Reflection BBT 402 year 20/21 by mohamad fadhli mad atari

Reflection BBT 402 year 20/21 by mohamad fadhli mad atari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix Made with mirth en-us 2020-12-29 04:15:24 UTC 2021-02-04 10:41:27 UTC hello@padlet.com Reflection (7 lectures, and 1 lab)- thus, there will be 8 groups with 8 students each. Please check your assigned group in the e learning. e.g group A for lecture 1, group B for lecture 2.. etc) fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1044847526 1. Lecture number?
2. take home message/ content from your understanding. (include picture if necessary)
3. questions (another student can answer these questions)
4. author name]]> 2020-12-29 04:16:59 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1044847526 Reflection on Lecture 1 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045003218 Genetic variation in a population is very important for the species to adapt to environment changes. A large gene pool allows suitable traits to be selected for survival of species.
Population genetics helps in the conservation of endanger species (exp. Cryptocoryne purpurea), the management of invasive species (exp. Dioecious hydrilla), and the development of commercial plants.

Leong Hui Lee (Group A)]]> 2020-12-29 06:45:38 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045003218 Reflection for First Lecture https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045003916 1. Lecture 1
2. One of the importance of studies in population genetics is to know the genetic variability (whether the population has large gene pool or small gene pool) in an organisms. Along with the understanding in genetic variability, it can helps in recognising and then conserving endangered organisms such as Cryptocoryne purpurea to prevent them from distinction. The variability is found higher among population than within population. Meanwhile, population genetics study also plays important role in management issue of organisms and protection of commercial plant.
3. I have no question for now, Dr.
4. Cheah Yining (Group A)]]> 2020-12-29 06:46:21 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045003916 Reflection: Lecture 1 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045005044 Low genetic variability will be resulted from narrow gene pool size. Thus, genetic variation is higher in larger population size. The study of population genetic is important as to enable the development of new strains of genetic, recognized the endangered species as well as for management and balancing purposes.
-Yong Wan Chen (Group A)- ]]> 2020-12-29 06:47:21 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045005044 Reflection Lecture 1 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045026013 Genetic variation is significant for the survivability of a population as low generic variability can cause extinction of the population. The study of population genetic is important for us to conserve , protect the endangered species, manage the invasive species and environmental problem by understand patterns in genetic variability and also develop commercial plants with high economical values.

LUI XIN JIE (139142)]]> 2020-12-29 07:06:29 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045026013 Lecture 1 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045033834 Population genetics describes the genetic variation within and among population. Endangered species such as cheetah suffers from low genetic variability with small gene pool.

We study population genetics to conserve endangered and threatened species, to deal with management issues such as invasive species and to protect commercial plant.

Mo Zhi Zhi (139144)

]]> 2020-12-29 07:14:39 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045033834 Reflection on Lecture 1 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045056662 According to my understanding, genetic variation has many importance in a population which allows the species to adapt to the changes happening surrounding it. Population genetics also teaches us on the proper way of conserving the threatened and endangered species, ways on overcoming management issues and teaching the proper methods to protect the economic and commercial plants (IP).

NUR SHARMILAH BT AHMAD (138881)]]> 2020-12-29 07:41:57 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045056662 Reflection on lecture 1 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045062908 A small population with similar gene species leads to less variation in the gene pool. This event will increase the offspring population with inherited conditions via inbreeding. Therefore, they are easily extinct even without any impact from the environmental factors. That is why large wild populations are important for species survival because having various genes is high.

Captive breeding can be used to increase endangered species.

NUR ARIFAH IZZATI BINTI KHAIRUDDIN (139170) ]]> 2020-12-29 07:50:26 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1045062908 Lecture 1 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1046087465 Population genetics describes the genetic variation in a particular population. Due to the overhunting and narrowing of habitat by humankind, some species are getting lesser in number, and therefore low generic variability occurred. This phenomenon is dangerous if environmental conditions changed. Therefore, studying population genetics is vital to conserve the endangered species, manage issues, protect the economy, and protect the commercial plants.

Tang Xin An (139205)]]> 2020-12-30 04:32:01 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1046087465 Reflection on lecture 1 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1046651988 Learn about genetic variation will help us to understand the population genetic more. Genetic variation help in explain the variation of origin, maintain and evolutionary importance. The importance of learning population genetics is can overcome all the problems occur because of human action. For example, low generic variability occur in some habitat of animal due to hunting activity. This make population of the animals become low. In addition, by learning the trends of genetic variability help us to increase the population of certain species of plant. This will help to protect the ecosystem.
Nurul Nadiah Binti Mohamad Nasir (139185) ]]> 2020-12-30 16:42:30 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1046651988 Lecture 2 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1047628899 DNA The genetic diversity among the populations is very important to adapt to different adverse environment. Different genetic composition among the plants can prevent the outbreak of insects and diseases.
Microsatellite is a codominant, polymorphic DNA loci. These loci are present in most eukaryotes and highly abundant throughout the genome. Microsatellite can act as marker to select interested trait such as drought tolerance, disease resistance in selective plant breeding.

