biology of organisms comparative...

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Biology of Organisms

•  Why is an introduction to life’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 thaliana

Zea mays

Caenorhabditis elegans Drosophila melanogaster Danio rerio

Xenopus laevis Mus musculus Macaca mulatta

Comparative Biology •  This is why we can

study human 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.

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Comparative Biology

•  Some of the most exciting recent discoveries in biology include the elucidation of common genetic elements of animal development.

•  HOX genes.


•  Interactions between life’s diversity underlie essentially all of biology.

•  How might this be relevant to your future interests?

•  Medicine?


•  Interactions between life’s diversity underlie essentially all of biology.

•  How many interactions are going on here?

Animals

Colonization of land

Paleozoic Meso-

zoic Humans

Ceno- zoic

Origin of solar system and Earth

Prokaryotes Proterozoic Archaean Billions of years ago

1 4

3 2

Multicellular eukaryotes

Single-celled eukaryotes

Atmospheric oxygen

Today, Module 1:

Origins, History, &

Unity of Life

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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 years

– Oldest rocks are 4.0-3.8 billion years •  Any thoughts?

What is life?

•  Reproduction

Asexual Sexual

What is life?

•  Reproduction •  Metabolism:

–  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

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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 •  Evolution, Adaptation, &

Extinction

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III. A hierarchy of organization

•  From atoms to grasslands

•  There are increasing levels of complexity –  An upside-down pyramid

of increasing structural and functional complexity.

•  At each increasing level, the whole is more than the sum of its parts

atom molecule organelle

cell tissue

organ

organ system organism population

ecosystem biome

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

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Mammalian Forelimb

•  The pentamerous (five-digit) arrangement of the mammalian forelimb indicates homology.

–  Features that are similar as a result of descent.


•  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?


•  Fungi and Animals diverged some 965 million years ago!

•  Evolution will, of course, obscure these relationships.

•  But they are all part of the hierarchy of life.

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•  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: Phylogenetics and Taxonomy

•  The study of diversity is known as SYSTEMATICS.

•  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. Fossils & Sedimentation

•  Fossils are the most readily observable record of the history of life.

•  Key to the field of macroevolution.

•  Paleontology is the study of fossils.

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•  Unfortunately, the fossil record is both biased and incomplete.

•  Why would it be biased?


•  Unfortunately, the fossil record is both biased and incomplete.

•  Why would it be biased?

•  Why would it be incomplete?


•  Taphonomic conditions must be appropriate. –  These are the

conditions that permit decaying organisms to become fossilized.

Will this wombat skeleton fossilize?


•  Taphonomic conditions depend upon:

•  Geological processes

•  Type of fossil •  Age of fossils Shales are particularly good

for preserving fossils

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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?


•  The vast majority are of hard parts. Why? –  Soft tisues are broken

down by bacteria and fungi

–  Hard parts become mineralized.

•  This includes animals AND plants.


•  Trace fossils provide information on interactions, ecology, behavior, functional morphology.

•  How? •  These are rare!

Dinosaur tracks Leaf-mining insects

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I. Fossils & Sedimentation •  Ages of Fossils

•  Older fossils are much more rare.

•  Why?

Fossilized stromatolite

Stromatolites

I. Fossils & Sedimentation •  Ages of Fossils

•  Older fossils are much more rare.

•  More opportunity for geological processes to obscure or destroy: weathering, subduction, etc.

•  Older rocks are rarer. Fossilized stromatolite

Stromatolites


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

•  Despite this, the fossil record provides remarkable insights into the history of life on earth.

“eBay insect fossil is new species”

II. Dating of major events

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

One second before the end of the dinosaurs…

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•  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.


Common isotope ratios used in radiometric dating


•  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

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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 Phanerozoic eons. The Archaean & Proterozoic together are commonly known as the Precambrian Era

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 origin) and first significant extinction at end of Archaean 2.5 bya

Fossilized stromatolite

Stromatolites

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.

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The Proterozoic: 2500-542 mya •  First Eukaryotes and

multicellular organisms appear.

•  Low diversity early (Snowball Earth)

•  Later characterized by the “Ediacaran” 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 eras: the Paleozoic, Mesozoic, and Cenozoic

•  Major boundaries between geological divisions correspond to extinction events in the fossil record

The Paleozoic Era: 542-251 mya

•  Began with the Cambrian 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.


