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      <title>SIL2006 POPULATION GENETICS by NURUL FARYANA BINTI MUSTAPA KAMA</title>
      <link>https://padlet.com/17207606/d07o2ence0ubf3x4</link>
      <description>Made with magic</description>
      <language>en-us</language>
      <pubDate>2021-10-20 01:34:16 UTC</pubDate>
      <lastBuildDate>2025-10-28 11:28:40 UTC</lastBuildDate>
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      <item>
         <title>Group B (4)</title>
         <author>17207606</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1831844828</link>
         <description><![CDATA[<div>AMEER HAKIM<br>LIM KHANG NING<br>NURUL FARYANA<br><br></div>]]></description>
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         <pubDate>2021-10-20 23:15:28 UTC</pubDate>
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         <title>Population genetics</title>
         <author>17207606</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1831868641</link>
         <description><![CDATA[<div>-The study of evolution from genetic point of view<br>-When evolution in population occurs at the genetic level, it is sometimes called micro evolution. It's change in the collective genetic material of a population</div>]]></description>
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         <pubDate>2021-10-20 23:33:06 UTC</pubDate>
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         <title>Side note</title>
         <author>17207606</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1831875081</link>
         <description><![CDATA[<div>- Population is a group of individuals of a same species that routinely interbreed<br>- Evolution did not happen in individual but happen among the group</div>]]></description>
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         <pubDate>2021-10-20 23:37:41 UTC</pubDate>
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         <title>Importantance of studying population genetics</title>
         <author>17207606</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1831889143</link>
         <description><![CDATA[<ol><li>&nbsp;Learn about human migration and history</li><li>To identify and localize disease genes</li><li>Difference in linkage disequilibrium for fine mapping</li><li>Avoid false positive date</li><li>Mapping of disease</li><li>Signature of natural selection</li></ol>]]></description>
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         <pubDate>2021-10-20 23:45:48 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1831889143</guid>
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      <item>
         <title>How population change over generations?</title>
         <author>17207606</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1834859439</link>
         <description><![CDATA[<ul><li><strong>Stabilizing selection</strong></li></ul><div>Natural selection will stabilise the population if it favours an average phenotype by selecting against extreme variation. Natural selection will favour individuals who blend in best with the forest floor and are less likely to be detected by predators in a population of mice living in the woods, for example. Assuming the ground is a fairly consistent shade of brown, mice with fur that is the most nearly matched to that colour will most likely survive and breed, passing on their brown coat genes. Mice with alleles that make them somewhat lighter or darker stand out against the ground and are more likely to be eaten by predators. The genetic variation of the population will diminish as a result of this stabilising selection.<br><br></div><ul><li><strong>Directional selection</strong></li></ul><div>When the environment changes, populations frequently go through directional selection, which favours phenotypes on one extreme of the current variation spectrum. The evolution of the peppered moth in eighteenth- and nineteenth-century England is a typical example of this form of selection. Prior to the Industrial Revolution, moths were mostly light in colour, allowing them to blend in with nearby light-colored trees and lichens. As industries began to spew soot, the trees darkened, making light-colored moths easier to spot for predatory birds.</div><div><br></div><ul><li><strong>Disruptive/diversifying selection</strong></li></ul><div>Natural selection can sometimes favour two or more unique phenotypes, each with its own set of advantages. The intermediate genotypes are generally less suited than their extreme counterparts in these situations. Diversifying or disruptive selection is evident in many populations of animals, such as lobsters, that have numerous male mating techniques. Large, dominant alpha males gain mates by brutal force, whereas little males can slip in for furtive copulations with the females in an alpha male’s domain.Both dominant males and “sneaking” men will be picked in this circumstance, but medium-sized males, who cannot surpass alpha males and are too large to sneak copulations, will be rejected.&nbsp;</div>]]></description>
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         <pubDate>2021-10-21 23:17:35 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1834859439</guid>
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      <item>
