Genome in Rainbow Trout and Steelhead

Genome in Rainbow Trout and Steelhead (lead author John Whitt) Abstract When being thrown into a different environment those new pressures can lead a population to have fast changes via natural selection. These evolutions can occur at a species level or can occur between two closely related species that have differentiated but share a common ancestor as long as the trait is beneficial for them. Population genetic and quantitative research methods have proven that certain linked areas of the genome in rainbow trout and steelhead are tied to the life history strategies of their species. Using genotype testing on 95 nucleotides it has been determined that the specific chromosome that is responsible for the life history strategies is Omy5. 1.   Introduction Being thrown into a new environment leads to quick changes in a population and the traits may even change in multiple species if they are being acted on be the same environmental forces. Different species who share a common ancestor that develop similar phenotype changes due to the habitat pressures acting on them are said to have parallel evolution. These physical changes may arise from the same genetic change in both species or can stem from different regions in both species that happen to cause the same phenotypic expression. While it is not impossible for parallel evolution to occur from a random new mutation it is much more likely to occur because of a sequence change in existing alleles. It is extremely important for researchers to determine the location of the genes they are testing for and without this, it is impossible to see how evolution is occurring at the genetic level.   It turns out most of the important traits are not controlled by a single genetic or habitat factor . They are often complex and difficult to locate.   The most difficult to genetically locate are traits that affect numerous physical changes, influence the behavior, or have a physiological effect on the species.   The researchers are using advanced techniques like genomic mapping and screening along with sequencing the entire genome of the animals being tested to help locate the area of the genome that is being affected from these rapid evolutions caused by new environments. There have been many genetic studies done on the migration of animals and it commonly accepted that genetics play a major role in the phenotypic differences that accompany these migration characteristics. These threshold traits are determined not only by the physical traits but also by the animals physiological traits. Though migration has all these complex traits that act on it researchers have also found single genes that have effect on the migration of animals as well, so it can also be quite simple at times. The single Clock gene in the Pacific salmonid is a large contributor on when the salmonid migrates.   One of the worlds most abundant and common fish is the Oncorhynchus mykiss. O. mykiss have one of the most comprehensive migratory variations. For example the rainbow trait never leaves freshwater whereas the steelhead are more located in the salt water.   It has been determined that these varying migration tendencies are genetically passed down. Though the differences be tween the steelhead and the rainbow trout are great they are the closest related O. mykiss. Steelheads have more of a complexity when it comes to factors affecting their migration. They have the typical traits that usually affect migration, but also have smoltification which gives them the traits required to go from freshwater to saltwater and ability to travel far.   The rainbow trout on the other hand only keeps the ability to swim in fresh water but gain the ability to sexually reproduce sooner. Past studies have been completed on two populations of O. mykiss that happened to be separated by an environmental barricade. They were then tested for Fst value and found that the loci had the highest values displayed linkage disequilibrium which means that they were not independently assorted. The loci were also genetically located at the same position in both fo the populations. When further tested it was determined that the two populations had 3 loci that had linkage disequilibrium as well as allelic frequency patterns that matched with gnomonic mapping tests that gave the same locations for characteristics growth rate and smoltification. These were all found on the Omy5. These determined that the Omy5 location was responsible for all the traits across populations even if they were separated, meaning that there was no genetic flow going on between the two.   Miller and colleagues goals are to find out how SNPs that coded for physical traits like maturation time, growth rate, an d smolting from past experiments are linked to the Omy5 gene. 2. Material and methods (a) Population samples Using locations from California and Oregon 21 samples of steelhead and rainbow trout were obtained from populations that were separated by natural or artificial barriers. They took the samples from above and below the barriers and also took samples from rainbow trout hatcheries, so that they could have samples from all the life stages. They believed that all of the fish samples that were obtained in the wild were of natural origin, but were not one hundred percent on the status of the hatchery samples. (b) Marker development, genotyping and analysis Miller and colleague discovered 344 single nucleotide polymorphisms that were linked to Omy5 with RAD sequencing from two of the hatchery strains. They created 55 unique SNPtype assays by adding 150bp from cloned BAC strains onto the flanking sequences of the SNP. They also utilized assays that were developed by other researchers.   Miller Pearse et al also used three loci found by Abadia Cardoso and his colleagues.   For the analysis part, they used EP1 systems and followed the recommended protocols. They used two control groups for every array. Linkage disequilibrium as well as, Hardy-Weinberg equilibrium were test for. Miller and colleagues only counted p-values that were under the Bonferroni-corrected value due to the large number of linked disequilibrium tests. They quantify the Omy5 in different ways. They ranked 55 loci of the Omy5 based on the r2 values and then compared those to rest of the loci. R2 value is calculated by checking to see if an allele is present at two di fferent loci. For example, one could look for allele 1 at locus 1 and locus 2 and then one would check to see if allele 2 is present at locus 1 and locus 2. These result could then be used to calculate r2.  Ã‚   Using statistical packages the researcher visualized linkage disequilibrium of the Omy5 in all of the population sampled. They also computed the amount of linkage association that was over the critical value that was shared between locus and loci. For a reference population Miller Pearse et al used the Scoot Creek steelhead because it had the biggest sample size and have had the greatest polymorphic loci.   To find if there was a link between Omy5 and life history Miller took allele frequencies from all the populations and compared them to one another still using the Scott Creek as a reference population he determined the frequency p for all the sample populations. 