Chapter 26: Phylogeny and the Tree of Life

Phylogeny

The evolutionary history of a species or group of related species

Systematics

Classifies organisms and determines their evolutionary relationships.

Carolus Linnaeus

He published a system of taxonomy based on resemblances in the 18th century

Binomial nomenclature

A two-part naming system for species, developed by Carolus Linnaeus.

Two-part names for species

Hierarchical classification

What are the two key features of the binomial nomeclature?

Genus

Specific Epithet

What are the two parts of a binomial name?

Phylogenetic tree

The evolutionary history of a group of organisms can be represented through

differ

Linnaean classification and phylogeny can __ from each other

Branch point

Represents the divergence of two evolutionary lineages from a common ancestor in a phylogenetic tree

Sister taxa

These are groups that share an immediate common ancestor that is NOT shared by any other group in the phylogenetic tree

Rooted tree

A phylogenetic tree that includes a branch point representing the most RECENT common ancestor of all taxa in the tree.

Basal Taxon

A lineage that diverges early in the history of a group and originates near the common ancestor of the group

patterns of descent

Phylogenetic trees show _______ not phenotypic similarity

Morphologies

Genes

Biochemistry of living organisms

To infer phylogenies, systematists gather information about the? (3)

Homology

Phenotypic and genetic similarities due to shared ancestry

Analogy

Phenotypic similarities due to convergent evolution, not from shared ancestry.

Convergent evolution

The process whereby different species develop similar traits independently due to similar environmental pressures and natural selection, rather than a shared ancestor.

Comparing fossil evidence

Nucleotide sequence

Homology can be distinguished from analogy by? (2)

Computer programs

Mathematical tools

Systematists use these two to analyze comparable DNA segments from different organisms

Molecular homoplasies

These are coincidental similarities that are similar molecular sequences that have evolved independently in different species, often due to convergent evolution.

Cladistics

A method of classifying organisms based on common ancestry and evolutionary relationships, focusing on shared derived characteristics.

Clade

A group of organisms that includes an ancestor and all its descendants, forming a branch on the tree of life.

Monophyletic

A valid clade. A group of organisms that includes a single common ancestor and all its descendants, representing a complete branch on the evolutionary tree.

Paraphyletic

A group of organisms that includes a common ancestor but not all its descendants, resulting in an incomplete branch on the evolutionary tree.

Polyphyletic

A group of organisms that includes distantly related species but does not include their most recent common ancestor.

Shared ancestral character

A character that originated in an ancestor of the group and is present in all its descendants, providing insight into evolutionary pathways.

Old traits shared by many groups

Shared derived character

An evolutionary novelty UNIQUE to a specific clade and NOT found in distant ancestors

New traits that makes a group special

Outgroup

A group that is closely related to the ingroup but not part of it. A group that has diverged before the ingroup

Ingroup

The group of organisms being studied or analyzed in a particular phylogenetic context, which shares more recent common ancestry.

Maximum parsimony

Assumes that the tree that requires the FEWEST evolutionary events is the most likelyto have occurred in the history of the studied groups.

The shortest path of evolution

Maximum likelihood

Based on probability rules about how DNA changes over time and assumes a tree can be found that reflects the most likely sequence of evolutionary events

The most realistic path of evolution

Phylogenetic bracketing

is a method used to infer characteristics of ancestor species by examining the traits of their descendants. It helps in understanding evolutionary relationships among closely related groups.

Fourchambered hearts, song, nest building and brooding

These are the shared features of birds and crocodiles (4)

genome

An organism’s evolutionary history is documented in its ____

Orthologous genes

Genes that are found in a single copy in the genome and are homologous between species

They can diverge only after speciation occurs

Keeps the SAME function across species

Genes are found in DIFFERENT species but came from a common ancestor

Paralogous genes

Genes that result from gene duplication and are found in MORE THAN one copy in the genome

Can diverge within the species that carries them and often evolve NEW functions

Come from the same species

Molecular clock

Uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change

last shared a common ancestor

In orthologous genes, nucleotide substitutions are assumed to be proportional to the time since they ____ ____ _ ____ ____

genes became duplicated

In paralogous genes, nucleotide substitutions are proportional to the time since the ___ _____ _____

Amino acid

A critical component to protein function and plays a key role in differentiating the clock rate for different genes

neutral

The molecular clock does not run as smoothly as expected if the mutations were _____

Irregularities

These result from natural selection in which some DNA changes are favored over others

Chimpanzees and primates

Phylogenetic analysis shows that HIV descended fromt hese animals

Molecular systematics

a way of classifying and studying the relationships between organisms using DNA, RNA, or protein (amino acid) sequences instead of just physical traits.

Monera

Protista

Plantae

Fungi

Animalia

What are the 5 kingdoms

Bacteria

Archaea

Eukarya

What are the three domains in the three-domain system

Horizontal gene transfer

The movement of genes from one genome to another

Exchange of transposable elements and plasmids

Viral Infection

Fusion of organisms

What are the 3 occurences of horizontal gene transfer?