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Overview: Investigating the Tree of Life
The discipline of systematics classifies organisms and determines their evolutionary relationships (phylogeny) and is the study of biodiversity Systematists use fossil, molecular, and genetic data to infer evolutionary relationships Phylogeny is the evolutionary history of a species or group of related species
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Phylogenies are inferred from morphological and molecular data
To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences
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Linking Classification and Phylogeny
Systematists use phylogenetic trees These diagrams are genealogies of probable evolutionary groups based on relationships of taxonomic groups
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A phylogenetic tree represents a hypothesis about evolutionary relationships
Each branch point represents the divergence of two species
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What We Can and Cannot Learn from Phylogenetic Trees
Phylogenetic trees do show patterns of descent Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage It shouldn’t be assumed that a taxon evolved from the taxon next to it
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Concept : Phylogenies show evolutionary relationships
Taxonomy is the ordered division and naming of organisms
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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: binomial nomenclature: two-part names for species and descending categories -hierarchical classification, taxons
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The two-part scientific name of a species is called a binomial
The first part of the name is the genus The second part, 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
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Hierarchical Classification
Linnaeus introduced a system for grouping species in increasingly broad categories The taxonomic groups in descending categories domain, kingdom, phylum, class, order, family, genus, and species A taxonomic unit at any level of hierarchy is called a taxon
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Figure 26.3 Hierarchical classification
Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Figure 26.3 Hierarchical classification Phylum: Chordata Kingdom: Animalia Bacteria Domain: Eukarya Archaea
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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
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Lizards and snakes Crocodilians Ornithischian dinosaurs Common
Fig Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs lFigure A phylogenetic tree of birds and their close relatives Birds
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Monophyletic – grouping consists of a single ancestor that gave rise gave rise to all descendents ( single tribe ) Ideal example for systematics
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(a) Monophyletic group (clade)
Fig a A B Group I C D E F Figure 26.10a Monophyletic, paraphyletic, and polyphyletic groups G (a) Monophyletic group (clade)
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A polyphyletic grouping consists of various species that lack a common ancestor
Do not reflect evolutionary history
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(b) Polyphyletic group
Fig c A B C D Group II E F Figure 26.10c Monophyletic, paraphyletic, and polyphyletic groups G (b) Polyphyletic group
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A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants
Do not reflect evolutionary history
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(c) Paraphyletic group
Fig b A B C D Group III E F Figure 26.10b Monophyletic, paraphyletic, and polyphyletic groups G (c) Paraphyletic group
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Sorting Homology from Analogy
When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology same structure different function, is similarity due to shared ancestry ex- bat skeleton to bird skeleton Analogy structure from a different ancestor with similar function, is similarity due to convergent evolution ex bat wing analogous to bird wing
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Fig. 26-7 Figure 26.7 Convergent evolution of analogous burrowing characteristics Australian mole, American mole have different internal anatomy, physiology, reproductive systems ex marsupial vs placental yes they have a common ancestor 140 million years ago but analogous characters developed in these lineages to adapt similar life styles
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Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages
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Shared characters are used to construct phylogenetic trees
Once homologous characters have been identified, they can be used to infer a phylogeny
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Molecular Support An organism’s evolutionary history is documented in its genome
Comparing nucleic acids or other molecules to infer relatedness is a valuable tool 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
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Tools of the trade Nucleic Acids
DNA hybridization measures a closely related species by the tightness between DNA H bonds Ex- found a giant panda is a bear a raccoon is a lesser panda Restriction maps are used to compare mitochondrial DNA because it mutates 10X faster than the genome Ex – used to study Native American groups DNA sequence of actual nucleotides analysis helps construct phylogenic trees
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Proteins Compare amino acid sequences
Hemoglobin c and cytochrome c are ancient proteins in all aerobic species Ex- humans compare to a chimp identical aa, dog differs by 13 aa However only 2% of the genome codes for protein
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Concept 26.5: 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
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Molecular Clocks A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change Valid if mutation rates are constant
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Molecular clocks are calibrated against branches whose dates are known from the fossil record
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Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates Comparison of HIV samples throughout the epidemic 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
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Index of base changes between HIV sequences
Fig 0.20 0.15 Computer model of HIV Index of base changes between HIV sequences 0.10 Range Figure Dating the origin of HIV-1 M with a molecular clock 0.05 1900 1920 1940 1960 1980 2000 Year
