Phylogeny and the Tree of Life Chapter 26 Phylogeny and the Tree of Life

Phylogeny and Systematics Phylogeny: the evolutionary history of a species – based on common ancestries inferred from: Fossil records Morphological & biochemical resemblances Molecular evidence Systematics: a discipline that focuses on classifying organisms and their evolutionary relationships.

The Fossil Record Sedimentary rock are the richest source of fossils. The fossil record is a substantial, but incomplete, chronicle of evolutionary history. The history of life on Earth is punctuated by mass extinctions Biologists draw on the fossil record Which provides information about ancient organisms

The Fossil Record Sedimentary rocks Are the richest source of fossils Are deposited into layers called strata 1 Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor. 2 Over time, new strata are deposited, containing fossils from each time period. 3 As sea levels change and the seafloor is pushed upward, sedimentary rocks are exposed. Erosion reveals strata and fossils. Younger stratum with more recent fossils Older stratum with older fossils Figure 22.3

The Fossil Record The fossil record Fossils reveal Is based on the sequence in which fossils have accumulated in such strata Fossils reveal Ancestral characteristics that may have been lost over time

Biologists also use systematics As an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct Currently, systematists use Morphological, biochemical, and molecular comparisons to infer evolutionary relationships

Morphological and Molecular Homologies In addition to fossil organisms Phylogenetic history can be inferred from certain morphological and molecular similarities among living organisms In general, organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences NOTE: DNA sequence comparisons are the BEST evidence of close relation.

Sorting Homology from Analogy A potential misconception in constructing a phylogeny Is similarity due to convergent evolution, called analogy, rather than shared ancestry It is important in phylogeny to sort HOMOLOGY from ANALOGY. Homologous structures – common ancestry Analogous structures – convergent evolution by similar environmental pressures

Convergent Evolution and Analogous Structures Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages Figure 25.10

Homoplasies Analogous structures or molecular sequences that evolved independently are also called homoplasies

Taxonomy Phylogenetic systematics connects classification with evolutionary history Taxonomy Is the ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences

Binomial Nomenclature Is the two-part format of the scientific name of an organism Was developed by Carolus Linnaeus The binomial name of an organism or scientific epithet Is latinized Is the genus and species

Hierarchical Classification Linnaeus also introduced a system for grouping species in increasingly broad categories If organisms A, B, and C belong to the same order but to different families and if organisms D, E, and F belong to the same family but to different genera, which pair of organisms would show the greatest degree of structural homology? Panthera pardus Felidae Carnivora Mammalia Chordata Animalia Eukarya Domain Kingdom Phylum Class Order Family Genus Species A and B? A and C? B and D C and F E and F Figure 25.7

Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees Panthera pardus (leopard) Mephitis mephitis (striped skunk) Lutra lutra (European otter) Canis familiaris (domestic dog) Canis lupus (wolf) Panthera Mephitis Lutra Canis Felidae Mustelidae Canidae Carnivora Order Family Genus Species Figure 25.8

Linking Classification and Phylogeny Each branch point Represents the divergence of two species Leopard Domestic cat Common ancestor

Linking Classification and Phylogeny “Deeper” branch points Represent progressively greater amounts of divergence Leopard Domestic cat Common ancestor Wolf

Cladistics Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics: A cladogram Is a depiction of patterns of shared characteristics among taxa A clade within a cladogram Is defined as a group of species that includes an ancestral species and all its descendants Cladistics Is the study of resemblances among clades

Cladistics Clades Can be nested within larger clades, but not all groupings or organisms qualify as clades

A valid clade is monophyletic Monophyletic Clades A valid clade is monophyletic Signifying that it consists of the ancestor species and all its descendants (a) Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A mono- phyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics. Grouping 1 D C E G F B A J I K H Figure 25.9a

Paraphyletic Clades A paraphyletic clade Is a grouping that consists of an ancestral species and some, but not all, of the descendants (b) Paraphyletic. Grouping 2 does not meet the cladistic criterion: It is paraphyletic, which means that it consists of an ancestor (A in this case) and some, but not all, of that ancestor’s descendants. (Grouping 2 includes the descendants I, J, and K, but excludes B–H, which also descended from A.) D C E B G H F J I K A Grouping 2 Figure 25.9b

