ECCB 400 Exam 1

Why are molecular markers important?

They allow ecologists to quantify genetic diversity, track the movements of individuals, measure inbreeding, identify remains of individuals, characterize new species and retrace historical patterns of dispersal.

Molecular ecology definition

Molecular ecology involves using molecular genetic techniques to better understand aspects of nature. It is an INTERDISCIPLINARY FIELD that combines evolutionary biology, population genetics, phylogenetics, and genomics to answer ecological questions often pertaining to conservation biology and the assessment of the diversity of life.

What are some questions that can be addressed with genetic data?

• Estimating population sizes of hard-to-count or cryptic species

• Detection of invasive species• Monitoring of species recovery plans

• Determining hybridization between closely related species

• Aiding in wildlife poaching or forensic cases

• Delineating species units within populations to better guide management decisions and resources

• Estimate how changing environmental conditions may influence species and populations

How is ecology typically studied?

Field observations and experimental manipulations

What type of data have ecologists typically used in the past?

phenotypic data

What is the major limitation of phenotypic data?

It often fails to provide accurate information about the genetic diversity of populations.

Phenotypic variation does NOT always reflect...

genotypic variation

While some phenotypes are under strict genetic control, others...

are strongly influenced by environmental conditions

There is rarely a clear relationship between an organism's genotype and its...

phenotype

Phenotypic plasticity

The potential for a single genotype to develop into multiple phenotypes under different environmental conditions

Phenotypic plasticity can lead to...

-Overestimates of genetic variation when these are based on morphological variation

-Obscuring the movements of individuals and their genes between populations

How can the consequences of plasticity be unveiled?

Using genomic data, which directly quantifies genetic variation and allows us to find genetic differences between individuals and populations

What experiment could be called "the origin of molecular ecology"?

Lewontin and Hubby experiment., 1966

What did the Lewontin and Hubby experiment accomplish?

They were able to experimentally quantify genetic variation between populations

What was Lewontin and Hubby's experiment?

They analyzed 18 loci of 6 different populations of fruit flies. In each population up to 6 of these loci were found to be polymorphic (containing multiple alleles). This means that there is a much higher level of genetic diversity in populations than previously believed.

Genetic diversity

The amount of DNA variation between organisms of the same species

Genetic divergence

The amount of DNA variation between organisms of different species

Molecular genetics

The study of DNA structure and function at the molecular level.

Why does DNA structure matter?

Understanding DNA structure is the key to understanding how DNA functions as genetic material

4 roles of genetic material

1. Information

2. Replication

3. Transmission

4. Variation

Why is it important that DNA carry information?

The genetic material must contain the information necessary to construct an entire organism. In other words, it must provide the blueprint for determining the inherited traits of an organism.

Why is DNA transmission important?

During reproduction, the genetic material must be passed from parents to offspring.

Why is DNA replication important?

Because the genetic material is passed from parents to offspring, and from mother cell to daughter cells during cell division, it must be copied.

Why is DNA variation important?

Genetic material must vary in ways that can account for the known phenotypic differences within each species.

Nucleotides

Repeating structural unit of nucleic acids

Nucleotides are linked together to form a...

strand

DNA strands are linked together to form a...

double helix

Three components of nucleotides

One or more phosphate group, a sugar, and a base (in DNA: A,G,C,T. in RNA: A,G,C,U.)

Two features of DNA (and RNA) structure that matter the most

1. Directionality

2. Specific sequence

Directionality

All sugar molecules have the same orientation (5' carbons are above 3' carbons)

Difference between DNA and RNA?

RNA has ribose sugar instead of deoxyribose sugar. Uracil is also substituted for thymine in RNA.

RNA molecule folding

Folds into specific structures

Chromosomes

physical structures within living cells that contain the genetic material

Genome

The entire complement of genetic material in an organism or species

In bacteria and archaea, the genome is typically in the form of...

a single circular chromosome

3 cellular components where genetic material is found in eukaryotes

1. Nuclear Genome (one haploid set of chromosomes in the nucleus)

2. Mitochondrial genome (most eukaryotes)

3. Chloroplast Genome (plants and algae)

Most bacterial species have what kind of chromosomal DNA...

circular

Typical chromosome length

A few million base pairs

Intergenic regions

Short regions between adjacent genes

Are eukaryotic chromosomes circular or linear?

Linear

Are most eukaryotic chromosomes haploid or diploid?

Diploid

How long is a typical chromosome?

Tens of millions to hundreds of millions of base pairs

How many genes does a typical chromosome have?

Between a few hundred and several thousand

Centromere

A necessary structure for the separation of homologous chromosomes during cell division

Telomeres

Specialized sequences located at both ends of the linear chromosomes

Repetitive sequences can be found...

in the centromeric and telomeric regions, but also may be interspersed throughout the chromosomes

Kilobase

1000 base pairs

Megabase

1,000,000 base pairs

Gigabase

1 billion base pairs

Two types of hypotheses as to why some species have larger genomes than others

Adaptive & non adaptive (neutralist)

Adaptive hypothesis

Genome sizes changes are important for adaptation and are dictated by natural selection (Example: small genomes in bats and birds due to metabolic constraints)

Non adaptive (neutral) hypothesis

Genome size varies regardless of natural selection

Genome size differences are mostly due to differences in the number of...

