7.2 megaset Macroevolution

Miller-Urey Experiment

• replicated chem of early Earth in experiment

• Inorganic mlc → impt organic mlc

• NH3, CH4, H2, H2O → amino acids, sugars, lipids

• the early oceans with these chemical rxns that provide the building blocks for life are called the “primordial soup”

those same conditions are no longer present (primordial soup)

BPQ

Life on Earth prob has 1 origin

Why has new life not appeared on Earth in the 4 bil yrs since it appeared?

3 Hypotheses for Origins of Life

1. Genes first hypothesis

   1. RNA world

2. Metabolism first hypothesis

3. Extraterrestrial hypothesis

   1. Somewhat cooky but not impossible

Genes first hypothesis

• RNA world hypothesis

• Origins of life start w/ self-replicating RNA

  • self-replicating RNAs would be under the influence of evolutionary forces

  • RNA organisms would later utilize other macromolecules

  • DNA became the base of the genetic code later

RNA abilities

• store info (viruses)

• store energy

• send signals - mRNA

• regulate - miRNA

• catalyze rxns - rRNA

Metabolism First hypothesis

• self-sustaining metabolic rxn formed first

  • energy and components provided by environment (e.g. hydrothermal vents)

    • other components came later to create more complex chemical networks

• Many metabolic rxns are cyclic

  • self sustaining rxns can continue

  • under the influence of evolution

Extraterrestrial Hypothesis

• More cooky

  • life came from space

  • extraterrestrial life just happened to end up on a planet that could form its own form of life???

• Less cooky

  • important components of life came from space

Evidence for Macroevolution

1. anatomy and embryology

2. molecular biology

3. biogeography

4. fossil record

Anatomy and Embryology

• Homology - features that are the same/similar due to common ancestor

  • Homologous characters

• Many specialized anatomical parts are just modifications of parts in other species

Homoplasy

• features that are the same/similar but NOT due to common ancestor

  • Analogous characters

  • Convergent Evolution!

• e.g. birds, bats, pterosaurs

  • Bones of the wing - Homology

  • Wing itself - Homoplasy

homology

BPQ

Human and chimp apposable thumbs - Homology or Homoplasy?

homoplasy

BPQ

Human and dinosaur bipedality - Homology or Homoplasy?

Embryology

• Homology among traits during development

  • some ancestral traits can still be found in embryos

• Development of these “old” traits sometimes goes wrong

Molecular biology

• genetic info can be homologous as well

  • Much of what we understand about evolutionary history comes from genetic similarities

Biogeography

• the geography distribution of organisms

Pangaea

ancient supercontinent

Gondwana

ancient southern continent

Laurasia

ancient northern supercontinent

Ratites

• large flightless birds

• only found in southern continents

No

BPQ
Flightlessness among Ratites is homology, so what can we infer about the most recent common ancestor? Could it fly?

Lung Fish

fish with lungs

only found in southern continents

Fossil Record

• largely incomplete

• but provides insight into what the past looked like

• changes as you go back in time

  • no mammals in jurassic

  • no angiosperms in triassic

  • no gymnosperms in carboniferous

  • no fish in the cambrian

Time Terms

• Eon

  • Era

    • Period

      • Epoch

Eons

• Phanerozoic

  • Present - 570*

• Proterozoic (Precambrian)

  • 570 Mya - 2500 Mya

• Archaean (Precambrian)

  • 2500 Mya - 4000 Mya

• Hadean (Precambrian)

  • 4000 Mya - 4500 Mya

Precambrian

• Hadean (Eon)

  • No life on Earth

• Archaean (Eon)

  • Prokaryotes appear

• Proterozoic (Eon)

  • Eukaryotes appear

  • Multicellular organisms appear

    • Coincides with rise of oxygen levels

Phanerozoic Eras

• Cenozoic

  • present - 65.5 Mya*

• Mesozoic

  • 65.5 Mya - 245 Mya *

• Paleozoic

  • 245 Mya - 570 Mya *

memorize dates

Paleozoic Periods

• Permian

  • 245 - 286 Mya

• Pennsylvanian (Carboniferous Pd)

  • 286 Mya - 318 Mya

• Mississippian (Carboniferous Pd)

  • 318 Mya - 360 Mya

• Devonian

  • 360 mya - 408 mya

• Silurian

  • 408 mya - 438 mya

• Ordovician

  • 438 mya - 505 mya

• Cambrian

  • 505 mya - 570 mya

Mnemonics

Cambrian, Ordovician, Silurian, Devonian, Mississippian, Pennsylvanian, Permian

Come Over Some Day, Maybe Play Poker?

