Chapter 26: Phylogeny and the Tree of Life
1. Key Concepts Pertaining to Phylogeny 2. Determining Phylogenies 3. Evolutionary History Revealed in Genomes 1. Key Concepts Pertaining to Phylogeny Cell PHYLOGENY – the evolutionary history division error Species: of species or group Panthera pardus Genus: TAXONOMY – system by which Panthera organisms are named and classified Family: Felidae • based on morphological and molecular Order: (DNA, proteins) data Carnivora
• not necessarily based on evolutionary Class: history, though it can be Mammalia Phylum: TAXONOMIC HIERARCHY – series of nested Chordata groupings used to categorize organisms Domain: Kingdom: Bacteria Animalia Domain: • Archaea developed by Carolus Linnaeus of Sweden Domain: th in the mid-18 century and still used today Eukarya TAXON – a specific category or level in the taxonomic hierarchy (e.g., “class” or “family”)
BINOMIAL NOMENCLATURE – how organisms are named
• genus & specific epithet (e.g., Homo sapiens, Escherichia coli, Tyrannosaurus rex)
o both terms are “latinized” and written in italics
o the specific epithet is an adjective and is not capitalized
o the genus is a noun and is capitalized
• also developed by Carolus Linnaeus
Order Family Genus Species Phylogenetic Trees
Panthera Felidae Panthera pardus A PHYLOGENITIC TREE is a branching (leopard)
Taxidea diagram representing a hypothesis Carnivora
Mustelidae Taxidea of evolutionary relationships taxus (American • each branch point indicates
Lutra badger) Lutra lutra divergence from a common ancestor (European 1 otter) • shows patterns of descent, NOT morphological similarity
Canis Canidae
Canis latrans 2 (coyote) SISTER TAXA – groups that share an Canis immediate common ancestor lupus (e.g., wolf and coyote) (gray wolf) BASAL TAXON – earliest Branch point: lineage to diverge where lineages diverge Taxon A from the remainder of a 3 Taxon B group Sister 4 taxa Taxon C 2 ROOTED – if all taxa in a Taxon D group have the same ANCESTRAL 5 Taxon E common ancestor they 1 LINEAGE are said to be “rooted” Taxon F Basal Taxon G POLYTOMY – more than taxon two lineages diverge from This branch point This branch point forms represents the a polytomy: an a single branch point (due common ancestor of unresolved pattern of to uncertain divergence) taxa A–G. divergence. Homology vs Analogy
HOMOLOGY – similarities due to common ancestry • Molecular Homology – similarity in DNA, protein sequences • Morphological Homology – skeletal & fossil similarities
ANALOGY – morphological similarity due to convergent evolution (e.g., bird vs bat wings) Australian marsupial “mole”
• analogous structures that arise independently are referred to as homoplasies North American eutherian mole 2. Determining Phylogenies All available information, molecular, morphological and physiological, are used in determining phylogenetic relationships. Geckos
ANCESTRAL No limbs LIZARD Snakes (with limbs)
Iguanas
Monitor lizard When molecular and morphological data contradict, Eastern glass lizard molecular data takes precedence. No limbs Cell 1 C C A T C A G A G T C C division Using DNA Homology to 2 C C A T C AerrorG A G T C C Construct Phylogenies
Deletion Sequences in non-conserved regions of DNA (i.e., 1 C C A T C A G A G T C C sequences not subject to Natural Selection) are 2 C C A T C A G A G T C C aligned since they are presumably free to mutate G T A Insertion o computers are used to find the best alignment accounting for deletions, insertions, etc
1 C C A T C A A G T C C The degree of homology in similar regions can 2 C C A T G T A C A G A G T C C be used to construct a phylogeny o greater homology = more recent common ancestor
1 C C A T C A A G T C C NOTE: Random chance would result in 25% homology 2 C C A T G T A C A G A G T C C between sequences, so true homology must be >25%. Using Cladistics to Construct Phylogenies
CLADE – an ancestral species and all descendants (a) Monophyletic group (clade) • all descendants have a single common ancestor • all members of clade have unique shared A derived characters • clades are a monophyletic groups 1 B Group I
C SHARED ANCESTRAL CHARACTERS (SAC) D • characters that originated before the clade E
SHARED DERIVED CHARACTERS (SDC) F • characters found only within the clade G PARAPHYLETIC group – consists Paraphyletic group Common of a single common ancestor and ancestor of some (not all) of its descendants even-toed Other even-toed ungulates ungulates (b) Paraphyletic group (c) Polyphyletic group Hippopotamuses A A
B B Group III Cetaceans C C 3 D D Seals E Group II E 2 F F Bears G G POLYPHYLETIC group – consists of Other organisms with more than 1 carnivores common ancestor Polyphyletic group Constructing phylogenies based on shared derived characters (SDCs):
• start with an outgroup (group that diverged before the lineage of interest) and construct the phylogeny based on multiple SDCs • a character table can be used to identify successive branch points, each being due to a SDC found in successively fewer members of the phylogeny
TAXA Lancelet (outgroup)
Lamprey
Lancelet (outgroup) Lamprey Bass Frog Turtle Leopard Vertebral column Bass (backbone) 0 1 1 1 1 1 Vertebral Hinged jaws 0 0 1 1 1 1 column Frog Hinged jaws 4 walking legs 0 0 0 1 1 1 Four walking legs Turtle
CHARACTERS Amnion 0 0 0 0 1 1
Hair 0 0 0 0 0 1 Amnion Leopard Hair (a) Character table (b) Phylogenetic tree Using the Principle of “Maximum Parsimony” to Construct Phylogenies
A phylogeny should be constructed based on maximum parsimony, i.e., the simplest solution that is consistent with the facts.
