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Chapter 26. Phylogeny and the Tree of Life

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Yun Doo Chung

on 3 September 2014

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Transcript of Chapter 26. Phylogeny and the Tree of Life

Chapter 26. Phylogeny and the Tree of Life
Taxonomy
is the ordered division and naming of organisms
New information continues to revise our understanding of the tree of life
Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics
Legless lizards have evolved independently in several different groups
Overview: Investigating the Tree of Life
What is this organism?
Phylogeny
is the evolutionary history of a species or group of related species
The discipline of
systematics
classifies organisms and determines their evolutionary relationships
Systematists use fossil, molecular, and genetic data to infer evolutionary relationships
An unexpected family treee
Key Concepts
Phylogenies show evolutionary relationships
Phylogenies are inferred from morphological and molecular data
Shared characters are used to construct phylogenetic trees
An organism's evolutionary history is documented in its genome
Molecular clocks help track evolutionary time
New information continues to revise our understanding of the tree of life

Phylogenies show evolutionary relationships
The two-part scientific name of a species is called a
binomial
The first part of the name is the
genus

The second part, called the specific epithet, is unique for each species within the genus
The first letter of the genus is capitalized, and the entire species name is italicized
Both parts together name the species (not the specific epithet alone)
Hirarchical Classification
Linnaeus introduced a system for grouping species in increasingly broad categories
The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
A taxonomic unit at any level of hierarchy is called a
taxon
The broader taxa are not comparable between lineages
For example, an order of snails has less genetic diversity than an order of mammals
Linnaean classification
Linking Classification
and Phylogeny
Systematists depict evolutionary relationships in branching
phylogenetic trees
The connection between classification and phylogeny
Linnaean classification and phylogeny can differ from each other
Systematists have proposed the
PhyloCode
, which recognizes only groups that include a common ancestor and all its descendents
A phylogenetic tree represents a hypothesis about evolutionary relationships
Each
branch point
represents the divergence of two species
Sister taxa
are groups that share an immediate common ancestor
Phylogenies are inferred from morphological and molecular data
To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms
Shared characters are used to construct phylogenetic trees
Once homologous characters have been identified, they can be used to infer a phylogeny
An organism's evolutionary history is documented in its genome
Comparing nucleic acids or other molecules to infer relatedness is a valuable approach for tracing organisms’ evolutionary history
DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago
mtDNA evolves rapidly and can be used to explore recent evolutionary events
Molecular clocks help track evolutionary time
To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time
Binomial Nomenclature
In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
Two key features of his system remain useful today: two-part names for species and hierarchical classification
What We Can and Cannot Learn from phylogenetic Trees
Phylogenetic trees show patterns of descent, not phenotypic similarity
Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage
It should not be assumed that a taxon evolved from the taxon next to it
A
rooted tree
includes a branch to represent the last common ancestor of all taxa in the tree
A
basal taxon
diverges early in the history of a group and originates near the common ancestor of the group
A
polytomy
is a branch from which more than two groups emerge
How to read a phylogenetic tree
Applying Phylogenies
Phylogeny provides important information about similar characteristics in closely related species
A phylogeny was used to identify the species of whale from which “whale meat” originated
Morphological and Molecular Homologies
Phenotypic and genetic similarities due to shared ancestry are called
homologies
Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences
Sorting Homology from Analogy
When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or
analogy
Homology is similarity due to shared ancestry
Analogy is similarity due to convergent evolution
Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages
Convergent evolution of analogous burrowing characteristics
Bat and bird wings are homologous as forelimbs, but analogous as functional wings
Analogous structures or molecular sequences that evolved independently are also called
homoplasies
Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity
The more complex two similar structures are, the more likely it is that they are homologous
Evaluating Molecular Homologies
Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms
Aligning segments of DNA
It is also important to distinguish homology from analogy in molecular similarities
Mathematical tools help to identify molecular homoplasies, or coincidences
Molecular systematics
uses DNA and other molecular data to determine evolutionary relationships
Molecular homology
Cladistics
Cladistics
groups organisms by common descent
A
clade
is a group of species that includes an ancestral species and all its descendants
Clades can be nested in larger clades, but not all groupings of organisms qualify as clades
A valid clade is
monophyletic
, signifying that it consists of the ancestor species and all its descendants
Monophyletic, paraphyletic, and polyphyletic groups
A
paraphyletic
grouping consists of an ancestral species and some, but not all, of the descendants
A
polyphyletic
grouping consists of various species with different ancestors
Shared Ancestral and Shared Derived Characters
In comparison with its ancestor, an organism has both shared and different characteristics
A
shared ancestral character
is a character that originated in an ancestor of the taxon
A
shared derived character
is an evolutionary novelty unique to a particular clade
A character can be both ancestral and derived, depending on the context
Inferring Phylogenies Using Derived Characters
When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared
constructing a phylogenetic tree
An
outgroup
is a species or group of species that is closely related to the
ingroup
, the various species being studied
The outgroup is a group that has diverged before the ingroup
Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics
Characters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor
Phylogenetic Trees with Proportional Branch Lengths
In some trees, the length of a branch can reflect the 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
Maximum Parsimony and Maximum Likelihood
Systematists can never be sure of finding the best tree in a large data set
They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood
Maximum parsimony
assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely
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
Tree with different likelihoods
Computer programs are used to search for trees that are parsimonious and likely
Applying parsimony to a Problem in Molecular Systemics
Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendents
For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs
Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding
These characteristics likely evolved in a common ancestor and were shared by all of its descendents, including dinosaurs
The fossil record supports nest building and brooding in dinosaurs
Biological Diversity
Endless Forms Most Beautiful