Campbell’s Onion Soup Doesn’t Make People Puke

Cambrian

• Cambrian Explosion

  • Rapid diversification of multicellular Eukaryotes

• Arthropods were the most dominant animal

  • Some ventured onto land

Ordovician

Ordovician radiation

• another diversification event close to the scale of the Cambrian explosion

• Appearance of jawless fish

Silurian

• Appearance of bony fish

• first vascular plants appear

• first fully terrestrial animals appear

  • Pneumodesmus

Devonian

• “Age of Fishes”

  • rapid diversification of fish

• Entire evolution of land walking tetrapods from jawed fish occurs

Carboniferous (Mississippian and Pennsylvanian)

• Amphibians diversified

• First amniotes appear

• Lycopsid forests

• Giant terrestrial arthropods

Permian

• Gymnosperms appear

  • begins to replace lycopsid and fern trees

• Synapsids become dominant

  • Mammals are synapsids

• First dinosaurs appear

• Ends with PT extinction

  • 95% life dies

Mesozoic era

• “Age of the Dinosaurs”

• Cretaceous

  • 65.6 Mya - 144 mya

• Jurassic

  • 144 mya - 208 mya

• Triassic

  • 208 - 245 mya

Triassic

• synapsids, crocs, dinosaurs compete for control after PT extinction

  • dinosaurs win

• dinosaurs begin to diversify

• mammals appear

Jurassic

• Gymnosperms are dominant

• first Angiosperms may have appeared

• first birds appear

• pangaea splits

• dinosaurs get big!

Cretaceous

• angiosperms become more common

• some groups of dinosaurs go extinct

  • stegosaurids

• some new groups appear

  • ceratopsids

• KT (KPg) extinction event

  • 65% life dies

  • All non-avian dinosaurs die

Cenozoic era

• “Age of Mammals”

• Quaternary Period (2 epochs)

  • Holocene

    • present - 11,000 ya

  • Pleistocene

    • 11,000 ya - 1.6 Mya

• Tertiary Period (5 epochs)

  • Pliocene

    • 1.6 mya - 5.3 mya

  • Miocene

    • 5.3 mya - 27.3 mya

  • Oligocene

    • 23.7 mya - 36.6 mya

  • Eocene

    • 36.6 mya - 65.5 mya

  • Paleocene

    • 57.8 mya - 65.5 mya

Mnemonics (epochs)

Paleocene, Eocene, Oligocene, Miocene, Pliocene, Pleistocene, Holocene

Pretty Eager Old Men Play Poker Hard

Mnemonics (all periods)

Cambrian, Ordovician, Silurian, Devonian, Mississippian, Pennsylvanian, Permian, Triassic, Jurassic, Cretaceous, Tertiary, Quaternary

Come Over Some Day, Maybe Play Poker? Three Jacks Can Take Queens

Paleocene

• Angiosperms are expanding

• Forests grow rapidly in absence of dinosaurs

• Mammals become dominant

  • Start out small but quickly grow larger

Eocene

• Very warm period

  • forest covered even the poles

• Ungulates (hooved mammals) become prominent

• Whales become more diverse

• Grasses appear in wet riverside habitats

• Ends with Oi1 event

  • first major cooling and expansion of arctic ice

Oligocene

• Antarctica becomes covered in ice

• Most modern families of mammals are present

• Hominids (Apes) appear

• Angiosperms are becoming more dominant

• Grasses are spreading away from waterside habitats

Miocene

• Grasslands appear

• Grazing animals become more common

• Hominins (bipedal apes) appear

• Earth warms then begins to cool again

Grasslands have C4 grasses that trap more carbon underground, and since Carbon is a greenhouse gas, it leads to global cooling

But Carbon from the ground comes back eventually and warm the atmosphere

BPQ

C4 grasses trap more Carbon underground and have lower water loss. How could the appearance of grasslands cause global cooling?

Pliocene

• Australopithecus appears

• “Great American Interchange”

  • Panama rose up from the sea floor

  • N & S America connected for first time since Cretaceous

Pleistocene

• “Ice Age”

• Modern humans appear

• Megafauna extinction

  • Mammoths

  • Mastodon

  • Glyptodon

  • Giant Ground Sloths

Humans evolved in Africa → Homo sapiens evolved with African wildlife

when humans migrated, they were invasive species

BPQ

Africa had much of its megafauna spared from this extinction event. We know that changing climate change prob had a big effect on these animals.

However, what other factors could also be apart of these extinctions and explain why Africa still has much of its megafauna?

Holocene

• Modern day

• Glacial retreat (end of ice age)

• Worldwide expansion of human population

• All of recorded human history

Phylogeny/Cladogram

figure that shows the evolutionary relationships among organisms

“phylogenetic tree”

Leaves

Selected Taxa of phylogenetic tree

Root

point where the tree connects back to the rest of the tree of life

Node

most recent “hypothetical” ancestor

• all taxa are leaves → we cannot tell what true ancestors are

• even fossils will always be leaves

• We cannot distinguish ancestors from relatives

Speciation

the process of one species becoming two or more species

Species

Difficult answer: the smallest evolutionary unit

AP Bio answer: a grp of organisms that can interbreed (and create viable, fertile offspring)