3. Results and analysis (a) Genetic data There was a total of 95 single nucleotide polymorphism tested eight of those failed due to not being amplified, did not show signs of polymorphism or werent in line with Mendelian segregation.   This left Miller with 87 loci which were comprised of 55 Omy5 loci and loci from the other 32 were on other linked groups. Of these 87 it was determined that 4 were not in Hardy-Weinberg equilibrium. (b) Population structure Based on the 32 loci from other linked groups it was determined that they followed a similar trend as that of past studies. Stating that the closer the populations were to each other the more related the populations would be. Miller found when looking at the Omy5 loci it was the opposite meaning the population displayed a high separation between the populations that were separated by the waterfalls or dams. (C) Linkage disequilibrium Miller performed a total of 495 linkage disequilibrium tests on the 32 other linked groups. After the tests were Bonferroni corrected for numerous attempts it was determined that none of those groups had a significant value.   Miller now looked at the loci of the 55 Omy5 groups and the results were that out of 1430 there were a total of 602 that were significant, which gave them a total of 42% of the test samples having a significant p-value. These results conferred that the linkage on Omy5 was, in fact strong. To visualize linkage disequilibrium in all of the populations Miller took the values for the r2 which went from 0.008 0.53 (no units) and used these to order the populations. Miller found that there were 14 loci with r2 values that exceeded the critical value which is 0.9. Once analyzed there obviously a cluster of loci that were in strong linkage disequilibrium. (d) Allele frequency and haplotype variation among populations The results for allelic frequency variations agreed with the linkage disequilibrium analysis performed on the 55 Omy5 loci.   The results also gave groups of the loci whose frequencies were closely related and were linked to populations that were above and below the natural or artificial barriers. Miller took the loci with the greatest average r2 values and labeled them as one linked haplotype. These 30 loci were linked to the steelhead and rainbow trouts life-history strategies.   Miller Pearse et al then used the haplotype to determine the haplotype frequency for the steelhead and rainbow trout by using their average allele frequencies. Miller Pearse et al found that rainbow trout haplotype frequencies were higher in the areas that were above the barriers and had significantly decreased haplotype frequencies in the below barrier populations. This was accurate with the collecting data of the rainbow trout as they were found in the four populations that were taken from above the natural and artificial barriers. Miller and colleagues then compared that new species versus the older species and found that the older species had a great number of Steelhead haplotypes. 4. Discussion Miller concludes that the results prove that adaptation in natural populations can occur rapidly and are caused by the environments pressures that act upon those populations. Miller also states that artificial factors have a higher evolutionary influence on the populations than is seen with natural selection. What is still unclear to Miller is that how these pressures affect the genetic evolution of the populations. For example, if species are undergoing parallel evolution are they just developing similar traits that are better suited for their environment, or are these changes also occur similarly at the genetic level. Miller Pearse et al results imply that the parallel pressures of natural selection are also having parallel affects genetically. These effects are occurring specifically on the Omy5. Which they have concluded to be linked to the life-history patterns of that population and used the data collected from the frequency haplotyping to demonstrate that the population respon ds to environmental pressures that are acting on them.   The Omy5 also acts as a command center of some sorts and controls actions like migration. Looking to the past Millers et al experiment is in line with others performed. There have been experiments that have used different populations of sticklebacks and moved them from their normal saltwater environment to a new freshwater environment which resulted in the loss of defensive traits like armor. There are also examples of Scott Creek population that went through a pigmentation change even though it resulted in a reduction in the fitness of the population.   Miller hypothesis that life-history strategies are linked to the genetic of the population, specifically at the Omy5 region is supported by his and these past experiments. There is also evidence from past experiments that suggest that Omy5 has resistance to recombination, and is likely due to chromosome inversion. This is interesting because the region that is responsible for the change in life-history patterns is resistant to change. Could look at this like the population of O. mykiss do not want to change those traits .   It is also important to note that it is not hundred percent sure exactly what traits are being affected by the Omy5 section of the genome. It is known that the Clock gene is within the Omy5 region. The Clock gene has been linked to smolting and it is hypothesized that sense smolting is extremely complicated that there are multiple genes that are responsible for its coding. (a) Conservation implication. Miller also states that his results are showing a decrease in rainbow trout in older above barrier location and the hypothesis that if enough time passes there might be no rainbow trout in above barrier locations due to the migration history patterns of these fish, so far his hypothesis seems to accurate, because all of the rainbow trout they collected were below the barriers.   He also states that because of the artificial barriers that do not allow the populations to make migration chooses of their own that it locks them into this cycle even more. Meaning that if they were natural barriers the fish might be able to find a way past them, but since they are artificial barriers like dams that are meant to block passage that the above barrier and below barrier populations are going to stay separated.   Miller Pearse et al discusses the effects of large closed bodies of waters or reservoirs and states that these could be the reason for the higher frequency of rainbow trout haplotype since these environments favor their population more so than the steelhead. Miller and his colleagues experiment give many facts about the rapid evolution due to environmental pressures caused by a change in habitat, but they also provide some more subtle information that may be lost in the numbers. Millers experiment shows declining number of rainbow trout in older areas and presents facts about how artificial barriers affect the different population of fishes. The article also discusses how only the fish that are below the barriers are protected.   This is probably not the best way to try and keep these fish population from being endangered. The reason being that both species share such a close ancestor that they are both able to produce the same phenotypes, which should result in both of them being protected.

