Background of the Study
Systematics and taxonomy involves identifying and resolving relationships among species. But with species today being more taxonomically complex, integrating molecular technology as an alternative tool in species identification has helped systematic s gain new perspective in evolutionary studies .Taxonomy has always been the forefront in the study of life and forever will be (Wheeler 2004). And with the increase in the development within the field of molecular biology and genetics, DNA is now used as a way in identifying species. DNA Barcodes are tags along a specific gene sequence that have been proposed in species identification. The use of DNA as a barcode that was developed by Hebert et al. (2003) has been the system used because of its accurate and stable method, that even a tiny tissue sample will suffice the identification of that species (Laiou et al., 2013). DNA Barcoding nowadays is being used as a universal system in identification and taxonomic clarification (Hollingsworth et al., 2011). The importance of DNA barcoding is evident in such a way that the pace of species discovery will emphasize sorting of species from different taxa classifications representing new species (Hebert et al., 2005). Barcoding promotes biological applications such as identification of medicinal plants and even plant nearing extinction (Muellner et al. 2011). DNA Barcoding defines the expansion and discovery of the world’s ever-expanding inventory of species’ diversity.
DNA barcoding requires it to be standard, scalable and minimal. Plants’ low rate of nucleotide substitution in the mitochondrial gene has been the source of major debate regarding a plant’s code for its identity. CO1 has been the standard gene used fo...
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... of plastid atpB and rbcL gene sequences. Systematic Biology 49: 306–362. doi:10.1093/sysbio/49.2.306
Tezcan, M., Vlachonasios, K., and Aki, C. (2010) DNA Barcoding study on Sideritis trojana Bornm. An endemic medicinal plant of Ida Mountain, Turkey. Fresenius Environmental Bulletin, PSP vol.19-no.7
Tamura, K., Peterson, D., Peterson, N., Stetcher, G., Nei, M., and Kumar S. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution. Retrieved February 01, 2014 from http://mbe.oxfordjournals.org/
Wang, Q., Yu., QS., Liu, JQ. (2011) Are nuclear loci ideal for barcoding plants? A case study of genetic delimitation of two sister species using multiple loci and multiple intraspecific individuals. Journal of Systematics and Evolution 49: 182-188
Wheeler (2004)
This information supports our hypothesis for the monohybrid cross, but it does not support our hypothesis for the dihybrid cross. In the monohybrid cross, it was expected that we would get a phenotype ratio of 3 plants with anthocyanin for every 1 plant with no anthocyanin. The plants with anthocyanin were easy to differentiate because of the purple color that is shown in the phenotype of plants with anthocyanin in them (Webb 2014). The results we observed were relatively close to this ratio, and the chi-square statist tells us that the monohybrid cross did follow mendelian inheritance patterns. In a different experiment done with Brassica rapa, it was found that when a set of plants with anthocyanin present were crossed with a set of the same species of plant but without anthocyanin present, the phenotypic ratio observed was 3 to 1 (Hayashi et al. 2010). This information just reinforces the idea that a monohybrid cross between Brassica rapa with anthocyanin and without anthocyanin does produce a F2 generation that follows Mendelian inheritance patterns with a 3 to 1 phenotypic ratio. The dihybrid cross we conducted was done with the anthocyanin gene, and the color gene. The dihybrid cross did not follow Mendelian inheritance patterns, so this leads us to believe there must have been a source
The samples of DNA were obtained by plucking individual hairs from students' heads and using the PCR device to replicate. the DNA from the roots of the hair. The replicated DNA samples were then placed into the electrophoresis gel and the device was turned on. Using the methods discussed above we found that three of the fourteen samples, 21%, were homozygous and the remaining eleven samples. 79% were heterozygous in their ancestors.
Amplification reaction was done in a 25.0 µL reaction mixture containing 0.4 µL DNA (from DNA extraction), 5.0 µL of 10X PCR reaction buffer, 14.2 µL of sterelized dH2O, 2.0 µL of magnesium chloride (MgCl2, 25 mM), 1.0 µL nucleotide/dNTP mix (10 Mm), and 0.4 µL of 5 u/µL Taq DNA polymerase for each primer namely respectively. The components and the volume used for the amplification reactions are listed in Table 3.2. For the reaction, PCR reaction was performed in a programmable gradient-enabled thermocycler (Bio-Rad MyCycler™ Thermal Cycler).