         <title>Marker system</title>
         <author>17207606</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1834864239</link>
         <description><![CDATA[<div><br></div><ol><li>Phenotypic/Morphological Marker<ul><li>First-generation of marker</li><li>Distinguishes based on morphological/physical characteristics.</li><li>Eg：<ul><li>Height (tall/short plant）</li><li>Resistance (resistant/susceptible plant to the certain environment)</li></ul></li></ul></li><li>Biochemical Marker<ul><li>The second generation of marker</li><li>Distinguish based on variation in the expressed product</li><li>Eg:<ul><li>Proteins</li><li>Isozymes</li><li>Disease resistant protein (A biochemical marker distinguishes individual)</li></ul></li><li>Major limitation 1st and 2nd marker:<ol><li>They are influenced by the environmental changes(very unstable)</li><li>The number of characters/proteins are very less.</li></ol></li></ul></li><li>Genetic markers/ DNA markers<ul><li>The third generation of marker</li><li>Distinguish based on variation in the DNA sequence/genome</li><li>Eg:<ul><li>RAPD, RFLP, AFLP, SSR &amp; SNP</li></ul></li><li>The variation detected by this marker:<ul><li>Deletion</li><li>Insertion</li><li>Duplication</li><li>Inversion</li></ul></li><li>Advantage:<ol><li>They are not influenced by the environment (very stable)</li><li>The number of markers is almost unlimited</li></ol></li></ul></li></ol>]]></description>
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         <pubDate>2021-10-21 23:21:33 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1834864239</guid>
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      <item>
         <title>RFLP (Restriction Fragment Length Polymorphism)</title>
         <author>khangning23</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1835485834</link>
         <description><![CDATA[<ol><li>First generation marker</li><li>Exploits variation in restriction sites of DNA</li><li>RFLP is a site in genome where the distance of 2 restriction site varies in every individuals</li><li>Process:<ol><li>Restriction enzymes recognised the restriction site</li><li>Restriction Site is cut/cleaved- become fragmented DNA</li><li>2 restriction fragments are separated on Gel Electrophoresis-forming bands pattern.</li><li>Fragments transferred to nitrocellulose membrane</li><li>DNA hybridization- Radiolabelled probes are applied at Southern Blot (Probes bind to complementary DNA on membrane)</li><li>X-ray film is applied to the blot- To visualise DNA fingerprint pattern</li><li>Allowed the probes to develop</li><li>Extra columns shows the restriction fragment pattern of 2 individuals</li></ol></li><li>Application:&nbsp;<ul><li>Identifying Parentage</li><li>Criminal Identification</li><li>Diversity/Phylogeny Analysis</li><li>Breeding</li><li>Marker assisted selection</li><li>Mapping</li></ul></li><li>Pros:<ul><li>Codominant- Can distinguish Homozygous &amp; Heterozygous DNA</li><li>Sequense specific- Probe is developed with sequence specifications</li><li>Genomic abundance- Restriction site are distributed throughout the genome</li><li>Reproducible &amp; Stable- Results are highly reproducible even across different labs</li><li>Simple—given the availability of suitable probes, the technique can readily be applied to plant</li></ul></li><li>Cons:<ul><li>Requires high quality &amp; large amount of DNA- Restriction enzymes activity is highly affected by impurities</li><li>Radiolabeled Probe is costly and working requires caution</li><li>Not automated</li><li>Tedious</li><li>Time Consuming</li><li>Low level of polymorphism</li></ul></li></ol>]]></description>
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         <pubDate>2021-10-22 04:44:58 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1835485834</guid>
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      <item>
         <title>RAPD (Randomly Amplified POlymorphic DNA)</title>
         <author>khangning23</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837569771</link>
         <description><![CDATA[<ul><li>10 nucleotides long arbitrary sequences added forwards/reversed</li><li>Amplify complimentary region in genome</li><li>RAPD amplification depends on template</li><li>2 other variants of RAPD:<ol><li>AP-PCR (Arbitrary Primed PCR)</li><li>DAF (DNA Amplification Fingerprint)</li></ol></li><li>Pros:<ul><li>Fast &amp; Easy Assay-can be completed with 4-5 hours</li><li>Sequence info not required for primer designing</li><li>Can be performed with few nanograms of DNA</li><li>High genomic abundance</li><li>Cheap</li></ul></li><li>Cons:&nbsp;<ul><li>Low reproducibility</li><li>Dominant markers</li><li>High quality of template DNA is required</li><li>Highly sensitive to reaction conditions.</li></ul></li></ul>]]></description>
         <enclosure url="" />
         <pubDate>2021-10-23 03:51:52 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837569771</guid>
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      <item>
         <title>AFLP (Amplified Fragment Length Polymorphism)</title>
         <author>khangning23</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837570123</link>
