gene pool is a valuable reservoir for enriching genetic improvement programs targeting higher yield, better quality, adaptability and resistance to pests and diseases.ST and gene flow were moderate to high among these populations. Endemic perennials often exhibit high levels of gene flow (Assessment of genetic diversity is a prerequisite for efficient genetic resource management, conservation of species in natural habitat and identification of suitable parental combinations, all of which produce perceptible impacts on genetic improvement of a crop species . Little ene flow . The higene flow . In contThe domesticated genotypes exhibited high heterozygosity, which may have accumulated due to clonal propagation and perpetuation of somatic mutations. Higher heterozygosity and decreased population differentiation are characteristic of clonality, while the opposite is true for sexual propagation . They alB. nivea. The findings will be useful for devising conservation strategies and for selecting a suitable gene pool for genetic improvement of this industrially important crop species.The present work is the first report on genetic variability of Indian ramie suggesting that the preservation of genetic variability in the natural populations should be given priority. Our work also establishes the usefulness of the SCoT marker system in genetic diversity studies, ancestry determination and population structure analysis of


Recent studies have identified genetic markers associated with risk for certain sports-related injuries and performance-related conditions, with the hope that these markers could be used by individual athletes to personalize their training and diet regimens. We found that we could greatly expand the knowledge base of sports genetic information by using published data originally found in health and disease studies. For example, the results from large genome-wide association studies for low bone mineral density in elderly women can be re-purposed for low bone mineral density in young endurance athletes. In total, we found 124 single-nucleotide polymorphisms associated with: anterior cruciate ligament tear, Achilles tendon injury, low bone mineral density and stress fracture, osteoarthritis, vitamin/mineral deficiencies, and sickle cell trait. Of these single nucleotide polymorphisms, 91% have not previously been used in sports genetics.We conducted a pilot program on fourteen triathletes using this expanded knowledge base of genetic variants associated with sports injury. These athletes were genotyped and educated about how their individual genetic make-up affected their personal risk profile during an hour-long personal consultation. Overall, participants were favorable of the program, found it informative, and most acted upon their genetic results.This pilot program shows that recent genetic research provides valuable information to help reduce sports injuries and to optimize nutrition. There are many genetic studies for health and disease that can be mined to provide useful information to athletes about their individual risk for relevant injuries. The regular demands of training and competition during a season make professional, collegiate, and recreational athletes alike highly susceptible to injury. From 1988 through 2003, the incidence rate of injuries in NCAA athletes was 15.47 per 1,000 athlete exposures.Recent genetic research has revealed specific markers associated with increased risk for sports injuries and performance-related conditions,8,9. UseIn this paper, we examine the possibility of applying genetic knowledge about health and disease to predicting risk of sports injury in athletes. We performed a literature search on genetic studies in three categories of health that had not been previously used in the context of sports genetics: stress fracture, vitamin and mineral deficiencies, and osteoarthritis. We found a large number of DNA polymorphisms (113) in these categories, along with 11 polymorphisms that had been previously associated with athletic injuries . We chose to focus on injuries whose risk factors could be addressed by modifications in training or diet, rather than non-actionable injuries, such as concussions. Through our literature search, we identified 113 SNPs that have previously not been discussed in relation to sports injuries and performance. A new sports genetic database was constructed, and used to help customize injury prevention and training for fourteen athletes. Fourteen elite triathletes from the Stanford University Triathlon Team were genotyped and given information that could lead to individualized changes in training routines and injury prevention programs.Genome-wide association studies (GWAS) from the NHGRI GWAS Catalog and candidate gene studies from PubMed (MEDLINE) were selected for their relevance to athletic health: bone mineral density, osteoarthritis, calcium levels, vitamin E, vitamin D, vitamin B12, folate pathway vitamin levels, homocysteine, and phytosterol levels. Single nucleotide polymorphisms (SNPs) from genome-wide studies that reached genome-wide significance were accepted, along with SNPs from candidate gene studies. The studies were rated according to the criteria established for the assessment of cumulative evidence on genetic associations and effect size estimates were based on odds ratios reported for published SNPs associated with each category .We wanted to test our sports genetics database on a small set of elite athletes and recruited nineteen athletes on the Stanford University Triathlon Team based on their commitment to training and athletic ability . AthletiThree and twelve months after their consultation meeting, athletes were sent surveys using REDCap (Research Electronic Data Capture) software to assesThe pilot program protocol was approved by the Research Compliance Office at Stanford University (IRB Protocol 24576). Written informed consent was obtained from all athletes to participate in the study, as well as verbal consent to use their deidentified information for study purposes.The literature review identified a total of 124 SNPs in the following categories: bone mineral density (BMD), osteoarthritis, vitamin and mineral deficiencies, ACL rupture, Achilles tendon injury, and sickle cell trait (SCT) .We analyzed the raw genotype files for SNPs associated with the six types of injuries identified in the extensive literature review . These iCOL1A1, COL5A1, COL12A1, and MMP12 genes that are associated with ACL tears[The first injury category, rupture of the ACL, is one of the most severe injuries sustained in active populations. CandidaACL tears,19,20,21ACL tears.MMP3, COL5A1, COL1A1, CASP-8, and GDF5 genes to be associated with Achilles tendon pathologies[COL1A1, which encodes type I collagen, the major protein component of tendons and ligaments[The second injury category, Achilles tendon injury, includes degenerative and painful conditions that affect athletes in a wide range of sports, including up to 18.5% of runners,24,25. Cthologies,29,30,31ligaments,33. The ligaments,35,36. Tet al. performed a large meta-analysis on lumbar spine and femoral neck bone mineral density, including 17 GWA studies involving a total of 32,961 individuals. They identified 64 SNPs associated with bone mineral density at genome-wide significance. An algorithm was developed summing the individual contributions from 63 of these SNPs into one combined genetic score. These scores were divided into five different risk categories based on the population distribution[et al. paper[The third injury category, stress fracture, is a common overuse injury in repetitive sports, and affects up to 20% of female athletes and military recruits. Bone mitribution. Individtribution. Three aal. paper,43,44.et