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Home , Phanerozoic

Biology of Organisms

• Why is an introduction to ’s diversity important? Comparative Biology

• Uses phylogenetic relationships to study the features that unite and distinguish different groups. • Allows us to understand everything in biology from genes to behavior to anatomy to ecology to distributions in a holistic manner. Escherichia coli Saccharomyces cerevisiae Arabidopsis Zea mays thaliana

Caenorhabditis elegans Drosophila melanogaster Danio rerio

Xenopus laevis Mus musculus Macaca mulatta Comparative Biology

• This is why we can study diseases using mouse models. • This is why principles of genetics derived from fruit flies are generalizable. • This all goes back to the unity of life. Comparative Biology

• Some of the most exciting recent discoveries in biology include the elucidation of common genetic elements of development. • HOX genes. Biology of Organisms

• Interactions between life’s diversity underlie essentially all of biology. • How might this be relevant to your future interests? • Medicine? Biology of Organisms

• Interactions between life’s diversity underlie essentially all of biology. • How many interactions are going on here? Ceno- zoic

Colonization of land

Animals Origin of solar Today, and Earth Module 1: Origins, 1 4

History, & Archaean Prokaryotes Unity of Life 2 3 Multicellular

Single-celled eukaryotes Atmospheric oxygen What is life?

• What would we look for in a life form? • What defines life? • It’s been around for 3.8-3.5 billion – Oldest rocks are 4.0-3.8 billion years • Any thoughts? What is life?

• Reproduction

Asexual Sexual What is life?

• Reproduction • : – the set of chemical reactions that occur in living organisms that manage the material and energy resources of the cell. What is life?

• Reproduction • Metabolism • Organization – Non-random – Hierarchies – Emergent properties What is life?

• Reproduction • Metabolism • Organization • Growth & Development – Heritability – Cells What is life?

• Reproduction • Metabolism • Organization • Growth & Development • Homeostasis – Regulating internal environment What is life?

• Reproduction • Metabolism • Organization • Growth & Development • Homeostasis • Responds to the environment – Temperature, moisture, sunlight, substrate What is life?

• Reproduction • Metabolism • Organization • Growth & Development • Homeostasis • Responds to the environment • , , & III. A hierarchy

organelle of organization atom molecule • From atoms to • There are increasing levels of

complexity tissue cell – An upside-down pyramid of increasing structural and functional complexity. • At each increasing level, the whole is more than the sum Population/ organism of its parts Species organ system

biome ecosystem Community IV. Emergent Properties • With increasing complexity the hierarchical level becomes more than the sum of its parts. • These are known as emergent properties. • These are novel properties that emerge from interactions at lower levels. • How is this cathedral termite mound an example of an emergent property? IV. Emergent Properties • As biologists, to understand the whole we need to break it down and examine its parts. • Reductionist perspective. • But we always must keep in mind that when we do this that the whole loses its emergent properties. V: Correlation: structure, function, diversity • Divergence through evolution. – a.k.a. descent with modification. • Organisms have both a shared ancestry and new attributes.

Mammalian Forelimb V: Correlation: structure, function, diversity • The pentamerous (five-digit) arrangement of the mammalian forelimb indicates .

– Features that are similar as a result of descent.

Mammalian Forelimb V: Correlation: structure, function, diversity

• This pentamerous arrangement has been subsequently been modified through adaptation. VI. Unity in diversity

• Sometimes it is difficult to see unity in diversity. • What, for example, could a hummingbird and a mushroom have in common? VI. Unity in diversity

• Fungi and diverged some 965 million years ago! • Evolution will, of course, obscure these relationships. • But they are all part of the hierarchy of life. VI. Unity in diversity

• Over 1.5 million species are named. • But more than 98% of all species that have ever existed have become extinct. • This also obscures relationships. VI. Unity in diversity: and Taxonomy

• The study of diversity is known as . • Phylogenetics is the practice of elucidating relationships. • Taxonomy is the practice of naming organisms. • Classification arranges organisms. VII: Pattern & Process

• Pattern: Description of the WHAT? • Process: Description of the HOW?