For the original analysis, the corrected pairwise distance will be calculated using the Jukes–Cantor and the Maximum Composite Likelihood Model. The Jukes–Cantor model assumes that the rate of nucleotide substitution or all nucleotides (C, A, T and G) are equal, that nucleotide frequencies are equal, that there is an equal rate of substitution among sites, and does not correct for the lower rate of transversion substitutes in comparison to transitional substitutions (Jukes and Cantor, 1969). The Maximum Composite Likelihood takes into account the phylogenic relationship between sequences, using the sum of the log likelihoods of the bases as the composite likelihood. Both pair wise distances and substitution parameters are estimated using the Maximum Composite Likelihood (Tamura et al. 2004). Both models should yield different maximum sequence divergence and average divergence that can then be compared to the original paper. With sequence divergence data, the temporal origin of the genus can be identified. The two alternate models to the Kimura-2 parameter will be analyzed to discuss which methods yield results closest to the expected time origin of the genus
Rienzo, Anna Di. Wilson, Allan. 1991. Branching pattern in the evolutionary tree for human mitochondrial DNA. Evolution 88: 1597-1601.
Evidence has shown that the corn we know today is quite different from the first time it was domesticated in Mexico. Although researchers and the academic world acknowledge that corn began its world journey in Mexico, they are unsure as to the time and location of the earliest domestication (American Society of Plant Biologist). Through genetics, teosinte is found to be corn’s wild ancestor. Although the two do not look much alike, at a DNA level they are surprisingly alike, such as having the same number of chromosomes and a remarkably similar arrangement of genes (The University of Utah).
As the population density increased, so did the male gametophytes of the wild type strain; but there were no male gametophytes at any population density in the Her ...
5.) Fraser et al., Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete. Science 1998 281: 375-388.
DNA Timeline: DNA Science from Mendel to Today. (2014). Retrieved May 29, 2014, from http://www.dnai.org/timeline/
Work Cited Colby, Chris. A. Web. " An Introduction to Evolutionary Biology." 28 August 2015.
Smith, A.M., Coupland, G., Dolan, L., Harberd, N., Jones, J., Martin, C., Sablowski, R. and Amey, A., 2010. Plant biology. New York: Garland Science; Taylor & Francis distributor.
A one-to-one correspondence of orthologs and paralogs can help to reconstruct evolutionary history of genes by comparing the sequences of all genes between genomes from different taxa and with each genome. However combination of speciation and gene duplication entangles orthologs and paralogs into complex web of relationships involving one-to-many and many-to-many correspondence. The emerging field of evolutionary genomics have also highlighted the importance of gene loss, horizontal gene transfer and gene rearrangements in genome evolution which can further complicate the evolutionary relationships of homologous genes [3].
The authors. Primarily members of the Sherlock lab at Stanford University, constructed a sequencing-based ultra-high-resolution lineage tracking system in Saccharomyces cerevisiae to allow monitoring of several cell population lineages simultaneously. A plasmid library containing, 500,000 random barcodes was inserted into the genome at a landing pad to act as a barcode. Barcoding requires 48 generations of growth from a common ancestor before analysis. To count the relative frequency of each lineage across time, genomic information including lineage barcodes were isolated from the DNA of pooled populations using a two- step PCR protocol, and sequenced amplicons. The population dynamics observed indicated that for mutations to fixate, they must provide advantages above the mean fitness and grow at a rate quick enough so that mutation establishment is not prevented. This paper served as one of the first primary examples of genetic bar coding, including the methods of inserting genetic barcoding via a restriction enzyme/cloning/ligating mechanism. The articles findings are strong, including theoretical computational models and physical samples analyzed with barcode
There are various computer programs that can aid in sequencing these segments of DNA and generate phylogenetic trees. The programs are specifically looking for intron indels, retroposon, gene duplications and linked genes (Rokas and Holland 2000). Researchers can use several supermatrix formations that have already been created to pair up species (Gatesy et al. 2012). In our example, DNA was extracted, purified and then sequences. The computer program was looking for the presence or absence of transposon sites when compared to one of the supermatrix formations(Gatesy et al. 2012). Additionally, as the computer program runs the sequences gathered from the whale and hippopotamus the sequences will align allowing for additional differences and similarities in the genetic code to be found. After the genetic code has been sequenced, the computer programs can run programs to make phyogenetic
The scientific and medical progress of DNA as been emense, from involving the identification of our genes that trigger major diseases or the creation and manufacture of drugs to treat these diseases. DNA has many significant uses to society, health and culture of today. One important area of DNA research is that used for genetic and medical research. Our abi...