Lecture 10: Phylogenetics I

Carl Linnaeus

• 1707-1778

• developed lifeform classification system (used to understand how species are related to each other) which is NOT derived from evolutionary thinking

• similar species can be grouped into hierarchical levels of similarity based on morphology

• 8 taxonomic ranks: DKPCOFGS

Binomial Nomenclature

• genus followed by species

• genus always capitalized, both always italicized

Phylogenetics

• study of relationships among taxa based on their evolutionary history

• goal: reconstruct evolutionary history of species and understand their pattern of descent

  • results are typically presented as a phylogeny/phylogenetic tree

• phylogenies built using characters

Systematics

• study of classifying organisms

Phylogenetic Systematics

• modern approach to classification using evolutionary relationships between organisms

Character

• any observable characteristics, or feature, of an organism

• morphological, behavioural, genetic, etc.

  • ex. coat colour in oldfield mice, genetic sequence, etc.

Trait

• the specific value of a character (i.e. the character state)

  • ex. brown or white coat, specific nucleotide (ACTG), etc.

• used to build trees so that we may infer patterns of descent among species/populations

Traits in Phylogenetics

• traits in phylogenetics are used to:

  • build trees

  • infer timing of evolutionary events by “mapping”

Phylogenetic/Evolutionary Trees

• built by mapping traits of interest to infer a pattern of descent among species/populations

• HYPOTHETICAL!

  • evolutionary histories are rarely directly observed

  • classifications will change as hypotheses about relationships change

Downside of Phylogenetic Trees

• do not account for strange things which happen in evolution:

  • horizontal gene transfer

  • hybridization

  • merges

• sometimes, trees are not great representations of evolutionary hisotries

  • however, they are still very useful tools!

Phylogenetic Tree Components

• all trees have:

  • branches

  • branch tips

  • internal nodes

  • an outgroup

  • a root

Taxon

• group of related organisms, placed at branch tip

  • could be species, genera, family, clades, etc.

Nodes

• hypothetical common ancestors

  • ancestors do not resemble present day species

  • ancestral population, not individual

Branch Tips

• represent decendents (following a node) on a phylogenetic tree

Derived Trait

• a trait that arises from changes to the ancestral state/trait

• characters therefore have polarity:

  • direction, or orientation

Ancestral → Derived Trait

Mapping Example: Tetrapod Opsins

• cone opsins: visual pigments

  • different animals have varied opsins, allowing them to see different wavelengths

• Opsins are mapped at branch tips

Orientation Phylogenetic Trees

• there are several ways to draw trees, but the information conveyed about relationships among taxa is the same

• relative positions from left to right do not indicate relatedness

  • distance to most recent common ancestor does (ie; the more recently that 2 groups share a common ancestor, the more closely related they are)

Pedigree vs. Phylogeny

• nodes:

  • pedigree: individuals

  • phylogeny: populaitons

• ancestors:

  • pedigree: 2 parents

  • phylogeny: 1 ancestral species

• progression over time:

  • pedigree: expands backwards in time

  • phylogeny: expands forwards in time

How to Build a Phylogeny

• select species/taxa of interest

• collect character/trait data

• determine which species have which traits in common:

  • which traits are ancestral? which are derived?

  • logic: species with many traits in common are more likely to be related than species with few traits in common

Apomorphy

• evolutionary innovation

  • derived trait

• what is called a plesiomorphy or apomorphy depends on context

Plesiomorphy

• pre-existing

  • ancestral trait

• what is called a plesiomorphy or apomorphy depends on context

Synapomorphy

• shared evolutionary innovation

  • derived trait

• ideal to build trees with these, as the presence of synapomorphies (rather than the retention of ancestral characters) tells us about branch order

Symplesiomorphy

• shared pre-existing

• ancestral trait

Causes of Phylogenetic Similarity

• homology

• homoplasy

Homology

• shared traits that are a result of common ancestry

  • homologous trait

  • ex. human eye and mouse eye

Homoplasy

• similar trait but not because of inheritance from a common ancestor

  • analogy or reversals

Analogy

• homoplasy

• similarity due to convergent evolution

  • ex. human eye and octopus eye, bird and bat wings

Reversals

• homoplasy

• loss of a derived trait through a return to the ancestral state

Divergent vs. Convergent Evolution

• divergent: homologous traits can take on different appearances or functions

• convergent: development of analogous triat

Divergent Evolution

• closely related organisms diverge from each other due to differing selective pressures

• homologous traits can take on different appearances or functions

  • ex. tetrapod limbs

Convergent Evolution

• two or more populations/species develop similarities due to similar selective pressures

• develop analogous traits

  • ex. body shape of aquatic predators

Issue of Homoplasy

• ideally build trees using synapomorphies, however convergence (or reversals) can be hard to identify

• how to avoid this issue:

  • including multiple outgroups

    • provides more info about trait polarity and the ancestral state

  • including many characters

    • reduces chance that all traits are reversals or analogous

How do we distinguish homology from homoplasy?

1. comparative embryology (look at traits before extensive modification during development)

2. fossil record (transitional fossils linking past and present)

3. agreement with other phylogenetic hypothesises (assume homoplasy vs. logy if ‘stronger’ evidence indicates groups are not sister taxa)

   1. number of features (inconsistent character most likely homoplasious)

   2. complexity of features (if 2 similar complex structures match in many details, it is unlikely they evolved independently)

Outgroup Analysis

• outgroup are a species (or group) that is less closely related to any member of the ingroup than the ingroup members are to each other

  • branched off earlier in history

• used to make inferences about common ancestor of ingroup

Parsimony Analysis

• under parsimony, our most likely tree is that which minimizes the # of evolutionary changes

• maximum parsimony= fewest changes

  • this approach gives no other cause for preferring one tree over another

Phylogeny

• a phylogeny is a hypothesis about inferred evolutionary relationships

• allow us to ask questions about trait origins

• based on characters that are homologous and emphasize shared derived characters

  • synapomorphies

• challenges include recognizing homology and direction of evolution

  • which is often unknown in ancestral states

Shoebills Evolutionary History

• phylogeny from morphological characters (80s)

  • shoebill and heron: sister taxa

• phylogeny from molecular genetics (2000s)

  • shoebill and pelican: sister taxa

• phylogeny from current morphological studies (20s)

  • shoebill and heron: sister taxa (still!)

• key point: phylogenies are hypotheses about evolutionary relationships, which can be continuously tested

Vestigial Traits

• traits that serve no known current function

  • problem with Darwin’s theory

• why do they remain?

  • not costly to remain

  • on its way out, just slowly

• useful in phylogenetic reconstruction, as they can infer common ancestry