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

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

Linking Classification and Phylogeny Systematists use phylogenetic trees These diagrams are genealogies of probable evolutionary groups based on relationships of taxonomic groups

A phylogenetic tree represents a hypothesis about evolutionary relationships Each branch point represents the divergence of two species

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

Concept : Phylogenies show evolutionary relationships Taxonomy is the ordered division and naming of organisms

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

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

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

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

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

Lizards and snakes Crocodilians Ornithischian dinosaurs Common Fig. 26-16 Lizards and snakes Crocodilians Ornithischian dinosaurs Common ancestor of crocodilians, dinosaurs, and birds Saurischian dinosaurs lFigure 26.16 A phylogenetic tree of birds and their close relatives Birds

Monophyletic – grouping consists of a single ancestor that gave rise gave rise to all descendents ( single tribe ) Ideal example for systematics

(a) Monophyletic group (clade) Fig. 26-10a A B Group I C D E F Figure 26.10a Monophyletic, paraphyletic, and polyphyletic groups G (a) Monophyletic group (clade)

A polyphyletic grouping consists of various species that lack a common ancestor Do not reflect evolutionary history

(b) Polyphyletic group Fig. 26-10c A B C D Group II E F Figure 26.10c Monophyletic, paraphyletic, and polyphyletic groups G (b) Polyphyletic group

A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants Do not reflect evolutionary history

(c) Paraphyletic group Fig. 26-10b A B C D Group III E F Figure 26.10b Monophyletic, paraphyletic, and polyphyletic groups G (c) Paraphyletic group

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

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

Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

Shared characters are used to construct phylogenetic trees Once homologous characters have been identified, they can be used to infer a phylogeny

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

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

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

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

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

Molecular clocks are calibrated against branches whose dates are known from the fossil record

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

Index of base changes between HIV sequences Fig. 26-20 0.20 0.15 Computer model of HIV Index of base changes between HIV sequences 0.10 Range Figure 26.20 Dating the origin of HIV-1 M with a molecular clock 0.05 1900 1920 1940 1960 1980 2000 Year

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)

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

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

A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

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

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

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

Amniotic (shelled) egg 1 1 Fig. 26-11a 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 26.11 Constructing a phylogenetic tree Amniotic (shelled) egg 1 1 Hair 1 (a) Character table

Vertebral column Hinged jaws Four walking legs Amniotic egg Lancelet Fig. 26-11b Lancelet (outgroup) Lamprey Tuna Vertebral column Salamander Hinged jaws Figure 26.11 Constructing a phylogenetic tree Turtle Four walking legs Amniotic egg Leopard Hair (b) Phylogenetic tree

Computer programs are used to search for trees that are parsimonious and likely

Three phylogenetic hypotheses: I I III Fig. 26-15-1 Species I Species II Species III Three phylogenetic hypotheses: Figure 26.15 Applying parsimony to a problem in molecular systematics I I III II III II III II I

Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II Fig. 26-15-2 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 26.15 Applying parsimony to a problem in molecular systematics

Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II Fig. 26-15-3 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 26.15 Applying parsimony to a problem in molecular systematics

Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II Fig. 26-15-4 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 26.15 Applying parsimony to a problem in molecular systematics I I III II III II III II I 6 events 7 events 7 events

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.

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

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

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 26.21 The three domains of life Spirochetes Halophiles Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria BACTERIA Methanobacterium Cyanobacteria ARCHAEA (Plastids, including chloroplasts)

BACTERIA Green nonsulfur bacteria (Mitochondrion) Spirochetes Fig. 26-21a Green nonsulfur bacteria (Mitochondrion) Spirochetes Chlamydia COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria Figure 26.21 The three domains of life BACTERIA Cyanobacteria (Plastids, including chloroplasts)

ARCHAEA Sulfolobus Thermophiles Halophiles Methanobacterium Fig. 26-21b Sulfolobus Thermophiles Halophiles Figure 26.21 The three domains of life Methanobacterium ARCHAEA

EUKARYA Dinoflagellates Land plants Forams Ciliates Red algae Amoebas Fig. 26-21c EUKARYA Land plants Dinoflagellates Green algae Forams Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Figure 26.21 The three domains of life Fungi

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 complicates efforts to build a tree of life

Bacteria Eukarya Archaea 4 3 2 1 Billions of years ago Fig. 26-22 Figure 26.22 The role of horizontal gene transfer in the history of life 4 3 2 1 Billions of years ago

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

Fig. 26-23 Eukarya Bacteria Archaea Figure 26.23 A ring of life

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