Evolution of Eukaryotic Genomes I

Flashcards covering key concepts in the evolution of eukaryotic genomes, including types of mutations, genome structure, homology relationships, and theories of genome size variation.

Neutral Theory of Molecular Evolution

A theory stating that most evolutionary changes at the molecular level, and most of the variation within and between species, are due to mutations that are neutral with respect to natural selection.

Phylogenetic Trees

Diagrams that represent the evolutionary history of a set of sequences, with branch lengths indicating the number of mutations or amount of time passed.

Sequence Homology

Two sequences that derive from a common evolutionary ancestral sequence in the past.

Homologs

Genes that are homologous, deriving from a common evolutionary ancestral sequence.

Orthologs

Homologous genes separated by a speciation event.

Paralogs

Homologous genes separated by a gene duplication event.

Ohnologues

Homologous genes separated by a whole-genome duplication event.

Xenologs

Homologous genes separated by a horizontal gene transfer event.

Sequence Similarity

A measure of how similar sequences are, regardless of their evolutionary relationship, often expressed as percentage identity.

Single-nucleotide Substitutions

A type of mutation where one base pair is replaced by another.

Insertions and Deletions (Indels)

A type of mutation involving the addition or removal of one or more nucleotide base pairs in a DNA sequence.

Structural Changes

Large-scale mutations such as inversions, translocations, and rearrangements that alter chromosome structure.

Copy Number Changes

Mutations where segments of DNA are duplicated or deleted, leading to an altered number of copies of certain genes or regions.

GC Content

The fraction of nucleotides in a genome that are Guanine (G) or Cytosine (C).

AT Content

The fraction of nucleotides in a genome that are Adenine (A) or Thymine (T), calculated as 1 minus GC content.

Recombination

The process by which genetic material is broken and rejoined to produce new combinations of alleles, leading to different evolutionary histories along the genome.

Telomeres

The very ends of chromosomes, composed of many short repeat sequences (e.g., TTAGGG in vertebrates).

Centromeres

Highly repetitive regions that link sister chromatids during cell division.

Euchromatin

Lightly packed chromatin that is accessible for transcription.

Heterochromatin

Tightly packed chromatin that is largely inaccessible for transcription and thus 'silent'.

Chromatin

The complex of DNA and proteins (histones) that forms chromosomes within the nucleus of eukaryotic cells, packaging genomes.

Histones

Proteins around which DNA is wrapped to form chromatin.

Prokaryotic Genes

Genes typically without introns, with a few hundred base pairs of regulatory sequence directly upstream, sometimes arranged in operons.

Eukaryotic Genes

Genes often containing many long introns and much more extensive regulatory sequences, which can be located far from the gene, and generally not arranged in operons.

Introns

Non-coding sequences within a gene that are removed by RNA splicing during the maturation of the RNA molecule.

Operons

A cluster of functionally related genes that are transcribed together from a single promoter, characteristic of prokaryotic genomes.

C-value

An older measure of the amount of DNA per cell in an organism.

C-value Paradox

The observation that genome size (C-value) does not correlate strongly with organismal complexity, largely due to variation in non-coding DNA.

Junk DNA

A term referring to sequences in the genome that do not serve any known function within the biology of the organism, often comprising a large fraction of eukaryotic genomes.

Evolutionary Conservation

The phenomenon where nucleotide positions important to biological function change less throughout evolution, as mutations at these positions are removed by purifying selection.

Purifying Selection

A type of natural selection that removes deleterious mutations from a population.

Effective Population Size (Ne)

A theoretical population size that accounts for factors like variations in reproductive success, influencing the efficiency of natural selection.

Evolvability

The capacity of a system (such as a genome or species) to generate adaptive variation.

Group Selection

A form of natural selection that acts on entire groups or populations, rather than on individuals, and is hypothesized by some to promote evolvability.