Lee Chia Qing 139131 (GroupB)]]> 2020-12-31 12:46:57 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1047628899 Lecture 2 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1047768267 Genetic Diversity promotes the survival of populations by eliciting the adaptations with response to environmental changes. High proportion of loci heterozygous (H) indicates higher heterozygosity, which refrain the species from being endangered or extinct. Microsatellites which have high levels of allelic variations are critical tools for the polymorphism analysis which drives the genetic diversity.

Leong May Heng 139136 (Group B)]]> 2020-12-31 17:41:33 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1047768267 Lecture 2 Reflection Genetic diversity is the study of different alleles and genotypes of a population to cope with the environment changes. A loss of genetic diversity will increase the risk of extinction of a population through inbreeding depression. Microsatellite is the repetitive DNA in a gene sequence which is mostly from non-coding region of vertebrate, insect and plant chromosomes. The number of repeats varies among individuals in a population, making microsatellites useful to the population geneticist. https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1047945466 Lee Hui Wen 139132 (Group B)]]> 2021-01-01 01:18:11 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1047945466 Lecture 2 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1049273951 Genetic diversity is actually the variability that we can find in a certain population or a specific species that occurs in gene level. GD is important as this is what makes the species to adapt unfavorable conditions and survive. GD can be measured by calculating proportion of loci polymorphic (p), average heterozygosity and allelic diversity. Microsatellites has high number of mutation and high level of polymorphism, therefore encourages variability.

Aneesha Melvina Sakayanathan 139103 (Group B)]]> 2021-01-03 03:09:48 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1049273951 Lecture 2 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1052146127 Genetic diversity is like genetic variability present within species. Genetic diversity is the product of recombination of genetic material in the process of inheritance. Genetic diversity gives rise to different physical attributes to the individual and capacity to adapt to stress, diseases and unfavorable environmental conditions. It changes with time. A microsatellite is a tract of repetitive DNA in which certain DNA are repeated. Microsatellites occur at thousands of locations within an organism's genome. They have a higher mutation rate than other areas of DNA leading to high genetic diversity.

Maryam Iryani Binti Zainal
139143
Group B]]> 2021-01-04 14:59:11 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1052146127 Reflection Lecture 1 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054234651 The study of population genetics is important in understanding genetic variation in a particular population. Also, through the study of population genetics, researchers or scientists can help in conservation of threatened and endangered species, management issues and protection of commercial or economic plant. ]]> 2021-01-05 02:30:08 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054234651 Lecture 2 Reflection: https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054402173 Genetic diversity is the variety of alleles and genotypes present in the group such as population and species. Genetic variation within a population depends on GD. It is required for populations to adapt with changes in environment.GD describes differences among member of a population. High GD means different kind of alleles present for each characteristic while low GD means nearly all individuals have same alleles. Inbreeding and reduction in reproductive fitness could cause the loss of GD. GD is measured for many traits such as quantitative characters, deleterious alleles, protein and DNA. Polymorphism, monomorphism and co-dominance are familiar terms to GD. Microsatellite method is used to identify high polymorphism. Microsatellite is divided into 4 categories which are uninterrupted and interrupted microsatellite, composite microsatellite and cryptic simple sequence.

Nurul Anis, 138889 (Group B)

]]> 2021-01-05 04:22:26 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054402173 Lecture 3 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054596643 Allele frequencies to genotype frequencies can be assume by using H-W formula :
p+q=1
when mating
(p+q)(p+q) = p2+2pq+q2 = 1
in this case, p2=AA 2pq=Aa and q2=aa
However, assumption need to be make, these include random mating between the individuals, no mutation among the population, natural selection is not affecting the locus, the population is infinitely large and no migration occur. Deviation from the H-W equilibrium genotype frequency are informative and will allow the detection of inbreeding, population fragmentation and migration among the population.

Non random mating consist of 2 types, first is inbreeding and second is assortative mating that increase homozygosity and disassortative mating that increase heterozygosity.

Random genetic drift will reduce genetic variation by reducing heterozygosity and remove a specific alleles.

Natural selection cause organism with alleles that have advantages in the environment to survive.
Mutation help increase genetic variation as if produce novel allele.
Fragmented population cause an overall deficiency of heterozygotes as they are separated by geographical barrier.

Heterozygosity are classified into observed heterozygosity and expected heterozygosity and can be calculated using 2 different formula.
Jaskhai Ng
139124
Group C]]> 2021-01-05 06:13:02 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054596643 Lecture 3 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054770532 Hardy-Weinberg Principle is a model that relates allele frequencies to genotype frequencies.

The allele frequencies, p + q = 1 and the expected genotypes frequencies p² + 2pq + q² = 1
AA = p², aa = q² and Aa = 2pq.