al., as well as the individual SNP results, for a total of 66 SNPs. Two participants had genetic scores on the extreme ends of the risk groups established by Estrada et al. The triathlete with the worst genetic risk score had a history of three previous stress fractures during his/her career as a collegiate runner. A DEXA scan, which directly measures BMD, indicated osteopenia for this athlete. The triathlete with the most protective score had no history of stress fracture, and only one stress reaction so far as a cross-country runner. Triathletes can easily redistribute training volume to cycling or swimming if they are predisposed to running injuries, such as stress fractures.We reported the combined genetic score developed by Estrada The fourth category, osteoarthritis, is a major cause of pain and disability in the elderly and is the most common form of arthritis worldwide. Sports The fifth category includes SNPs associated with vitamin and mineral deficiencies. Exercise results in biochemical adaptations in muscle that place metabolic pathways under stress and increase the need for micronutrients. Routine training increases the loss of micronutrients, thus requiring greater intake of micronutrients for building, maintaining, and repairing lean body mass. Moreoveet al. performed a GWAS on vitamin D involving 33,996 individuals and found SNPs that explain 1–4% of the variance in serum levels[et al. performed a GWAS on 20,611 individuals and found SNPs that account for 0.54% of the variance in serum calcium concentrations[We reported on 39 SNPs associated with levels of: iron status biomarkers, circulating vitamin E, circulating vitamin D, serum calcium, magnesium, vitamin B12, vitamin B6, vitamin B9, phytosterol, and plasma homocysteine,62,63,64um levels. O'Seaghntrations. Geneticntrations. One of The last category, sickle cell trait, is a Mendelian condition caused by the inheritance of one normal allele of the hemoglobin gene (hemoglobin A), and one abnormal allele ,67,68. ITwelve of fourteen athletes were recommended training interventions. The 3-month and 12-month questionnaires showed that eight of those twelve athletes acted upon their genetic results. Two of the remaining four who had not started an intervention indicated that they plan on taking action in the future. Moreover, seven believe that the implemented changes have had, or will have, a positive impact on their athletic careers. Importantly, after one year, four athletes were still actively following their interventions. In the year preceding this pilot study, ten of the fourteen total athletes (71%) sustained an injury . HoweverThere is a rich compendium of genetic studies that can be used to study sports injury risk in elite athletes. By including genetic studies of health and disease, we have greatly expanded the database of DNA variations that can be applied to sports genetics. We performed a literature search and identified 124 SNPs that have been associated with six different risk categories: ACL rupture, Achilles tendon injury, low bone mineral density, osteoarthritis, vitamin and mineral deficiencies, and sickle cell trait. To our knowledge, 113 of these SNPs have not previously been used in sports genetics,8,10,71.et al. studied low bone mineral density, osteoporosis, and fractures in older women. We propose that these findings may also be relevant for athletes. Training creates a physical stress that, together with genetic predispositions, may lead to an injury that normally only occurs when older. Genetic information linked to vitamin and mineral deficiencies can be useful to help optimize micronutrient intake. Testing for sickle cell trait is already mandatory for all Division I and Division II NCAA athletes. We included the rs334 variant in our report because the DNA test is more accurate and cost-effective than the hemoglobin solubility tests recommended by the NCAA[We looked at large genetic studies investigating health traits that could be of interest to athletes. Most published gene association studies investigate disease in the general population rather than athletes. For example, studies on bone mineral density and vitamin/mineral deficiencies have not been previously used in sports genetics. Estrada  the NCAA.st and 10th for the Elite Men was 1.5 minutes, or about 1.4% of the total race time for each event[We began by recruiting elite collegiate triathletes for several reasons. First, triathletes are at increased risk for developing a wide range of injuries due to the three different disciplines of the sport. Second, Stanford University triathletes are club athletes in an individually scored sport, and hence ethical considerations regarding student-athlete scholarships and starting line-ups were not a concern. Athletes were individually motivated to participate (or not) in the genetic testing program, and independently chose whether or not to share their genetic results with third parties. Finally, these athletes are highly dedicated to athletic performance and could benefit from a new competitive edge. Although the genetic associations described here only contribute a small amount to overall risk for injury, they may still be important to elite athletes looking for every edge they can get. Over the 2011 and 2012 ITU World Triathlon Series race seasons, the average time difference between 1ach event. OptimizNevertheless, the small effect from genetic testing for athletic injury may mean that it is currently premature for use in the general athletic population. Injury This pilot program was limited to only fourteen athletes, which is too small to perform a rigorous trial to show the effectiveness of the sports genetics program in reducing injury incidence and to draw meaningful conclusions about the effectiveness of the genetic testing. Our goal was to simply observe the athletes' responses to the new genetic knowledge. Nevertheless, there was positive feedback about the benefits of genetic testing. Fourteen of the nineteen athletes that were contacted decided to participate. Of those that replied to the 3- and 12-month follow up questionnaires, all responded positively to the program and thirteen indicated that they found the genetic results both useful and informative. Moreover, all but one athlete reported sharing their genetic information with their coaches, trainers, physicians and/or teammates, highlighting that genetic information can be used to benefit athletes through multiple channels. Eight out of twelve athletes that were recommended training changes actually modified their training based on their genetic data. Besides prompting athletes to include new modifications in their training or diet, genetic knowledge may also increase compliance with currently prescribed prehabilitation strategies. GeneticThere is a rich source of new genetic knowledge that can be applied to athletic injury risk. Many health risks, such as low bone mineral density in the elderly, may also be pertinent to athletes. Athletes push themselves to the limit, which increases their chance for injury, and small effects in physiology can have meaningful consequences in competition. Through our literature search, we identified 113 SNPs that have previously not been discussed in relation to sports injuries and performance. A new sports genetic database was constructed, and used to help customize training and injury prevention for fourteen triathletes. In the future, additional categories of injury can be included in the sports genetics database, and personalized genetic consultation can be expanded to other types of athletes.S1 FileText copy of survey questions distributed to athletes three and twelve months after initial results consultation.(PDF)Click here for additional data file.


