Phylogeny and Systematics: Understanding Evolutionary Relationships

Phylogeny

the evolutionary history of a species or group of species

Systematics

discipline focusing on classifying organisms and determining their evolutionary relationships

Taxonomy

how organisms are named and classified

Binomial Nomenclature

the two-part format of the scientific name

Genus

first part of the binomial; species belong to a genus

Specific Epithet

second part of binomial; unique for each species within the genus

Taxon

the named taxonomic unit at any level of the hierarchy (ex: Panthera is taxon at genus level and Mammalia is taxon at class level)

Phylogenetic Tree

branching diagram that represents the evolutionary history of a group of organisms

Branch points

represent the divergence of two evolutionary lineages from a common ancestor

Sister Taxa

groups of organisms that share an immediate common ancestor

Basal Taxon

lineage that diverges early in the history of the group, and lies on a branch that originates near the common ancestor of the group

Polytomy

a branch point from which more than two descendent groups emerge

Morphological Homologies

The more elements that are similar in two complex structures, the more likely it is that they evolved from a common ancestor

Homologies

phenotypic and genetic similarities due to shared ancestry

Analogy

similarities due to convergent evolution

Homoplasies

analogous structures that arose independently

Molecular Homologies

If genes in two organisms share many portions of their nucleotide sequence it is likely the genes are homologous

Molecular systematics

uses data from DNA and other molecules to determine evolutionary relationships

Cladistics

an approach to systematics where common ancestry is the primary criteria used to classify organisms

Clades

groups, each of which includes an ancestral species and all of its descendants (clades are nested within larger clades)

Monophyletic group

consists of an ancestral species and all of its descendants (clade)

Paraphyletic group

consists of an ancestral species and some, but not all of its descendants

Polyphyletic group

includes taxa with different ancestors; does not include the most recent common ancestor of all members of the group

Shared ancestral character

a character that originated in an ancestor of the taxon; arose prior to the common ancestor

Shared derived character

an evolutionary novelty unique to a clade; inherited from the most recent common ancestor of an entire group

Outgroup

a species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying (ingroup)

Maximum Parsimony

A method used by scientists to narrow down and find the most accurate tree in a data set.

Maximum Likelihood

A statistical method used to estimate the parameters of a model that best explains the observed data.

Gene Duplication

The process that increases the number of genes in a genome, providing more opportunities for further evolutionary changes.

Gene Families

Groups of related genes within an organism's genome that result from repeated duplications.

Orthologous Genes

Genes found in different species, whose divergence traces back to the speciation events that produced the species.

Paralogous Genes

Genes that result from gene duplication, where multiple copies have diverged from one another within a species.

Molecular Clock

A method that measures the absolute time of evolutionary change based on the observation that some genes evolve at constant rates.

Irregularities in the Molecular Clock

Likely the result of natural selection where certain DNA changes are favored over others.

Nucleotide Substitutions in Orthologous Genes

Assumed to be proportional to the time that has elapsed since the species branched from their common ancestor.

Substitutions in Paralogous Genes

Proportional to the time since the ancestral gene was duplicated.

Neutral Theory

The theory that much evolutionary change in genes and proteins has no effect on fitness and is therefore not influenced by natural selection.

Clock Rate Differences

Differences in the clock rate for different genes are a function of how important a gene is.

Essential Amino Acid Sequence

If the sequence specified by a gene is essential to survival, most mutational changes will be harmful and only a few will be neutral.

Less Critical Amino Acid Sequence

If the sequence is less critical, fewer new mutations will be harmful and more will be neutral, leading to quicker changes.

Domains

Categories of life including Bacteria, Archaea, and Eukarya.

Bacteria

Contains most of the currently known prokaryotes, including those closely related to chloroplasts and mitochondria.

Archaea

A diverse group of prokaryotic organisms that inhabit a wide variety of environments.

Eukarya

All organisms that have cells containing true nuclei.

Horizontal Gene Transfer

The process in which genes are transferred from one genome to another through various means such as transposable elements and plasmids.

Phylogenetic Trees

Trees built using different genes that can give inconsistent results due to horizontal gene transfer.

Genome Comparisons

Show that there have been substantial movements of genes between organisms in different domains, facilitated by horizontal gene transfer.