Who is to blame Essay -- essays research papers

Who Is To Blame? â€Å"Frankenstein†, one of the key texts in modern literature, was written by Mary Shelley in 1818 when she was only 21. The novel was first published anonymously, and the author was only later revealed to be Shelley. When she republished the book in 1831, with changes to the story, Shelley had finally answered the question she had been asked several times: how could such a young girl write about such horrible things? Her answer describes her literary sources, as well as a disturbing dream that was the kernel of inspiration for the story. â€Å"Frankenstein† is a tale about a man named Victor Frankenstein who creates life out of ‘raw materials’. As the story unfolds, the creature comes to life and ends up, out of revenge, killing several members of Frankenstein’s family. Although ...

Describe and Evaluate Two Theories for the Maintenance of Relationships Essay

Social exchange theories exist in various forms but the underlying theme is that people may be selfish. Social exchange theories argue people may view relationships in a â€Å"profit† or â€Å"loss† way. Thibaut & Kelley believed people will look to see how rewarding a relationship is and then how much it costs to be in the relationship. If there is a profit left over (rewards – costs = profit) then that may encourage them to continue the relationship where as if there is a loss – this may motivate them to end the relationship. Blau argued that interactions are â€Å"expensive†, as they take time, energy and commitment and may involve unpleasant emotions and experiences. Therefore what we get out of a relationship must exceed what goes in. Walster et al believed that social interactions involve an exchange of rewards, like affection, information, status. The degree of attraction or liking reflects how people evaluate the rewards they receive in relative to those given. SET is therefore an economic theory explaining relationships in terms of maximising benefits and minimising costs. The â€Å"Social exchange† is the mutual exchange of rewards between partners; like friendship, sex and the costs of being in the relationship may be freedoms given up, time, effort. A person may make their assessment of their rewards by using two comparisons: The comparison level (CL) – where rewards are compared to costs to judge profits. This may be based on past experiences and relationships as well as what we expect to get from a relationship. The comparison level for alternative relationships (CLalt) – Where rewards and costs are compared against perceived alternative relationships and how they compare. A relationship is maintained if profit is perceived in both these two comparisons. Thibaut & Kelley proposed a four-stage model setting how relationships could be maintained, predicting that over time people develop a predictable and mutually beneficial pattern of exchanges assisting the maintenance of relationships; Sampling – Rewards and costs are assessed in a number of relationships Bargaining – A relationship is â€Å"costed out† and sources of profit and loss are identified Commitment – Relationship is established and maintained by predictable exchange of rewards Institutionalisation – Interactions are established and the couple â€Å"settle down†. Mills et al identified two kinds of intimate relationships; (a) The communal couple where each partner gives out of concern for the other and (b) The Exchange couple who keep mental records of who is ahead and who is behind. This indicates that there are different types of relationships and SET may apply to some of them but not universally to all. Rusbult asked participants to complete questionnaires over a 7-month period concerning rewards and costs and found that SET did not explain the early â€Å"honeymoon† phase of the relationship when balance of exchanges was ignored. However later on relationship costs were compared with degree of satisfaction which suggests that the theory is best applied to the maintenance of relationships. Rusbult found that costs and rewards from a relationship were weighed up in comparison to possible alternative relationships when deciding whether they should be maintained which supports that social exchange models idea that people assess rewards by making comparisons. However a third element of investment (Commitment) was also a factor in this in which people compared how much they had invested into the relationship and what they stood to lose – which SET does not fully recognise suggesting it does not explain such things. Rusbults Investment model looks at this however and better explains this. Hatfield looked at people who felt over or under-benefited. The under-benefitted felt angry and deprived while the over-benefited felt guilty and uncomfortable. This