• This course will mainly be about the description. • Because we must know what exists before we attempt to explain I. & Sedimentation

• Fossils are the most readily observable record of the . • Key to the field of . • is the study of fossils. I. Fossils & Sedimentation

• Unfortunately, the record is both biased and incomplete. • Why would it be biased? • Why would it be incomplete? I. Fossils & Sedimentation

• Taphonomic conditions must be appropriate. – These are the conditions that permit decaying organisms to become fossilized.

Will this wombat skeleton fossilize? I. Fossils & Sedimentation

• Taphonomic conditions depend upon: • Geological processes • Type of fossil

• Age of fossils Shales are particularly good for preserving fossils I. Fossils & Sedimentation

• Geological Processes

• Most fossils are found in sedimentary rock. • How are sediments formed? What are the implications of this for the abundance of fossils? • Also mineralized amber and ice. I. Fossils & Sedimentation

• Types of Fossils

• The vast majority are of hard parts. Why? I. Fossils & Sedimentation

• Types of Fossils

• Trace fossils provide information on interactions, ecology, behavior, functional morphology. • How? • These are rare! tracks Leaf-mining insects I. Fossils & Sedimentation

• Ages of Fossils

• Older fossils are much more rare. • Why?

Stromatolites

Fossilized stromatolite I. Fossils & Sedimentation

• The rarity of appropriate taphonomic conditions results in this bias and incompleteness.

• Despite this, the fossil “eBay insect fossil is new species” record provides remarkable insights into the history of life on earth. II. Dating of major events

• How do paleontologists estimate fossil/strata ages? – Relative – Absolute

One second before the end of the … II. Dating of major events

• Relative dating: • Usually older fossils at bottom of strata, younger towards top. II. Dating of major events

• Absolute dating. • Radioactive elements: isotopes that decay at a constant rate. • The ratio of these versus the stable isotopes that they decay into gives us a metric of the age that the sediment was formed – or the fossil itself if any organic Carbon is lucky enough to be preserved. II. Dating of major events

Common isotope ratios used in radiometric dating II. Dating of major events

• Generalizations: • Index fossils help correlate ages of strata over wide areas. • Based on well- documented fossils of short-lived (but abundant) species.

Viviparus glacialis is an index fossil for 2.3-1.8 mya III. The Geological Time Scale IV. Major Episodes

• A combination of: – Relative dating – Absolute dating – Major events in the history of life • Give us the Geological Time Scale – You should become familiar with the names, dates, and major events in this time scale. I highly recommend that you study Table 25.1 from your book!

The geologic record is divided into the Archaean, the Proterozoic, and the eons.

The Archaean & Proterozoic together are commonly known as the The Archaean: 4.6-2.5 bya

• Probably absent of life until 3.5 bya (first rocks 3.8 bya) • Prokaryotes appear (3.5 bya) • Massive increase in Oxygen (of biological Stromatolites origin) and first significant extinction at Fossilized end of Archaean 2.5 stromatolite bya The Proterozoic: 2500-542 mya

• First Eukaryotes and multicellular organisms appear. • Familiarize yourself with pages 516-517 and figure 25.9 in the textbook for this. The Proterozoic: 2500-542 mya

• First Eukaryotes and multicellular organisms appear. • Low diversity early (Snowball Earth) • Later characterized by the “” or “Vendian” biota. • Mass extinction of these forms at the end of this boundary. • Why? Phanerozoic: 542 mya-present

• The Phanerozoic encompasses multicellular eukaryotic life • The Phanerozoic is divided into three : the , , and • Major boundaries between geological divisions correspond to extinction events in the fossil record The Paleozoic Era: 542-251 mya

• Began with the Explosion. • Sudden appearance of modern animal phyla in the fossil record. • Localized fossils and DNA evidence suggest earlier origins (Conway Morris’ long fuse). • BUT the explosion refers to their widespread emergence and dominance. The Paleozoic Era: 542-251 mya

• Major features: – Colonization of land – Appearance of vascular – Origins of seed plants – Diversification of insect orders – Radiation of vertebrates The Paleozoic Era: 542-251 mya

• Ended with the extinction. • Correlated with formation of PANGEA. Continental Drift • The movement of earth’s continents relative to each other. • Based on the theory of . • Tectonic plates move in relation to each other causing continental drift, earthquakes, volcanoes, mountain-building, and oceanic trench formation The Paleozoic Era: 542-251 mya