Betula papyrifera) is an open pollinate species that is, dominant in the Northern Ontario after land reclamation. In fact, this species represents 65% of all trees in the region. We hypothesized that the exchange of genetic information between fragmented populations by range-wide paternal introgression is possible in wind-pollinated species such as B. papyrifera. On the other hand, the effects of heavy metal contamination from the mining activities on plant growth and population dynamics are well documented. The main objectives of this study were (1) to assess the level of genetic variation, gene flow, and population sustainability of B. papyrifera after land reclamation; and (2) to determine the level of phytoavailable metals in soil and their accumulation in trees. We found that B. papyrifera is a Ni and Zn accumulator with a translocation factor of 6.4 and 81, respectively, and an indicator of Cu and Pb. The level of polymorphic loci, Shannon index, Nei's genetic diversity, observed number of alleles, and gene flow were determined for the fragmented populations within the targeted region. The percent of polymorphic loci ranged from 28% to 56%; the gene flow was also low with a value of 0.89, and the population differentiation was very high with a value of 0.36. Two population–diagnostic ISSR markers were identified. They were cloned, sequenced, and converted to SCAR markers. Overall, the fragmented populations of B. papyrifera in Northern Ontario are genetically sustainable based on the moderate level of intrapopulation variability.White birch ( Betula belonging to the Betulaceae family, consists of roughly 60 species of hardwood. Betula papyrifera (white birch), is a major component of the boreal forest of North America. It is found in every Province of Canada, except Nunavut, as well as the northern United States  is an open pollinate species that is, dominant in the Northern Ontario after land reclamation. In fact, this species represents more than 50% of all trees in the region. Because of the long-distance pollen dispersal, gene flow among the fragmented populations is expected to be high. We hypothesized that the exchange of genetic information between fragmented populations by range-wide paternal introgression is possible in wind-pollinated species such as B. papyrifera and that the population differentiation will be low.White birch (B. papyrifera (white birch) after land reclamation; and (2) to determine the level of phytoavailable metal in soil and accumulation in B. papyrifera.The main objectives of this study were (1) to assess the level of genetic variation, gene flow, and population sustainability of The distribution and percentage of each plant species was determined for every site. Three quadrants with a radius of 5 m were randomly selected across the sites. They were 1 m apart. Tree species richness in each quadrant of each tree species was calculated based on direct counting. Individuals with trunks larger than 10 cm were counted as trees and those smaller as saplings.3 and HCL using a MARS 5 microwave oven. The supernatant was transferred and brought up to 50 mL with deionized water. Metal levels were measured using an inductively coupled plasma optical emission spectrometry (ICP-OES), inductively coupled plasma mass spectrometry (ICP-MS), and hydride generation atomic emission spectrometry (HG-AAS).Soil samples were collected across the twelve sites Fig.. These s3 to 50-mL centrifuge tubes. Tubes were placed in a shaker under ambient lighting conditions for 24 h at 20°C  of the suspension was measured prior to centrifugation at 1100 × g for 20 min, with filtration of the supernatant through a 0.45-μm filter into a 20-mL polyethylene tube and made to volume with deionized water. The filtrate was preserved at approximately 3°C for chemical analysis by ICP-MS. The quality control program completed in an ISO 17025 accredited facility (Elliot Lake Research Field Station of Laurentian University) included analysis of duplicates, internal reference materials (IRMs), procedural and calibration blanks, with continuous calibration verification, and use of internal standards  to correct for any mass bias. All concentrations were calculated in mass/mass dry soil basis.Bioavailable (phyto) metals were measured by adding 5 g of soil with 20 mL of 0.01 mol/L LiNOP ≥ 0.05) among the sites. The translocation factors (TF) were determined according to the equations described by Singh and Agrawal  was added into the tubes. The tubes were then vigorously mixed by inversion for 5 min and centrifuged . The aqueous phase (top) was transferred to a new set of tubes and washed twice more with equal volumes of 24:1 chloroform/octanol . An equal amount of isopropanol was added to the tubes and gently inverted to allow the DNA to precipitate. The tubes were then stored overnight at −20°C. The next day, the tubes were centrifuged . Afterwards, they were decanted and the DNA pellet was washed with 5 mL of 70% ethanol. Once completely dry, the pellet was dissolved in TE buffer (1:10 EDTA/Tris-HCl), transferred into 1.5-mL properly labelled microcentrifuge tubes, and stored at −20°C until further use.4, 1× PCR buffer, 0.5 ng/μL of primer, 0.5 ng/μL of dNTP stock , 0.8 ng/μL of DNA, 0.8 units/μL of Taq polymerase (Bio Basic Inc.), and autoclaved distilled water to a final volume of 25 μL. Blanks were adjusted with autoclaved distilled water instead of DNA. A drop of mineral oil was added to each tube before initiating the PCR to minimize evaporation. The PCR program consisted of an initial denaturation of 5 min at 95°C followed by a 2-min incubation at 85°C at which point the polymerase was added; 42 cycles of 1 min at 95°C, 2 min 55°C, and 1 min 72°C; a final incubation of 7 min at 72°C followed by a cooling period until 4°C.A total of 18 different ISSR primers synthesized by Invitrogen were used to screen a few samples from each white birch population. The DNA amplification was carried out in 0.5-mL tubes. Each reaction contained 1.5 mmol/L MgSOLoading buffer was added to the PCR product ran on 2% agarose gels (3.16 V/cm). Seven primers that showed strong and reproducible amplification pattern were selected for the amplification of all the genomic DNA. The gels were documented, and bands were scored by their presence or absence using a 1 and 0 system.h), Shannon's information index (I), and the percent of polymorphic loci per primer. The distance matrix was generated using the Jaccard's similarity coefficient analysis with the Free Tree program.Data were analyzed using the computer-based software, POPGENE 32 and Free Tree program. Popgene 32 is able to calculate multiple genetic parameters when using dominant or codominant marker systems. The following parameters were estimated, including Nei's gene diversity (B. papyrifera) and red maple (Acer rubrum) being the predominant species. Conifers represent only a small percentage (<5%) of tree populations. Overall, B. papyrifera represents 53% of all trees and shrub species in the targeted region.The number of trees and shrubs was measured for each of the 12 sites. The data were pooled together to give a general idea of the distribution of the different species found in the sites Fig.. The fraDetailed data on total and bioavailable heavy metals for the five elements of interest are presented in TableThere were significantly higher levels of Zn and Ni in leaves compared with the bioavailable amount in soil. In fact, the translocation factors were 81 and 6.4 for Zn and Ni, respectively , Shannon's information index (I), and the percentage of polymorphic loci (%) were also calculated (TableGenetic diversity was measured across 12 white birch populations. The selected ISSR primers are described in Tableted Table.h) ranged from 0.08 (Kingsway) to 0.13  with a mean of 0.11. Shannon's information index (I) ranged from 0.13 (Kingsway) to 0.22  with a mean of 0.18. The percent of polymorphic loci (%) ranged from 28.4 (Kingsway) to 56.0  with a mean of 43.9. The gene flow was low across populations with a value of 0.89, and the population differentiation (Gst) was high with a value of 0.36. No significant difference was found between the contaminated and reference sites for all the genetic parameters estimated  ranged from 1.28 (Kingsway) to 1.56  with a mean of 1.44. The effective number of alleles (Ne) ranged from 1.13 (Kingsway) to 1.221 (Dam) with a mean of 1.18. Nei's gene diversity index  because previous studies have shown that this is where most of the airborne metal particulates reside  might therefore play a role in the phytoextraction of Zn and Ni. It can be considered as indicator of Cu and Pb because the amount in leaves was similar to the bioavailable content in soil. As it represents up to 53% of all tree species in the targeted sites, it can contribute to the phytostabilization of restored forests, because it is able to grow and survive on heavily contaminated soil.Genetic variation is one of the key characteristics of forest sustainability. If genetic variation is low, the overall gene pool of a population will be small and could result in its extermination or a population bottleneck if a stress occurs  used in the present study is designed specifically for the analysis of codominant and dominant markers using haploid and diploid data.h) and Shannon's information index (I) were low (0.113 and 0.177) indicating a low allelic frequency and uneven distribution. In the present study, the two generations were compared for genetic variation, and no significant differences in polymorphism were observed between the parental and the offspring generation. Likewise, no significant difference in genetic variation was found between white birch growing in heavy metal contaminated and reference sites. This is consistent with other studies performed on other tree species  belonging to the order Fagales are wind-pollinated trees, generating vast amounts of pollen to ensure a sufficient level of fertilization of female flowers over receptor regions. Their pollen grains are quite small and light to facilitate the transportation of a substantial fraction (up to 1% for some plumes) of the released material over thousands of kilometers if weather conditions are suitable (Sofiev et al. It is, however, well established that the bulk of pollen is deposited near the source plant (Tampieri et al. The fact that only two population diagnostic markers were identified in one reference sites suggests that the level of gene flow, although small, remains adequate to prevent population divergence. It should be pointed out that gene flow is an extremely complex phenomenon that can occur in many ways and that can fluctuate over time. The lack of a generally applicable direct method for measuring gene flow hinders its evaluation as a potential cohesive force among conspecific populations (Larson et al. The two population–diagnostic bands that were identified were sequenced and transformed to SCAR markers. The primers designed that flanked SCAR sequence amplified genomic DNA from all the populations, suggesting that the sequences were not truly population specific. This is an indication that the sequences are present in low copy number in all the populations, but in a higher frequency in the original population where it was identified with ISSR primers.There exist, however, other reasons that could explain why diagnostic marker once converted to a SCAR marker is not specific. The appearance of a band in one population or species and its absence in another could be the result of competition among DNA fragments during amplification Nkongolo . AmplifiWhite birch represents more than 50% of the tree species in the targeted region following soil restoration. The total heavy metal levels were found to be high, but the availability of these metals was much lower. Compared with previous data, heavy metal levels are decreasing, possibly due to leaching and the phytoextraction by surrounding vegetation. White birch is accumulating zinc and nickel in their leaves and is indicator of Cu and Pb. The levels of genetic variation were low to moderate. Contrary to our hypothesis, the gene flow among the fragmented populations was low and population differentiation was relatively high in the reclaimed mining region. Populations within the targeted region were distantly related, and diagnostic markers were identified only for one of the 12 populations. No association between the levels of genetic variation in white birch populations and heavy metal content in the soil was established. The genetic analysis revealed that white birch populations from the Greater Sudbury region are genetically sustainable.


