Lecture 1 Phylogeny the Tree of Life DM

Lecture #1: Phylogeny & the “Tree of Life” DM Hillis, D Zwicki, R Gutell. University of Texas

Aristotle’s Scala Naturae

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

Taxonomy • how organisms are named and how they were classified before phylogeny • the field of biology that determines phylogeny, names organisms and places them into groups is systematics • taxonomy = method of systematics

Taxonomy • biologists refer to organisms using Latin scientific names – – – binomial nomenclature instituted in the 18 th century by Carolus Linnaeus more than 11, 00 binomial names 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”)

Taxonomy • 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/genetics being used

Phylogeny and Taxonomy • 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 – Phylo. Code: 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”

Morphological and Molecular Homologies • phylogenies are inferred from both morphological and molecular data • phenotypic and genetic similarities due to a shared ancestry = homologies • homologous characteristic = characteristics of different species that have evolved from the same origin – 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!!!

Morphologic Homologies • 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

Morphologic Homologies • 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 – but the more similar a structure is and the less complex – the more likely the structures are analogous – e. g. wing of a bat and bird

Morphologic Homologies • 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 immediate ancestors

Molecular Homologies • 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 Homologies species #1 • evaluating 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) species #2 over evolutionary time insertion of DNA bases + deletion of others occurs computer programs are still able to align these sequences and find commonalities Molecular Homology

Molecular Homology • molecular homology is determined through molecular systematics = comparison of nucleic acids and other molecules (e. g. proteins) to deduce relatedness • helps us create phylogenetic relationships when comparative anatomy can’t help – e. g. molecular homologies can be found between humans and mushrooms! – e. g. Hawaiian silversword plants – very different phenotypic appearance throughout the islands – but very similar in terms of their DNA sequences = homologous

Molecular Homology • molecular homology 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

• two types of homologous genes: – 1. orthologous = genes in two (or more) species that evolve from a gene in a common ancestor • e. g. cytochrome c genes – found in humans and dogs – they show high levels of sequence alignment or homology – didn’t change much from their common ancestor • orthologous genes are found between species • these genes can only diverge after speciation has taken place • if they are highly homologous – rate of evolutionary change is slow • if they lose homology – rate of change is high Homologous Genes

• two types of homologous genes: – 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 • result of gene duplication • one gene stays the same • the other “duplicated” gene has changes to its sequence & gives rise to a new gene individual species evolution Homologous Genes A 1’ and A 2’ are paralogous A 1’ and A 1’’ are orthologous

Homologous Genes speciation (within the same species) (within the ancestor)

Phylogenetic Trees • the evolutionary history of a group of organisms – intended to show patterns of descent NOT phenotypic similarities • a phylogenetic tree represents a hypothesis about evolutionary relationships – depicted as branch points or nodes – each branch point is a divergence of evolutionary lineages from a common ancestor

– e. g. Mustelidae and Canidae are clades within the larger clade of Carnivora because they share a common ancestor Genus • common ancestry is the primary criterion to classify organisms into a clade • smaller clades are nested within larger clades Family – “subdivision” of a phylogenetic tree Panthera Mephitis Lutra lutra Canis pardus mephitis (European familiaris lupus (leopard) (striped skunk) otter) (domestic dog) (wolf) Panthera Felidae Order • field of biology that creates phylogenetic trees = cladistics • phylogenists now place organisms into clades = includes the ancestral species and all of its descendants Species Phylogeny & Cladistics Mephitis Lutra Mustelidae Canis Canidae Carnivora • we still use the taxonomic names for these clades • e. g. order, family, genus

Phylogenetic Trees • taxon: taxonomic group of any rank • branch points or nodes: evolution of a single lineage into different ones • sister taxa = groups of organisms that share an immediate common ancestor • basal taxon = lineage that diverges early in the history of a group (and has no other branch points)

Phylogenetic Trees • polytomy = many temporal based branches connected to a single node – branch point where more than two descendant groups emerge – scientists haven’t yet identified all the relationships between these organisms