Gene Duplications and Gene Families
Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes
Repeated gene duplications result in gene families
Like homologous genes, duplicated genes can be traced to a common ancestor
Orthologous genes
are found in a single copy in the genome and are homologous between species
They can diverge only after speciation occurs
Two types of homologous genes
Paralogous genes
result from gene duplication, so are found in more than one copy in the genome
They can diverge within the clade that carries them and often evolve new functions
Genome Evolution
Orthologous genes are widespread and extend across many widely varied species
For example, humans and mice diverged about 65 million years ago, and 99% of our genes are orthologous
Gene number and the complexity of an organism are not strongly linked
For example, humans have only four times as many genes as yeast, a single-celled eukaryote

Genes in complex organisms appear to be very versatile, and each gene can perform many functions
Molecular Clocks
A
molecular clock
uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change
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
Molecular clocks are calibrated against branches whose dates are known from the fossil record
Individual genes vary in how clocklike they are
A molecular clock for mammals
Neutral theory
states that much evolutionary change in genes and proteins has no effect on fitness and is not influenced by natural selection
It states that the rate of molecular change in these genes and proteins should be regular like a clock
Neutral Theory
The molecular clock does not run as smoothly as neutral theory predicts
Irregularities result from natural selection in which some DNA changes are favored over others
Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty
The use of multiple genes may improve estimates
Problems with Molecular Clocks
Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
HIV spread to humans more than once
Comparison of HIV samples shows that the virus evolved in a very clocklike way
Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s
Dating the origin of HIV-1 M with a molecular clock
From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals
Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia
More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya
The three-domain system is supported by data from many sequenced Classification Schemes genomes
Three domains of Life
A Simple Tree of All Life
The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria
The tree of life is based largely on rRNA genes, as these have evolved slowly
There have been substantial interchanges of genes between organisms in different domains
Horizontal gene transfer
is the movement of genes from one genome to another
Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms
Horizontal gene transfer complicates efforts to build a tree of life
The role of horizontal gene transfer in the history of life
Is the Tree of Life Really a Ring?
Some researchers suggest that eukaryotes arose as an fusion between a bacterium and archaean
If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life
A ring of life
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