Genome Evolution I

comparative genomics

the study of differences and similarities in genome structure and organization in different organisms

combines genome biology and evolutionary biology

what does analysis of differences in genomes by a phylogenetic framework allow us to do?

we can study how genomes change over time and how those changes relate to observed biological diversity

hypotheses generated with a robust and independent phylogenetic framework are

more likely to provide better explanations for the observed traits

mutation, in the case of genomes

anything that generates variation at the genome level

why do genomes evolve?

mutation leads to natural selection and drift/sorting/luck

mutation process examples

polyploidy

segmental/chromosomal duplications

chromosomal rearrangements

retroviral insertions

transposition

endosymbiosis

change/effect of polyploidy

whole genome duplication

change/effect of segmental/chromosomal duplications

other large-scale duplications, gene shuffling, gene order alterations

change/effect of chromosomal rearrangements

mutagenesis, gene shuffling

change/effect of retroviral insertions

changes in genome size, shuffling, mutagenesis, altered gene expression

change/effect of endosymbiosis

genome reduction, EGT

long term (evolutionary) consequences are determined by

multiple strongly interdependent factors, such as population size, type of reproduction, phenotypic manifestation of the mutations, habitats (stable vs variable), etc

factors may not be generators of variation but instead

create conditions that are conducive to and modulate genome evolution

genome evolution factors (but not generators of variation) examples

radical lifestyle/environmental changes

composition of the ecosystem

exposure to pathogens

becoming a parasite or endosymbiont

acquiring endosymbionts

“nothing”

radical lifestyle/environmental changes

increased exposure to environmental stressors (heat, radiation) can lead to increased rates of mutation and rearrangements and/or alter nucleotide composition

changes in population structure and/or population size affect probability of fixation of rare chromosomal changes, including large duplications

composition of the ecosystem

e.g. invasive spp. increase competition pressure; arrival of predators do the same

exposure to pathogens

affect population structure (e.g. bottlenecks); favour fixation of low-frequency genomic changes; microorganisms can introduce active TEs into genome

becoming a parasite or endosymbiont

massive gene loss due to pressure for small genome and/or redundancy of gene function, and/or increased rates of mutation—result in genome reduction and overall sequence divergence

acquiring endosymbionts

induce massive acquisition and replacement of genes; affects gene size and gene complement

in a stable environment, continuous supply of resources basal rates of mutations result in

genome change over time (e.g. base substitutions, DNA damage, recombination)

what traits can we look at?

genome architecture, base composition (related to codon usage and amino acid content)—but there are many characteristics

genome architecture

number and shape of chromosomes; distribution of non-coding DNA; order of the genes

base composition

usually expressed as %GC or %AT

most eukaryotic genomes are at around 50% GC but due to multiple factors the composition can become strongly biased

many intracellular parasites exhibit strong AT biases, probably because they have poor DNA repair efficiency, resulting in right rates of certain mutations, especially those that turn C→A

complications with nucleotide composition

it is tightly related with codon usage and amino acid content of the encoded proteins

therefore, these 3 parameters are strongly interdependent, and this means that figuring out what exactly causes a particular bias is usually very difficult

what does “shared genes” mean?

homologs, ideally orthologs

minimal gene set/core eukaryotic genes

a given organism’s gene catalog that consists of a group of genes for components (proteins, RNAs) that are essential for the basic functions of the cell

e.g. ribosome components, DNA/RNA pols, other DNA/RNA synthesis and processing proteins, components of basic cellular mechanisms, etc.

we can expect to find the gene encoding these components in any eukaryotic organisms

generalized gene set

for genes involved in central metabolism and other cellular activities that are more or less ubiquitous

e.g. synthesis of macromolecules such as nucleotides and AAs, intracellular transport, etc.

found in most euk species

specialized gene set

for genes involved in specific pathways and systems that are restricted to certain groups of organisms

e.g. photosynthesis, assimilation of nutrients present in certain habitats, cellular structures involved in specific activities such as feeding, mobility, etc

rules for the layers of gene sets and distributions across lineages

most organisms will have genes from all layers

most genes in the core layer can be found in all organisms

most genes in the generalized layer will be found in most free-living organisms

genes in the specialized layer tend to show restricted taxonomic distribution

genes in a specific functional role that are found in different organisms are not necessarily homologous

EGT

like proks, euk genomes can take up foreign genes from various sources and through various mechanisms

contribution from this has been significant, bringing in thousands of genes of bacterial ancestry into euk genomes (e.g. from mitochondria and plastids)

LGT and euks

uncertain in extent and is sporadic compared to proks, but it still constitutes a significant source of metabolic innovation that enabled many organisms to colonize new environments

how can we count shared genes?

use specialized tools for classifying genes into orthologous groups, e.g. OrthoFinder

gene complement and counting shared genes

can be done at different evolutionary distances

with closely related species, complement will be very similar

as distance becomes larger, the number of genes in common becomes smaller

phylogenetic framework

allows us to infer rates of expansion and contractions (i.e. gains and losses) of genes and gene families that occurred on individual lineages

data and parameters considered for phylogenetic frameworks

number of genes in existing species

topology of the tree (branching order)

length of the branches (amount of evolution sustained by each lineage)

absolute time (calibrated with external data such as fossils)

we can also analyzed what ______ are represented in shared genes

functions