Phylogenetic Trees • rooted phylogenic tree: single lineage at the base representing the common ancestor – branching indicates evolutionary relationships – branch points indicate the evolution of different lineages from a common ancestor • unrooted phylogenic tree: no common ancestors but relationships among organisms can be determined

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 – must 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)

• sister taxa = e. g. Mephitis and Lutra – e. g. Mustelidae and Canidae • basal taxon = e. g. Felidae Genus Panthera Mephitis Lutra lutra Canis pardus mephitis (European familiaris lupus (leopard) (striped skunk) otter) (domestic dog) (wolf) Panthera Family – so Mustelidae is the common ancestor to Mephitis & Lutra and to their descendants the skunk and the otter Felidae Order • branch points or nodes: e. g. Mustelidae dividing into Mephitis & Lutra Species Phylogenetic Trees Mephitis Lutra Mustelidae Carnivora Canis Canidae

• common ancestor to Caniformia and Feliformia? ? ? • consider the Caniformia branch of the tree - example of a sister taxa? ? • consider the Feliformia branch of the tree - example of a basal taxon? ? Species Genus Family Suborder Order

Phylogenetic Trees • 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 Monophyletic Grouping 2 Paraphyletic Grouping 3 Polyphyletic

Phylogenetic Trees • when examining a phylogenetic tree you will find shared derived characteristics = a character found within a clade but not necessarily within their shared common ancestor Turtle Leopard Hair Salamander Amniotic egg Tuna – e. g. hair – shared derived Four walking legs character for mammals (e. g. the Lamprey leopard) but NOT for reptiles Hinged jaws (the turtle) Lancelet (outgroup) Vertebral column – one way to look at it is to think that shared derived characteristics are unique to specific clades

Phylogenetic Trees • you will also find shared ancestral characteristics = a character that originates within the ancestor and is found in the descendents TAXA Leopard Turtle – e. g. vertebral column – shared ancestral character found in the vertebrate ancestor PLUS the lamprey, the tuna, the salamander, the turtle and the leopard but NOT to the lancelet Hair Salamander Amniotic egg Tuna Four walking legs Lamprey Hinged jaws Lancelet (outgroup) Vertebral column

• we use the shared derived characteristic 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 characteristic of hinged jaws to create the next etc…. – this makes the lamprey the next outgroup • we use shared derived characters to create phylogenetic trees TAXA Turtle Leopard Hair Salamander Amniotic egg Tuna Four walking legs Lamprey Hinged jaws Lancelet (outgroup) Vertebral column

M rd Hu m an Ra t Bi ou se n ia Am ph Fi sh ib el nc La 65. 5 Millions of years ago Neoproterozoic 542 Paleozoic 251 Mesozoic Cenozoic Dr os op et hi la • phylogenetic trees can be constructed to also denote the amount of evolutionary change or the time when the change happened – by changing the branch length • 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

Maximum Parsimony and Maximum Likelihood • • you are analyzing data for 50 species there are 3 x 1076 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 • proposes that the tree with equal rates of change is more likely • computer programs now search for trees maximize BOTH of these principles

Maximum Parsimony and Maximum Likelihood 25% 15% 20% 15% 10% 5% Tree 1: More likely Comparison of possible trees 5% Tree 2: Less likely • how do we arrange a human, a tulip and a mushroom on a phylogenic tree based on their DNA sequences? ? • two possible trees given • both trees are equally parsimonius (equally simple) • remember equal rates of changes are more likely!! • so tree 1 assumes that the rate of change in DNA sequences between all three species are equal – rate of change in human and mushroom DNA = 20%; change in tulip DNA 20% • more likely than tree 2 which proposes rates of change for the mushroom (5%), for humans (25%) and tulips (35%)

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

• 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

• recently the application of molecular analysis to this classification has resulted in a reclassification • adoption of a three domain system 1. Bacteria – most of the currently known prokaryotes (or Eubacteria) 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! 1 Billion years ago • includes the cyanobacteria (bluegreen algae), the spirochetes and the ancestors to mitochondria and chloroplasts 0 Bacteria Eukarya gene transfer 2 3 common ancestor of all life 4 Origin of life Archaea

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.

• 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

• 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.