Biological species concept

• requires reproductive barriers

  • Prezygotic barriers

    • prevents mating

  • Postzygotic barriers

    • prevents creation of viable, fertile offspring

Allopatric Speciation

new species appear in different areas

Vicariance

areas move

Migration

species move

Sympatric Speciation

New species appear in the same areas

Extinction

when all members of a species dies off

• sometimes opens up niche that new species can inhabit

Mass extinction

when a large percentage of Earth’s species die off at once

• 5 major ____ ____ events

• Humans might be causing the 6th

Adaptive Radiation

a rapid rate of speciation from a common ancestor, often associated with ecological and morphological diversity (Divergent evolution)

Gradualism

speciation associated with slow, gradual morphological changes

Punctuated Equilibrium

speciation associated with rapid morphological changes

Speciation-Extinction Equilibrium

a constant state of biological diversity

• speciation rate = extinction rate

cant tell if fossils could produce viable offspring/reproduce at all

BPQ

What are some problems with the biological species concept?

Linnaean Classification System

• Organisms are grouped into hierarchies

• Still used today but w less emphasis

• Kings Play Cards On Fat Green Stools

Binomial Nomenclature

• Scientific names for species

• always italicized or underlined

• 2 parts

  • Genus → can NOT be reused

  • species epithet → can be reused for other genuses

1. we don’t have enough taxonomic levels to show ALL relationships

2. or over-generalize by placing all organisms into one group → eliminates relationships

BPQ

What are some of the problems w the Linnaean Classification system?

Taxonomy

process of naming and classifying organisms

based on phylogeny

loosely fit into Linnaean classification

Monophyletic Group

• consists of 1 common ancestor and all the descendants

• good taxonomic names are ones that are monophyletic

Paraphyletic group

Consists of 1 common ancestor but is missing some descendants

Polyphyletic group

consists of distantly related organisms

Paraphyletic

BPQ

Think about what you consider a fish

Are fish monophyletic, paraphyletic, or polyphyletic?

Cladistics

a sound method for developing hypothesis of evolutionary relationships

• ALL phylogeny are hypotheses

Cladistics is NOT just based on organisms looking similar

Cladistics requirements

1. Informative characters (traits)

2. Parsimony

Characters

1. Synapomorphies

2. Plesiomorphies

3. Autapomorphies

Synapomorphies

• shared derived (new) characters

• Informative

Plesiomorphies

• shared ancestral (old) characters

• Uninformative

Autapomorphies

• unshared derived (new) characters

• uninformative

Outgroup

distantly related group that is used to distinguish synapomorphies from plesiomorphies

without an ____, we dont know which traits are synapomorphies and which are plesiomorphies

• presence (1) or absence (0) of a trait are arbitrary

If this has the trait, it is considered a Plesiomorphy

• evolved before the ingroup did

Looking like a lizard is a plesiomorphy (uninformative) bc all amniotes looked like lizards

BPQ

how can we explain how crocs can be more closely related to birds even tho they look more like lizards?

AP way to make a phylogeny

group by similarities

Parsimony Analysis

assumption = evolutionary change

• phylogeny w least number of evolutionary changes is probably the correct one

Character Matrix

columns: characters/traits

rows: organisms/taxa

1: presence of trait

0: absence of trait

Ingroup: Organisms/taxa being studied

Outgroup: distant relative

• used to determine synapomorphy/plesiomorphy

• not shown in picture

• all the traits listed on the slide are not informative

• human’s traits are autapomorphies

• chimps, gorillas, orangutan traits are plesiomorphies

BPQ

how is it possible chimps are more closely related to humans?

Homoplasy

shared characters NOT due to common ancestry

Goal of cladistics

• maximize homology

• minimize homoplasy

  • homoplasies require extra evolutionary steps

Competing Hypotheses

• different sets of data can create multiple phylogenies

• many problems in phylogenetics are still unresolved

• All phylogenies are hypotheses

  • phylogenies are often reassessed as new data comes in

each tree is arranged differently, but have the SAME relationships

BPQ What is the difference in relationships between the following phylogenies?

Tree Topology

• nodes on a tree can rotate without changing relationships

• Polytomy

Polytomy

an unresolved tree - when there is more than one most parsimonious solution, so a node splits into 3+ branches

• Hard Polytomy - Results from actual evolutionary processes that happened (real)

• Soft Polytomy - Results from bad data/not enough data (not real)

Taxonomic Definitions

3 ways to define a taxonomic group (clade)

• Apomorphy-based Clade

• Node-based Clade

• Stem-based Clade

Apomorphy-based clade

the first ancestor to evolve a synapomorphy and all of its descendants

Node-based clade

the most recent common ancestor of two taxa and all of its descendants

• when both taxa are extant, it is called a crown clade

Stem-based Clade

all organisms more closely related to one taxa than to another

Character Optimization

• placing characters on phylogenies in a way to yield the most parsimonious evolution

• Process

  1. If the outgroup is 1, place that character at the root

  2. Add characters to the tree use the least number of steps

  3. Use (-) in front of a character to show loss of the character

DELTRAN optimization

• delayed optimization

• prioritizes convergent evolution

• in phylogeny, draw the trait evolving/being lost twice

• only equally parsimonious to ACCTRAN during polytomy