Precambrian and Paleozoic, Mesozoic and Cenozoic, Genome Evolution

Know the approximate dates and general kind of fossils found in the Ediacaran Biota and Burgess Shale

Ediacaran Biota:

• 565-544 Ma. End of Proterozoic.

• Mostly impression and almost none of them have shells or other hard parts.

• Lichens, algae, life no longer represented. Fauna: sponges, jellyfish, comb jelly relatives.

• Rangeomorphs. Bilaterally symmetrical like todays mollusks, worms, and crustaceans.

• Small bilaterians.

Burgess Shale Fauna:

• Lagerstatte (extrodinarily rich deposit). 505 Ma

• Preserve soft-bodied animals in detail.

• Large colonial cnidarians present in both. Cambrian species: arthropods, trilobits, segmented worms, wormlike priapulids, sipunculids, mollusks, chordates,

• Cnidarians, arthropods, segmented worms, molluscs, chordates, and even phyla that may be unknown among extant organisms

When did Kingdom Animalia appear on the planet?

approximately 800 Ma

What happened to the Ediacarans?

Mass extinction at the end of the Proterozoic eliminated much of the ediacaran fauna

Describe the key morphological features of the transitional fossils that illustrate the fish-tetrapod transition

Tetrapods have similar forelimbs because they descended from a single lineage, inherited fundamental design of their appendages.

• Devonian

• All sarcoperygians (lobe-fin bony fish) are characterized by a proximal bone in the fin/limb - humerus (forelimb) or femur (hindlimb).

• Well developed joints between consecutive vertebrate and enlarged rib attatchments.

• Pelvis attatched by novel sacral ribs.

• Respiration, osmoregulation.

• fin rays → digits

• the loss of dorsal and anal fins and a flattened skull with dorsally facing orbits.

What happened during the Cambrian Explosion? Are these animals representatives of living phyla? (The jury’s still out, so just support your argument & compare the textbook & Wonderful Life!)

The Cambrian explosion filled many of the ecological niches present in shallow marine habitats.

sudden increase in atmospheric oxygen occurred during the mid-Cambrian and made large size and rapid movement possible. They also posited that a mass extinction eliminated much of the Ediacaran fauna at the end of the Proterozoic, creating an opportunity for the tiny deuterostomes and protostomes present at the time to evolve in response to the changed conditions.

an explosion of morphological diversity, but not necessarily an explosion of lineages, which occurred much earlier. The idea that the major animal lineages existed long before they diversified and produced large-bodied forms is captured in the quip that the Cambrian explosion had a “long fuse.”

During the Cambrian Explosion (~541 million years ago), there was a rapid diversification of animal body plans, many of which resemble those of living phyla. While the textbook presents these forms as early members of modern groups, Wonderful Life argues that many were experimental and later extinct lineages, suggesting greater early evolutionary disparity than seen today.

Why did the Cambrian Explosion occur?

a rise in atmospheric oxygen levels, changes in ocean chemistry, and perhaps a mass extinction event.

Transition from diffusion-deploying Precambrian detritivores or
microbe-munchers to Cambrian animals that exploited many niches
• Rising oxygen concentrations & extinction of Ediacaran fauna (Knoll &
Carroll 1999

How old are the earliest land plants? Did they look like modern plants? Why/Why not?

470 Ma. No, they were small, simple, and lacked true roots, leaves, or vascular tissue, resembling mosses or liverworts. This simplicity reflects their early adaptation to land, before the evolution of more complex structures seen in later vascular plants.

Who were the earliest land plants?
• Bryophytes
• Rhyniophytes, zosterophylls, and trimerophytes!

Why do you think we don’t have lots of representatives of fossil fungi & other tiny organisms?

We don't have many fossil fungi and other tiny organisms because their soft bodies and microscopic size make them unlikely to fossilize, especially without hard parts like bones or shells. Additionally, the environments where they lived often didn’t favor preservation, and even when fossilized, they're hard to detect and identify in the rock record.

What happened at the end of the Devonian?

