1. Lecture #1: Phylogeny & the “Tree of Life”

2. Phylogeny how do biologists classify and categorize species? by understanding evolutionary relationships evolutionary history of a species or a group of species = phylogeny phylogenies are constructed using systematics – uses data ranging from fossils to molecules to genes to derive evolutionary relationships

3. Species Panthera pardus Panthera Genus Family Felidae Carnivora Order Mammalia Class Phylum Chordata Kingdom Animalia Eukarya Domain Taxonomy how organisms are named and classified biologists refer to organisms using Latin scientific names – binomial nomenclature – instituted in the 18 th century by Carolus Linnaeus – more than 11,00 binomials still in use today – 1 st part - genus to which the species belongs (plural = genera) – 2 nd part – specific epithet – unique for each species e.g. panther = Panthera pardus e.g. human = Homo sapiens (“wise man”) Linnean system – grouped species into a well organized hierarchy of categories – named unit at any level of the hierarchy = taxon – taxa = domain, kingdom, phylum, class, order, family, genus, species – species that are closely related – belong to the same genus – related genera are in the same family etc…… – the characters that are used to classify organisms are determined by taxonomists – not just physical characteristics now – but molecular/genetic being used

4. Phylogenetic Trees the evolutionary history of a group of organisms – intended to show patterns of descent NOT phenotypic similarities while the Linnean system distinguishes groups it tells us nothing of the groups’ evolutionary relationships to each other proposal: that classifying organisms should be based entirely on evolutionary relationships – PhyloCode: a system that names groups that include a common ancestor and all of its descendants – changes the way taxa are defined but keeps the taxonomic names of most species – eliminates ranks like “family” and “class” a phylogenetic tree represents a hypothesis about evolutionary relationships – depicted as dichotomies or two-way branch points – each branch point is a divergence of two evolutionary lineages from a common ancestor

5. Phylogenetic Trees branch points: divides Mustelidae into Mephitis & Lutra – so Mustelidae is the common ancestor to Mephitis & Lutra and to their descendants the skunk and the otter sister taxa = groups of organisms that share an immediate common ancestor – e.g. Mephitis and Lutra – e.g. Mustelidae and Canidae basal taxon = lineage that diverges early in the history of a group – e.g. Felidae polytomy = branch point where more than two descendant groups emerge Carnivora Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Species Genus Family Order FelidaeMustelidaeCanidae PantheraMephitisLutraCanis

6. branch points: Carnivora is the common ancestor to Caniformia & Feliformia and all of their descendents on the tree sister taxa = Canidae and Arctoidea; common ancestor = Canoidea basal taxon = Nimravidae – branched early off of Feliformia

7. Phylogenetic Trees THREE THINGS: #1: phylogenetic tress shown patterns of decent – NOT phenotypic similarities – closely related organisms may NOT look like each other because their lineages evolved at different rates or faced different environmental conditions #2: the sequence of branching in a tree does not indicate the absolute age of the species – interpret the tree in terms of patterns of descent – unless dates are given #3: do NOT assume a taxon on a tree evolved from the taxon next to it – instead look at the common ancestor (branch point)

8. Morphological and Molecular Homologies phylogenies are inferred from both morphological and molecular data phenotypic and genetic similarities due to a shared ancestry = homologies – similarities in the number of forelimb bones in mammals is due to their descent from a common ancestor with the same bone structure = morphological homology – similarities in DNA sequences between humans and other primates is due to their descent from a common ancestor = molecular homology large changes in morphological homology do NOT mean divergence in molecular homology!!!

9. be careful with morphological homology! just because two species look the same does NOT mean there are homologous (shared ancestor) – e.g. Australian mole (marsupial) and a North American mole (eutherian) look the same phenotypically – but a quite different in terms of internal anatomy the two moles are similar due to convergent evolution similar environmental pressures and natural selection produce similar (analogous) adaptations in two organisms of different evolutionary lineages you have to be able to distinguish between homology and analogy to construct a phylogenetic tree – analogy = two structures look alike but no common descent – e.g. bird and bat wings are analogous structures –bird and bat wings arose independently from the forelimbs of different ancestors homoplasy = analogous structures that arise independently an easy way to distinguish homology and analogy – is complexity – the more things that are similar in a structure between two organisms and the more complex the structure is – the better chance the structure is homologous – e.g. skull of humans & chimps Morphologic Homologies