In Hardy-Weinberg equilibrium, we must follow the assumption, which is random mating, no mutation, natural selection is not affecting the locus, population is infinitely large and no migration.

If any assumptions underlaying the H-W equilibrium are violated, deviation from equilibrium genotype frequencies will occur. Deviation from H-W equilibrium genotype frequency are informative allowing to detect inbreeding, population fragmentation and migration. The action that violates H-W equilibrium are non-random mating, random genetic drift, selection, mutation, and fragmented populations.

Non-random mating consists of two situations which is inbreeding and assortative & disassortative mating. Inbreeding and assortative mating will reduce heterozygosity and increase homozygosity.

Random genetic drift reduces genetic variation in 2 ways which is heterozygosity is reduced and alleles are lost.

Selection is the differential survival & reproduction of phenotypes that are better suited to the environment or obtaining mating success. Generally, remove genetic variation from the population

Mutations is a process that produces a gene/chromosome set differing from wild type. Therefore, tends no to pull pops very far from H-W equilibrium.

Fragmented population, in isolated populations, allele frequency diverges due to chance and selection. Thus, fragmented pops with restricted gene flow show deficiency of heterozygotes compare to H-W expectation.

Heterozygosity can be divided into 2 which is observed heterozygosity (H_o) and expected heterozygosity (H_e). H_e is less affected by sampling as opposed to H_o.

Nurul Zakirah Ismail

138895

Group C

]]> 2021-01-05 07:47:21 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054770532 Lecture 3 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054788178 The Hardy-Weinberg Principle is derived by two different person G. H. Hardy and Wilhelm Weinberg. This principle helps to relates the frequencies of allele to the genotype frequencies.

In using the Hardy-Weinberg Equation to find the frequency of allele and genotype, five assumptions need to be followed. The assumptions are random mating of population, large population size, no natural selection occur, no mutation in the population and no migration in the population.

The important equation in Hardy-Weinberg Principle is;
p + q = 1 (allele frequencies)
p2 + 2pq + q2 = 1 (expected genotype frequencies)

There are five violation of the Hardy-Weinberg assumption; non-random mating, random genetic drift, selection, mutation and fragmented populations.

The observed ( H_o)and expected (H_E) heterozygosity are calculated by using different formula;
H_oequal to the number of heterozygotes at a loci over the total no of individual sampled.
H_Eequal to one minus sum of power off two of the allele frequencies (if allele more than 2), if 2 alleles, H_E equal to 2pq.

Siti Nur Hanis Syazana Mohd Azemi (138904)
Group C

]]> 2021-01-05 07:56:19 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1054788178 LECTURE 3 REFLECTION: https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1055448114 Based on HARDY-WEINBERG PRINCIPLE which relates the allele frequencies to genotype frequencies, we assume:

the formula for allele frequency is:
p + q = 1, which is p is allele freq of A and q is for allele freq of a.

the expected genotype frequencies would be:
p(^2) + 2pq + q(^2) = 1
with p(^2) is the freq of AA
2pq is the freq of Aa
and q(^2) is the freq of aa

This particular genotype frequencies formula explained that if the allele is rare, most of its alleles are heterozygotes, while if the allele is in high freq, most of the alleles are in homozygotes.

The principles predicts the unchanged of allele freq between generations only if the assumptions are satisfied. In order to meet the the equilibrium, there are few assumptions to be noted such as:
there is random mating, large population, no natural selection, no mutation and no migration.

Deviation from equilibrium genotype freq will occur if any assumptions are violated, allowing to detect inbreeding, population fragmentation and migration. Therefore, H-W equilibrium provides Ho to detect if the populations has non random mating, migration etc. The violations include, non random mating, random genetic drift, selection, mutation and fragmented populations.

Heterozygosity is used to express the extend of genetic diversity at a locus. Ho, observed heterozygosity, is the number of heterozygotes at a loci over the total no of ind sampled. HE, expected heterozygosity, is 2pq.

AMIRAH IZZATI BT ABDULLAH ZAHRI, 138806
GROUP C]]> 2021-01-05 13:38:12 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1055448114 Lecture 3 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1060082438 Hardy-weinberg equation is a principle that relates the allele frequencies to genotype frequecies. There is some assumption needed to be fulfil for Hardy-weinberg equation which includes random mating, no mutation, no natural selection, no migration and large population. The formula of this Hardy-weinberg equation is
p² + 2pq + q² = 1 which AA = p²aa = q² and Aa = 2pq

There are observed and expected heterozygosity which can be calculated with following equation:
Ho = number of heterozygotes at a loci divide with total no of individuals sampled
H_E= 1- total of power of two of the allele frequencies (more than 2 alleles)
= 2pq (2 alleles)

Ling Jia Yi 139139 Group C

]]> 2021-01-06 16:43:25 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1060082438 Lecture 4 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061685991 Chi-squared test (X² test) is used to determine the differences between observed (O) and expected (E) numbers in a populations. The formula of X² test is X² = ∑ (O - E)²/ E where O refers to observed number and E refers to expected numbers.