Scutiger ningshanensis were studied using the combined data mtDNA cytochrome b (cyt b) and the mtDNA cytochrome c oxidase subunit I (COI) as the molecular markers. This species has high genetic variation. There was a significant genetic differentiation among most populations. Three lineages were detected. The phylogenetic relationship analyses and the SAMOVA  results showed significant phylogeographic structure. 82.15% genetic variation occurred among populations whereas differentiation within populations only contributed 17.85% to the total. Mantel test results showed a significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations   = 0.0185<0.05), indicating the existence of isolation-by-distance pattern of genetic divergence for cyt b + COI sequence, which suggests that the distribution of genetic variation is due to geographical separation rather than natural selection. The population expansion or contraction and genetic differentiation between populations or lineages could be explained by topography and the repetitive uplifts of the Tsinling Mountains and the climatic cycles during the late Pliocene and Pleistocene. S. ningshanensis experienced a rapid population expansion about 40,000 years before present. The current decline in population size was probably caused by anthropogenic disturbance. Current populations of S. ningshanensis are from different refugia though the location of these refugia could not be determined in our study. Topography, climatic changes and repetitive population expansion/contraction together led to the high level of genetic variation in S. ningshanensis. A total of three management units (MUs) was determined, which must be considered when conservation policy is made in the future.Population genetic structure, historical biogeography and historical demography of the alpine toad  Scutiger ningshanensis were studied using the combined data mtDNA cytochrome b (cyt b) and the mtDNA cytochrome c oxidase subunit I (COI) as the molecular markers. This species has high genetic variation. There was a significant genetic differentiation among most populations. Three lineages were detected. The phylogenetic relationship analyses and the SAMOVA  results showed significant phylogeographic structure. 82.15% genetic variation occurred among populations whereas differentiation within populations only contributed 17.85% to the total. Mantel test results showed a significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations   = 0.0185<0.05), indicating the existence of isolation-by-distance pattern of genetic divergence for cyt b + COI sequence, which suggests that the distribution of genetic variation is due to geographical separation rather than natural selection. The population expansion or contraction and genetic differentiation between populations or lineages could be explained by topography and the repetitive uplifts of the Tsinling Mountains and the climatic cycles during the late Pliocene and Pleistocene. S. ningshanensis experienced a rapid population expansion about 40,000 years before present. The current decline in population size was probably caused by anthropogenic disturbance. Current populations of S. ningshanensis are from different refugia though the location of these refugia could not be determined in our study. Topography, climatic changes and repetitive population expansion/contraction together led to the high level of genetic variation in S. ningshanensis. A total of three management units (MUs) was determined, which must be considered when conservation policy is made in the future.Population genetic structure, historical biogeography and historical demography of the alpine toad http://en.wikipedia.org/wiki/Genetic_drift - cite_note-Masel_2011-1#cite_note-Masel_2011-1Genetic drift may lead to disappearance of gene variants and thereby reduce genetic diversity.Population genetic structure refers to the geographical pattern of genetic diversity within or among populations. It could be influenced by gene flow, genetic drift, selection, mutation and recombination. Gene flow is caused by the movement of individuals from one population to another Phylogeography connects historical processes in evolution with spatial distributions The Tsinling Mountains are located in the central part of China, stretching from west to east . These MScutiger ningshanensis was described from the western part of the Tsinling Mountains S. ningshanensis.The alpine toad http://www.iucnredlist.org). Actually, in addition to the type locality, this species was reported later in 2009 from a variety of localities including the Baiyunshan Mountains (bys), Shirenshan Mountains (srs) and Laojunshan Mountains (ljs) This study was approved by the Institutional Animal Care and Use Committee (IACUC) of Shaanxi Normal University. Only the clipped toes or tail tips of tadpoles were used for extraction of total DNA. No specific permissions were required for these locations/activities. This species was ranked “Endangered B2ab(iii)” in “The IUCN Red List of Threatened Species™ 2013” based on an outdated information that this species was only found at the type locality (nsc) Scutiger boulengeri were collected from Jone County (34.539922N 103.491647E), southern Gansu Province, China. S. boulengeri will be used as outgroup in phylogenetic relationship analysis.Our sampling covers the entire known distribution of this species. Furthermore, to make an extensive sampling, we explored the whole Tsinling Mountains, and fortunately collected this species at two locations where the distribution of this species has not been recorded. A total of 99 samples were collected from 6 localities during 2011 and 2013 , Fig. 1.5′-TGATCTGAAAAACCACCGTTG-3′ and FrogThr-r 5′- CTCCATTCTTCGRCTTACAAG-3′ S. ningshanensis cyt b), KF757392–KF757439 (S. ningshanensis COI); KJ082065– KJ082072 (S. boulengeri cyt b), KJ082073–KJ082080 (S. boulengeri COI). Indicators of nuclear mitochondrial pseudogenes (numts), such as indels, stop codons and double peaks in sequence chromatograms The clipped toes or tail tips of tadpoles were preserved in 100% ethanol and stored at −20°C. A continuous fragment (1009 bp) of the mitochondrial cytochrome b (cyt b) was amplified using PCR , with primers FrogGlu-f S. ningshanensis was conducted. The clipped phalanges were stored in 95% ethanol solution. The phalanges were washed in running tap water, then decalcified in 3% nitric acid for 12 to 24 hours. The mid-diaphyseal region of the phalanges was cross-sectioned at 12–20 µm using a microtome and stained with hematoxylin for two min. Sections were examined under a light microscope and the number of lines of arrested growth (LAGs) was counted A skeletochronological study of longevity of http://darwin.uvigo.es). The number of variable and parsimony informative sites was determined using the program DnaSP 5.10.01 Hd) and nucleotide diversity (Pi) were determined through Arlequin 3.5.1.2 The sequences were aligned with Clustal X1.83 S. boulengeri was used as outgroup.The substitution model selection was implemented in jModelTest 2.1.4 FST values and the geographical distances. Pair-wise FST values between populations were estimated using Arlequin3.5.1.2, while geographical distances between populations were calculated online at http://www.gpsvisualizer. com/calculators#distance.The population comparisons using pairwise difference as distance method, and the partition of genetic diversity within and among populations were analyzed by analysis of molecular variance (AMOVA) http://web.unife.it/progetti/genetica/Isabelle/samova.html) with 1,000 permutations. The number of initial conditions was set to 100 as recommended by Dupanloup et al. K of groups of populations ranged from 2 to 4. The K with the highest Fct represents the best number of groups and the best population configuration.The spatial genetic structure of haplotypes was analyzed using the program SAMOVA1.0 Ne) of each clade  for coalescent simulations was converted from Theta using the equation θ = Neµ with µ = 0.65×10−8 (per lineage per million years) ×6 (generation time of S. ningshanensis). The θ-values were estimated using maximum likelihood method in the program Lamarc2.7.5 Ne was the sum of the Ne for all groups and the proportion of total Ne that each group comprised were used to scale the branch width of hypothesized trees (models of population divergence) (The effective population size (ergence)  [49]–[51S. ningshanensis. The clades were