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Difficulties with Molecular Clocks
The molecular clock does not run as smoothly as neutral theory predicts Neutral evolution means that mutation rates are constant Adaptation doesn’t fit into this idea Irregularities result from natural selection in which some DNA changes are favored over others Working with DNA has it problems (2 in notes)
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Science of Systematics
Two new approaches Phenetics and Cladistics Phenetics – bases taxonomy difference on measurable similarities and differences Compares anatomical characteristics Doesn’t sort out homology from analogy Phenetics contends that if enough phenotypes are examined homology will prevail
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Cladistics Cladistics phylogenic systematics, groups organisms by common descent A clade is a group of species that includes an ancestral species and all its descendants
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A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants
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An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics Outgroup is clearly not related
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Maximum parsimony assumes that the tree that requires the fewest evolutionary changes (appearances of shared derived characters) is the most likely Synamorphies -appearances of shared derived characters
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Shared Ancestral and Shared Derived Characters
In comparison with its ancestor, an organism has both shared and different characteristics
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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
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Inferring Phylogenies Using Derived Characters
When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared
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Amniotic (shelled) egg 1 1
Fig a TAXA (outgroup) Lancelet Salamander Lamprey Leopard Tuna Turtle Vertebral column (backbone) 1 1 1 1 1 Hinged jaws 1 1 1 1 CHARACTERS Four walking legs 1 1 1 Figure Constructing a phylogenetic tree Amniotic (shelled) egg 1 1 Hair 1 (a) Character table
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Vertebral column Hinged jaws Four walking legs Amniotic egg Lancelet
Fig b Lancelet (outgroup) Lamprey Tuna Vertebral column Salamander Hinged jaws Figure Constructing a phylogenetic tree Turtle Four walking legs Amniotic egg Leopard Hair (b) Phylogenetic tree
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Computer programs are used to search for trees that are parsimonious and likely
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Three phylogenetic hypotheses: I I III
Fig Species I Species II Species III Three phylogenetic hypotheses: Figure Applying parsimony to a problem in molecular systematics I I III II III II III II I
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Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig Site 1 2 3 4 1/C Species I C T A T I I III 1/C Species II C T T C II III II 1/C Species III A G A C III II I 1/C 1/C Ancestral sequence A G T T Figure Applying parsimony to a problem in molecular systematics
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Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig Site 1 2 3 4 1/C Species I C T A T I I III 1/C Species II C T T C II III II 1/C Species III A G A C III II I 1/C 1/C Ancestral sequence A G T T 3/A 2/T 3/A I I III 2/T 3/A 4/C II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A Figure Applying parsimony to a problem in molecular systematics
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Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig Site 1 2 3 4 1/C Species I C T A T I I III 1/C Species II C T T C II III II 1/C Species III A G A C III II I 1/C 1/C Ancestral sequence A G T T 3/A 2/T 3/A I I III 2/T 3/A 4/C II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A Figure Applying parsimony to a problem in molecular systematics I I III II III II III II I 6 events 7 events 7 events
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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 Phylogeny gained strength with cladistics using morphology, biochemistry, paleontology and comparative biology.
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Concept 26.6: 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
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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 genomes Animation: Classification Schemes
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EUKARYA BACTERIA ARCHAEA Fig. 26-21 Land plants Dinoflagellates
Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Fungi Sulfolobus Green nonsulfur bacteria Thermophiles (Mitochondrion) Figure The three domains of life Spirochetes Halophiles Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria BACTERIA Methanobacterium Cyanobacteria ARCHAEA (Plastids, including chloroplasts)
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BACTERIA Green nonsulfur bacteria (Mitochondrion) Spirochetes
Fig a Green nonsulfur bacteria (Mitochondrion) Spirochetes Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria Figure The three domains of life BACTERIA Cyanobacteria (Plastids, including chloroplasts)
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ARCHAEA Sulfolobus Thermophiles Halophiles Methanobacterium
Fig b Sulfolobus Thermophiles Halophiles Figure The three domains of life Methanobacterium ARCHAEA
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EUKARYA Dinoflagellates Land plants Forams Ciliates Red algae Amoebas
Fig c EUKARYA Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Figure The three domains of life Fungi
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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
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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 complicates efforts to build a tree of life
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Bacteria Eukarya Archaea 4 3 2 1 Billions of years ago Fig. 26-22
Figure The role of horizontal gene transfer in the history of life 4 3 2 1 Billions of years ago
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Is the Tree of Life Really a Ring?
Some researchers suggest that eukaryotes arose as an endosymbiosis 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
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Fig Eukarya Bacteria Archaea Figure A ring of life
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Monophyletic group A A A B B B C C C D D D E E E F F F G G G
Fig. 26-UN3 Monophyletic group A A A B B B C C C D D D E E E F F F G G G Paraphyletic group Polyphyletic group
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