The coefficient of inbreeding, F, is used to describe genetic diversity within and among populations by measuring the probability that two alleles of a given gene are derived from a common ancestral allele. The formula of F is F= = H_exp - H_obs / H_expwhere H_exprefers to expected frequency in H-W and H_obsrefers to observed frequency in heterozygotes.

The formula of average deviation in heterozygotes within subpopulations is F_IS = (H_S- H_I) / H_S = 1 - H_I/ 2pq where H_I refers to average of observed heterozygosity, H_S refers to average of expected heterozygosity and IS = deviation among individuals relative to their subpopulations.

The formula of deviation in heterozygosity is due to subdivision alone is F_ST = (H_T- H_S) / H_T = 1 - H_S/ 2pq where H_T refers to expected heterozygosity in the total population, H_S= average of expected heterozygosities and ST refers to deviation among subpopulations relative to the total populations.

The formula of overall deviation in heterozygosity in total populations is F_IT = (H_T- H_I) / H_T where HT refers to expected heterozygosity in total populations, H_I refers to observed heterozygosity in total populations and IT refers to deviation among individuals relative to the total population.

Wong Bao Yi 139213 (Group D)

]]> 2021-01-07 02:10:00 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061685991 LECTURE 4 REFLECTION: https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061701820 Chi-squared test is mean to test agreement between observed and expected numbers which is used to determine the difference of statistical significant of deviation between observe and expected numbers.

Meanwhile, inbreeding coefficient, F is used to measures the probability that two alleles of a given gene are derived from a common ancestral allele. There are factors that can increase or decrease heterozygosity over H-W population which are natural selection and genetic drift. Besides, overall deviation in heterozygosity in total population can be calculated using formula derived of expected heterozygosity and observed heterozygosity in total population.

Furthermore, Wahlund Effect is related to the reduction of heterozygosity in a large population due to subpopulation structure. For example, with two or more different alleles frequency of subpopulations show the decrease number of the overall heterozygosity due to geographic barriers to gene flow and genetic drift.

Muhammad Asyhraf Bin Razak (139156)]]> 2021-01-07 02:18:23 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061701820 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061785082 Lecture 4 Reflection

The chi-squared test can test the agreement between the observed and expected number whereby to determine the significant difference of the deviation between observe and expected numbers.

X²= ∑ (O-E)²/E

The subpopulation overall deviated from the Hardy-Weinberg expected heterozygosity is due to the factors acting within the subpopulation and subpopulation division. F is referred to as the inbreeding coefficient to describe the genetic diversity within and among the populations. F measures the probability that two alleles of a gene are derived from a common ancestral allele. The factors that can affect the subpopulation by increasing or decreasing the heterozygosity over the Hardy-Weinberg expectation are genetic drift, natural selection, and inbreeding.

The Wahlund effect is the reduction of heterozygosity in a population due to the sub-population structure. The factor that can cause the population subdivision is the geographic barriers to gene flow and genetic drift in the subpopulation.

Wan Jia Hui (139210)

]]> 2021-01-07 03:07:35 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061785082 LECTURE 4 REFLECTION https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061997006 In this lecture, I had learnt about chi-squared test that is used to test the differences between observed (O) and expected (E) numbers and thus to determine the difference of statistical significant of deviation between observe and expected numbers. Formula of X² test is X² = ∑ (O - E)²/ E in which O represents observed number and E represents expected numbers.

Next, the coefficient of inbreeding, F, used to describe genetic diversity among populations by measuring the probability that two alleles of a given gene are derived from a common ancestral allele. The formula of F is F= = H_exp - H_obs / H_expwhere H_exprefers to expected frequency in H-W and H_obsrefers to observed frequency in heterozygotes.

Formula of average deviation in heterozygotes within subpopulations is F_IS = (H_S- H_I) / H_S = 1 - H_I/ 2pq where H_I represents average of observed heterozygosity, H_S represents average of expected heterozygosity and IS represents deviation among individuals relative to their subpopulations.

The deviation formula in heterozygosity is due to subdivision alone is F_ST = (H_T- H_S) / H_T = 1 - H_S/ 2pq in which H_T represents expected heterozygosity in the total population, H_S= average of expected heterozygosities and ST represents deviation among subpopulations relative to the total populations.

The overall deviation in heterozygosity formula in total populations is F_IT = (H_T- H_I) / H_T in which HT represents expected heterozygosity in total populations, H_I represents observed heterozygosity in total populations and IT represents deviation among individuals relative to the total population.

The conclusion that were made are FIS (range from -1 (inbred) to 1 (outbred) while FST (range from 0 (no genetic structure; inbred) to 1 (maximal structure; gene flow is high) and FIT (ranged from -1 to 1 depending on values of FIS & FS.