treated as taxon states and each haplotype as character states. The haplotype trees by coalescence within a diverging population tree (model of population divergence) were simulated, and fit of a haplotype tree to a population tree was calculated to search for population trees that optimize fit of gene trees.A single-refugium hypothesis of population divergence during the Dali glaciation (the last maximum glaciation in China which occurred about 50 ka before present) was tested using the maximum likelihood estimation implemented in Mesquite2.75 FS test DSSD) and Harpending's raggedness index (R) between observed and expected mismatches.Neutrality tests were calculated in Arlequin3.5.1.2 The site-frequency spectrum (for segregating sites) was calculated in DnaSP5.10.01 Furthermore, the Bayesian Skyline Plot (BSP) approach was used to estimate the demographic history in BEAST v1.8.0 To detect the existence of potential cryptic species, uncorrected p-distances S. ningshanensis is three years S. ningshanensis is nine years. The average generation time (GT) of S. ningshanensis is six years.The average longevity of tadpoles was estimated by Lu et al. S.ningshanensis and eight of S. boulengeri. A total of 1009 base pairs of cyt b gene and 631 base pairs of COI gene was obtained, 67 haplotypes were identified for the combined gene sequences (cyt b+COI) of S. ningshanensis. Of the combined 1640 nucleotide sites, 181 were variable (polymorphic sites or segregating sites), 121 were parsimony informative, and 60 were singleton variable. The haplotype diversity of total and most sampled population was very high, however, the nucleotide diversity of every sampled population was low   in  of 0.74 . An impo of 0.74 .p-value  = 0.0±0.0)  while differentiation within populations only contributed 17.85% to the total . The fix0.0±0.0) .FST) between most local populations except the population comparison between hby and lfy (Population comparisons showed a significant genetic differentiation ( and lfy .p (rrand≥robs)  = 0.0185<0.05), indicating the existence of isolation-by-distance pattern of genetic divergence for cyt b+COI sequence, which suggests that the distribution of genetic variation is due to geographical separation rather than natural selection. The Mantel test results provided the evidence for large-scale geographical population structure in this species.Mantel test results showed a significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance  of the pFCT equals to 0.84285   = 0.01662±0.0) when K = 3, showing that the most likely number of populations is three.Results from SAMOVA analysis indicated that the highest s is 55 which doesn't fall within the model of single-refugium indicating that the fragmentation model of population divergence was rejected  further estimated the demographic history. The effective sample size (ESS) for all parameters of the BSP was greater than 200, showing that the 20 million generations were sufficient to determine the demographic history for each examined lineage. All lineages and the total population experienced population expansion. The hby-lfy lineage, nsc lineage and the total population experienced quick population growth after about 40,000 years ago, while the ljs-bys-srs lineage experienced a slow population growth after about 15,000 years ago. Noticeably, the hby-lfy lineage and the total population experienced a recent sharp decline in population, the ljs-bys-srs lineage showed a more recent population decline, while the nsc lineage maintained basically constant population size after the population expansion .S. ningshanensis probably contains three cryptic species or at least three subspecies.The lineage hby-lfy and the lineage nsc were highly divergent from each other with an uncorrected p-distances of 4.2%, the lineage hby-lfy and ljs-bys-srs were also highly divergent with an uncorrected p-distances of 4.37%. Similarly, there was an high divergence between the lineage nsc and ljs-bys-srs, with an uncorrected p-distances of 2.37%. These values were similar to those p-distances (3%) reported between two different frog species S. ningshanensis. High-level genetic diversity in narrowly endemic species could be associated with the factors such as the long species history, the high-level gene flow, having experienced a recent contraction in population, multiple founder events, the maintenance of genetic diversity in refugia, the hybridization, and the ability to survive in a range of different habitats. S. ningshanensis. This species has probably undergone a long history through which many mutations were accumulated since their origin. High-level gene flow is beneficial to fix the mutations in population. Multiple founder events were another alternative explanation for the high-level genetic diversity in this species. There is a possibility that multiple founder events, which accumulated more and more mutations, occurred in the history of this species. The two congeners of S. ningshanensis are S. boulengeri and S. liupanensis. The nearest localities of these two species are 167 km or 361 km respectively away from the locality hby of S. ningshanensis, which makes it impossible for the occurring of hybridization among these three species S. ningshanensis. The distributing region of S. ningshanensis include a range of different habitats such as high mountains with different elevation, streams, and different vegetations. High-level diversity in habitats also contributed to the high-level genetic diversity.Our results showed high levels of genetic diversity in FST values are high and statistically significant. Thus, the Ningshan alpine toad appears to exhibit substantial population differentiation across the Tsinling Mountains.Significant population structure occured based on the statistics pairwise differentiation. Most pairwise S. ningshanensis. It is not possible that a significant Mantel test provided the evidence for discontinuity in the distribution of genetic variation. It rather showed a continuous distribution of the variation due to individuals mating preferentially with individuals from nearby populations Mantel test results showed a significant correlation between the genetic distance and geographical distance of the populations, indicating the presence of IBD pattern of genetic divergence for cyt b+COI sequences, suggesting that the distribution of genetic variation is due to geographical separation rather than natural selection. The Mantel test results provided the clear evidence for large-scale geographical population structure in S. ningshanensis. SAMOVA results and the phylogenetic relationship analysis further affirmed the existence of phylogeographic structure in this species.AMOVA results indicated that 82.15% genetic variation occurred among populations, while differentiation within the populations only made 17.85% contributions. The high genetic variation among populations affirmed the presence of phylogeographic structure in Amphibians have poor dispersal capabilities and are sensitive to fine-scale landscape structure, topographic and altitudinal variation and climatic changes S. ningshanensis that distributed in the areas with low elevation disappeared during the interglacial in the Quaternary since it is an alpine species. In addition, S. ningshanensis retreated to a few refugia during glacial period. At the end of the Dali glaciation, S. ningshanensis experienced a rapid population expansion which occurred about 40,000 years before present, and it is experiencing a population contraction now probably due to anthropogenic disturbance. Topographic features, climatic fluctuation and anthropogenic activity together led to the current patchy geographic pattern for S. ningshanensis. This geographical distribution pattern also seen in other montane organisms Topography and Pleistocene climate changes drive population genetic differentiation forming genetic structure pattern Finally, there is the possibility that unsampled populations between nsc and ljs may be genetically intermediate among the three groups.S. ningshanensis. The Tibetan Plateau experienced three phases of rapid uplifts S. ningshanensis though we could not determine the number and location of the refugia based on the statistical phylogeography analyses. Most species of the genus Scutiger inhabit in the eastern Tibetan Plateau S. ningshanensis evolved when the Scutiger species dispersed eastward along the Tsinling Mountains. The hby-lfy