Chapter 14 & 15 ~ BSC2010L

Molecular Evolution and Origin of New Features

Kimura’s Neutral Theory

Kimura suggested that accumulation of neutral mutations due to genetic drift played a considerable role in generating variation in the genome.

Genome size varies greatly among taxa because…

differences in the amount of non-coding DNA, number of genes (coding DNA) may also vary among taxa

What percent of human DNA are protein coding sequences

Only 3%

How are genomes measured?

in base pairs (bp)

If only the protein and RNA coding portions of genomes are considered then…

there is much less variation in genome size

Is there a correlation between gene number and organismal complexity?

There is usually some but not always.

Pseudogenes

component of noncoding DNA that has lost their original function

Non-coding DNA in genomes

May alter the expression of surrounding genes or occasionally develop novel functions, some sequences may help maintain chromosome struct and consist of transposons

Transposons

jumping genes

The amount of noncoding DNA may be related to…

population size

Noncoding sequences that are only slightly deleterious are likely to be…

purged by selection most efficiently in species with large population sizes.

In small populations what would genetic drift to do these sequences?

may overwhelm selection against them

Sexual reproduction

involves combining gametes from two individuals

Asexual reproduction

involves producing genetically identical copies of oneself

The “two-fold cost of sex”

A female only passes 50% of her genes to each offspring (cost of meiosis)

Dividing offspring into genders reduces a female’s overall reproductive rate (cost of males)

Also, recombination can break up adaptive combinations of genes

In a sexually-reproducing populations, a single asexual mutation will…

have higher fitness, and should be able to quickly spread, asexual mutants arise often

Possible advantages of sexual reproduction?

Elimination of deleterious mutations through recombination followed by selection

The variety of genetic combinations in each generation can be advantageous

Facilitates repair of damaged DNA (possible advantage of sexual reproduction)

damage on one chromosome can be repaired by copying intact sequences on the other chromosome

Muller’s ratchet

in a non-recombining genome deleterious mutations accumulate in each successive generation, only death of the lineage can eliminate deleterious mutations in asexual species

Sexually reproducing species avoid Muller’s ratchet because…

individuals can produce gametes/offspring with fewer deleterious mutations than themselves.

Sex (meiosis and fertilization)

generates new combinations of alleles on which natural selection can act, does not directly influence the frequencies of alleles.

Lateral (horizontal) gene transfer

individual genes, organelles, or genome fragments move horizontally from one lineage to another.

Novel traits

qualitatively new, complex, or individualized structures, patterns, or behaviors not found in an organism's ancestors, often emerging through the reorganization of existing developmental pathways

Gene duplication

major mechanism by which new genetic material is generated

Gene copies may have different fates:

1. both copies retain original function (may increase amount of gene product)

2. Each copy may specialize in part of the original function or expression, or may be expressed in different tissues or at different times in development

3. One copy may accumulate deleterious mutations and become a functionless pseudogene

4. One copy retains original function, the other changes and evolves a new function

phylogeny

the evolutionary history of a group

Phylogenetic tree

a diagrammatic reconstruction of that history

Systematics includes

phylogenetics

taxonomy

• 2 different & relevant ways to classify taxa

Taxonomy

hierarchical way of categorizing species

Binomial nomenclature

gives every species a unique name consisting of two parts: the genus to which it belongs, and the species name. ex: Homo sapiens

Carolus Linnaeus

started the biological classification system in the 1700s

Principle of parsimony

simplest path uses the fewest evolutionary changes

A phylogenetic tree may potray the evolutionary history of

• all life forms

• major groupings of taxa

• small groups of closely related species

• populations

• individuals

• genes & proteins

shared features

indicate that all life is related through a common ancestor, but major differences have also evolved

root

represents the ancestral lineage

branch points (or nodes)

represent speciation events

Sister taxa

two taxa that are each other’s closet relatives (the two branches off a single node)

sister species

two species that are each other’s closet relatives

sister clades

any two clades that are each other’s closet relatives

Paraphyletic

a group that does not include all the descendants of a common ancestor

Polyphyletic

a group that does not include its common ancestor

Monophyletic

a group that includes all the descendants of a common ancestor

synapomorphies

shared, derived characters

found in more recently evolved species or groups and not present in ancestral lineage

ancestral characters

found in more recently evolved species or groups and not present in ancestral lineage

Outgroup

serve as reference group, should be closely related without shared derived characters that unite the ingroup

Convergent evolution

when superficially similar traits may evolve independently in different lineages

Evolutionary reversal

when a character reverts from a derived state back to an ancestral state

homologous structures

physical features in different species that share a common evolutionary ancestor, even if they serve different functions

analogous structures

biological features in different species that perform the same or similar functions but did not originate from a common ancestor

synonymous

a DNA change that alters a codon but encodes the same amino acid, often called a "silent" mutation. While previously thought to be neutral, these changes can affect gene expression, mRNA stability, and protein folding due to the degeneracy of the genetic code

nonsynonymous

a nucleotide substitution in DNA that alters the amino acid sequence of a protein, often impacting its structure and function