DNA repetitive sequences, which are mostly non-genic

Invasive plants usually have smaller...

genomes

Do bacteria or eukaryotes have larger genomes?

Eukaryotes

Sequence complexity

the number of times a particular base sequence appears throughout the genome.

Unique or nonrepetitive sequences

found once or a few times within a genome. Many protein-encoding genes are unique sequences of DNA. Human genome: unique sequences makeup ~41% of the entire genome

Moderately repetitive sequences

found a few hundred to several thousand times in a genome.

Highly repetitive sequences

found tens of thousands or even millions of times throughout a genome. Mostly transposable elements.

When were transposable elements discovered?

Discovered first by B McClintock in the 1940s

What are transposable elements made of?

They are short DNA sequences containing one to several genes

How do TEs make so many copies?

They are basically genomic parasites. When they colonize a new genome, TEs tend to make as many copies of themselves as possible

What are the end results of of TE genomic invasion?

In eukaryotes, genome size correlates with the number of TEs.

About ______% of our own genomes are made of TEs.

60

What percentage of the TEs inour genome are inactive?

99%

How do TEs spread?

They can spread between species like viruses (known as horizontal DNA transfer)

Why should we care about transposable elements?

1. They generate a lot of DNA variation.

2. They can alter phenotypes by changing the activity of nearby genes.

3. They play a major role in variation of genome size between species. This variation can have a role in adaptation and ecological consequences.

4. They are major sources of adaptation and evolutionary innovation.

5. They are important to calibrate molecular clocks because they accumulate mutations at a more regular pace than genes.

6. They can cause mutations that lead to disease in humans and other organisms.

TEs can make new copies that change...

how genes work and eventually change the phenotype.

What did the Arabidopsis thaliana experiment prove?

Populations including more TE lines were phenotypically more diverse, productive (biomass) and effective in competing with other plants.

Two types of genes

1. Genes that encode for proteins

2. Genes that encode for RNA with specific functions in the cell

Relationship between gene number and genome size in prokaryotes

Nearly linear

Relationship between gene number and genome size in eukaryotes

Not linear

Number of protein encoding genes in prokaryotes

about 1,000-5,000 protein coding genes. Larger genomes have more genes.

Number of protein encoding genes in eukaryotes

about 5,000-100,000 protein coding genes. No relationship between genome size and number of genes.

In prokaryotes, is most of the DNA protein encoding or not?

Yes. In prokaryotes, genes are compactly arranged, with little or no spacer sequences in between (short intergenic regions)

In eukaryotes, is most of the DNA protein encoding or not?

In eukaryotes, there is considerable space in DNA between genes (large intergenic regions) and within genes (introns)

operons

In prokaryotes, genes with similar functions are next to each other

Each gene within an operon contains enough information to...

encode a protein

Do eukaryotes have operons?

No. Each gene is separated from other genes.

Exons

Where the gene sequences that encode protein sequences are found

What are exons separated by?

Introns, which are still part of the genes but do not encode proteins.

Gene expression can be regulated by DNA sequences...

up and downstream.

Lines with arrows

Introns

Thin bars

Exons

Prokaryotic protein coding genes summary (4 points)

1. Organized in operons

2. From a few hundreds bp up to a few kb

3. Each gene in the operon encodes a distinct protein

4. No introns

Eukaryotic protein coding genes summary (5 points)

1. No operons

2. From a few hundreds bases up to >1 Mb

3. From a few to many exons and introns

4. Exons contain information to encode a protein

5. Regulatory regions at both sides of exons

Process from genes to species characteristics

1. Genes are expressed in order to produce a particular protein.

2. Proteins function affects the structure and workings of cells.

3. Organism's traits are determined by the characteristics of its cells.

4. A species is a group of organisms that maintains a distinctive set of attributes in nature. Natural selections on individuals determine if traits are maintained or removed.

The central dogma of genetics

1. Genes are DNA segments containing genetic information to make proteins

2. Genes are transcribed into messenger RNAs (mRNAs) in the process called transcription

3. mRNAs are used as templates for the synthesis of proteins, which occurs in the ribosomes in a process named translation

transcription

refers to the process of synthesizing RNA from aDNA template

Regulatory sequences

site for the binding of regulatory proteins; the role of regulatory proteins is to influence the rate of transcription. Regulatory sequences can be found in a variety of locations.

Promoter

site for RNA polymerase binding; signals the beginning of transcription.The RNA polymerase is the enzyme that synthesizes mRNA.

Terminator

signals the end of transcription

Regulatory sequences, promoters, and terminators are all at the __________ level.

DNA

Ribosome-binding site

site for ribosome binding.

Start codon

specifies the first amino acid in a polypeptide sequence.

Codons

3-nucleotide sequences within the mRNA that specify particular amino acids. The sequence of codons within mRNA determines the sequence of amino acids within a polypeptide.

Stop codon

specifies the end of polypeptide synthesis.

Ribosome-binding sites and codons (including start and stop) are all at the _________ level.

mRNA

transcription factors

control the rate of transcription.

Transcription factors recognize...

regulatory sequences, or regulatory elements—short stretches of DNA involved in the regulation of transcription. (some transcription factors increase the rate of transcription while others inhibit.)