BIOL 286: Lecture #2, Pt. 1 Review (Population Genetics & Hardy Weinberg Equilibrium)

population

A group of one species living in a particular area

What determines where species live? (2)

(1) The environment (temperature, water availability, sunlight, soil, etc.); (2) interactions with other species (parasitism, predation, competition)

population range

The geographical area in which a specific species can be found

Population ranges are not . . . and may . . .

static; change over time (e.g. expansion, contraction)

Population range changes (expansion/contraction) may be caused by . . . (2)

(1) environmental change; (2) species colonizing suitable but previously uninhabited areas

Explain population range change (expansion/contraction) due to the specified cause/case study: Cause- Environmental change; Case study- Spruce-fir/mixed conifer forests

15,000 years ago, Earth was coming to the end of an ice age with much cooler temperatures. As a consequence, spruce-fir and mixed conifer forests adapted to survive in cold environments could inhabit vast swathes of the mountainside. However, to the present day, temperatures have cooled, and these trees have shifted their range to higher altitudes (with cooler temperatures) to suit their temperature needs. This phenomenon constitutes a population range contraction, as the total area inhabited by the species depreciated over time.

Explain population range change (expansion/contraction) due to the specified cause/case study: Cause- Species colonizing suitable but previously uninhabited areas; Case study- Cattle egret

Cattle egret are native to Africa, Asia, and Europe. In the late 1800s, these birds arrived in South America, a previously uninhabited area with a suitable environment to support egret residence. The species subsequently underwent a large range expansion, as the total area inhabited by the species increased over time.

Population spatial patterns: (3)

(1) uniformly spaced; (2) clumped; (3) randomly spaced

Population spatial patterns: uniformly spaced

A population spatial pattern in which individuals of a species are evenly distributed throughout their habitat, with roughly equal distances between each organism

What phenomena typically produce a uniformly spaced population?

Uniformly spaced population distributions often arise due to phenomena such as allelopathy, territoriality, or competition. Broadly, this pattern aims to mitigate competition for limited resources.

allelopathy

The chemical inhibition of one plant (or other organism) by another, due to the release into the environment of substances acting as germination or growth inhibitors; serves to reduce spatial competition for limited resources

territoriality

The defense of an area by an organism or group of similar organisms for various purposes such as mating, nesting, roosting, or feeding. It can be viewed as both an ecological and behavioral concept, with exclusive use of space leading to a more or less uniform distribution of organisms across the species.

Population spatial patterns: clumped

A population spatial pattern in which individuals of a species are aggregated in patches rather than being evenly distributed across a habitat

What phenomena typically produce a clumped population?

Clumped population distributions often arise due to phenomena such as uneven resource availability across a habitat (e.g. desert oases) or certain social interactions that produce survivability benefits (e.g. packs of wolves (group hunting), herds of elephants (defense against predation)).

Population spatial patterns: randomly spaced

A population spatial pattern in which individuals of a species are scattered across a habitat without a predictable or ordered pattern; in other words, the location of one organism does not influence the location of another

What phenomena typically produce a randomly spaced population?

Randomly spaced population distributions typically arise when individuals of a population do not interact strongly or there are not strong effects of the environment promoting an alternative population arrangement with survivability benefits.

What is the rarest population distribution type and why?

randomly spaced; it is rare that there are not strong interspecies or environmental factors influencing population spatial dynamics

population genetics

The study of genetic variation within and among populations

Population genetics allow us to . . .

track changes in a population over time

Mutations arise from . . .

errors in DNA replication

Mutations can occur in . . . or . . .

somatic cells; germ line cells (sex cells: sperm and oocyte cells)

Mutations in sex cells will be . . .

incorporated into all cells that develop from them

duplication mutation

A type of mutation occurring when a region of a chromosome is duplicated

inversion mutation

A type of mutation occurring when a region of a chromosome breaks at two points and is re-inserted in the opposite orientation; can change gene order or regulatory regions of genes

Genetic variation from meiosis (sexually reproducing species): (4)

(1) crossing over; (2) independent assortment- different arrangements of chromosomes at the metaphase plate; (3) mutations in germline DNA; (4) random fertilization- different combinations of gametes can combine

Genetic variation from meiosis: Crossing over

During crossing over, homologous chromosomes pair up in prophase I of meiosis and exchange corresponding segments of DNA. This recombination shuffles alleles into new combinations that did not exist in either parent. Because each crossover event produces chromatids with unique genetic content, crossing over greatly increases the genetic diversity present in gametes and, ultimately, in populations.