A polyphyletic grouping Polyphyletic Clades A polyphyletic grouping Includes numerous types of organisms that lack a common ancestor Grouping 3 (c) Polyphyletic. Grouping 3 also fails the cladistic test. It is polyphyletic, which means that it lacks the common ancestor of (A) the species in the group. Further- more, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A. D C B E G F H A J I K Figure 25.9c

Cladograms Phylogenetic trees are constructed to reflect the hierarchial classification of taxonomic groups nested within more inclusive groups. Today, most systematists practice cladistics. A phylogenetic diagram based on cladistics is called a cladogram – and a valid cladogram is monophyletic. 22

Anatomy of the Cladogram

Characters and Cladograms The term “character” is referring to any feature that a particular taxon possesses. 2 Types: Shared Primitive Characters: a homology common to a taxon more inclusive than the one being defined. Shared Derived Characters: an evolutionary novelty unique to a particular clade (also called synapomorphies). The sequence of branching in a cladogram represents the sequence in which SHARED DERIVED CHARACTERS evolved. 24

Shared Primitive and Shared Derived Characteristics In cladistic analysis Clades are defined by their evolutionary novelties A shared primitive character Is a homologous structure that predates the branching of a particular clade from other members of that clade Is shared beyond the taxon we are trying to define A shared derived character Is an evolutionary novelty unique to a particular clade also called synapomorphies

Classification Using Cladograms To refine evolutionary classification, biologists now prefer a method called cladistics Cladistics considers only those characteristics that are new characteristics that arise as lineages evolve over time Characteristics that appear in recent parts of a lineage but not in its older members are called derived characters (synapomorphies). 26

Outgroups Systematists use a method called outgroup comparison To differentiate between shared derived and shared primitive characteristics As a basis of comparison we need to designate an outgroup which is a species or group of species that is closely related to the ingroup, the various species we are studying Outgroup comparison Is based on the assumption that homologies present in both the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor

The outgroup comparison Outgroup Comparisons The outgroup comparison Enables us to focus on just those characters that were derived at the various branch points in the evolution of a clade Salamander TAXA Turtle Leopard Tuna Lamprey Lancelet (outgroup) 1 Hair Amniotic (shelled) egg Four walking legs Hinged jaws Vertebral column (backbone) Amniotic egg Vertebral column (a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present. (b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny. CHARACTERS Figure 25.11a, b

Performing Outgroup Comparison See text page 543 See figure 26.11 Understand outgroup v/s ingroup and how both are used to build cladograms. 29

Phylogenetic Trees and Timing Any chronology represented by the branching pattern of a phylogenetic tree Is relative rather than absolute in terms of representing the timing of divergences

Maximum Parsimony and Maximum Likelihood Systematists can never be sure of finding the single best tree in a large data set Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood Among phylogenetic hypotheses The most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters

Parsimony Create “tree” that explains data envoking the fewest number of evolutionary events.

Principle of Maximum Likelihood The principle of maximum likelihood States that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events APPLICATION In considering possible phylogenies for a group of species, systematists compare molecular data for the species. The most efficient way to study the various phylogenetic hypotheses is to begin by first considering the most parsimonious—that is, which hypothesis requires the fewest total evolutionary events (molecular changes) to have occurred. TECHNIQUE Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird species. Species I Species II Species III Species IV I II III IV Sites in DNA sequence Three possible phylogenetic hypothese 1 2 3 4 5 6 7 A G T Bases at site 1 for each species Base-change event 1 First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here). 2 Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases). 3 Now focus on site 1 in the DNA sequence. A single base- change event, marked by the crossbar in the branch leading to species I, is sufficient to account for the site 1 data. Species Figure 25.15a

Principle of Maximum Likelihood 4 Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of these possible trees requires a total of four base-change events (marked again by crossbars). Thus, the first four sites in this DNA sequence do not help us identify the most parsimonious tree. I II III IV GG AA T G 10 events 9 events 8 events 5 After analyzing sites 5 and 6, we find that the first tree requires fewer evolutionary events than the other two trees (two base changes versus four). Note that in these diagrams, we assume that the common ancestor had GG at sites 5 and 6. But even if we started with an AA ancestor, the first tree still would require only two changes, while four changes would be required to make the other hypotheses work. Keep in mind that parsimony only considers the total number of events, not the particular nature of the events (how likely the particular base changes are to occur). Two base changes 6 At site 7, the three trees also differ in the number of evolutionary events required to explain the DNA data. RESULTS To identify the most parsimonious tree, we total all the base-change events noted in steps 3–6 (don’t forget to include the changes for site 1, on the facing page). We conclude that the first tree is the most parsimonious of these three possible phylogenies. (But now we must complete our search by investigating the 12 other possible trees.) Figure 25.15b

