Chapter 10: Phylogenetics and Macroevolution

taxonomy

the theory and practice of classification + naming

taxon

a single named taxonomic unit at any level (plural = taxa)

systematics

the study of biodiversity and the evolutionary relationships among organisms

• in modern practice, taxonomic names are assigned such that they are consistent with our present understanding of evolutionary relationships

Carolus Linnaeus (1707 - 1778)

• father of taxonomy

• binomial nomenclature

• hierarchical system of classification

biological classification

1. kingdom

2. phylum

3. class

4. order

5. family

6. genus

7. species

What is the purpose of biological classification?

• a name is a key to shared information on an organism → has predictive power

• enables interpretation of origins and evolutionary history

*systematics research requires a robust and stable system for classifying organisms

phylogenies

evolutionary history of species

1. individual organisms within a population

2. parents produce offspring

3. lines of descent persist across generations

4. a population is an aggregation of the genetic lineages of the individual they contain

5. a species is made of many populations, linked by gene flow

6. individual species split to give rise to multiple species

7. a phylogeny shows the relationships and evolutionary history of species

components of phylogenetic tree

• nodes

• branches

• tips

• external branches

• internal branches

• sister groups

• parent/daughter

• root

• ingroup

• outgroup

• MRCA

• clade

nodes

correspond to historical lineages splitting events, when one lineage splits into 2

branches

correspond to single-ancestor-descendant lineages

• all branches are connected by nodes

tips

individuals, species, clades that do not have represented descendants

external branch(terminal branch)

connect a tip and a node

internal branch

connect 2 node

sister groups

those that are the immediate descendants of same ancestor

parent/daughter

parent branches give rise to daughters

root

a node representing earliest time point in the diagram

• often represented by an unlabeled branch

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 help determine what character states are ancestral

MCRA = most recent common ancestor

youngest node that is ancestral to all lineages in a given group of taxa

clade

any piece of a phylogeny that includes an MCRA and all of its descendants

• i.e. any piece of a phylogeny that exhibits monophyly

• a phylogenetic tree can contain many clades

grouping concepts

• monophly

• paraphyly

• polyphyly

monophyly

describes a group made up of an ancestor and all its descendants

• i.e. monophyletic group or clade

paraphyly

describes a group made up of an ancestor and some (but not all) of its descendants

• i.e. paraphyletic group, or grade

polyphyly

describes a group that does not contain the most recent ancestor of all members

• i.e. polyphyletic group

scissor test

snip a branch → makes a group

phylogenies and trait evolution

• ancestral

• derived

• homology

• homoplasy

• synapomorphy

• terms refer to the inheritance of traits for a given group of species

• do not describe species themselves

• the same trait can be ancestral for a clade, but derived within a larger clade

ancestral

a trait inherited in its present form from the MCRA of the clade, for the species in a clade

derived

a trait originated within the clade, for that clade

synapomorphy

a shared, derived trait for a clade

• it is a treat that all species in the clade share, and that evolved on the branch leading to the clade (i.e. it’s derived within the context of more inclusive clades)

homology

when structures observed in diff taxa can be traced to a single structure present in a shared evolutionary ancestor

• similarity due to common ancestor

homoplasy

when a character or character state arises more than once on a phylogenetic tree (convergence is one kind)

• similarity evolved independently

Why conduct a phylogenetic analysis?

• understand history of life

• understand large-scale patterns of evolution

• understand how many times trait has evolved, how fast, under what condition

• practicals

  • where/when did parasites spread?

  • which flu strain was the most successful last year?

  • what are the driver mutations as SARS-COV-2 evolves?

Reconstructing phylogenies

1. gather info on variation we observe among the species

2. ignore all characters present in just 1 species because they don’t say anything about relationships

3. Venn diagram of nested relationships - what patterns of relatedness are indicated by these shared, derived characters?

4. make phylogenetic tree with shared characters and the independent characters

notes about phylogeny reconstruction

• modern phylogenetic methods fit models of evolution to observed trait data

• train data can be genetic or phenotypic

• phylogenetic relatedness is inferred from homologous trait

• homoplasy (e.g. convergent trait evolution) can mislead phylogenetic inference

e.g. DNA sequencing has enabled rapid progress towards constructing the tree of life

OneZoom web projects provides phylogenetic info about more that 2 million species

macroevolution

study of evolutionary processes and patterns among species

2 principal sources of macroevolutionary insights

• paleontology

  • provides a direct record of past evolutionary change

  • inference is strongest for groups that fossilize well

• phylogenetics

  • provides an indirect record of past evolutionary change

  • inference is strongest for groups that have living representatives

e.g. mass extinction periodically restructure life on earth

mass extinction: extinction of more than 75% of earth’s species in a geographically short period

fossil record

• provides only evidence for completely extinct clades

• documents long-term patterns of global biodiversity

• provides evidence for catastrophic extinctions during earth’s history

phylogeny

• provides evidence for explosive diversification following mass extinction

* diversification rate = speciation rate - extinction rate

Other features associated with increased diversification

• herbivory

• species with more sexual selection

• animal polination in plants

• increased dispersal

• increased range size