Genetic variation from meiosis: Independent assortment

During independent assortment, homologous chromosome pairs line up randomly at the metaphase I plate. Because each pair orients independently of the others, the maternal and paternal versions of different chromosomes are assorted into gametes in many possible combinations. This random arrangement produces a huge number of genetically distinct gametes, increasing variation within populations.

Genetic variation from meiosis: Germline mutations

Germline mutations arise when errors occur in DNA replication or repair within the cells that give rise to gametes. Unlike somatic mutations, these changes can be passed to offspring, adding entirely new alleles to the gene pool. Although most mutations are neutral or harmful, occasional beneficial mutations provide raw material for evolution by creating novel traits that selection can act on.

Genetic variation from meiosis: Random fertilization

Random fertilization increases genetic variation because any one of the many genetically distinct sperm can fuse with any one of the many genetically distinct eggs. Since each gamete already carries a unique combination of alleles from crossing over and independent assortment, the pairing of two random gametes produces an enormous number of possible genetic outcomes in offspring. This randomness further expands the genetic diversity present in populations.

horizontal gene transfer

The movement of genetic material between organisms that are not directly related through parent-offspring inheritance. This process contrasts with vertical gene transfer, where genetic information is passed down from parents to offspring during reproduction. HGT enables organisms, particularly bacteria, to acquire new traits from distantly related species, significantly influencing their genetic makeup and evolutionary trajectory

HGT can occur between . . . and the acquired DNA can . . . and

distantly related microbes; alter the niche of the bacteria; change how bacteria interact with their host or environment

Methods of horizontal gene transfer: (3)

(1) transformation; (2) transduction; (3) conjugation

Methods of horizontal gene transfer: transformation

A natural process in which competent bacterial cells take up free DNA from their environment and incorporate it into their genome through homologous recombination, thereby acquiring new genetic traits

Methods of horizontal gene transfer: transduction

A type of horizontal gene transfer in which bacteriophages (viruses that infect bacteria) act as vectors to transfer bacterial DNA from one bacterium to another, allowing bacteria to acquire new genetic material (e.g. genes for antibiotic resistance, virulence, or metabolic capabilities) without reproducing. Depending on the phage type, a lytic cycle (killing the host to release new viruses) or a lysogenic cycle (integrating their DNA into the bacterial chromosome) may be adhered to.

Methods of horizontal gene transfer: conjugation

A process of horizontal gene transfer (HGT) where genetic material is transferred between bacteria through direct contact. It involves the formation of a pilus that connects two bacterial cells, allowing the transfer of DNA, often in the form of plasmids.

Although it is less common than HGT between bacteria, HGT can occur . . .

between bacteria and other taxa

epigenetics

changes in DNA expression that do not entail changes to the DNA sequence itself

Epigenetic changes can be . . . and . . .

heritable; passed on across multiple generations

Epigenetic changes can be caused by . . . or . . .

acetylation; methylation

acetylation

A process by which an acetyl group is added to lysine of histone proteins, altering the charge of the amino acid to negative such that negatively charged DNA is repelled. As a result, DNA is packed less tightly and more accessible to transscription factors, in turn upregulating gene expression.

methylation

A process by which a methyl group associates with GC rich regions (cytosine specifically) around promoters, preventing transcription factors from binding as effectively. As a result, gene expression is downregulated, since promoters are rendered less accessible to requisite cellular machinery for expression.

diploid

An organism or cell containing two complete sets of chromosomes, one from each parent.

haploid

An organism or cell having only one complete set of chromosomes.

locus

The specific location where a given gene resides on a chromosome

allele

Different versions of a gene having distinct DNA sequences coding for different versions of a given genetic product

Maternal and paternal alleles can . . . but . . .

be the same; do not need to be the same

Punnett square

A graphical tool used to predict the possible genotypes and phenotypes of offspring from a genetic cross, effectively predicting the probability of inheriting specific traits (genotypes) and their observable characteristics (phenotypes). It is named after Reginald C. Punnett, a British geneticist who developed the method in 1905 to visually represent Mendelian inheritance.