GATE Ecology and Evolution Applied Ecology & Evolution Syllabus

What is cryopreservation and at what temperature is it typically carried out?

Cryopreservation is the long-term storage of viable cells, gametes, embryos, or tissues at ultra-low temperature, usually in liquid nitrogen at about $-196\,^{\circ}\mathrm{C}$, halting metabolism so material can be revived later.

What is conservation genetics concerned with?

Conservation genetics applies genetic theory and techniques to preserve species, focusing on maintaining genetic diversity, minimizing inbreeding, managing small/fragmented populations, and preventing loss of evolutionary potential and extinction.

Why is genetic diversity important for the long-term survival of a population?

Genetic diversity supplies the variation natural selection acts on, enabling adaptation to changing environments, disease, and climate. Low diversity reduces adaptive potential and raises extinction risk.

State the Hardy–Weinberg expected heterozygosity for a biallelic locus with allele frequencies $p$ and $q$.

Expected heterozygosity is $H_e = 2pq$, where $p + q = 1$. It is a common measure of genetic diversity at a locus.

How does effective population size $N_e$ relate to loss of heterozygosity per generation?

Heterozygosity is lost by genetic drift at a rate of about $\frac{1}{2N_e}$ per generation, so retained heterozygosity after $t$ generations is approximately $H_t = H_0\left(1 - \frac{1}{2N_e}\right)^{t}$. Small $N_e$ means rapid loss of diversity.

Define inbreeding depression.

Inbreeding depression is the reduction in fitness (lower survival, fertility, growth, or disease resistance) in offspring of related individuals, caused mainly by increased homozygosity that exposes deleterious recessive alleles and reduces heterozygote advantage.

What is the inbreeding coefficient $F$ and what is its value for offspring of a full-sib mating?

$F$ is the probability that the two alleles at a locus in an individual are identical by descent. For offspring of a full-sibling mating, $F = \frac{1}{4} = 0.25$.

How does inbreeding change genotype frequencies relative to Hardy–Weinberg?

With inbreeding coefficient $F$: homozygote frequencies increase to $p^{2}+pqF$ and $q^{2}+pqF$, while heterozygotes decrease to $2pq(1-F)$. Heterozygosity falls as $H = H_0(1-F)$.

What is DNA fingerprinting and what type of sequences does it exploit?

DNA fingerprinting is a technique to identify individuals from their unique DNA pattern. It exploits highly polymorphic repetitive sequences — Variable Number Tandem Repeats (VNTRs), including minisatellites and microsatellites (STRs) — that vary in repeat number among individuals.

Who developed DNA fingerprinting and name two of its applications.

Alec Jeffreys (1984) developed DNA fingerprinting. Applications include forensic identification, paternity/parentage testing, and in conservation: detecting poaching, assessing relatedness, and measuring genetic diversity in wild populations.

What is DNA barcoding and which gene is the standard barcode for animals?

DNA barcoding identifies species using a short, standardized DNA sequence. For animals the standard barcode is a ~$650$ bp region of the mitochondrial gene cytochrome c oxidase subunit I (COI / cox1).

Which marker regions are standard DNA barcodes for plants and for fungi?

Plants: chloroplast genes rbcL and matK (often combined). Fungi: the nuclear ribosomal Internal Transcribed Spacer (ITS) region.

Contrast DNA fingerprinting and DNA barcoding in terms of purpose.

DNA fingerprinting distinguishes individuals within a species (uses hypervariable repeats). DNA barcoding distinguishes species from one another (uses a conserved standardized gene region with interspecific variation).

Define epidemiology and distinguish incidence from prevalence.

Epidemiology is the study of the distribution and determinants of health/disease in populations. Incidence is the rate of new cases over a period; prevalence is the proportion of the population having the disease at a given time (existing cases).

Write the formula for the basic reproduction number $R_0$ and state its epidemiological threshold.

$R_0$ is the average number of secondary infections from one case in a fully susceptible population, e.g. $R_0 = \beta \, c \, d$ (transmission probability $\times$ contact rate $\times$ duration). If $R_0 > 1$ an epidemic spreads; if $R_0 < 1$ it dies out.

State the herd immunity threshold in terms of $R_0$.

