Bio445 Chapter 4 study guide

What are the 2 historical points where significant increases in the toolkit gene content evolved?

regulatory changes over gene invention and conserved toolkits

Homologs

genes/proteins/structures that share a common evolutionary origin

Orthologs

genes in different species that evolved from 1 ancestral gene via speciation event

Paralogs

genes within the same genome that arose via gene duplication event

Pseudogenization

1 gene copy accumulates loss of function mutation and becomes a non-functional pseudogene

Subfunctionalization

original gene had many functions/domains following duplication, each copy accumulates mutations disabling a subset of original functions

Neofunctionalization

1 copy retains ancestral function under constraint, redundant copy accumulates mutations, allowing it to acquire a completely novel function/expression

The evolutions of hox genes by the number

Cnidaria posessed 3 primitive hox genes → Bilateria 7/8 → protostomes ~10 → deuterostomes 14 → vertebrates up to 39

7 major ancestral Hox genes: 5 anterior, 1 central, 1 posterior

Living fossils

Extant organism that closely resembles ancient fossilized ancestors → allows inferences on genetic and physiological traits on common ancestors, morphological stasis, and deciphering the genetic toolkit

Evolution of Hox clusters

Invertebrate chordates (1 hox cluster) → 1R duplication split into 2 clusters, 2R duplication split into 4 clusters (a,b,c,d) and present in jawed vertebrates

Why are the outer genes the oldest in Hox clusters?

The 3’/5’ ends represent the ancestral pair whereas the center genes were added via duplication

What is the Parahox cluster?

sister gene to hox cluster: derived from endoderm

Colinearity: expressed anterior (Gsx), central (pdx), posterior (Cdx)

Clade

organism group including 1 common ancestor and all descendants

Basal

describes lineage that branches off earlier (more ancestor-like)

Outgroup

taxon closely related to, but outside of, studied organismal group

Tetraploidization events

Events where organism’s genome is doubled, resulting in 4n chromosomes

How is BLAST used as a tool to find orthologs and paralogs in animal genomes?

Aligns each search against target sequences and generates similarity/E (signifiance) scores to prove homology and not just similarity

Subfunctionalization of Gsb vs. Gsb-n

Gsb: retained for epidermal segment polarity and ectoderm cuticle patterning

Gsb-n: neural specialization within developing CNS

Who has the most toolkit genes of Cnidarians, Fruit flies, and humans?

Humans (39)