Other than that, I had also learnt on Wahlund effect which is the reduction of heterozygosity or increase in frequency of homozygotes in a huge population due to subpopulation structure. The cause of the population subdivision might be geographic barriers to gene flow and genetic drift in subpopulation. For instance, if two or more subpopulations have different allele frequencies then the overall heterozygosity is reduced, even if the subpopulations themselves are in a HardyWeinberg equilibrium.

SHARMILA D/O ARUMUGAM 144718
GROUP D

]]> 2021-01-07 05:20:56 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1061997006 Lecture 4 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1062320334 In this lecture, I have learned three main things which are the Chi-square test, inbreeding coefficients, and the Wahlund effect.

The Chi-square test is used to study the difference between observed and expected numbers. The formula of the Chi-square test:

X2= ∑ (O-E)2/E

Inbreeding coefficients (F) are used to measures the probability of two alleles of a gene derived from a common ancestral allele. There are three F:

1. The average deviation in heterozygotes within subpopulation:
FIS = ( Hs – HI )/ Hs = 1-HI/2pq

2. Deviation in heterozygosity due to subdivision alone:
FST = ( HT – HS )/ HT = 1-HS/2pq

3. Overall deviation in heterozygosity in total population:
FIT = ( HT – HI )/ HT

The Wahlund effect refers to the reduction of heterozygosity in a population due to the subpopulation structure. In other words, excess of homozygotes or the deficit in heterozygotes observed in a sample of individuals obtained from a structured population, even when the local populations are in Hardy-Weinberg equilibrium.

THAMAYANTHI MOORTHY (140122)

]]> 2021-01-07 08:14:32 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1062320334 Lecture 1 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064337740 Write your question in the comment section]]> 2021-01-07 17:50:48 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064337740 Lecture 2 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064340326 Write your question in the comment section]]> 2021-01-07 17:51:16 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064340326 Lecture 3 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064342498 Write your question in the comment section]]> 2021-01-07 17:51:37 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064342498 Lecture 4 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064345602 Write your question in the comment section]]> 2021-01-07 17:52:12 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1064345602 Lecture 4 reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1072285796 From this lecture, i learned about chi-squared test. It was used to test agreement between observed and expected numbers and also can be used to determine the difference of the deviation between observe and expected. There are two components of overall deviation which are deviation due to factors acting within subpopulations and deviation due to division of subpopulations.

The Wahlund effect means reduction of heterozygosity in population because of subpopulation structure. This means if more subpopulations have different allele frequencies, overall heterozygosity is reduced.

Nurul Nadiah (139185)
Group D

]]> 2021-01-10 23:34:44 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1072285796 Hardy-Weinberg Principle (Lecture 4 Reflection) fadhlijohan https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077084358
In this lecture, three Hardy-Weinberg Principle were covered which are:

1. Chi-squared test

2. Population fragmentation and inbreeding coefficients

3. Wahlund effect

Chi-squared test (X²) is used to test agreement between observed & expected numbers. The formula for Chi-squared test is:

X²= Ʃ(O-E)²/ E

In a subdivided pops (subpopulations) overall deviation from H-W expected heterozygosity has 2 components which are:

1. Deviation due to factors acting within subpopulations.

2. Deviation due to division of subpopulations

Inbreeding coefficients is used to describe genetic diversity within and among populations. It measures the probability that two alleles of a given gene are derived from a common ancestral allele.

The formula for inbreeding coefficients is:

F = H_exp- H_obs/ H_exp

The formula for average deviation in heterozygotes within subpops is:

F_IS= (H_S – H_I) / H_S = 1 – H_I / 2_pq

The formula for heterozygosity due to subdivision alone is:

F_ST = (H_T – H_S) / H_T = 1 – H_S / 2_pq

The overall deviation in heterozygosity in total pop is:

F_IT = (h_T – H_I) / H_T

Wahlund effect refers to the reduction of heterozygosity in a population due to subpopulation structure which means there are fewer heterozygotes than in the average for the set of subdivided populations. This is caused by geographic barriers to gene flow followed by genetic.

MUHAMMAD FADHLI BIN JOHAN (140021)

GROUP D

]]> 2021-01-12 05:20:04 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077084358 Lecture 5 reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077187644 2.take home message
The gene status result from cumulative effect of many generation.

When predicting the heterozygosity with time in different size population

Inbreeding
the plant will tend to reproduce by inbreeding when the population is small. This will increase the homozygosity , expose rare deleterious alleles and also tend to result for offspring with higher mortality rate.

Inbreeding coefficient ,F is the probability that it carries alleles at a locus that are identical by other descent. F=1 is the inbreed while 0 is outbreed.
Usually in small population inbreeding will occur from time.

The expectation of inbreeding F can be determine by the comparison of observed heterozygote with Hardy-Weinberg expectation

Why F is important is because of it is equal with the loss of genetic diversity.

