PHYOGENY & THE TREE OF LIFE

Campbell and Reece, Chapter 26

definitions

The evolutionary history of a species or group of species

Discipline focused on classifying organisms & determining their evolutionary relationships

Phylogeny Systematics

Taxonomyhow organisms are classified and named

each step called a taxon (plural: taxa)

BINOMIAL NOMENCLATURE

Man’s Genus species: Homo sapiens

used to avoid ambiguity

the Latin scientific name for each individual species

is the Genus species portion of taxonomy

3 DOMAINS

DOMAIN ARCHAEA Prokaryotes many live in Earth’s extreme environments

as molecularly close to eukaryotes as Domain Bacteria

includes multiple kingdoms

(notice position of domain Archaea)

Domain Archaea

methanogen thermophile

Domain Bacteria

Prokaryotic very diverse group use every major mode of nutrition &

metabolism beneficial: photoautotrophs,

alcoholic fermentation, Vit K production

pathologic: strep throat, flesh-eating disease, ulcers, Rheumatic fever

Domain Bacteria

Gram Positive BacteriaStretococcus

Gram Negative BacteriaLegionella pneumophilia

Domain Bacteria

Spirochetes

Domain Eukarya

Eukaryotic cells more complex, become specialized able to form multicellular organisms greatest diversity

Domain Eukarya

Plants Fungi

Domain Eukarya

Animal Protozoa

Domain Eukarya

Algae Cells Algae

Linnean Classification

PHYLOGENETIC TREES

show the evolutionary history of a group of organisms

represented by a branching diagram

each branch point represents the divergence of 2 evolutionary lineages from a common ancestor

Phylogenetic Trees

Branch Point

sister taxa

basal taxa

What you can learn

What you cannot learn

patterns of descent

common ancestors

does not show phenotypic similarity

cannot tell ages of species based on where branches are in the “tree”

Sister taxa did not evolve from each other; they have a common ancestor (that could be extinct)

Phylogenetic Trees

Uses of Phylogenetic Tree

1. If “close” relatives found they could be source of beneficial alleles that could be transferred to hardier taxa via genetic engineering

2. Using DNA samples are now able to differentiate legal species from illegal species of whale, tuna

Phylogenies are inferred from morphological & molecular data

Homology: similarity in characteristics resulting from a shared ancestry

Homologous Chromosomes in same species When

chromosomes duplicate in S Phase of Cell Cycle see genes in same loci of each sister chromatid

Homologous Chromosomes across Species with Common Ancestor

Genes or certain DNA sequences can also be homologous if they descended from sequences carried by a common ancestor

Organisms that share very similar morphologies or DNA sequences are likely to be more closely related than organisms with vastly different structures

There are examples of organisms that look very different but have very similar DNA sequences because species underwent adaptive radiation.

Homology vs. Analogy

Analogy is similarity due to convergent evolution: occurs when similar environmental pressures & natural selection produce similar (analogous) adaptations even though organisms have different ancestors.

homoplasies: analogous structures that arose independently (Greek: to mold in same way) Examples:

bird & bat wing: their common ancestor did not fly

The more complex the structure found in 2 species the more likely it is that they have a shared ancestor

Molecular Evidence of Evolutionary Relationships

DNA sequence similarities have been documented among prokaryotes & eukaryotes: (comparative genomics)

High degree of sequence similarity noted in some eukaryotic nuclear genes to Archaea & mitochondrial genes are similar to Bacteria

Using DNA to map an organism’s evolutionary history

The more recently 2 species have branched from a common ancestor, the more similar their DNA sequences should be

The longer ago 2 species have been on separate evolutionary paths, the more their DNA should have diverged

Different genes evolve at different rates

changes slowly useful for

investigating relationships between taxa that diverged hundreds of millions of yrs ago

evolves rapidly useful to

investigate more recent evolutionary events

Nuclear DNA Mitochondrial DNA

Eukaryotic genes consist of numerous coding regions (exons) that are separated by noncoding regions (introns)

Both are transcribed into pre-mRNA and then intron sequences are removed

In humans 90% of the exons are homologous to exons found in Drosophila & Caenorhabditis (nematode worms

Puffer Fish is vertebrate with smallest known genome (1/7th human genome) & yet has all exons present in humans

In chromosomes “homologous” means sequences are so similar that they are not likely due to chance so are considered the result of common ancestry

Duplication in human genome

both of genes & chromosome segments

Based on these duplications & new combinations of exons it seems that

1. the vertebrate evolution has required very few new proteins

2. evolutionary change involves making new genes by rearranging functional domains into novel combinations (called “exon shuffling”)

Exon Shuffling

Important source of genetic variation (in addition to mutations & crossing over)

Still investigating mechanism

Homologous Genes

60% of human genes that encode proteins are homologous to genes from other organisms

The high degree of conservation of both genes & exons among widely diverse organisms from all 3 Domains is strong evidence for their common ancestry

Nonfunctional Sequences

Another bit of strong evidence for relatedness among diverse organisms is the similarity in DNA sequences that have no apparent function.