lineage split apart at first, split between the lineages nsc and ljs-bys-srs occurred when this species continued dispersing from west to east on the Tsinling Mountains, while no further split occurred after the second split.The uplifts of the Tsinling Mountains promoted genetic differentiation among lineages of S. ningshanensis, and the expansion began simultaneously 40,000 years before present, which corresponds to the end of the Dali glaciation. Retreat of glacier led to population expansion in species on the Tsinling Mountains. A noteworthy phenomena is that S. ningshanensis is experiencing a distinct recent population contraction  as shown by the BSP analyses  in the future.All potential cryptic species should be considered for conservation. Different conservation strategies should be accepted for different species, therefore, it is inappropriate to protect a cryptic species complex using a single conservation strategy Management units (MUs) are used to make conservation strategy for threatened species S. ningshanensis experienced a rapid population expansion about 40,000 years before present. The current decline in population size was probably caused by anthropogenic disturbance. Current populations of S. ningshanensis are from different refugia though the location of these refugia could not be determined in our study. Topography is very important in shaping genetic connectivity. Topography, climatic changes and repetitive population expansion/contraction together led to the high level of genetic variation in S. ningshanensis. At least two putative cryptic species were detected. A total of three MUs were determined, which must be considered when conservation policy is made in future.Three lineages were detected. The phylogenetic relationship analyses showed significant phylogeographic structure. The population expansion or contraction and genetic differentiation between populations or lineages could be explained by topography and the repetitive uplifts of the Tsinling Mountains and the climatic cycles during the late Pliocene and Pleistocene.


Connecting genotype to phenotype is a grand challenge of biology. Over the past 50 years, there have been numerous and powerful advances to meet this challenge, including next-generation sequencing approaches . Domestiwww.bdebate.org) and the Center for Research in Agricultural Genomics , with the support of the US National Science Foundation. The meeting was divided into three scientific sessions. The first concentrated on the mechanisms that generate genomic diversity in plants, with a particular emphasis on transposable elements and polyploidy, while the second and third sessions were devoted to the evolution of plant phenotypes in wild and domesticated species, and to domestication and plant improvement processes, respectively.With the objective of reviewing the most recent advances and identifying unanswered questions at this interface, a group of scientists met in Barcelona in March 2015 for a workshop organized by B-Debate  emphasized the importance of WGD events in angiosperm evolution. He tested whether WGDs coincide with radiation events, and he presented data to support a lag-time between WGD events and increases in species diversification  , and tha as well . PolyloiMuDR, is partially released, as are genes regulated by trans-acting RNA silencing mechanisms. His data stressed the close intertwining of TE and gene silencing, and the high sensitivity of these processes to developmental changes  introduced the idea that the genome of a plant species can be divided into the pan genome (PG), which includes the core genomic features common to all individuals of a species, and the dispensable genome (DG), composed of genetic elements that are not shared by all individuals. The DG comprises the youngest and most dynamic fraction of the genome, and may be a key factor for adaptation. TEs are an important part of the DG, and Morgante showed that they can contribute not only to structural but also epigenetic differences between alleles in crops such as grapevine. Damon Lisch (Purdue University), presented data on the developmental control of TE silencing. He showed that during the transition from juvenile to adult stages of maize leaves, the silencing of some transposons, such as e family . FinallyArabidopsis as a model. She described a silencing event of a transgene that depends on the presence of repeats and that only occurs in tetraploids. She concluded that any structural change in the genome may have epigenetic consequences and could create diversity, and stressed the tight link between genetic and epigenetic changes  presented the work that his lab is doing to decipher the complexity of the quantitative natural variation in response to environmental changes. He is using a QTL mapping approach with crosses between individuals from wild populations. He discussed the difficulties of analyzing quantitative variation of small effects with enough precision to tackle the genotype by environmental interactions, and presented his laboratory phenotyping facilities that have helped them to start dissecting the quantitative genetics of plant growth  presented her work on the analysis of the role of genetic and epigenetic variation in ecological adaptation, using different species such as Spartina and Fallopia, and discussed to what extent epigenetic adaptation was similar to genetic selection  gave a talk on the costs of maintaining an ecologically relevant trait in nature. She shared her recent analysis on adaptation of weedy plants in agroecosystems to develop herbicide resistance, and discussed the nature of the costs that accompany a new adaptive trait  presented work on the molecular basis of quantitative traits, using The session ended with a general discussion on the future of characterization of complex traits. It was generally acknowledged that many tools – from genomics to high-throughput phenotyping – are now available that make it easier to map genes in both crop and wild species. The role of stable epigenetic changes in trait variation and its importance in wild and agricultural conditions remains unclear, and it is evident that more data as well as conceptual clarity in this area will be welcome. Finally, the growing information from plant systems biology provides opportunities to link genetic mapping with genetic networks, which could lead to greater understanding of the connections between genotypes and phenotypes.Brassica napus (oilseed rape) genome, an allopolyploid species resulting from a recent cross of B. rapa and B. oleracea. The B. napus genome reveals that there is substantial crosstalk between the two parental genomes, resulting in concerted homeologous exchanges, and shows that selection under domestication has resulted in a loss of undesirable glucosinolate genes and an expansion of oil biosynthesis genes  presented his work on the characterization of QTL related to climacteric fruit ripening and the accumulation of sugars in melon fruits using genetic and genomic tools, such as the melon genome sequence and near isogenic lines (Oryza Map Alignment Project) consortium toward building reference genome assemblies for 11 wild Oryza species. Finally, Wing also presented the progress of his laboratory in dissecting the domestication of the African O. glaberrima, which took place independently of that of the Asian rice. He showed that in both species, the same shattering gene (sh1) was the target of human selection. The causal mutations are a SNP and a deletion for the Asian and the African species, respectively. Michael Purugganan (New York University) presented several population genomic analyses toward the characterization of several traits of agricultural importance, such as the analysis of 95 landraces of O. glaberrima to dissect the salt tolerance phenotype, and the analysis of the domestication of date palm through resequencing data of 62 varieties.The third session of the meeting was devoted to the challenge of applying our understanding of plant genomic diversity and architecture to crop improvement. Maud Tenaillon  discussed recent work in her laboratory aimed at characterizing the genetic basis of flowering time in maize. She described the strategy used that consists of obtaining two maize populations from the same inbred line through divergent selection for flowering time. She showed that a significant response to selection in both directions was obtained. Her results point to