• Ended with the PERMIAN extinction. • Correlated with formation of PANGEA. • Correlated with high levels of volcanism. • Loss of approximately 90% of all animal species. • Transition into the Mesozoic Era The Mesozoic Era: 251-65mya

• Divided into three Periods: – (251-200 mya) – (200-145 mya) – (145-65 mya) • End of each characterized by The Mesozoic Era: 251-65mya

• Characterized by rise and dominance of Gymnosperms (Triassic and Jurassic). • Rise, diversification, and extinction of most dinosaur groups. • Origins and early diversification of and Angiosperms. The Mesozoic Era: 251-65mya • Ended with Cretaceous Extinction. • Significant evidence for massive impact event at Chicxulub crater in the Yucatán Peninsula. • Worldwide Iridium layer at Cretaceous-Tertiary boundary (a.k.a. K-T boundary). • Extinction of 50% of all marine and terrestrial species, including all but Cenotes in the Yucatán indicate one lineage of dinosaurs. the rim of the ancient crater The Cenozoic Era: 65mya-present

• Divided into two periods: – (65-23 mya) – (23mya- present) • Rise of angiosperms, mammals, and extreme diversification of insects. What is the objective of systematics? A. Objectives of Taxonomy

Cranial features; 1. Sort and identify brain size; brain organisms into morphology species. • This includes the unique derived characteristics that distinguish them. A. Objectives of Taxonomy

Small canine teeth; language 1. Sort and identify Presence of a chin organisms into species. • This includes the unique derived Advanced tool- characteristics that making distinguish them.

Dimensions of pelvis; upright gait; s-shaped spine A. Objectives of Taxonomy

Skull balanced upright on vertebral column 1. Sort and identify Reduced cover organisms into species. • This includes the unique derived Elongated characteristics that thumb and shortened distinguish them. finger; • This includes Limb length giving a name to undescribed species. Species: Panthera A. Objectives pardus of Taxonomy Genus: Panthera 1. Sort and identify organisms into Family: Felidae species. 2. Arrange (classify) Order: Carnivora species into broader hierarchical Class: Mammalia taxonomic categories • From genera to : Chordata domains

• What is our Kingdom: Animalia classification?

Bacteria Domain: Eukarya Archaea B. How to classify--the rationale

1. Classification should as much as possible reflect evolutionary history. • Provides the most information. • Becomes predictive. B. How to classify--the rationale Older: 1. Classification should as much as possible reflect Family Pongidae evolutionary history. Subfamily Ponginae Family Tribe Pongini 2. Single should be Hominidae composed of all species derived from a common ancestor. 1. This is known as Current: monophyletic 2. Contrast older notion of Hominidae families Pongidae + Hominidae vs current notion of Hominidae 3. Illustrates concepts of paraphyly and polyphyly B. How to classify--the rationale • Paraphyletic: A taxon that does not include all of the descendants of the most recent common ancestor. B. How to classify--the rationale • Polyphyletic: A taxon that includes members derived from two or more ancestors. Note that this is part of a continuum with paraphyletic. C. The Importance of Homology

• Structures that share a common ancestor. – forelimb of . – opposable thumb of – flower of angiosperms • These provide information into relationships via monophyly. C. The Importance of Homology

• Similar structures that do not share a common ancestry are analogous or are homoplasies. • These result from . • Are not informative to relationships. Informative to adaptation. PHYLOGENETICS

• The study of evolutionary relatedness between organisms. • (Contrast with taxonomy) • Without phylogenetics, comparative biology would not exist and diversity would make no sense. PHYLOGENY

• Graphical representation of the evolutionary history of a group as expressed in terms of relatedness. • Classifications based on phylogenies are known as natural classifications. • Phylogenies are based on shared, derived (or unique) homologous features. These are known as synapomorphies. Phylogenies

Change through time Change through time Change through time Phylogenies Change through time Change through time

Relative position is the only thing that matters! Nodes, Tips, Internodes Sister groups The two taxa on either side of a split Lancelet (outgroup)