• this is the principle of “Occam’s Razor” in which the hypothesis with the fewest assumptions is favored
Applying the principle of maximum likelihood to phylogenies based on DNA sequences:
• the hypothesis that requires the least number of mutational events is favored Technique 3 1/C 1/C I I III II III II 1/C III II I 1/C 1/C Species I Species II Species III
Three phylogenetic hypotheses: 3/A 2/T 3/A 1 4 I I III I I III 2/T 3/A 4/C II III II II III II 4/C 4/C 2/T III II I III II I 3/A 4/C 2/T 4/C 2/T 3/A
Site 2 1 2 3 4 Results I I III Species I C T A T Species II C T T C II III II Species III A G A C III II I 6 events 7 events 7 events Ancestral A G T T sequence Phylogenetic Bracketing
Phylogenetic bracketing is the process of inferring unknown characters in extinct species based on the principle of maximum parsimony:
• in this example the shared characters of crocodiles and Lizards and snakes birds are also attributed to 2 groups of dinosaurs Crocodilians
• this example of phylogenetic bracketing exhibits maximum Ornithischian Common dinosaurs parsimony since the simplest ancestor of explanation for these shared crocodilians, Saurischian dinosaurs, characters would be a single dinosaurs and birds common ancestor from which Birds all 4 groups evolved Evidence Supporting a Case of Phylogenetic Bracketing
This fossil supports a prediction based on phylogenetic bracketing – that Front limb dinosaurs, like crocodiles and birds, Hind engaged in brooding, the bodily limb warming of eggs.
Eggs
(a) Fossil remains of Oviraptor (b) Artist’s reconstruction of the and eggs dinosaur’s posture based on the fossil findings Phylogenetic Branch Lengths can be used to Indicate the Degree of Genetic Differences…
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse Phylogenetic Branches can also Indicate Time
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
CENO- PALEOZOIC MESOZOIC ZOIC 542 251 65.5 Present Millions of years ago 3. Evolutionary History Revealed in Genomes Orthologous vs Paralogous Genes ORTHOLOGOUS GENES – homologous genes in different species PARALOGOUS GENES – homology between different genes in the same species due to duplication Formation of orthologous genes: Formation of paralogous genes: a product of speciation within a species Ancestral gene Ancestral gene Gene families result from repeated Ancestral species Species C duplication of an original gene followed Speciation with Gene duplication and divergence divergence of gene by subsequent mutation.
Orthologous genes Paralogous genes Species A Species B Species C after many generations Molecular Clocks Certain genes or other regions of genomes tend to change (i.e., evolve) at a constant rate and thus serve as a molecular clock. For example, the number sequence differences (i.e., nucleotide substitutions) in orthologous genes can reveal: • the amount of time that has passed 90 since 2 species diverged from a common ancestor 60 • the amount of time that has passed since the gene was duplicated 30
Number of mutations of Number This is best determined with 0 neutral mutations (mutations that 0 30 60 90 120 are neither selected for or against). Divergence time (millions of years) Problems with Molecular Clocks
A molecular clock will not give accurate predictions if the rate of mutation is not constant which will be the case if:
• there is natural selection (i.e., a mutation is not neutral)
• changes in selective factors over time (i.e., under some conditions a mutation may be neutral and under other conditions it may not be)
• for these or other reasons the mutation rate may change over time
One can increase the number of genes and taxa analyzed as molecular clocks to dilute any inaccuracies associated with any particular gene, however the problems indicated above can never be entirely eliminated. Cell Euglenozoans Current Model of the division Forams error Diatoms Domain Domain Eukarya “Tree of Life” Ciliates Red algae Green algae • this model, as with previous models, Land plants will no doubt change over time as Amoebas Fungi more information pertaining to
Animals current and extinct species becomes Archaea Nanoarchaeotes Domain available Methanogens COMMON Thermophiles ANCESTOR Proteobacteria OF ALL LIFE • as new information becomes (Mitochondria)* Domain Bacteria available, we get closer and closer to Chlamydias Spirochetes the true evolutionary relationships Gram-positive bacteria among all species, both past and Cyanobacteria present (Chloroplasts)*