Biology II- Chapter 26

Phylogeny

-the evolutionary history of a species or group of related species

-If you can determine the phylogeny of an organism, you
are likely to know many of it's characteristics

The discipline of systematics

-classifies organisms and determines their evolutionary relationships

-Systematists use fossil, molecular, and genetic data to infer evolutionary relationships

Taxonomy

the ordered division and naming of organisms

Binomial nomenclature: 4 important facts

-Binomial nomenclature
avoids this confusion

-Binomial nomenclature
is hierarchical and divided
into taxa

-Note capitalization and
italics

-The higher levels do
not always reflect phylogeny

How do you Link Classification and Phylogeny

Systematists depict evolutionary relationships in branching phylogenetic trees

What does a phylogenetic tree represent?

-a hypothesis about evolutionary relationships

What does each branch point represent on a phylogenetic tree?

-represents the divergence of two species

-where lineages diverge

-represents the common ancestor of taxa

-forms a polytomy

What are sista taxa?

-groups that share an immediate common ancestor

What is a polytomy?

-an unresolved pattern of divergence

*see notes

What is Basal Taxon?

least related to the rest

What phylogenetic trees can and can't tell you:

-Organisms that share a common ancestor often resemble one another, but not always.

This can be due to different rates of evolution or
different selective pressures

Example: Crocodiles are more closely related to birds than other reptiles

Does the sequence of branching and length of the branches of the tree mean anything?

-No

-The sequence of branching and length of the branches of the tree mean nothing about the age of the organisms unless specific data about age is provided

-Do not assume that any taxon evolved from the adjacent taxon

What can phylogenies be used for?

-to identify relatives or ancestors of current species that may carry useful genes

-Identify organisms based on sequence similarities

How are phylogenies concluded?

-from morphological and molecular data

-To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms

-organisms that are similar morphologically will be
genetically similar, but this isn't always true

Homology

-is similarity due to shared ancestry

Analogy

-is similarity due to convergent evolution

How do you evaluate Molecular Homologies?

Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

What is Molecular homoplasy?

Two genes that share about 25%
sequence identity due to chance

What is Cladistics?

groups organisms by common descent

What is a clade?

-Groupings within trees

-a group of species that includes an ancestral species and all its descendants

IMPORTANT:A taxon is a clade ONLY if it is monophyletic (all of the organisms in the clade are from a common ancestor)

What is a valid clade?

monophyletic

What is monophyletic?

-signifying that it consists of the ancestor species and all its descendants

what is paraphyletic?

it does not include all of the descendants of the common ancestor

What is polyphyletic?

it does not include the most recent common ancestors of its members

what is a shared ancestral character?

a character that originated in an ancestor of the taxon

What is a shared derived character?

an evolutionary novelty unique to a particular clade

In some trees, the length of a branch can reflect what?

-Branch lengths can represent genetic change

-Branch lengths can represent chronological time

-number of genetic changes that have taken place in a particular DNA sequence in that lineage

-In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record

What does Maximum parsimony do?

-assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely

-least # of changes to the next

What is the principle of maximum likelihood?

-states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events

-how like this happened this way

Phylogenetic bracketing allows us to predict what?

features of an ancestor from features of its descendants

An organism's evolutionary history is documented where?

-in its genome

DNA similarities can reveal?

-relationships that are otherwise not obvious (example animals and fungi)

-Useful when fossils aren't available

What about DNA that codes for rRNA?

-DNA that codes for rRNA changes relatively slowly

-is useful for investigating branching points hundreds of millions of years ago

What about DNA that codes for mtDNA?

-evolves rapidly

-can be used to explore recent evolutionary events

what are orthologous genes?

the result of a speciation event and hence occurs btwn genes found in different species

ex. gene shared btwn humans and dogs

what are paralogous genes?

the result from gene duplication, hence multiple copies of these genes have diverged from one another within a species

what does a molecular clock used for?

-help track evolutionary time

-uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change

ex. was used to to estimate the approximate time when HIV jumped from animals to humans

In orthologous genes, nucleotide substitutions are?

proportional to the time since they last shared a common ancestor

In paralogous genes, nucleotide substitutions are?

-proportional to the time since the genes became duplicated

The 5 kingdoms (plants, animals, fungi, protists and monera)
has been broken down due to?

-molecular evidence

What are the 3 domains?

-Bacteria

-Archaea

-Eukarya
Plants animals and fungi are now kingdoms in the domain
Eukarya

What is horizontal transfer?

picking up DNA from somewhere else that isn't your parents

What is vertical transfer?

directly from parents