Lecture 10 Flashcards
Define taxonomy
the theory and practice of classification and naming
define systematics
the study of biodiversity and the evolutionary relationships among organisms
Carolus Linnaeus
1707-1778
- father of taxonomy
- binomial nomenclature
- hierarchical system of classification
define a taxon
a single named taxonomic unit at any level (plural = taxa)
7 taxa
kingdom (kingdoms)
phylum (phyla)
class (classes)
order (orders)
family (families)
genus (genera)
species (species)
what is the purpose of a biological classification?
- a name is key to shared information on an organism (eg scientific literature, field guides)
- therefore has predictive power
- enables interpretation of origins and evolutionary history
systematics research requires
a robust and stable system for classifying organisms (i.e. taxonomy)
describe how phylogenies arise/what they are made up of
- individual organisms within a population
- parents produce offspring
- lines of descent persist across generations
- a population is an aggregation of the genetic lineages of the individuals they contain
- a species is made of many populations, linked by gene flow
- individual species split to give rise to multiple species
- a phylogeny shows the relationships and evolutionary histories of species
node
corresponds to historical lineage splitting events, when one lineage splits into two
branches/ edges
correspond to single ancestor-descendant lineages. All branches are connected by nodes
tips/leaves/terminals/OTUs
tips do not have represented descendants. can be individuals, species, clades
internal vs external branches
external branches (aka terminal branches) connect a tip and a node. internal branches connect two nodes
root
- a node representing earliest time point in the diagram
- often represented by an unlabelled branch
sister groups/taxa
those that are immediate descendants of the same ancestor, eg sister species, sister branches, sister clades
parents and daughters
parent branches give rise to daughter branches
ingroup
consists of the focal species in a phylogenetic study
outgroup
a more distant relative of the in-group taxa; can help to root the phylogeny and determine what character states are ancestral
MRCA
most recent common ancestor; the youngest node that is ancestral to all lineages in a given group of taxa
clade
- any piece of a phylogeny that includes a MRCA and all of its descendants
- i.e. any piece of a phylogeny that exhibits monophyly
monophyly
- describes a group made up of an ancestor and all its descendants
- ie a monophyletic group or clade
paraphyly
- describes a group made up of an ancestor and some (but not all) of its descendants
- ie a paraphyletic group or grade
polyphyly
- describes a group that does not contain the most recent common ancestor of all members
- ie. a polyphyletic group
for the species in a clade a trait is ancestral if
it was inherited in its present form from the MRCA of the clade
for the species in a clade, a trait is derived if
it originated within the clade, ie in a descendant of the clade’s MRCA
relationship between ancestral and derived clades
the same trait can be ancestral for a clade, but derived within a larger clade
define a synapomorphy
a shared, derived trait for a clade. it is a trait that all species in the clade share, and that evolved on the branch leading to the clade (ie its derived within the context of more inclusive clades)
homology
when structures observed in different taxa can be traced to a single structure present in a shared evolutionary ancestor
homoplasy
when a character or character state arises more than once on a phylogenetic tree (convergence is one kind)
why conduct a phylogenetic analysis?
- understand history of life
- understand large scale patterns of evolution
- understand how many times traits have evolved how fast, under what conditions
- practical: where/when did parasites spread? which fly strain is most successful? what are the driver mutations as covid evolves?
why is phylogenetic relatedness inferred from homologous traits and not homoplasy?
homoplasy (eg convergent trait evolution) can mislead phylogenetic inference
2 principal sources of macroevolutionary insights?
palaeontology
- provides a direct record of past evolutionary change
- inference is strongest for groups that fossilise well
phylogenetics
- provides an indirect record of past evolutionary change
- inference is strongest for groups that have living representatives
mass extinction
extinction of >75% of earth’s species in a geologically short period
uses of fossil record
- provides only evidence for completely extinct clades
- documents long-term patterns of biodiversity
- provides evidence for catastrophic extinctions during earth’s history
diversification rate
speciation rate minus extinction rate
what happens after mass extinctions and how do we know?
explosive diversification; phylogenetic provides evidence for this
features associated with increased diversification
- herbivory
- species with more sexual selection
- animal pollination in plants
- increased dispersal
- increased range size