Lamprey

Fish Vertebral column Amphibians Hinged jaws

Four walking legs

Amniotic egg Mammals Hair, mammary glands, 3 bones in the middle ear Polytomies When resoluon of the branching diagram is difficult Outgroups Not part of the group in queson, but is closely related to the group Lancelet (outgroup)

Lamprey

Fish Vertebral column Amphibians Hinged jaws

Four walking legs Reptiles

Amniotic egg Mammals Hair, mammary glands, 3 bones in the middle ear Terminology

• Phylogenies are based on shared, derived (or unique) homologous features. These are known as apomorphies. • Synapomorphies are traits that are unique, derived, and indicate relaonships. They denote clades. • Autapomorphies are traits that are unique and derived, but do not indicate relaonships. They denote ps. • Plesiomorphies are traits shared by a number of groups, and are inherited from ancestors older than the last common ancestor. They do not denote clades. Synapomorphies, Autapomorphies, & Plesiomorphies Lancelet (outgroup)

Lamprey

Fish Vertebral column Amphibians Hinged jaws

Four walking legs Reptiles

Amniotic egg Mammals Hair, mammary glands, 3 bones in the middle ear Lancelet (outgroup)

Lamprey

Fish Vertebral column Amphibians Hinged jaws

Four walking legs Reptiles

Amniotic egg Mammals Hair, mammary glands, 3 bones in the middle ear

Phylogenetic tree: Endothermic vertebrates with hair, mammary glands, three bones in the middle ear (etc.) are all related and thus called MAMMALS. Lancelet (outgroup)

Lamprey

Fish Vertebral column Amphibians Hinged jaws

Four walking legs Reptiles

Amniotic egg Mammals Hair, mammary glands, 3 bones in the middle ear

Is the vertebral column a defining feature of mammals? How or how not? Lancelet (outgroup)

Lamprey

Fish Vertebral column Amphibians Hinged jaws

Four walking legs Reptiles

Amniotic egg Mammals Hair, mammary glands, 3 bones in the middle ear

Tree-thinking questions: Which is most closely related to a fish: amphibians, reptiles, or mammals? Which is most evolved: amphibians, reptiles, or mammals? Understanding the branching diagram

• Recall that species arise from a splitting of an ancestral (parent) population (); • Thus, all life could be represented by millions of such branches going back to the first organisms. Understanding the branching diagram

All the way to the relationships linking all species of cats (Johnson et al 2006) D. CHARACTERS • A set of alternative conditions (character state) that are considered able to evolve one to another. • Must search for and evaluate homologous structures. – Must follow Recognition Criteria of Homology: 1. Similarity in position 2. Detailed resemblance 3. Continuance through intermediate forms D. CHARACTERS

• Types of • Morphological Characters: Characters – Must be products of • Physiological evolutionary process characters – Must be heritable • Molecular characters – What kinds of things fall under this? • Behavioral characters • Ecological characters • Geographic characters D. CHARACTERS

A simple rule for hypothesis testing • The more data, the better! – This applies to testing phylogenetic relationships as well: the more characters, the better – Also, the more character systems, the better. Phylogenetic Analysis

• How do we reconstruct phylogenetic trees? • Based on using characters to test hypotheses of phylogenetic relationships. • Remember that the branching diagram is the hypothesis. Phylogenetic Analysis

1. A set of data (character X taxon matrix) 2. A set of possible evolutionary trees 3. A means of evaluating the alternative trees given the data. Phylogenetic Analysis

1. A set of data • Identify homologous (character X taxon characters and matrix) delineate alternative 2. A set of possible character states. evolutionary trees 3. A means of evaluating the alternative trees given the data. Phylogenetic Analysis

1. A set of data • These are the (character X taxon alternative matrix) hypotheses. 2. A set of possible evolutionary trees 3. A means of evaluating the alternative trees given the data. Phylogenetic Analysis

1. A set of data • Based on distribution of using shared derived characters (character X taxon (apomorphies) to identify matrix) clades. • Evaluated based on maximum 2. A set of possible parsimony or maximum evolutionary trees likelihood as the optimality criterion. 3. A means of evaluating the alternative trees given the data. Which tree is preferred?

