EVE 100 MT2

Phylogeny

• A visual representation of the evolutionary history of populations, genes, species, taxa, etc

• Depicts the history of events by which species/taxa/genes have arisen from common ancestors

• Hypothesis of relationships between taxa

Rooted Trees/Phylogenies

Contain information about the flow of time, which allows us to discern the pattern of descent from common ancestry and the direction of trait evolution

Polytomy

Indicate uncertainty in the correct branching pattern & can have an unlimited # of nodes

Phylogram

A tree in which branch lengths are proportional to the amount of change attributed to the branch.

Ultrametric tree

A rooted tree in which units of branch length accumulate evenly on all branches so that contemporaneous tips are equidistant from root node.

Monophyletic group

Clade: a part of a phylogeny that includes an ancestral lineage and all the descendants of that ancestral lineage.

Paraphyletic group

characterized by shared ancestral character states, symplesiomorphies, & does not include all descendants of the ancestral lineage

Polyphyletic group

Taxa united by similar but not homologous character states (resulting from convergent evolution)

Apomorphy

Derived character state

Plesiomorphy

Ancestral character state

Synapomorphy

A shared derived character state

Symplesiomorphy

A shared ancestral character state

Homoplasious character

A character state that evolved 2+ times (convergence)

Ingroup

Group of taxa for which relationships will be analyzed

Outgroup

Taxa more distantly related to the ingroup than any members of the ingroup are to each other

Maximum Parsimony

The best estimate of the true phylogeny requires us to postulate the fewest evolutionary changes (i.e. minimize the number of repeated changes, homoplasies).

Homoplasy

Repeated evolutionary change

Strict consensus

The tree composed ONLY of clades that occur on all input trees

Consensus tree

The combination of equally parsimonious trees to represent uncertainty in relationships among taxa

Orthologous gene

Homologous members of gene family in two or more species (separated by speciation events only)

Paralogous gene

Gene copies that originated via ancestral gene duplications (separated by at least one duplication event)

Mutation

A change in the nucleotide sequence from the parent to the offspring

Substitution

A change between species at the DNA level.

The molecular clock method

Assuming a constant rate of change at the molecular level:

• S_CA: substitutions between A and C

• S_AD: substitutions between A and D

A and C are known to have split t2 years ago

→ Substitution Rate = S_AC / (2 t₂)

*Units are in substitutions per year

S_AC / (2 t₂) = S_AD / (2 t₁)

so: t₁ = t₂ *(S_AD/S_AC)

Substitution Rate (Molecular Clock)

S_AC / (2 t₂)

Why 1^st and 2^nd codon position evolve at a slower rate than 3^rd codon positions?

The third codon positions are the most “degenerate;” the least constrained to evolve. Natural selection allows for more changes in the position; thus the codon exhibits the highest substitution rate

Why does sequence divergence in 3^rd codon positions plateau after 100 million years in this data set?

Because the 3rd codon position evolves faster, eventually the sequence divergence saturates, and it’s impossible for a short sequence to accumulate more substitutions. “Multiple hits” start to appear (mutations on mutations causing reverse evolution?)

Non-synonymous substitutions

Changes in protein sequence

Synonymous substitutions

No changes in protein sequence

dN /dS

The ratio of non-synonymous substitutions per non-synonymous site divided by the number of synonymous substitutions per synonymous site

This analysis can only be applied to protein-coding genes

dN /dS << 1

Consistent with negative (purifying) selection. The  vast majority of nonsynonymous mutations are deleterious and thus removed by natural selection

dN / dS = 1

Consistent with neutral evolution (no selection). (e.g. pseudogenes)

dN / dS >> 1

Consistent with positive selection

Species concept

What we mean by species

Species diagnosis

Defining criteria that can be used to delimit a particular species, and the traits that separate that species from other similar species

Morphological Species Concept

Defines a species as a group of organisms that look similar to each other & are distinct from other groups of organisms

– Uses phenotypes & morphology

Phylogenetic Species Concept

Defines a species as a group of organisms that share a pattern of ancestry/descent & that form a single branch on the tree of life

– Uses DNA/molecular data

Biological species concept (BSC)

Species are groups of actually or potentially interbreeding populations in nature, reproductively isolated from other such groups.

Critical observations that contributed to the formulation of BSC:

• Variation within species.

• Geographic variation

• Existence of sibling/cryptid species

Allopatric speciation

Geographically separated populations

Populations diverge while separated by a geographic barrier that prevents/reduces gene flow between populations. After the two populations become so different that reproductive isolation evolves, the two can coexist without interbreeding

Reproductive isolation

Any of several biological differences between the groups greatly reduces gene exchange between them, even if they are not geographically isolated

Parapatric speciation

Neighboring populations diverge while still exchanging some genes (but not freely). Adjacent populations adapt to different habitats/niches and selection favors divergence. Reduction of gene flow is due to strong selection preventing colonization of the other habitat or the formation of hybrids

Sympatric speciation

Two new species emerge from a single ancestor without any geographic isolation and while exchanging genes freely. This requires extremely strong divergent selection. This speciation mode is highly controversial and unlikely to happen in nature

Copulatory behavioral isolation

Behavior of an individual during copulation is insufficient to allow normal fertilization

Prezygotic reproductive barrier

Gametic isolation

Transferred gametes unable to fertilize eggs

Prezygotic reproductive barrier

Intrinsic isolation

Reflects a developmental problem in hybrids that is relatively independent of the environment

Postzygotic reproductive barrier

Extrinsic isolation

Reflects a developmental problem in hybrids caused by the environment

Postzygotic reproductive barrier

Reproductive Isolation (RI) Index

1 - (frequency of heterospecific matings ÷ frequency of conspecific matings)

Gametic incompatibility

Sperm or pollen from one species fails to fertilize the egg or ovule of another species

Gametic Isolation

Pollen tube growth in plants

Pollen from one species fails to fertilize the ovule of another species

Gametic Isolation

Hybrid inviability

Hybrids die before or shortly after birth

Intrinsic isolation

Physiological hybrid stability

Hybrids suffer problems in the reproductive system or gametes

Intrinsic isolation

Behavioral hybrid sterility

Hybrids suffer neurological or physiological defects that prevent them from finding mates

Intrinsic isolation

Ecological inviability

Hybrids develop normally but they suffer lower viability because they cannot find an appropriate ecological niche

Intrinsic isolation

Behavioral sterility

Hybrids can produce normal gametes but cannot obtain mates

Intrinsic isolation

Dobzhansky-Muller Incompatibilities (DMIs)

Incompatible genotypes that come from substitutions at two or more loci

The Dobzhansky-Muller model (for the evolution of intrinsic hybrid sterility/inviability)

Reproductive barriers are based on differences at two or more loci that have complementary effects on fitness

Functional divergence between interacting loci

Yields incompatible interactions in hybrids

Haldane’s rule

When in the F1 offspring of two different species a sex is absent, rare, or sterile, that sex is the heterogametic sex

Heterogametic hybrids

Affected by all X-linked alleles (recessive or dominant) that cause incompatibilities, as they carry only one copy of X-linked genes

Homogametic hybrids

Only affected by dominant deleterious X-linked alleles

Hybrid chromosome mismatches (during meiosis)

Result in the formation of chromosome chains, causing irregular segregation, unbalanced gametes and low fertility