•  Major features: –  Colonization of land –  Appearance of

vascular plants –  Origins of seed

plants –  Diversification of

insect orders –  Radiation of

vertebrates

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•  Ended with the PERMIAN extinction.

•  Correlated with formation of PANGEA.

Continental Drift •  The movement of

earth’s continents relative to each other.

•  Based on the theory of plate tectonics.

•  Tectonic plates move in relation to each other causing continental drift, earthquakes, volcanoes, mountain-building, and oceanic trench formation


•  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: –  Triassic (251-200 mya) –  Jurassic (200-145 mya) –  Cretaceous (145-65

mya) •  End of each

characterized by extinctions

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•  Characterized by rise and dominance of Gymnosperms (Triassic and Jurassic).

•  Rise, diversification, and extinction of most dinosaur groups.

•  Origins and early diversification of mammals and Angiosperms.


•  Ended with Cretaceous Extinction


•  Ended with Cretaceous Extinction.

•  Significant evidence for massive impact event at Chicxulub crater in the Yucatán Peninsula.

A split second before the extinction of the dinosaurs

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 one lineage of dinosaurs.

Cenotes in the Yucatán indicate the rim of the ancient crater

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The Cenozoic Era: 65mya-present

•  Divided into two periods: –  Paleogene (65-23

mya) –  Neogene (23mya-

present) •  Rise of angiosperms,

mammals, and extreme diversification of insects.

What is the objective of systematics?

1.  Sort and identify organisms into species.

•  This includes the unique derived characteristics that distinguish them.

Cranial features; brain size; brain morphology

A. Objectives of Taxonomy A. Objectives of Taxonomy



Presence of a chin

Advanced tool-making

Small canine teeth; language

Dimensions of pelvis; upright gait; s-shaped spine

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A. Objectives of Taxonomy



•  This includes giving a name to undescribed species.

Reduced hair cover

Elongated thumb and shortened finger; Limb length

Skull balanced upright on vertebral column

A. Objectives of Taxonomy


2.  Arrange (classify) species into broader hierarchical taxonomic categories

•  From genera to domains

•  What is our classification?

Species: Panthera pardus

Genus: Panthera

Family: Felidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Kingdom: Animalia

Archaea Domain: Eukarya Bacteria

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 1.  Classification should as

much as possible reflect evolutionary history.

2.  Single taxon should be composed of all species derived from a common ancestor.

1.  This is known as monophyletic

2.  Contrast older notion of primate families Pongidae + Hominidae vs current notion of Hominidae

3.  Illustrates concepts of paraphyly and polyphyly

Current: Hominidae

Older: Family Pongidae

Subfamily Ponginae

Tribe Pongini Family Hominidae

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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 tetrapods. –  opposable thumb of

primates –  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 convergent evolution.

•  Are not informative to relationships. Informative to adaptation.

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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

Cha

nge

thro

ugh

time

Change through tim

e

Phylogenies

Cha

nge

thro

ugh

time

Cha

nge

thro

ugh

time

Relative position is the only thing that matters!

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Nodes, Tips, Internodes

Hair, mammary glands, 3 bones in the middle ear

Hinged jaws

Vertebral column

Four walking legs

Amniotic egg

Amphibians

Mammals

Reptiles

Lamprey

Fish

Lancelet (outgroup)

Sister groups The two taxa on either side of a split

Polytomies When resolu<on of the branching diagram is difficult

Outgroups Not part of the group in ques<on, but is closely related to the group


Hinged jaws

Vertebral column

Four walking legs

Amniotic egg

Amphibians

Mammals

Reptiles

Lamprey

Fish

Lancelet (outgroup)

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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 rela<onships. They denote clades.

•  Autapomorphies are traits that are unique and derived, but do not indicate rela<onships. 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.


Hinged jaws

Vertebral column

Four walking legs

Amniotic egg

Amphibians

Mammals

Reptiles

Lamprey

Fish

Lancelet (outgroup)

Synapomorphies, Autapomorphies, & Plesiomorphies


Hinged jaws

Vertebral column

Four walking legs

Amniotic egg

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

Amphibians

Mammals

Reptiles

Lamprey

Fish

Lancelet (outgroup)


Hinged jaws

Vertebral column

Four walking legs

Amniotic egg

Is the vertebral column a defining feature of mammals? How or how not?