One category of these are pseudogenes

Pseudogenes 2 kinds:

1. arises from DNA replication mutations STOP codons in one of duplicates; other no mutation

2. Processed Pseudogenes:

arise during transcription or translation: lack a promoter sequence so cannot be transcribed

To date, 2909 pseudogenes in human genome

Other functionless DNA

Long Interspersed Nucleotide Element

Families: 1,2,3 Are

retrotransposons

Short Interspersed Nucleotide Element

Also 3 families in humans

Specific LINEs & SINEs found only in cloven-hooved mammals & whales

LINEs SINEs

Retroviruses

RNA virus Infects cell and turns its single

strand double strand which inserts into host genome

RetrovirusRetrotransposon

Retrovirus inserts self into host genome but somewhere along the way genes for capsids lost

If LINEs in different species are homologous it is considered to be strong evidence that these 2 species share a common ancestor where that particular LINE first became established

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Review:

Phylogeny can be inferred from –the fossil record, –morphological homologies, and –molecular homologies

Phylogenetic trees are used to depict hypotheses about the evolutionary history of a species

Shared characters are used to construct phylogenetic trees Shared ancestral characters group

organisms into clades Shared derived characters distinguish

clades & form branching points in the tree of life

Shared Characteristics are used to Construct Phylogenetic Trees

Cladistics: an approach to systematics in which organisms are placed into groups based primarily on common descent

Clades: groups organisms are placed in 1 clade will include ancestor & all its

descendants 3 types:

1. Monophyletic Group

equivalent to a clade

ancestral species & all its descendants

2. Paraphyletic Group

consists of an ancestral species & some of its descendants

3. Polyphyletic Group

Some members of this group will have different ancestors

Name That Group:

A character that originated in an ancestor of the taxon

An evolutionary novelty unique to a clade.

Shared Ancestral Character

Shared Derived Character

Shared Ancestral Character

Shared Derived Character

Making a Phylogenetic Tree

SHOULD BE POSSIBLE TO DETERMINE THE CLADE ANY SHARED DERIVED CHARACTER 1ST APPEARED

Construct a CHARACTER TABLE: 1 axis has list of organisms, 1 has

characters

CHARACTER TABLE

FROG IGUANA DUCK-BILLED PLATYPUS

KANGAROO BEAVER

AMNION

HAIR, MAMMARY GLANDS

GESTATION

LONG GESTATION

Important step in cladistics is the comparison of the Ingroup: the taxa whose phylogeny is

being investigated Outgroup: the taxon that diverged

before the lineage leading to the members of the ingroup

Use to identify the derived characters that define the branch points in the phylogeny of the ingroup

PHYLOGENETIC TREES

WHEN CONSTRUCTING A PHYLOGENETIC TREE, SCIENTISTS USE PARSIMONY, LOOKING FOR THE SIMPLEST EXPLANATION FOR OBSERVED PHENOMENA

SYSTEMATISTS USE MANY KINDS OF EVIDENCE, BUT EVEN THE BEST TREE REPRESENTS ONLY THE MOST LIKELY HYPOTHESIS

Shared characters are used to construct phylogenetic trees

The phylogenetic tree of reptiles shows that crocodiians are the closest living relatives of birds

Crocodiles & Birds share: 4-chambered heart “singing” to defend territories Parental care of eggs within nests

Phylogenetic Trees with Proportional Branch Lengths

branch lengths are proportional to the amount of genetic change in each lineage

So the longer the line the more genetic changes have occurred

Principle of Maximum Parsimony

1st investigate the simplest explanation that is consistent with the facts

aka “Occum’s Razor”

For phylogenies based on DNA: the most parsimonious tree requires the fewest base changes

Principle of Maximum Likelihood

Given certain probability rules about how DNA sequences change over time, a tree can be made that reflects the most likely sequence of evolutionary events

Currently using computer programs to search for trees that are parsimonious & have a high probability

Phylogenetic Trees as Hypotheses

Scientists can make & test predictions based on the assumption that a phylogeny (the hypothesis) can be supported or not.

Prediction: features shared by 2 groups of closely related organisms are also present in their common ancestor & all of its descendants

An organism’s evolutionary history is documented in its genome: 2 Types of Homologous Genes

Exact copies found in different species

Origin: common ancestor

Homology result of gene duplication: multiple copies of a gene in same species all came from same gene

Orthologous Genes Paralogous Genes

Genome Evolution

By investigating entire genomes of different species see 2 patterns:

1. Lineages that diverged long ago can share orthologous genes

2. # of genes a given species has does not seem to increase thru duplication at same rate as increase in phenotype changes

Molecular Clocks

is a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes & other regions of genomes appear to evolve at constant rates.

is based on assumption that the # of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from their common ancestor (known as divergence time)

Molecular Clocks

Calibration of a molecular clock is done by graphing the # of genetic differences against the dates of evolutionary branch points that are known from fossil record

Finding the average rates of genetic change from such graphs can be used to estimate dates of events that cannot be discerned from fossil record

Genes that appear to follow molecular clock are really only acting in statistically average rate of change

Of course parts of the genome appear to have evolved in irregular bursts

Some genes seem to have different rates of change in different organisms

Some genes evolve a million times faster than others

Neutral Theory

States much of the evolutionary change in genes & proteins has no effect on fitness & therefore is not influenced by natural selection

Many new genes are harmful so are quickly removed

Differences in the clock rate for different genes are a function of how important a gene is

Problems with Molecular Clocks

Natural selection favors some DNA changes

Many scientists remain skeptical about:

1. the “Neutral Theory”, 2. about using the molecular clock

beyond time span documented by fossil record (about 550 million years)

Dating the Origin of HIV with a Molecular Clock

HIV is descended from viruses that infected chimps & other primates but did not cause same AIDS-like illness

When did this happen?

HIV Strains

Multiple strains have infected humans

Multiple strains implies multiple origins

Most widespread strain in HIV-M

Using molecular clock best guess is HIV-M strain 1st spread to humans in the 1930’s

Is the tree of Life Really a Ring of Life?

there has been substantial movements of genes between organisms in the 3 domains

mechanism: horizontal gene transfer: plasmids, viral infection, maybe even fusion of organisms

Ring of Life

some scientists think horizontal gene transfer so common that early history of life should be represented as a ring with 3 domains emerging from the ring