CHANG QI HAN
139107
GROUP E]]> 2021-01-12 06:22:10 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077187644 Lecture 5 reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077216353 Population size will be recovered over many generations but it is not applied to genetic variation. Self incompatibility is happened to prevent self-fertilisation between population containing SI alleles. Therefore, SI allele in population increases, the number of sucessfully fertilised pollen also increases. Besides, inbreeding is the mating of individual related by ancestry. It is more often found in small population. It can be measured as probability that two alleles at a locus are identical by descent (F) and the inbreeding coefficient of individuals resulting from
selfing = ½.

TAI YI JIA
139202
GROUP E]]> 2021-01-12 06:37:37 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077216353 Lecture 5 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077415717 The genetic status of a population is derived from cumulative effects of many generations, which means, the loss of genetic diversity depends on generations instead of years.

The loss of genetic diversity is more severe in a small population if genetic drift or inbreeding occurs.

However, the influence of genetic diversity loss in polyploid population is smaller than in diploid population provided with the equivalent population size due to higher polymorphism and allelic diversity.

Inbreeding is a process that is unavoidable even though in outbreeding species. The inbreeding levels can be estimated from genotype frequency and inbreeding coefficients.

IVY TING MENG YING
139122
GROUP E ]]> 2021-01-12 07:59:28 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1077415717 Lecture 5 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1078927711 Write your question in the comment section]]> 2021-01-12 15:17:38 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1078927711 LECTURE 4 REFLECTION https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1081917081 in this lecture, i learnt about the usage of the chi-square test, population fragmentation & inbreeding coefficient and Wahlund effect.

First, Chi-square test is used to test the agreement between the observed and expected number and the formula for the chi-square test used is
X² = ∑ (O - E)²/ E

Next, for the population fragmentation & inbreeding coefficients. The subdivided population is caused by deviation which are factors acting within subpopulations and division of subpopulations. the usage of inbreeding coefficient is to measure the probability of two alleles of given gene that are derived from common ancestral allele and this is use to describe genetic diversity within/among population itself. There are 4 formula used for inbreeding coefficient:
1. General formula used is
F = H_exp - H_obs / H_exp
2. the formula for average deviation in heterozygotes within subpops is
F_IS = (H_S - H_I ) / H_S = 1 - H_I / 2pq 3. the formula for the deviation that happen in heterozygosity due to subdivision alone is
F_ST = (H_T - H_S ) / H_T = 1 - H_S / 2pq.
4. The formula for overall deviation in heterozygosity in total pop is
F_IT = (H_T - H_I ) / H_T

Lastly is the Wahlund Effect. it refers to reduction of heterozygosity in a population due to subpopulation structure that can be causes by geographic barriers to gene flow followed by genetic drift that occured in the subpopulation.

Nurul Syazwani Binti Azahar
138894
Group D]]> 2021-01-13 08:00:40 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1081917081 Lecture 5 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1082700889 Inbreeding in the plant will happen when the population is small. When inbreeding happened, plants tend to reproduce by selfing. This might result in a high inbreeding coefficient (F) and very low heterozygosity (H). All individuals eventually become related by descent. Thus, in a small population, inbreeding is unavoidable. Hence, in a random mating population of stable size, loss of genetic diversity equals the inbreeding coefficient.

Both inbreeding and drift reduce genetic diversity, which has been related to an increased likelihood of population loss, decreased population growth rate, decreased capacity for environmental change response, and decreased vulnerability to pathogens, which has an effect on the ability of released plants to survive and reproduce in the wild.
Pang Wei Quan
139187
GROUP E

]]> 2021-01-13 12:33:50 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1082700889 Lecture 6 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1085487537 Inbreeding depression (ID) refers to reduction in reproductive fitness as a result of inbreeding in naturally outbreeding species. Generally, ID will produce progeny plants that are shorter, less weight, late flowering and producing less seeds. The effect of ID is significant for traits that are associated with reproduction than those that are not. Studies had shown that ID influence greater in field than in the greenhouse.

In calculation of ID, F is used to represent the rate of inbreeding. Overall,
Mo=a(p-q)+2pdq
Mf=a(p-q)+2pdq(1-F)
therefore, ID can be calculated by 2pdqF. From the calculation, ID can be observed reduce the heterozygosity.

The magnitude of ID depends on heterozygosity, dominance deviation and inbreeding coefficient. The deleterious allele must be partial/complete recessive or partial dominance. Selection pressure can reduce the frequency of dominance deleterious allele but not in the case of overdominance. The effect of ID is greater in diploid and tetraploid than in polyploid due to relative rates of fixation, genetic loads and effect of dominance or overdominance.

To detect ID, individuals should be maintained under same environment. Moreover, detection also can be done by outcross populations and microsatellite loci. Finally, the ID can be predicted by using equation: δ = 1 – (fitness of inbred offspring/fitness of outbred offspring)

HEW WEI HENG
139120
Group F ]]> 2021-01-14 01:18:40 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1085487537 Lecture 6 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1085653603 Inbreeding depression (ID) is the reduction in biological fitness (shorter, few seeds production, lower survival rates, etc.) due to the breeding of related individuals.