• Parsimony • We should first investigate the simplest explanation for • Maximum-likelihood observed character state distributions. • We will spend time in lab on • Minimizes the number of these AND your book is evolutionary events on a quite thorough with this (pp tree. 542-547) • Maximizes apomorphic characters while mimizing homoplasious characters. How would we draw a phylogeny of these lizards with only the information we have right here?

C

A B Which tree is preferred? • Parsimony A – Data matrix & alternative hypotheses. B

C B Tail Legs Back Front black blue orange red A

A C C B A C B Which tree is preferred? • Parsimony A – Minimize character changes on the trees. B

C B Tail Legs Back Front black blue orange red A

A C C B A C B Which tree is preferred? • Parsimony A – Minimize character changes on the trees. B

C B Tail Legs Back Front black blue orange red A

A C C B A C B Which tree is preferred? • Parsimony A – Minimize character changes on the trees. B – Do so for every character. C B Tail Legs Back Front black blue orange red A

A C C B A C B Which tree is preferred? • Parsimony A – Minimize character changes on the B trees. C – Do so for every character. B – Count the number of A changes. – Which is most C parsimonious? C

A

B Which tree is preferred?

• Parsimony • Similar, but now • Maximum-likelihood optimality no longer based on principle of • We will spend time in lab on parsimony. these AND your book is • Optimality based on quite thorough with this (pp specified model of 542-547) evolution. • Generally applied to molecular data. • Uses external information. Using Phylogenies

• Now that you have a tree, what can you do with it? – Testing hypotheses about evolution – Learning about the characteristics of extinct species and ancestral lineages – Classifying organisms (later) Testing evolutionary hypotheses

Mapping evolutionary transitions

Some horned lizards squirt blood from their eyes when attacked by canids.

How many times has blood-squirting evolved? This phylogeny suggests a single evolutionary gain and a single loss of blood squirting

Blood squirting? No Yes Testing evolutionary hypotheses

Mapping evolutionary transitions

But a new phylogeny using multiple characters suggests that blood squirting has been lost many times in the evolution of this group

Our interpretation of these evolutionary scenarios depends on phylogeny

Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644 Testing evolutionary hypotheses

Reconstructing ancestral characters

This phylogeny also shows how we can use data from living species to infer character states in ancestral taxa

? ?

Ancestral state could be blue, purple, or intermediate…outgroup comparison indicates blue is most parsimonious

Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644 Testing evolutionary hypotheses

Mapping evolutionary transitions

How many times has venom evolved in squamate reptiles?

Once in the large “venom clade”

Groups within this clade then evolved different venom types e.g., different proteins found in versus Gila monsters

Even non-venomous lizards in this clade (Iguania) share ancestral toxins

Fry et al. (2006) Nature 439: 584-588 Testing evolutionary hypotheses

Convergence and modes of speciation

What can this phylogeny tell us about homology/analogy and speciation? Lake Tanganyika Lake Malawi

1. Similarities between each pair are the result of convergence 2. more likely than Testing evolutionary hypotheses

Coevolution Aphids and bacteria are symbiotic Given this close relationship, we might expect that speciation in an aphid would cause parallel speciation in the bacteria When comparing phylogenies for each group we see evidence for reciprocal (but also contradictions) Clark et al. (2000) Testing evolutionary hypotheses

Geographic origins Where did domestic corn A (Zea mays maize) originate? Populations from Highland Mexico are at the base of each maize clade B

Matsuoka et al. (2002) Testing evolutionary hypotheses

Geographic origins Where did humans originate? Each tip is one of 135 different mitochondrial DNA types found among 189 individual humans African mtDNA types are clearly basal on the tree, with the non-African types derived Suggests that humans Vigilant et al. (1991) Science originated in The power of Phylogenetic Biology • From understanding physiological processes to identifying endangered species. • To understanding dinosaur behavior… (?!) Phylogenetics and Dinosaur behavior

• Belinda Chang and colleagues began by reconstructing a phylogeny of vertebrates using numerous genes. • They then sequenced a rhodopsin gene from all of these species and tested their photoactive properties. Phylogenetics and Dinosaur behavior

• Using this information, they reconstructed what the ancestral protein looked like. • They then synthesized this protein, expressed it in a mammalian cell line tissue culture, and tested its photoactive properties. • The photoactive properties were significantly red-shifted from modern , suggesting that early hunted at dawn and dusk!