few mutations with strong epistatic interactions as the genetic basis of the flowering time differences . Boulos The session ended with a general discussion in which the notion of the pan genome and the dispensable  genome was discussed. The need for better genome sequences and standardized methods for genome annotation, in particular for TEs, was also emphasized during the discussion. Similarly, the need for good repositories of phenotypic data were also acknowledged. In summary, while during the last few years, whole genome data for crop species have become available, there is still a need for improvement of the sequences and their annotation, together with a proper description of the associated phenotypes to be able to bridge the gap between the genotype and the phenotype that will make possible a paradigm shift in crop improvement.In total, the presentations at the conference revealed the extraordinary advances in our understanding of plant genome structure and the genesis of phenotypically relevant genetic variation. While connections to agronomically important phenotypes remain elusive in many cases, the meeting highlighted the promise of merging the often disparate disciplines of plant genomics and plant breeding, toward the goal of sustainably feeding a growing human population


Zeuxapta seriolae, is a host-specific parasite that has an extensive geographical distribution on its host, Seriola lalandi, and is considered highly pathogenic in farmed fish. In recent years, developing cultures of S. lalandi in different coastal localities in Southeastern Pacific Ocean (SEP) have been affected by moderate and heavy infections of this parasite, attributed to contagion from wild to farmed fish. Here, we evaluated the pattern of genetic variations and biological traits of Z. seriolae in a spatial and temporal scale across its geographical distribution in SEP to determine its genetic status and biological traits, which could affect its transmission dynamics from wild to farmed fish.The monogenean, c oxidase subunit I (COI) gene was sequenced for 112 individuals from NCC and 63 from JFA and compared using AMOVA. Prevalence and intensity of Z. seriolae were calculated for each area. The parasite body size, fecundity and size at sexual maturity were estimated for 177 parasites from NCC and 128 from JFA, and significant differences were evaluated using GLM.Wild fish and their parasites were sampled from fisheries in the northern Chilean coast (NCC: 24°S-30°S) and Eastern islands  between 2012 and 2014. Fragments of 816 bp of the cytochrome Z. seriolae across SEP, with a population in NCC and the other in JFA, both with the same high haplotype diversity. Neutrality tests and mismatch analyses indicated that both Z. seriolae populations are stable. Parasite biological traits such as fecundity, body size, and size at sexual maturity, and population parameters varied significantly between geographical areas.Geographical genetic structuring was detected for Z. seriolae were detected in wild fish across SEP. Because of the seasonal migration of wild host and temporal contact with farming, quantifying the genetic diversity and level of gene flow or isolation between parasite populations is useful for fish health management in farming. The smallest size of sexual maturity in parasites from NCC is predictive of shorter life cycles, and their high genetic diversity suggests high evolutionary potential and high transmission of this parasite to farmed hosts.Two genetic groups of  Therce genes .The genetic structure of parasite populations is associated with host specificity, host mobility and environmental conditions . The disIn marine systems, oceanographic conditions and the distance between populations can determine the geographic genetic patterns in parasites , 19 and,Zeuxapta seriolae, is reported in Seriola lalandi from Australia, New Zealand, Japan and California and in S. dumerili from the Mediterranean Sea [Zeuxapta is specific to the genus Seriola, and Z. seriolae, and shows a particularly wide geographic distribution in both farmed and wild fish. Additionally, Z. seriolae is considered highly pathogenic in farmed fish because at high intensities, it can kill its host by causing anaemia [Population genetic studies provide insight into parasite evolutionary histories and aid in the identification of the causal factors contributing to disease dynamics and distribution . The monnean Sea –26. The  anaemia , 27–30.S. lalandi is a pelagic fish and is highly migratory and widely distributed in temperate and subtropical waters of the world. In the SEP, S. lalandi present a permanent population in an archipelago approximately 700 km from continental Chile (80°W), where it is captured year-round. On the northern continental Chilean coast (NCC: 20°S to 30°S), this species arrives annually in the summer, most likely to feed, as occurs in the southwest Atlantic Ocean [S. lalandi have been initiated at different localities in the NCC, where farmed fish are affected by moderate and heavy infection levels of this parasite, which has been attributed to contagion from wild to farmed fish.The yellowtail kingfish ic Ocean . No spawZ. seriolae is a host specific parasite that has an extensive geographic distribution (cosmopolitan) and affects the aquaculture of S. lalandi worldwide it is important to know its evolutionary potential, which can be useful for understanding the dynamic of the disease. Here, we evaluated the patterns of genetic variation of this monogenean on spatial and temporal scales using mitochondrial DNA markers. Additionally, we estimated several life history traits, such as fecundity and size at sexual maturity, beside population parameters of infection across the geographic distribution in the SEP. Taking into account that the host population migrates in the summer to the coast in the SEP (extending the fishery from 20 °S to 30 °S) but the host migratory route, fish origin and the effect of physical barriers on the dispersal of parasite population are not known, we can expect that parasite populations correspond to a single panmictic population. Alternatively, if physical barriers or host segregation affect the genetic flow of parasites, we can expect genetic structure of Z. seriolae across the SEP.Because S. lalandi fish captured by commercial fishers from two geographical areas  across the SEP. Fish from the oceanic area  were collected between April and August of 2013–2014. Fish from the coastal area were collected from different sites during summer (January and April) between 2012 and 2014 because fishing of S. lalandi extends from 20 °S to 30 °S varying the fish landing sites between years. The sampled sites/year in the NCC were: Antofagasta/2013, 2014 , Chañaral/2012  and Coquimbo/2014   was amplified using forward primer JB3 (5′-TTTTTTGGGCATCCTGAGGTTTAT-3′) and reverse primer COX1 (5′AATCATGATGCAAAAGGTA-3′) as described by Leung et al. [http://www.macrogen.com).DNA was extracted using the QIAamp Tissue kit  according to the manufacturer’s instructions. The DNA was then eluted into 50 μl of nuclease free water. Mitochondrial gene cytochrome g et al. . Each PCSequences were edited using ProSeq v 2.9 beta  and aligd: a measure of the frequencies and numbers of haplotypes among individuals [Z. seriolae between geographical areas.Molecular diversity was estimated through the following indices: number of haplotypes (H), number of polymorphic sites (S), haplotype diversity , nucleoividuals ) and meaividuals  and Arleividuals . Geneticividuals . Mann Whct), among populations within years (Fsc) and within populations (Fst). The significance of the covariance component associated with different possible levels of genetic structure was permuted 10,000 times. Pairwise genetic differentiation between populations was estimated using the fixation index Fst and statistical significance was tested with 10,000 permutations. Both analyses were performed in Arlequin v3.1.Genetic population structures were examined through AMOVA to determine the amount of genetic variability using F-statistics in three temporally subdivided hierarchical levels: the proportion of variations among years  previous construction of a neighbour-joining tree (TN93 + G model) in Mega v6. All sequences were deposited in GenBank under accession number: KP119183-KP119357.Finally, a haplotype network was constructed using HaploViewer , which was connected to an Olympus camera. The total length (in