Reconstructing Using Phylogenies/Evo of Genes and Genomes

Taxon-

group of organisms

Nodes represent

MRCA

Sister lineages

the two adjacent lineages following a branch point

Basal lineage

an early diverging lineage in a clade

Clades are composed of

related species, their MRCA and all the descendants

Maximum parsimony

the simplest tree is most likely

Morphological homologies

similarities in external (scales, feathers, hair, etc.) or internal (bones, teeth, etc.) structures

Molecular homologies

similarities in nucleotide sequence (DNA) or amino acid sequence (protein)

“ontogeny recapitulates phylogeny”

Related organisms share considerable morphological homologies during

embryonic development

Analogous traits

similar traits may evolve independently in different lineages (ex. streamlined bodies of sharks and dolphins)

Ancestral vs derived

Ancestral is a trait that is common in the ancestors, derived is a deviation from this, such as lack of tails in a primate

Clade levels ordered (largest to smallest)

1. Domain

2. Supergroup

3. Kingdom

4. Phylum

5. Class

6. Order

7. Family

8. Tribe

9. Genus

10. Species

During Strangerthings, King Phillip Cried Out For Tasty Great Soup

Binomial nomenclature structure

Genus then species

Paraphyletic group

Includes MRCA but is missing some descendants

Polyphyletic group

Does not include MRCA, occurs when organisms are grouped together using analogous traits that are a product of convergent evolution

Monophyletic group

MRCA and all descendants

For molecular analysis, percent similarities are determined using entire

coding sequences of genes or their corresponding amino acid sequences of the

proteins encoded by those genes

A gene duplication is

gene gets duplicated in the genome, due to unequal crossing over during meiosis in gametes

Paralogs:

similar genes in the same organism that arise via gene duplications (ex. All globin genes evolved from one ancestral globin gene and are the product

of numerous gene duplications followed by mutations and the action of

evolutionary mechanisms/drivers over hundreds of millions of years)

Pseudogene:

does not get expressed and is non-functional

Lateral gene transfer:

a way for organisms to acquire genes, mainly occurs between viruses and their hosts and between bacteria but has been shown to occur between eukaryotes

Hox genes

control body patterning along the anteroposterior axis

What are transcription factors

proteins that bind the regulatory sequences of other genes to control their expression

Changing the spatial temporal expression of genes…

has dramatic phenotypic effects ex. legs growing on the face

Ubx genes

inhibits expression of wing genes in the third thoracic segment of fruit flies

Orthologs

similar genes in different species that arise from an ancestral gene in their MRCA that was passed down and modified as speciation occurred, have similar functions

pax6 genes

serve as master regulators of eye development