Hangberg Event: Loss of ~95% of vertebrate species

Know what a placoderm is, an ostracoderm, and a tetrapodomorph sarcopterygian

Ostracoderms: Jawless, heavily armored early fishes

Placoderm: The earliest gnathostomes (jawed fishes), anterior ½ of the fish covered by heavy dermal bone armor; first vertebrate group with internal fertilization and first viviparous vertebrates! Originated in them (intercourse)

• Acanthothoraciformes: most basal order; “oldest known jawed vertebrates”

• Rhenaniformes: Extreme dorsoventral compression; look like rays/skates, but swam differently. Why? lacked the flexible, wing-like pectoral fins and muscular fin control that rays use for undulating motion. Instead, their movement was likely more rigid and limited, relying on body undulations or tail propulsion

• Antiarchiformes: mainly freshwater, global distribution; very heavily armored; piral valve intestine; jointed, muscular pectoral appendages.

  • Bothriolepis: tail isn’t preserved in the fossil because it was made of softer less mineralized tissue

• Petalichthyformes: dorsoventrally compressed; bottom-dwellers. Resemble rheananiforms

• Pyctordontiformes: Holocephlan-like; 1st claspers, 1st evidence of viviparity

  • Materpiscis

• Anthrodiriformes: Largest placoderm order; craniovertebral joint allowed opening of mouth; diverse dentition; reached large sizes (at least 6 m)

Terapodomorph Sarcopterygian: Lobe-finned fishes on the lineage that gave rise to tetrapods.

Chondrichthyans: Early chondrichthyans like Cladoselache had more gill slits, more fin spines, and weirder teeth than any sharks alive today. Teeth are most likely to be found as shark fossils.

What’s great about teeth?

Great for diagnosing a fossil to family or species, but their morphology is often convergent - they aren’t so good for untangling deeper-level phylogenetic relationships.

When you only have strange tooth fossils—like in Helicoprion, which is known for its bizarre spiral "tooth whorl"—it makes reconstructing the animal's full anatomy and lifestyle very difficult and speculative. CT scanning revealed jaw cartilage. Was probably a holocephala, related to the edestids.

How did the Paleozoic end? Are there parallels between the Permian extinction event and what’s going on today? Who diversified after the Permian mass extinction?

The Permian-Triassic (P-T) extinction marked the end of the Paleozoic large-scale volcanic activity, combined with lowered oxygen levels and runaway greenhouse conditions, was the likely culprit. The results of this work indicate that the extinction interval was less than 200,000 years, was synchronous on land and in the ocean, and was centered on a date of 252.3 Ma. The synchronous nature of the extinction suggests a common cause and greatly limits potential mechanisms. characterized by massive fluctuations in the global carbon cycle, indicating long-term environmental instability. The term Lilliput effect is commonly used to characterize body-size reductions in the wake of mass extinctions, which seem to be a common feature of the fossil record. fluvial changes were caused by the extinction of ground vegetation, Siberian eruptions elevated CO2 levels and produced short-term effects like acid rain, wildfires, global cooling (from dust and sulfates ejected in the atmosphere), and ocean acidification.

Some rapidly evolving groups (e.g., ammonoids, conodonts) were able to diversify within 1–2 million years after the extinction. After the Permian mass extinction, marine groups like bivalves, ammonoids, and corals rapidly diversified, along with marine reptiles like ichthyosaurs. On land, archosaurs (including early dinosaurs and crocodile relatives) and therapsids (mammal ancestors) evolved new forms. Seed plants like conifers also became dominant, reshaping ecosystems in the Triassic.

• Both involve rapid climate change, especially global warming driven by high CO₂ levels—then from volcanic activity, now from human emissions.

• Massive loss of species and ecosystem disruption occurred, with modern extinction rates now comparable to past mass extinctions.

• In both cases, ocean acidification, deoxygenation, and habitat loss play major roles

Who died at the end of the Triassic? and what big group diversified after that?

Triassic saw the rise of dinosaurs. Coelophysis! many marine and terrestrial species became extinct, including various marine reptiles, phytosaurs, aetosaurs, and synapsids. Following this extinction event, dinosaurs diversified and became a dominant group. 

What makes a dinosaur pelvis different form the pelves of other reptiles?

the orientation of the pubis bone and the presence of a perforate acetabulum (open hip socket).

Where did amniotes come from? What’s a synapsid, anapsid, and diapsid? Which one are we?

Amniote Origins
• Amniotes evolved from a lineage of “amphibians” related to anthracosaurs in the Carboniferous (about 350 mya)
• Amniote groups based on holes in skull (fenestrae):
Synapsids: 1 fenestra
Diapsids: 2 fenestrae
Anapsids: no fenestrae

Humans are synapsids

Who’s the best Permian synapsid? Be ready to support your answer ;)

Which clade of dinosaurs gave rise to birds?