The critical proportion of the population that must be immune to halt spread is $p_c = 1 - \frac{1}{R_0}$. Above this fraction, sustained transmission cannot occur.

What are the compartments of the basic SIR epidemic model?

S = Susceptible, I = Infected (infectious), R = Recovered (or removed/immune). Individuals flow $\ce{S -> I -> R}$, governed by transmission rate $\beta$ and recovery rate $\gamma$, with $R_0 = \frac{\beta}{\gamma}$.

Define a zoonotic disease and give three examples.

A zoonotic disease (zoonosis) is an infectious disease transmitted from vertebrate animals to humans. Examples: rabies (dogs/bats), plague (rodents), and avian/swine influenza; also COVID-19, Nipah (bats), and brucellosis.

Distinguish a reservoir host from a vector in disease transmission.

A reservoir host is an animal in which a pathogen is maintained long-term (the source of infection), whereas a vector is an organism (often an arthropod) that transmits the pathogen from reservoir/host to a new host without necessarily being the disease's reservoir.

Name the pathogen, vector, and reservoir for plague.

Pathogen: the bacterium $\textit{Yersinia pestis}$; vector: the rat flea ($\textit{Xenopsylla cheopis}$); reservoir: rodents (especially rats). It is a classic vector-borne zoonosis.

What is antibiotic resistance and what is its primary evolutionary driver?

Antibiotic resistance is the ability of bacteria to survive and grow despite antibiotic exposure. Its primary driver is natural selection: antibiotics kill susceptible cells while resistant variants survive and proliferate, especially under overuse/misuse of antibiotics.

List four biochemical mechanisms by which bacteria resist antibiotics.

(1) Enzymatic inactivation of the drug (e.g., $\beta$-lactamase), (2) target-site modification, (3) reduced uptake / decreased membrane permeability, and (4) active efflux pumps that expel the drug.

How does horizontal gene transfer accelerate the spread of antibiotic resistance?

Resistance genes (often on plasmids/transposons/integrons) spread between bacteria — even across species — via conjugation, transformation, and transduction, so resistance disseminates without requiring new mutations in each lineage.

Distinguish vertical from horizontal gene transfer of resistance genes.

Vertical transfer passes resistance genes from parent to daughter cells during division (clonal inheritance). Horizontal transfer moves genes between unrelated cells via conjugation, transformation, or transduction, enabling rapid cross-lineage spread.

What is vector control and name four major strategies.

Vector control is the limitation or eradication of disease-transmitting organisms to interrupt pathogen transmission. Strategies: (1) chemical (insecticides, larvicides, indoor residual spraying, treated bed nets), (2) biological (predators like Gambusia fish, Bti), (3) environmental (source reduction, draining stagnant water), and (4) genetic (sterile insect technique, Wolbachia).

What is the Sterile Insect Technique (SIT) in vector control?

SIT releases large numbers of sterilized (e.g., irradiated) male insects that mate with wild females, producing no viable offspring. This reduces the next generation's population and suppresses vector numbers without insecticides.

How does the larvivorous fish Gambusia function as a biological vector-control agent?

$\textit{Gambusia}$ (mosquitofish) is introduced into water bodies where it eats mosquito larvae and pupae, reducing the emergence of adult mosquitoes and thus malaria/dengue vector populations. (Note: it can itself become invasive.)

What is the Red List, and which IUCN category lies just above 'Extinct in the Wild'?

The IUCN Red List classifies species' extinction risk. The threatened categories, from least to most severe, are Vulnerable (VU) → Endangered (EN) → Critically Endangered (CR); above CR are Extinct in the Wild (EW) and Extinct (EX).

Define a keystone species and explain its relevance to conservation.

A keystone species has a disproportionately large effect on community structure relative to its abundance. Its removal triggers major ecosystem change or collapse, so conserving keystone species (e.g., sea otters, top predators) protects whole communities.

What is the rivet-popper hypothesis and what does it illustrate about biodiversity loss?

Proposed by Paul Ehrlich, it compares species in an ecosystem to rivets holding an airplane (ecosystem) together. Losing a few rivets (species) may be tolerated, but progressive loss eventually causes catastrophic collapse — illustrating that each species contributes to ecosystem stability and that loss of keystone species is especially damaging.