Amphibians

Mammals

Reptiles

Lamprey

Fish

Lancelet (outgroup)

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Hinged jaws

Vertebral column

Four walking legs

Amniotic egg

NO! This is a shared ancestral trait or plesiomorphy. At what level does this become an synapomorphy?

Amphibians

Mammals

Reptiles

Lamprey

Fish

Lancelet (outgroup)


Hinged jaws

Vertebral column

Four walking legs

Amniotic egg

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

Amphibians

Mammals

Reptiles

Lamprey

Fish

Lancelet (outgroup)

Understanding the branching diagram

•  Recall that species arise from a splitting of an ancestral (parent) population (speciation);

•  Thus, all life could be represented by millions of such branches going back to the first organisms.




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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




Criteria of Homology: 1.  Similarity in position ✔ 2.  Detailed resemblance 3.  Continuance through

intermediate forms

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Criteria of Homology: 1.  Similarity in position ✔ 2.  Detailed resemblance ✖ 3.  Continuance through

intermediate forms




Criteria of Homology: 1.  Similarity in position ✔ 2.  Detailed resemblance ✖ 3.  Continuance through ✖

intermediate forms

D. CHARACTERS

•  Types of Characters: –  Must be products of

evolutionary process –  Must be heritable –  What kinds of things

fall under this?

•  Morphological Characters

•  Physiological characters

•  Molecular characters •  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.

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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.


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.





•  Identify homologous characters and delineate alternative character states.





•  These are the alternative hypotheses.

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•  Based on distribution of using shared derived characters (apomorphies) to identify clades.

•  Evaluated based on maximum parsimony or maximum likelihood as the optimality criterion.

Which tree is preferred? •  Parsimony •  Maximum-likelihood

•  We will spend time in lab on these AND your book is quite thorough with this (pp 542-547)



•  We should first investigate the simplest explanation for observed character state distributions.

•  Minimizes the number of evolutionary events on a tree.

•  Maximizes apomorphic characters while mimizing homoplasious characters. A

B

C

How would we draw a phylogeny of these lizards with only the information we have right here?

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Which tree is preferred? •  Parsimony

–  Data matrix & alternative hypotheses.

B

A

C C

A

B

A

B

C

Tail black

Legs blue

Back orange

Front red

A

B

C


–  Minimize character changes on the trees.

B

A

C C

A

B

A

B

C

Tail black

Legs blue

Back orange

Front red

A

B

C



B

A

C C

A

B

A

B

C

Tail black

Legs blue

Back orange

Front red

A

B

C



–  Do so for every character.

B

A

C C

A

B

A

B

C

Tail black

Legs blue

Back orange

Front red

A

B

C

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–  Do so for every character.

–  Count the number of changes.

–  Which is most parsimonious?

B

A

C C

A

B

A

B

C



•  Similar, but now optimality no longer based on principle of parsimony.

•  Optimality based on specified model of 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)

Blood squirting? No Yes

Mapping evolutionary transitions

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

How many times has blood-squirting evolved?

Testing evolutionary hypotheses

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Blood squirting? No Yes

This phylogeny suggests a single evolutioary gain and a single loss of blood squirting


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

How many times has blood-squirting evolved?


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

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

Testing evolutionary hypotheses Mapping evolutionary transitions

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

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



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 Snakes versus Gila monsters Even non-venomous lizards in this clade (Iguania) share ancestral toxins

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Lake Tanganyika

Convergence and modes of speciation

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

Lake Malawi

1. Similarities between each pair are the result of convergence

2. Sympatric speciation more likely than allopatric speciation


Clark et al. (2000)

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 cladogenesis (but also contradictions)

Matsuoka et al. (2002)

A

B


Geographic origins

Where did domestic corn (Zea mays maize) originate?

Populations from Highland Mexico are at the base of each maize clade


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 originated in Africa

Vigilant et al. (1991) Science

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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.


Using this information, they reconstructed what the ancestral protein looked like.

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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 birds, suggesting that early archosaurs hunted at dawn and dusk!

biology of organisms comparative...

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