chapter 20: phylogenies and the history of life

shared characteristics between organisms

composed of one or more cells, carry out metabolism, transfer energy with ATP, encode hereditary information in DNA

group organisms based on shared characteristics

fossil records, ,morphology, physiology, behavior, embryological development, DNA/RNA sequences

systematics

field that scientists use to organize and classify organisms based on evolutionary relationships

taxonomy

science of classifying organisms

Linnanean system

named after Carl Linnaeus, moving from the root on a cladogram, each group (taxa) becomes more specific (more

restricted), at each sublevel in the taxonomic classification

system, organisms become more similar

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

binomial nomenclature

a system for giving each organism a two-word scientific name that consists of the genus name followed by the species name (epithet), genus is capitalized, entire species name is italicized (also subspecies names)

phylogeny

the evolutionary history and relationship of an organism or group of organisms, important because it enriches our understanding of how genes, genomes, species (and molecular sequences more generally) evolve

rooted phylogenic tree

single lineage (at base) represents common ancestor

unrooted phylogenic tree

show relationships but not a common ancestor

root

indicates that an ancestral lineage gave rise to all organisms on the tree

branch point (node)

splitting represents single lineage evolving into two clades, nodes are most recent common ancestor (MCRA) of subsequent clades, taxa that share a node also share a common ancestor

taxon

a group of organisms in a classification system

basal taxon

a lineage that diverges early in the history of a group

sister taxon

any taxa derived from a common ancestral node

clade (monophyletic group)

evolutionary branch of a cladogram that includes a single ancestor and all its descendants, monophyletic taxon

paraphyletic group/taxon

a group that includes an ancestral population and some of its descendants, but not all, leaves out a common descendant

polyphyletic group/taxon

an unnatural group that does not include the most recent common ancestor, includes species with different ancestors

polytomy

a branch point from which more than two descendant groups emerge

cladistics

a phylogenetic classification system that uses shared derived characters (homologous characters) and ancestry as the sole criterion for grouping taxa, goal is to produce cladograms where all clades are monophyletic

shared characteristics

traits of structures shared by all or most species in a group because they are inherited from a common ancestral species, used to determine relatedness when constructing a cladogram

shared ancestral character

a character that is shared by members of a particular clade but that originated in an ancestor that is not a member of that clade

shared derived character

an evolutionary novelty unique to a particular clade, used to identify branch points (nodes) within the larger clade, distinguishes those that share it from those who do not

rule of parsimony

choose the simplest cladogram with the fewest steps or events

confusion in phylogeny

convergent evolution and evolutionary reversal

limitations to the classic model of inheritance

mendelian inheritance and its modifications assume that genes are transferred from parent to offspring (vertical gene transfer), and mutations are the primary sources new genetic information

this is not the complete story in prokaryotes, and even some eukaryotes because of horizontal gene transfer

horizontal gene transfer

transfer of genetic material between unrelated species, more prevalent in prokaryotes

transformation

naked DNA uptake by bacteria

transduction

genes transferred by virus

conjugation

genes transferred between to bacteria via pilus

endosymbiotic theory

a theory that states that certain kinds of prokaryotes began living inside of larger cells and evolved into the organelles of modern-day eukaryotes, mitochondria and chloroplasts

genome fusion

fusion of two prokaryotic genomes, presumably by endosymbiosis

web of life

phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution

ring of life models

proposed that all three domains evolved from a pool of prokaryotes swapping genes via horizontal gene transfer, may help explain how certain eukaryotic genes more resemble those of bacteria while others resemble archeans