Birds are a branch of theropod dinosaurs

What are the two main clades of dinosaurs and how do we tell them apart based on their pelves?

Ornithischian “Bird-Hipped” Dinosaurs
• Pelvis has ilium, ischium, and pubis
• Pubis points backward, runs parallel with ischium
• Birds also have backward-pointing pubis, but
this is due to convergence
• Many groups:
• Ornithopoda: hadrosaurs ("duck-billed dinosaurs"),
iguanodontids, heterodontosaurs, and
hypsilophodontids
• Ceratopsia (horned dinosaurs)
• Ankylosauria (armored ankylosaurs)
• Stegosauria (stegosaurs)
• Pachycephalosauria (pachycephalosaurs)

Saurischian “Lizard-Hipped” Dinosaurs
• Pelvis has ilium, ischium, and pubis
• Grasping hand, asymmetrical
fingers, more mobile neck
• Pubis at an angle to the ischium
• Two major groups:
1. Sauropods
2. Theropods
• Birds derived from this group,
rather than the ornithischian
dinosaurs
• “Bird-hipped” condition
(backward-pointing pubis) is an
example of convergent evolution

Why is Archaeopteryx a great example of a transitional fossil?

Archaeopteryx had flight feathers like a modern bird’s and a dinosaur-like skeleton with teeth and a long tail. Could glide or do rudimentary powered flight.

What bird features were already present in theropod dinosaurs?

Current phylogeny puts birds as branch of theropod dinosaurs, related to animals like Velociraptor and Tyrannosaurus
• Many bird features had already evolved in dinosaurs:
1. feathers
2. furcula (wishbone)
3. pneumatic (hollow) bones
4. tridactyl foot with big toe pointed backward

Dinosaurs were endothermic/warm-blooded. Generated their own body heat through metabolism.

When did angiosperms appear in the fossil record? When did putative angiosperm fossils appear?

Probably Late Jurassic or Early Cretaceous (conflicting interpretations
of fossil pollen grains). 110 Ma
• Early angiosperms likely had simple flower organography

What happened at the end of the Cretaceous? How do we know, and how do we spot this event in the fossil record?

Cretaceous (65 mya): 76% of species; bolide impact in Yucatan resulting in
rapid cooling, probably combined with Deccan volcanism, ultimately a shift to
global warming, eutrophication and anoxia of the oceans

K-Pg Boundary can be recognized in the field by:
• rare element iridium
• shocked quartz grains
• glassy microtektites
• decrease in angiosperm
pollen
• “fern spike” (lots of fern
spores!)

Cretaceous–Paleogene

What was the Great American Biotic Interchange and what kind of awesome mammals did North America get out of it?

• Giant Ground Sloths - South America 35 Ma; migrated into N. America 8 Ma.

• Glyptodonts

  • Xenarthans (rel. to armadillos)

  • hunted? Climate change?

• Fossil Camels

• Fossil Rhinoceroses

  • Climate change

• Chalicotheres

• Mammoths and Mastodons

What happened at the end of the Pleistocene?

End of the Pleistocene (~12,000 years ago): extinction of megafauna, arrival of humans, end of glaciation. End of last ice age and began Holocene epoch. Expansion of modern humans.
• What remains from this time?

• Fossils of megafauna in permafrost, caves, and tar pits

• Stone tools and archaeological sites left by early humans

• Some survivors, like bison and reindeer, which adapted to post-Ice Age environments
  • Are we living in the Anthropocene
  

Know that we can sequence DNA from ancient animals (but not very ancient animals!)

Would you expect a ‘simple’ or a small organism to have a small genome?

Yes?

Why do eukaryotes have such a gigantic genome?

a high amount of non-coding DNA, repeated sequences, and the retention of gene duplicates

• Non-coding DNA – Much of the genome doesn't code for proteins but includes regulatory elements, introns, and repetitive sequences.

• Gene duplication – Eukaryotes often duplicate genes, leading to larger gene families and raw material for evolution.

• Endosymbiosis and genome mergers – The incorporation of whole genomes from symbiotic events (like mitochondria and chloroplasts) added complexity.

• Transposable elements – "Jumping genes" can replicate themselves and inflate genome size over time.

Are introns useless? Why/why not?