         <description><![CDATA[<ul><li>PCR amplification based<ul><li>Combination of both restriction based &amp; PCR based method</li></ul></li><li>Process：<ol><li>Involve in the digestion of genomic DNA using Restriction Endonucleases (Eco R1- 6bp cutter &amp; Mse I-4bp cutter)</li><li>Followed by Adapter Ligation and PCR Amplification</li><li>Amplified products are visualized on high-resolution polyacrylamide gels.</li><li>Amplification (2 phases)<ol><li>Pre-selective amplification<ul><li>The first round of amplification</li><li>Few fragments are selectively amplified</li><li>20 PCR cycle is set</li></ul></li><li>Selective amplification<ul><li>The second round of amplification</li><li>More primers + 3 extra nucleotide bases are used</li><li>Few cycles of Touch Down PCR is set - to improve the amplification efficiency</li></ul></li></ol></li><li>Fragment separation- Bending pattern of the fragment is analyzed manually/with analytical software</li></ol></li><li>Pros:&nbsp;<ul><li>Multilocus-Restriction sites are present across the whole genome, can analyze multiple-locus at once</li><li>Universal primers- sequence information is not essential as primers complementary to adapter sequences are designed.</li><li>Simplicity</li><li>Low temperature</li><li>Can detect Polymorphisms</li></ul></li><li>Cons:&nbsp;<ul><li>High-quality DNA is required</li><li>Dominant- Cannot detect homozygous/heterozygous</li><li>Locus unknown</li><li>Expensive</li><li>Time consuming</li></ul></li></ul>]]></description>
         <enclosure url="" />
         <pubDate>2021-10-23 03:52:22 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837570123</guid>
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      <item>
         <title>SSR (Simple Sequence Repeats)</title>
         <author>khangning23</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837570400</link>
         <description><![CDATA[<ul><li>Short Tandem Repeats of 1-6 base&nbsp;</li><li>Others name:<ul><li>STR (Short Tandem Repeat)</li><li>Microsatellites</li><li>SSLP (Simple Sequence Length Polymorphism)</li></ul></li><li>Types of SSR:<ul><li>Genomic SSR<ul><li>Found in coding, intronic/intergenic regions</li><li>More variability</li><li>Less cross- transferability</li></ul></li><li>Genic SSR<ul><li>Only found in the coding region</li><li>Lesser Variability</li><li>High cross-transferability</li></ul></li></ul></li><li>Cause of SSR:<ol><li>Replication slippage is a major cause for SSR</li><li>Mutations &amp; Recombination during meiosis</li></ol></li><li>Pros:<ul><li>Co-dominant</li><li>Hyper variable</li><li>Stable</li><li>Low quantity of DNA required</li><li>Sequence-specific</li><li>Automation, Fast , multiplexing</li><li>Transferable between species</li></ul></li><li>Cons：<ul><li>High cost</li><li>Shadow/shutter bands appear</li><li>Presence of null alleles</li><li>Too many alleles at certain loci</li><li>Microsatellite flanking regions contain the length mutation (sometimes)</li></ul></li></ul><div><br></div>]]></description>
         <enclosure url="" />
         <pubDate>2021-10-23 03:52:43 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837570400</guid>
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      <item>
         <title>SNP (Single Nucleotide Polymorphism)</title>
         <author>khangning23</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837570808</link>
         <description><![CDATA[<ul><li>Latest Generation markers</li><li>Types of SNP:<ol><li>Transition &amp; Transversion: Purine mutated to Purine &amp; Purine mutated to Pyrimidine</li><li>Coding: Synonymous (Do not alter the amino acids) &amp; Non-synonymous</li><li>Non-coding</li><li>Homozygous</li><li>Heterozygous</li></ol></li><li>Protocols of SNPs:<ol><li>Amplification of target fragment (PCR &amp; Strand displacement amplification)</li><li>Allele discrimination reaction (DNA polymerases, DNA ligases, hybridization)</li><li>Detection &amp; Identification (Fluorescence intensity, Microarray, Mass spectrometry, Gel Electrophoresis)</li></ol></li></ul><div><strong><mark>*To improve resolution &amp; accuracy of results, most SNP technologies separate protocols 2 &amp; 3<br></mark></strong><br></div><ul><li>Pros:<ul><li>PCR products can be very small (markers work with degraded DNA)</li><li>Many possibly multiplex hundreds/thousands on a chip</li><li>Reproducible</li><li>Sequence-Specific</li><li>Genome-wide detection</li></ul></li><li>Cons:<ul><li>Less allele- marker less informative</li><li>Need more SNP- to get the same level of information about DNA</li><li>Hard to use</li><li>Expensive</li></ul></li></ul>]]></description>
         <enclosure url="" />
         <pubDate>2021-10-23 03:53:13 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837570808</guid>
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      <item>
         <title>Introduction</title>
         <author>khangning23</author>
         <link>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837697865</link>
         <description><![CDATA[<div>In bio, the Marker system is used to distinguish individuals, populations, varieties and species.</div><div><br></div>]]></description>
         <enclosure url="" />
         <pubDate>2021-10-23 07:27:29 UTC</pubDate>
         <guid>https://padlet.com/17207606/d07o2ence0ubf3x4/wish/1837697865</guid>
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