supports SET theory by suggesting that regardless of whether individuals benefitted, they do not wish to maintain a relationship which is unfair. Equity Theory may better explain this however and how it may that that theory is better suited to explain such as if, as SET proposes, it is all about profit – then surely when people feel they are over-benefiting they are more inclined to maintain the relationship. Rubin believed that although people are not fundamentally selfish – attitudes towards others are determined to a large extent by how rewarding we think they are for us supporting the theory. Argyle criticised methodologies that evaluate SET as being contrived and artificial with little relevance to real life relationships. Sedikides claimed that people are capable of being completely unselfish in relationships and do things for others without expecting anything in return – which is most evident in relationships with those emotionally close to us. Sedikides believed that individuals could bolster their partners self-esteem when faced with failures or stress and therefore SET’s theory of humans being out for what they can get is simplistic and inaccurate. Fromm argued against the theory also arguing that true â€Å"love† was about giving as opposed to false love where people expect to have favours returned. Most research has tended to concentrate on short-term consequences of relationships rather than the long-term maintenance and what drives them. This theory may apply to those that keep â€Å"score†. Mustein et al devised the exchange orientation tool, identifying such scorekeepers; who are suspicious and insecure suggesting that the theory only suits relationships lacking confidence and mutual trust. Equity Theory Equity does not mean equality; instead it perceives individuals as motivated to achieve fairness in relationships and to feel dissatisfied with inequity (unfairness). Definitions of equity within a relationship can differ between individuals. Maintenance of relationships occurs through balance and stability. Relationships where individuals put in more than they receive or receive more than they put in are inequitable, leading to dissatisfaction and possible dissolution. The recognition of inequity within a relationship presents a chance for a relationship to be saved – that is, maintained further by making adjustments so that there is a return to equity. Relationships may alternate between periods of perceived balance and imbalance, with individuals being motivated to return to a state of equity. The greater the perceived imbalance, the greater the efforts to realign the relationship, so long as a chance of doing so is perceived to be viable.

Which Type of US Visa Is Right for You

Citizens of most foreign countries must obtain a visa to enter the U.S. There are two general classifications of U.S. visas: nonimmigrant visas for temporary stays, and immigrant visas to live and work permanently in the U.S.   Temporary Visitors:  Nonimmigrant US Visas Temporary visitors to the U.S. must obtain a nonimmigrant visa. This type of visa allows you to travel to a U.S. port-of-entry. If you are a citizen of a country thats part of the Visa Waiver Program, you may come to the U.S. without a visa if you meet certain requirements. There are a number of reasons why someone would come to the U.S. on a temporary visa, including tourism, business, medical treatment and certain types of temporary work. The State Department lists the most common U.S. visa categories for temporary visitors. These include: Australian (E-3) in Specialty OccupationBorder Crossing Card - Mexican TravelersBusiness, Tourist, and VisitorsChile Free Trade Agreement (FTA) ProfessionalDiplomats and Government OfficialsExchange VisitorsFiancà ©(e) to Marry U.S. Citizen/SpouseInternational Organizations NATOMedia JournalistsMexican and Canadian NAFTA Professional WorkerReligious WorkersSingapore Free Trade Agreement (FTA) ProfessionalStudentsTemporary Workers OverviewTreaty Traders Treaty InvestorsVisa Renewals Living  and Working in the U.S. Permanently: Immigrant US Visas To live permanently in the U.S., an immigrant visa is required. The first step is to petition the U.S. Citizenship and Immigration Services to allow the beneficiary to apply for an immigrant visa. Once approved, the petition is forwarded to the National Visa Center for processing. The National Visa Center then provides instructions regarding forms, fees, and other required documents to complete the visa application.  Learn more about  US visas  and find out what you need to do to file for one and how long the process will take. The major immigrant US visa categories include: Immediate RelativesSpecial ImmigrantsFamily-sponsoredEmployer-sponsored Source: The U.S. Department of State