10. Molecular Homologies to evaluate molecular homology requires analysis of DNA sequences – extract the DNA, sequence the DNA and align them in terms of similar sequences – alignment done by powerful computer programs that take into account deletions of bases or additions of bases that can “shift” the coding and non-coding sequences back or forward – also determine if the similarities are just a coincidence (molecular homoplasy or analogy) so looking at the DNA sequences of the Australian and N.A. moles identifies numerous differences in DNA sequences that can’t be aligned – do not share a common ancestor and their phylogenetic trees will differ molecular analysis also helps us identify organisms with very different phenotypes as being closely related – e.g. Hawaiian silversword plants – very different phenotypic appearance throughout the islands – but very similar in terms of their DNA sequences = homologous over evolutionary time insertion of DNA bases + deletion of others occurs computer programs are still able to align these sequences and find commonalities species #1 species #2 Molecular Homology

11. Molecular Homology molecular homology is determined through molecular systematics = comparison of nucleic acids and other molecules to deduce relatedness helps us create phylogenetic relationships when comparative anatomy can’t help – molecular homologies can be found between humans and mushrooms! also allows us to reconstruct phylogenetic trees when the fossil record is absent so molecular biology has allowed us to add many more “branches” and “twigs” to phylogenetic trees keep in mind - different genes evolve at different rates – the evolution of ribosomal genes are slow – allows us to investigate further back in time – the evolution of mitochondrial genes are fast – investigation of more recent events

12. Homologous Genes Ancestral gene Speciation Orthologous genes Ancestral gene Gene duplication Paralogous genes as species evolve - genes duplicate some duplicated genes found in many species do not change significantly over the course of evolution – these genes retain a high level of homology over the course of their evolution other genes change so much – there is very little homology left so many species within a phylogenetic tree can share many homologous genes and have many distinct genes but an individual species can also possess homologous genes as a result of their evolution two types of homologous genes: – 1. orthologous = genes are duplicated as species evolve e.g. cytochrome c genes – found in humans and dogs they show high levels of sequence alignment or homology orthologous genes are a product of speciation these genes can only diverge after speciation has taken place for them to be highly homologous – rate of evolutionary change is slow – 2. paralogous = genes are duplicated within a species as it evolves e.g. olfactory receptor genes in humans – numerous types of receptors each coded for by different genes but these genes have regions of homology when compared to one another paralogous genes are within a species these genes can diverge within a species because they are present in more than one copy in the genome

13. Clades & Cladistics inferring phylogeny from homologous characteristics = cladistics common ancestry is the primary criterion to classify organisms biologists place organisms into clades = includes the ancestral species and all of its descendants – “subdivision” of a phylogenetic tree smaller clades are nested within larger clades – e.g. Mustelidae and Canidae are clades within the larger clade of Carnivora three types of groupings possible with a phylogenetic tree – 1. monophyletic (“one tribe”) = ancestor (B) and all of its descendants (C – H) – 2. paraphyletic (“beside the tribe”) = ancestor (A) and some of its descendants (I, J K & not B – H) – 3. polyphyletic (“many tribes”) = different ancestors and their descendants (F, G, H & I, J, K) Grouping 1 MonophyleticParaphyletic Grouping 2 Polyphyletic Grouping 3

14. Clades TAXA Turtle Leopard Hair Amniotic egg Four walking legs Hinged jaws Vertebral column Salamander Tuna Lamprey Lancelet (outgroup) within clades you will find shared derived characters = a character found within that clade but not necessarily within their shared common ancestor – e.g. hair – shared derived character for mammals (the leopard) but NOT for reptiles (the turtle) within larger clades you will find shared ancestral characters = a character that originates within the ancestor – e.g. backbone – shared ancestral character to the vertebrates: the lamprey, the tuna, the salamander, the turtle and the leopard but NOT to the lancelet but also the backbone is also a shared derived character found within the clade of vertebrates and not within the lancelet (clade chordata) one way to look at it is to think that shared derived characters are unique to specific clades we use shared derived characters to create the phylogenetic tree

15. so we use the shared derived character of a vertebral column to determine the first branch point – the lancelet (no vertebral column) is called the outgroup and the remaining organisms are the ingroup use the derived character of hinged jaws to create the next etc…. – this makes the lamprey the next outgroup phylogenetic trees can be constructed to also denote the amount of evolutionary change or the time when the change happened – changing the branch length TAXA Turtle Leopard Hair Amniotic egg Four walking legs Hinged jaws Vertebral column Salamander Tuna Lamprey Lancelet (outgroup) Drosophila Lancelet Fish Amphibian Bird Human Rat Mouse Cenozoic Mesozoic Paleozoic 65.5 251 542 Neoproterozoic Millions of years ago common ancestor of the fish and the human arose 542 MYA!! so there has been 542 million years of evolution for both the fish and the human

