LECTURE 1: Phylogeny and Systematics

What is Phylogeny? the evolutionary history of a species Evolutionary biology is about both process and history A major goal of evolutionary biology is to reconstruct the history of life on earth To reconstruct phylogeny, scientists use SYSTEMATICS The study of biodiversity in an evolutionary context

How are Phylogenies Constructed? The Fossil Record Morphological similarities Homologous Structures (remember those?) Molecular similarities DNA Organisms with very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences

How can Scientists determine whether structure are Homologous or Analagous? HOMOLOGY is similarity due to SHARED ANCESTRY ANALOGY is similarity due to CONVERGENT EVOLUTION CONVERGENT EVOLUTION: two organisms develop similarities as they adapted to similar environmental challenges – not because they evolved from a common ancestor EXAMPLE: both birds and bats have adaptations that allow them to fly However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb than to a bird’s wing Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing

HOW DO THESE ORGANISMS DISPLAY EXAMPLES OF CONVERGENT EVOLUTION?

How would you compare the fins in these 2 organisms?

What are Homoplasies? Analogous structures or molecular sequences that evolved independently Example: the four-chambered heart of birds & mammals is analogous

What are Molecular Homologies? Systematists compare long stretches of DNA and even entire genomes to assess relationships between species If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous In closely related species, sequences may differ at only one or a few base sites Distantly related species may have many differences or sequences of different length

How is Phylogeny linked with Classification? Systematists explore phylogeny by examining various characteristics in living and fossil organisms They construct branching diagrams called PHYLOGENETIC TREES to depict their hypotheses about evolutionary relationships The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups

LE 25-9 Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Species Genus Panthera Mephitis Lutra Canis Family Felidae Mustelidae Canidae Order Carnivora 10

Each branch point represents the divergence of two species LE 25-UN497 Leopard Domestic cat Each branch point represents the divergence of two species Common ancestor Wolf Leopard Domestic cat “Deeper” branch points represent progressively greater amounts of divergence Common ancestor 11

LE 25-13 Drosophila Lancelet Amphibian Mouse Fish Bird Human Rat Cenozoic 65.5 Mesozoic 251 Paleozoic 542 Neoproterozoic Millions of years ago 12

What is Cladistics? classifying organisms based on RESEMBLANCES among clades Determining which similarities between species are relevant to grouping the species in a clade is a challenge It is especially important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy CLADISTICS enables us to identify the sequence of the evolution of derived characteristics

What is a Cladogram? depicts patterns of shared derived characteristics among taxa Synapomorphies the chronological sequence of branching during the evolutionary history of a set of organisms This chronology DOES NOT indicate the TIME of origin of the species that we are comparing, only the groups to which they belong A cladogram is NOT a phylogenetic tree To convert it to a phylogenetic tree, we need more information from sources such as the fossil record, which can indicate when and in which groups the characters first appeared

What is a Clade? THREE TYPES OF CLADES: MONOPHYLETIC PARAPHYLETIC a group of species that includes an ancestral species and all its descendants THREE TYPES OF CLADES: MONOPHYLETIC single ancestor that gives rise to all species in that taxon and to no species in any other taxon; legitimate cladogram PARAPHYLETIC members of a taxa are derived from 2 or more ancestral forms not common to all members; does not meet cladistic criterion POLYPHYLETIC lacks the common ancestor that would unite the species; does not meet cladistic criterion

Grouping 1 Monophyletic LE 25-10a Grouping 1 A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants Monophyletic 16

Grouping 2 Paraphyletic LE 25-10b Grouping 2 A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants Paraphyletic 17

Grouping 3 Polyphyletic LE 25-10c Grouping 3 A polyphyletic grouping consists of various species that lack a common ancestor Polyphyletic 18

How are Cladograms Constructed? In cladistic analysis, clades are defined by their evolutionary features (novelties) A CHARACTER any feature that a particular taxon possesses A SHARED DERIVED CHARACTER (SYNAPOMORPHIES) an evolutionary novelty unique to a particular clade A SHARED PRIMITIVE CHARACTER found not only in the clade being analyzed, but also in older clades Systematists must also sort through homologous features, or characters, to separate shared derived characters from shared primitive characters

SHARED DERIVED CHARACTERISTICS Need to differentiate between shared primitive characters and shared derived characters ANALOGIES All similar characters PRIMITIVE (ANCESTRAL) HOMOLOGIES DERIVED (UNIQUE TO A CLADE) 21

SHARED PRIMITIVE & SHARED DERIVED CHARACTERISTICS EXAMPLE: the presence of hair is a good character to distinguish the clade of mammals from other tetrapods. It is a shared derived character that uniquely identifies mammals However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals. Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates SHARED DERIVED CHARACTERS ARE USEFUL IN ESTABLISHING A PHYLOGENY, BUT SHARED PRIMITIVE CHARACTERS ARE NOT 22

How are Cladograms built Using Outgroups? OUTGROUP COMPARISON used to differentiate shared primitive characters from shared derived ones OUTGROUP a species or group of species that is closely related to the INGROUP (the various species being studied) ASSUMPTION: homologies shared by the outgroup and ingroup must be a primitive character that predate the divergence of both groups from a common ancestor

PERFORMING OUTGROUP COMPARISON What is the shared primitive characteristic? DOES NOT MEAN THAT TURTLES EVOLVED MORE RECENTLY THAN SALAMANDER 24

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BUILDING A CLADOGRAM 26

THE CHARACTER TABLE: 27

THE RESULT: 28

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AND SOMETIMES THE SIMPLEST EXPLANATION IS NOT THE BEST… Parsimony does not always work, nature does not always take the simplest course 30

Much of an organism’s evolutionary history is documented in its genome 31

What are Gene Duplications and Gene Families? increases the number of genes in the genome, providing more opportunities for evolutionary changes GENE FAMILIES groups of related genes within an organism’s genome Like homologous genes in different species, duplicated genes have a common genetic ancestor There are two types of homologous genes: ORTHOLOGOUS genes and PARALOGOUS genes 32

TWO REMARKABLE FACTS ABOUT GENE FAMILIES All living things share many biochemical and development pathways The number of genes seems not to have increased at the same rate as phenotypic complexity Humans have only five times as many genes as yeast, a simple unicellular eukaryote, although we have a large, complex brain and a body that contains more than 200 different types of tissues Many human genes are more versatile than yeast and can carry out a wide variety of tasks in various body tissues 33

What are Orthologous Genes? genes found in a single copy in the genome They can diverge only after speciation occurs i.e. The ß hemoglobin genes in humans and mice are orthologous Orthologous genes are widespread and can extend over enormous evolutionary distances Approximately 99% of the genes of humans and mice are demonstrably orthologous, and 50% of human genes are orthologous with those of yeast

What are Paralogous Genes? result from gene duplication, so they are found in more than one copy in the genome They can diverge within the clade that carries them, often adding new functions i.e. Olfactory receptor genes have undergone many gene duplications in vertebrates Humans and mice each have huge families of more than 1,000 of these paralogous genes

Ancestral gene Speciation Orthologous genes LE 25-17a Ancestral gene Speciation Orthologous genes 36

Ancestral gene Gene duplication Paralogous genes LE 25-17b Ancestral gene Gene duplication Paralogous genes 37

What are Molecular Clocks? The MOLECULAR CLOCK is a yardstick for measuring absolute time of evolutionary change They are based on the observation that some regions of the genome evolve at constant rates For these regions, the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the two species last shared a common ancestor In the case of paralogous genes, the number of substitutions is proportional to the time since the genes became duplicated Proteins and mitochondrial genomes have constant rate of change over time 38

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 39