Characteristics of ID:
Dependent to heterozygosity, dominance deviation and inbreeding coefficient. The deleterious alleles must be partial or complete recessive, and partial dominance.

Impact:
Inbreeding leads to decline in heterozygosity

Detection of ID:
Outcross populations of suspected suffering from ID, utilization of multiple microsatellite loci.

Measurement can be done using the formula:
ID; δ = 1 – (fitness of inbred offspring/fitness of outbred offspring)

Teoh Siew Chin
139206
Group F]]> 2021-01-14 03:14:02 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1085653603 Lecture 6 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1085687062 Write your question in the comment section]]> 2021-01-14 03:41:48 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1085687062 Lecture 5 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1094072447 From the topic Effect of Population Size Reduction- Loss of Genetic Diversity in Small Populations and Inbreeding, I gain a lot of new information and knowledge. Firstly, I know a big reason why human cannot inbreeding or married or mating with individual related by ancestry (sibling-sibling or father-daughter or mother-son) but animal can. Besides that, I also know why some of the plant cannot successfully breeding. This is because if the plant mating between plants carrying the same self incompatibility (SI) genotypes are incompatible. If the number of S alleles increase, the percentages of plant successfully fertilized also increase.
Intan Sakinah binti Zulkifli
139121
Group E

]]> 2021-01-16 16:18:40 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1094072447 Lecture 7 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1094661576 Write your question in the comment section]]> 2021-01-17 04:38:49 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1094661576 Lab Practical 5 fadhliatari https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1094662128 2021-01-17 04:39:23 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1094662128 LECTURE 3 REFLECTION https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1095682305 Based on Hardy-Weinberg Principle, as long as all the assumption made in Hardy-Weinberg Principle are followed, the frequency of allele will not change over the generation. These assumptions including random mating, no mutation on the allele that can cause loss or addition of allele in the population, no natural selection and migration involved and the population size is large. This is to retain the gene pool. Smaller population tend to have genetic drift which violate these principle.

from Hardy-Weinberg Principle, we have Hardy-Weinberg equation that are used to calculate the frequency of the allele involve using the formula
p2+2pq+q2=1
where
p2 is for the homozygous dominant allele
q2 for the homozygous recessive allele
pq is for the heterozygous

If any violation occurs, the information such as the occurrence of inbreeding, population fragment and migration can be detected.

Umi Natra, 138911, Group C]]> 2021-01-17 15:56:10 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1095682305 Lecture 6 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1097477081 According to Husband and Schemke, Inbreeding refers to the mating of closely related individuals and inbreeding depression can be defined as the reduction in the fitness of progeny derived from such mating, as compared with those derived from outcrossing.

Characteristics of ID plants can be identified through pollen quality, number of ovule, amount of seed, germination rate and more.

The magnitude of ID depends on the species, trait and population size among others. For example, it depends on the heterozygosity of deleterious alleles, dominance deviations of allele and the amount of inbreeding.

Munirah Binti Mahadzan (144707)

]]> 2021-01-18 10:08:00 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1097477081 Lecture 7 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1099861729 Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together from one generation to the next. Genes are linked if they are located closely to each other on the same chromosome.

Linked genes do not assort independently but tend to stay together in the same combinations as they were in parents.

Chromosome mapping can determine which segments of DNA came from which ancestor, by measuring the measuring the frequency of recombinant (RF) between linked genes, the relative position of genes on a
chromosome.

Lim Wei Heng
134646
Group G]]> 2021-01-19 06:53:14 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1099861729 Lecture 7 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1099918795 Linkage is the tendency of alleles of different genes to be inherited together from one generation to the next. Genes that are closed to each other on the same chromosome and fail to assort independently are known as linked genes. However, two genes on the same chromosome are called synteny genes.

Chromosome mapping is used to identify the relative position of genes on a chromosome by measuring the recombinant frequency (RF) between the linked genes.

Test cross ratio (assort independently): 1:1:1:1

Test cross ratio (linked genes): 1:1

Two factors linkage analysis:

Recombinant frequency between 2 genes
= Number of recombinant chromosomes / Total number of chromosomes

Chi-square test can be performed to know that whether the two genes are linked.

Three factors linkage analysis:

Map distances are calculated twice as those done in a two factors testcross. However, the correct order of the genes must be determined first.

Multifactorial chromosome mapping:

For four and more linked genes, with each added factor, number of possible genotypes in testcross doubles.

Chang Li Ying
139106
Group G

]]> 2021-01-19 07:15:46 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1099918795 Lecture 6 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1100036656 Inbreeding depression (ID) is the reduction in biological fitness including shorter, few seeds production, lower survival rates, etc. due to the breeding of related individuals.