Phylogenetic Trees as Hypotheses The best hypotheses for phylogenetic trees Are those that fit the most data: morphological, molecular, and fossil Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious See figure 25.16

Tools for Tracing Evolutionary History Much of 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

Molecular Clocks Molecular clocks help track evolutionary time The molecular clock Is a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates Neutral theory states that Much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection And that the rate of molecular change in these genes and proteins should be regular like a clock Does not run as smoothly as neutral theory predicts

Applying a Molecular Clock: The Origin of HIV Phylogenetic analysis shows that HIV Is descended from viruses that infect chimpanzees and other primates A comparison of HIV samples from throughout the epidemic Has shown that the virus has evolved in a remarkably clocklike fashion

The Universal Tree of Life The tree of life Is divided into three great clades called domains: Bacteria, Archaea, and Eukarya The early history of these domains is not yet clear Bacteria Eukarya Archaea 4 Symbiosis of chloroplast ancestor with ancestor of green plants 1 3 Symbiosis of mitochondrial ancestor with ancestor of eukaryotes 4 Billion years ago 3 2 2 Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells 2 3 1 Last common ancestor of all living things 1 Origin of life 4

Timeline of Classification 1. 384 – 322 B.C. Aristotle 2 Kingdom Broad Classification – Plants or Animals 2. 1735 - Carl Linnaeus 2 Kingdom Multi-Divisional Classification (Kingdom, Phylum, Class, Order, Family Genus, Species) 3. Evolutionary Classification – (After Darwin) Group By lines of Evolutionary Descent 4. Five Kingdom System – 1950s (Whittaker) – 1950s – Plantae, Fungi, Animalia, Protista, Monera 6. Three Domain System – late 1990s late 1990s – Bacteria, Archaea, Eukarya 40

Linnaeus System Evolves from TWO Kingdoms to FIVE As we learned more about different kinds of life, there needed to be more Kingdoms 1800’s – Added Kingdom Protista Amoeba, Slime Molds 1950’s – Added Fungi and Monera Fungi distinguished from Plants Prokaryotes (no nucleus) bacteria given category 1970’s – Split Kingdom Monera into 2 separate Kingdoms Eubacteria – bacteria with peptidoglycan Archaebacteria – bacteria without peptidoglycan 41

The Five-Kingdom System Reflected increased knowledge of life’s diversity Kingdom is highest – most inclusive taxonomic category Five Kingdoms include: Monera Protista Plantae Fungi Animalia Recognized 2 types of cells: prokaryotes & eukaryotes 42

The Five-Kingdom System Described classification as: Plantae, Fungi, Animalia, Protista, Monera recognizes only 2 types of cells: prokaryotic and eukaryotic sets all prokaryotes apart from eukaryotes prokaryotes are in their own kingdom (Monera) distinguished 3 kingdoms of eukaryotes based on mode of nutrition protista were all eukaryotes that did not fit the definition of plants, fungi, or animals

Whittaker’s five-kingdom system

Figure 26.16 Our changing view of biological diversity

The Three-Domain System Molecular analyses have given rise to the most current classification system – the Three Domain System Domain is larger than kingdom (superkingdoms) The 3 Domain System is the most recent classification system and includes: Bacteria Archaea Eukarya http://bcs.whfreeman.com/thelifewire/content/chp27/27020.html 46

The Three Domain System Describes classification as: Not all prokaryotes are closely related (not monophyletic) Prokaryotes split early in the history of living things (not all in one lineage) Archaea are more closely related to Eukarya than to Bacteria Eukarya are not directly related to Eubacteria There was a common ancestor for all extant organisms (monophyletic) Eukaryotes are more closely related to each other (than prokaryotes are to each other)

Classification of Living Things Section 18-3 Classification of Living Things Go to Section: 48