BIOL 286: Lecture #8 Review (Phylogenetics)

Historically, species relatedness was based on . . ., . . ., . . ., . . ., . . ., etc.

appearance; behavior; ecology; habitat; biochemistry

Potential issues with assessing species relatedness based on factors such as morphology, behavior, ecology, habitat, biochemistry, etc.: (3)

(1) cryptic species; (2) convergent evolution; (3) difficulty with microbes

cryptic species

Groups of organisms that are genetically distinct and do not interbreed, but are morphologically nearly indistinguishable

systematics

The study of evolutionary relationships

phylogeny

An evolutionary tree that represents a hypothesis on patterns of relatedness

Elements of a phylogenetic tree: (4)

(1) tips; (2) nodes; (3) branches; (4) roots

Phylogenies are also known as . . .

phylogenetic trees

Elements of a phylogenetic tree: Node

In a phylogenetic tree, the junction points where branches meet, symbolizing evolutionary events such as speciation or divergence from a common ancestor

Elements of a phylogenetic tree: Tips

In a phylogenetic tree, the terminal nodes representing the most recent descendants, which can be species, taxa, populations, or genes

Elements of a phylogenetic tree: Branches

In a phylogenetic tree, the lines that connect nodes, representing a lineage (which may include one or more species or taxa that share a common ancestor) connecting a common ancestor to its descendants

Elements of a phylogenetic tree: Roots

In a rooted phylogenetic tree, the node that corresponds to the ancestral lineage from which all other nodes descend, making it the oldest part of the tree

Phylogenetic trees can be . . . or . . .

rooted; unrooted

The root of a phylogenetic tree represents . . ., while the tips represent . . .

the most recent common ancestor of all entities in the tree; current species or sequences

In rooted phylogenetic trees, roots provide . . ., allowing for determination of . . . That is, roots specify . . . of relatedness

a reference point for interpreting evolutionary relationships; the sequence of divergence events; directionality

A rooted phylogenetic tree shows . . ., whereas an unrooted tree . . .

the direction of evolutionary time from the ancestor to descendants; only illustrates relationships without specifying ancestry

In unrooted phylogenetic trees, only . . . is shown, as . . .

relatedness among taxa; the direction of evolution cannot be inferred

Branches of a phylogenetic tree indicate . . ., while nodes-- . . . --represent . . . or . . .

lineages; where branches split; speciation events; points of divergence from a common ancestor

sister taxa

Lineages that share an immediate common ancestor and are therefore each other's closest relatives (i.e. they diverged from the same node)

DNA sequence data can be used to determine . . .

the hypothesized relatedness of species

DNA sequencing can include: (3)

(1) sequencing a single gene; (2) sequencing the entire genome; (3) sequencing the genome of an organelle (e.g. mitochondrial or chloroplast genome)

How do we use DNA to create phylogenies? (3)

(1) Compile DNA sequences of species of interest; (2) Align DNA sequences; (3) Input aligned DNA sequences to software to assemble a phylogenetic tree

multiple sequence alignment

The process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.

Multiple sequence alignments highlight . . . such as . . ., . . ., and . . . and are used to . . . . and . . . of . . ., . . ., . . ., and . . . or . . .

mutation events; point mutations (single amino acid or nucleotide changes); insertion mutations; deletion mutations; assess sequence conservation; infer the presence and activity; protein domains; tertiary structures; secondary structures; individual amino acids; nucleotides.

clade

A group of biological taxa that includes all descendants of one common ancestor

monophyletic clade

A taxonomic grouping that includes all descendants from one common ancestor

paraphyletic clade

A taxonomic grouping that includes the common ancestor and some of its descendants, but not all

polyphyletic clade

A taxonomic grouping that does not include the common ancestor of the taxon

outgroup

On a phylogenetic tree, a species that is more distantly related to the other species in the tree

Sometimes we cannot determine the relationship between species in a clade with existing DNA sequences. As a result, . . . are observed in the phylogenetic tree

polytomies

polytomy

A node in a phylogenetic tree or cladogram where three or more lineages diverge from a single ancestral lineage at the same time. In other words, it represents a branching point with more than two branches, rather than the typical two-branch split (dichotomy)

When polytomies are observed, . . . may help infer true evolutionary relationships

more sequencing efforts

ancestral state

A state shared by a common ancestor (i.e. it arose prior to lineages diverging)

shared derived state

A trait or mutation that arose after a common ancestor; a derived characteristic among multiple taxa

Shared derived state is also called . . .

symapomorphy

homoplasious state

A mutation that arose twice in each lineage

Gene selection factors for creating phylogenies: (3)

(1) the gene must be present among all species of interest; (2) the gene must have the same function; (3) rate of evolution

When choosing a gene for creating phylogenies, choose a gene found . . . with . . .

in all species of interest; the same function

Explain the importance of considering the rate of evolution of genes when selecting a gene to assembly a phylogeny.

When assembling a phylogeny, it is essential to consider the rate of evolution of the genes being analyzed because different genes accumulate mutations at different speeds. Slow‑evolving genes (such as many nuclear protein‑coding genes) are most informative for resolving deep evolutionary relationships, since their sequences remain conserved over long time scales. By contrast, fast‑evolving genes—including many mitochondrial genes—accumulate mutations rapidly and are therefore better suited for distinguishing closely related species or recent divergences. Selecting an appropriate gene ensures that the phylogeny reflects the correct temporal scale of evolutionary change.

When assembling phylogenies, what sort of genes are best to elucidate deep evolutionary relationships? Why?

slow-evolving genes (e.g. nuclear genes and rDNA); because their sequences remain conserved over long time scales

When assembling phylogenies, what sort of genes are best to distinguish closely related species or recent divergences?

fast-evolving genes (e.g. mitochondrial genes)

positive selection

An evolutionary paradigm by which alleles that increase fitness quickly increase in frequency in a population

Under positive selection, the allele tends to . . . until . . .

increase over time; reaching fixation

purifying selection

An evolutionary paradigm by which alleles that decrease fitness tend to disappear from populations

balancing selection

An evolutionary paradigm by which an allele tends to remain in the population at an intermediate frequency owing to expressed advantage only in heterozygotes

Neutral theory of evolution (Kimura)

Asserts most variation at the molecular level does not affect fitness (i.e. is neutral) and, therefore, the evolutionary fate of genetic variation is best explained by stochastic processes (i.e. genetic drift alters allele frequencies)

Per Kimura's neutral theory of evolution, mutations will either . . . or . . . and the rate of mutation . . .

become fixed; lost from the population; is equivalent to the rate of fixation

molecular clock

The concept that, with the knowledge of when lineages diverged, we can estimate the mutation rate (mutations/time) for lineages by examining how different the DNA sequences are between extant taxa

Molecular clocks are calibrated with . . . (e.g. . . . or . . .)

known evolutionary events; from fossil records; major evolutionary events

What is a limitation of molecular clocks?

Mutation rates may vary among taxa (will yield incorrect divergence estimates)

Phylogenies can be used to track . . . and . . . over time

the appearance of traits; trends of changes in a trait

allometry

Differential growth of body parts that results in a change of shape or proportion with size (i.e. traits scale with size)

Encephalization Quotient (EQ)

Quantifies the relationship between brain size that is not explained by the allometric relationship between brain and body size

zoonotic diseases

Diseases that can be transmitted from animal to human populations, or vice versa