millimeters) included the opisthaptor length.Prevalence and intensity of h et al.  for yearh et al. . Three hParasite fecundity was measured as number of eggs per parasite. For this, the parasite uterus was dissected and an entire chain of eggs was removed and counted using a manual counter. To evaluate differences in fecundity, only those parasites whose uteri contained over 50 eggs were considered to exclude those parasites just starting their egg production.Z. seriolae contained at least one egg within the uterus [NCC = 590; nJFA = 158). The parasite length was categorized in mm (1 mm to 25 mm).The size at first sexual maturity (= first size egg production) was measured as the parasite length when 50 % of the population of e uterus  for eachZ. seriolae between geographical areas and to compare the parasite total length between the NCC and JFA samples. The Spearman correlation was used to evaluate the association between parasite body length and number of eggs [2x2 contingency tables with Yates correction were used to evaluate prevalence between geographical areas and temporal variations for sites AF  and JF (oceanic). Mann Whitney U tests were used to evaluate differences in intensity of  of eggs . General of eggs . All anaZ. seriolae individuals sampled from the two geographical areas: 112 sequences from the NCC and 63 sequences from the JFA , but nucleotide diversity was significantly lower in JFA . Eighty-seven percent of the variance was explained by variability within populations and 13 % of the remaining genetic variation was attributed to variability among populations within years  occurring in each site and geographical area, but it was more predominant in JFA where H5 was surrounded by a large number of unique haplotypes. The group 2 included three highly frequent haplotypes  that were predominant in the NCC  and for entire geographical area of study deviated significantly from the expected distribution under expansion model, exhibiting a bimodal distribution of pairwise differences Fig. . Neutral2 = 31.7; df = 1; p < 0.001) and intensity  of Z. seriolae were significantly higher in JFA, considering the entire period of study  but not in the oceanic area . Among years, median intensity varied between 2 and 14 in the NCC and between 8 and 15 in the JFA , year  and co-variable fish size .Prevalence . Z. seriolae fecundity variations were explained by geographical area  and mostly by the co-variable parasite body length .Fecundity correlated with parasite body length . This parasite population genetic structure may be explained by oceanographical barriers to parasite dispersion and/or by host population segregation.For the effective management and health maximization of cultured fish, it is essential to have a clear understanding of the levels of gene flow, the connectivity of parasite populations or metapopulations, the sources of larval infestations, and the relative fluxes of parasites between wild and farmed fish , 2. To sZ. seriolae populations are stable and consistent with populations that are geographically subdivided and have limited or low migration [Z. seriolae populations [Mazocraeoides gonialosae along the coast of China [Population structure in space and time is the result of both present processes and past history . Populatigration . Additioigration , while Figration ; this laigration . Thus, tulations , 54 has ulations  or when ulations , 57 as hof China .S. lalandi, could reach remote locations as well as its host. However, geographical barriers can affect either the host or parasite distribution [Trachurus murphyi [. However, factors such as the Chile–Peru Current (Humboldt Current), surface gradients of temperature and salinity, and the great depths of the Chile–Peru Trench (more than 4000 m in the region) [Z. seriolae population there.Parasites infecting highly mobile hosts such as ribution , 58. JFAribution . These iribution . Studiesribution , 62. Unt murphyi , have no region) , 65 may M. gonialosae and Gotocotyla sawara, which are considered generalist parasites that infect more than one host fish species, did not show a geographical genetic structure based on COI mtDNA in the western Pacific Ocean. The absence of different genetic structures between the populations of these parasite species was attributed to a high gene flow favoured by their host range [Z. seriolae consist of a string of eggs that can entangle in the gills of fish or join together to form light masses of numerous eggs that have a wide surface area, which allows the eggs to stay in the water column for a short time [The dispersal ability and genetic flow of ectoparasites is influenced by host specificity . Host spst range , 15. Theort time , with paort time .S. lalandi is a cosmopolitan species distributed in the Pacific, Indian and Atlantic Oceans (www.fishbase.org). This species arrives at the NCC annually between December and April, where it is captured by artisanal fishermen, whereas S. lalandi is captured in the JFA year-round. In other geographical areas, S. lalandi shows a reproductive strategy with limited migration; specifically, only a subset of the reproductive fish migrates [S. lalandi can migrate considerable distances, but most juveniles are relatively sedentary [S. lalandi are unknown in the SEP, the geographical genetic differences between Z. seriolae from JFA and NCC as well as the temporal genetic differentiation of Z. seriolae between localities from NCC could be indicative of different host subpopulations. Alternatively, the short generation time of the parasites combined with the subdivision of the host populations during prolonged time periods may contribute to the generation of structured parasite populations.Host behaviour is an important factor for parasite dispersal . Therefomigrates . Additioedentary , 71. HowZ. seriolae from the NCC area showed a smaller first size at sexual maturity and was significantly smaller and produced fewer eggs than did parasites from the JFA. Tubbs et al. [in vitro fecundity of Z. seriolae because egg production decreases at other temperatures yet sexual maturity is reached more quickly at higher temperatures. The seawater in NCC varies between 18 °C and 20 °C in summer [Z. seriolae populations across the SEP; however, it is also possible that genetic differences among the parasite populations are reflected in different biological traits. Regardless, the biological trait differences between populations of Z. seriolae may involve differential infestation dynamics  on host populations from different geographical areas, as demonstrated for different ectoparasites in fish farming [Throughout a latitudinal gradient, variations in environmental parameters, such as temperature and salinity, can modify the biological traits of a species , 73. Mons et al.  suggesten summer  and betwn summer . Therefo farming , 80. Sim farming , 82.Z. seriolae infesting the wild fish S. lalandi across the SEP. In each area, the parasites showed different biological characteristics, such as fecundity, body size, and size at first sexual maturity, and population parameters suggesting different dynamics of infestation. Because of the seasonal migration of wild hosts in the SEP, and consequent temporal contact with farmed hosts in NCC, the quantification of diversity and genetic differentiation and level of gene flow (or isolation) between parasite populations, as well as potential parasite adaptations, is useful for fish health management in farming. The smallest sizes of sexual maturity observed in parasites from the NCC predict shorter life cycles, which along with the high genetic diversity suggest high evolutionary potential and high transmission of this parasite to farmed hosts.In this study, we detected two different populations of the parasite


Cbfb/MYH11 leukemia from blood, spleen and bone marrow within 12 days of treatment  that drive tumor progression and immune evasion, such as STAT3, remains a challenge for pharmacological drugs. Blocking STAT3 binding to DNA using specific decoy oligodeoxynucleotides (dODN) provides an alternative targeted inhibitory strategy. To achieve STAT3 inhibition specifically in antigen-presenting cells, we linked STAT3dODN to a TLR9 ligand, CpG ODN as successfully done before for delivery of siRNA molecules ,2. The Ct Figure . The twot Figure . The potThis project described was supported by the National Cancer Institute of the National Institutes of Health under award number R01CA155367 to M.K.