16. phylogenetic trees can be constructed to also denote the amount of evolutionary change or the time when the change happened – changing the branch length or they can be constructed to denote the amount of genetic change Drosophila Lancelet Fish Amphibian Bird Human Rat Mouse Cenozoic Mesozoic Paleozoic 65.5 251 542 Neoproterozoic Millions of years ago common ancestor of the fish and the human arose 542 MYA!! so there has been 542 million years of evolution for both the fish and the human Drosophila Lancelet Fish Amphibian Bird Human Rat Mouse BUT the rate of genetic change in fish and humans is different

17. Maximum Parsimony and Maximum Likelihood you are analyzing data for 50 species there are 3x10 76 different ways to arrange these specific into a tree! with DNA sequencing it gets more complicated you can narrow the possible trees by using the principles of – 1. maximum parsimony = the tree uses the simplest explanation consistent with the facts “Occam’s razor” = if you have several theories based on facts, the one that is the simplest is likely to be right! in other words = “KISS” – keep it simple stupid! – 2. maximum likelihood = the tree reflects the most likely sequence of evolutionary events uses rather complex methods based on the differences between DNA sequences and the rate of changes in these sequences – equal rates of change are more likely computer programs now search for trees maximize BOTH of these principles Comparison of possible trees 15% 20% 5% 10% 15% 25% Tree 1: More likelyTree 2: Less likely both trees are equally parsimonius (equally simple) but tree 1 assumes that the rate of change in DNA sequences are equal – rate of change in human and mushroom DNA = 20%; change in tulip DNA 20% which is more likely than tree 2 which assumes that the rate of change in the mushroom (5%) is slower than that of humans (25%) and tulips (35%)

18. From Kingdoms to Domains earliest taxonomists just had two kingdoms: Plants and Animals with the discovery of bacteria – things got a bit more complicated but bacteria were classified as plants since they were found to have a cell wall since algae underwent photosynthesis – considered plants also fungi also classified as plants – despite having nothing in common with plants organisms that consumed were considered animals – including single celled organisms like protozoans

19. in 1969: five-kingdom classification system – Robert Whittaker – recognized the existence of two fundamental cell types: prokaryotes and eukaryotes – created a separate kingdom for prokaryotes and divided up the eukaryotes – 1. Monera - prokaryotic – 2. Protista – unicellular organisms including algae – 3. Fungi – 4. Plantae – 5. Animalia – based on the nutritional requirements and methods of these domains plants = autotrophs fungus and animals = heterotrophs fungus = decomposers animals = digestors within the body

20. recently the application of molecular analysis to this classification has resulted in a reclassification – some prokaryotes can differ dramatically from each other – as much as they differ from plants and animals – construction of phylogenetic trees based on molecular data adoption of a three domain system of superkingdoms – 1. Bacteria – most of the currently known prokaryotes (or Eubacteria) includes the cyanobacteria (blue- green algae), the spirochetes and the ancestors to mitochondria and chloroplasts – 2. Archaea – prokaryotes that inhabit a wide variety of environments – 3. Eukarya - eukaryotes contains the “old” kingdoms of protists, fungi, plants and animals these kingdoms no longer exist! BacteriaEukaryaArchaea Billion years ago Origin of life 0 1 2 3 4 gene transfer common ancestor of all life

21. Team Problems Question: The correct sequence from the most to the least comprehensive of the taxonomic levels listed here is – A) family, phylum, class, kingdom, order, species, and genus. – B) kingdom, phylum, class, order, family, genus, and species. – C) kingdom, phylum, order, class, family, genus, and species. – D) phylum, kingdom, order, class, species, family, and genus. – E) phylum, family, class, order, kingdom, genus, and species.

22. Answer? B

23. Question: If organisms A, B, and C belong to the same class but to different orders and if organisms D, E, and F belong to the same order but to different families, which of the following pairs of organisms would be expected to show the greatest degree of structural homology? – A) A and B – B) A and C – C) B and D – D) C and F – E) D and F

24. Answer? E

25. QUESTION) Hawaiian silverswords have very different phenotypes as you travel from island to island. On the basis of their morphologies, how might Linnaeus have classified the Hawaiian silverswords? – A) He would have placed them all in the same species. – B) He probably would have classified them the same way that modern botanists do. – C) He would have placed them in more species than modern botanists do. – D) He would have used evolutionary relatedness as the primary criterion for their classification. – E) Both B and D are correct.

26. Answer? C