Characteristics of ID depends on heterozygosity, dominance deviation and inbreeding coefficient. The deleterious alleles must be partial or complete recessive and partial dominance.

The individuals should maintain under the same environmental condition at the same time in order to detect ID and compared the ID of Inbred and outbred individuals. There are several approach including outcross populations of suspected suffering from ID and use multiple microsatellite loci.

Inbreeding depression (ID) usually measured as the proportionate decline in mean per unit, increase in inbreeding depression. Since plants can be selfed, by comparing selfed & outcross progeny, the usual estimate of ID is obtained.

Nurfatin Lidyya (139179)
Group F

]]> 2021-01-19 07:54:59 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1100036656 Lecture 7 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1100224536 Linkage is the tendency of alleles of different genes to be passed on from one generation to the next. Only genes situated on the same chromosome can show linkage. Genes that are closed to each other on the same chromosome and do not assort independently are linked. Genes on the same chromosome are called synteny genes.

Chromosome mapping measures the frequency of recombinant between the linked genes and the relative position of the genes.

LIM HONGQI
127277
GROUP G

]]> 2021-01-19 08:51:09 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1100224536 Lecture 7 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1100856569 Linkage is the tendency for alleles of different genes to be passed on from one generation to the next generation. Only genes that situated on the same chromosome can show linkage. If the allele located at the other side of the centromere, it cannot be considered as linked gene but called as synteny genes. Linked genes do not assort independently but tend to stay together as their parents.

Genetic mapping measured the distance between two genes and can be calculated by dividing the number of recombinant progenies by the total number of progenies. The unit is in cM (centimorgan).

Nurul Iffah ASR
138891
Group G]]> 2021-01-19 12:12:07 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1100856569 Lab Practical 5 Reflection jinyie0418 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1101578715 Population genetics is the study of genetic variations in populations, including the change of allele frequencies, genotype frequencies and phenotype frequencies. There are several factors which contribute to the population diversity such as selection, mutation rate, mating system, genetic drift and effective population size. To describe a variation in a population, genetic markers like microsatellites are commonly employed.

The advancement in software programs helps in estimating population genetics parameters by analyzing microsatellite genotype data. For instance, POPGENE can be used to determine the allele frequency, allele number, effective allele number and polymorphic loci. Furthermore, ARLEQUIN can be used to study test of Hardy-Weinberg equilibrium, expected and observed heterozygosity, genetic structure (AMOVA), population specific heterozygosity F_IS and pairwise differences F_ST.

CHEE JIN YIE (139109)
GROUP H]]> 2021-01-19 15:02:29 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1101578715 Linkage and Chromosome Mapping https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1103192357 In this lecture, we learned about the relationship between linkage with chromosome mapping. We also learned how to calculate genetic map distance and change it to cM. We also learned that frequency of crossing over is high when genes are further apart and they result in the different independent assortment ratios. From the ratios, we can calculate genetic map distance provided there is a linkage group. Linkage group includes 2 factor linkage and 3 factor linkage

Linkage is the tendency for alleles of different genes to be passed together from 1 generation to the next. synteny genes are referred to genes on located on the same chromosome. Multifactorial chromosome mapping is possible to be calculated with 4 or more linked genes.

Muggunna Bala
139150
Group G]]> 2021-01-19 20:04:16 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1103192357 Lab 5 Reflection https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1104251481 Population genetics is the analysis of genetic variation within populations and includes the study and simulation over space and time of shifts in the frequencies of genes and alleles in populations. Many of the genes present in a population would be polymorphic, which means that they will appear in various forms. Mathematical models, based on advances in the molecular understanding of genetics, Mendel's laws of inheritance and modern evolutionary theory, are used to analyses and forecast the occurrence of unique alleles or combinations of alleles in populations. The population or the species is the focal point.

POPGENE is a user-friendly kit for computers. Analysis of genetic variation by co-dominant and dominant markers and quantitative traits among and within natural populations. Arlequin is a free programmed for population genetics distributed as an integrated data analysis software for the GUI. It conducts many types of tests and calculations, including genetic distance computation of the fixation index, Hardy-Weinberg equilibrium, linkage imbalance, distribution of mismatch, and tests of pairwise discrepancy.
Mohamad Nor Aizat (139147)

Gp H

]]> 2021-01-20 05:48:15 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1104251481 Lecture 5 Reflection syahiratul_suhardi185 https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1104349646 This lecture topic is about "Effect of population size reduction-loss of genetic diversity in small populations and inbreeding". Inbreeding is the mating of individuals linked by ancestry. When the population is small, the plant may appear to reproduce by inbreeding. The effects from inbreeding will increase homozygosity, exposes rare deleterious alleles and reduce reproductive fitness (offspring of inbreeds have high mortality rate compared to non-inbreed offspring).

Syahiratul Syamimi Suhardi
138909
Group E]]> 2021-01-20 06:35:59 UTC https://padlet.com/fadhliatari/3sxjuh1zas7il7ix/wish/1104349646