Introns aren’t useless!
• Presence of introns highly conserved across distantly related organisms
(Rodriguez-Trelles et al. 2006, Roy & Gilbert 2006) & presence of introns
creates a burden on the host
• Excision of spliceosomal introns requires spliceosome (among largest
molecular complexes, = 5 snRNAs & >150 proteins)
• Book says “we can only speculate as to their function, if any,” BUT introns
modify expression level of their host gene in many different ways

Why do people suspect introns may be adaptive or beneficial?

It could be that introns are simply excess

genetic material that serves no purpose in the organism, like mobile elements.

But if introns do not do anything, their presence would likely be quite variable.

Instead, the positions of introns are well conserved across distantly related organ-

isms

Why are mobile genetic elements considered genome parasites? Can you think of any situations in which mobile genetic elements might be advantageous to the individual?

Mobile Genetic Elements = DNA sequences that have the ability to
move from location to location within a genome,
aka transposable elements, transposons
• Transposons that leave a copy of themselves behind = retrotransposons
• Fitness of the element increases as it is spread through a population of
genes in a genome, but can have negative effects on genome fitness;
transposons often called genome parasites

• Creating beneficial mutations – In rare cases, their insertion can improve gene function or regulation.

• Driving genetic diversity – They increase variation, which may help in adapting to changing environments.

• Altering gene expression – They can introduce new regulatory sequences that fine-tune how genes are turned on or off.

• Providing raw material for evolution – Some mobile elements become co-opted into useful genetic functions (e.g. immune system genes, placental genes in mammals).
  

Explain how a mobile genetic element’s fitness might be high, while its’ host’s fitness might be low

If the new loca-

tion is an intergenic region, there may be no effect on the phenotype of the host.

But if a mobile element lands within the coding sequence of a gene, deleterious

knock-out mutations usually result. Carrying mobile elements in the

genome appears to be neutral at best and maladaptive at worst.

The answer is that while se-

lection at the level of hosts may select against mobile elements, selection at the

level of the elements themselves favors their spread. mobile el-

ements that replicate themselves most efficiently and with the least fitness cost to

the host genome are, on balance, favored by natural selection and tend to spread.

How do host genomes defend against mobile genetic elements? (explain this in terms of post-transcriptional and pre-transcriptional silencing)

Post-transcriptional
silencing using
interference mRNAs
to silence mobile
elements

Pre-transcriptional
silencing using
methylation: methyl
groups attached to DNA
prevent its transcription
to RNA

exaptation—traits that originally evolved for one purpose (like regulating gene expression in single-celled organisms) but were later co-opted

Where do new genes generally come from?

Gene duplication = primary source of new genes
• Polyploidization = duplication of whole genome
• Segmental duplication = duplication of small sections of genome
(a gene, piece of gene, stretch of DNA containing several genes)
• Caused by mobile genetic elements or unequal x-ing over

How does segmental duplication happen?

Segmental duplication happens when a section of DNA—often thousands to millions of base pairs long—is copied and inserted elsewhere in the genome. This can occur through:

1. Unequal crossing over during meiosis, where misaligned chromosomes exchange unequal segments.

2. Replication errors, such as slipped-strand mispairing, where the DNA replication machinery accidentally copies the same region twice.

3. Transposable elements or retrotransposons, which can carry nearby DNA with them when they move.

Know the Roma tomato example of a mobile genetic element resulting in a new phenotype

In tomatoes, a mobile genetic element called Rider caused a segmental duplication that inserted the SUN gene into another gene, DEFL1, on a different chromosome. This disrupted DEFL1 and gave SUN new cis-regulatory elements, causing it to be expressed during fruit development. As a result, tomatoes that carry this duplication develop oval-shaped fruits instead of round ones. This example shows how a transposable element can drive morphological change by altering gene regulation.

What can happen to a duplicated gene? How can subfunctionalization lead to an escape from adaptive conflict? (i.e. know the Lycodichthys example!)

Subfunctionalization can lead to an escape from adaptive conflict when a gene with two conflicting functions is duplicated, allowing each copy to specialize in one task and improve independently.

In the Antarctic eelpout, the SAS-B gene originally performed two functions: sialic acid synthesis and weak ice-binding. These functions conflicted—improving one impaired the other. After gene duplication, one copy retained and enhanced the catalytic function (SAS-B), while the other (which became AFPIII) lost catalytic activity but evolved into a highly effective antifreeze protein. This division of labor allowed both functions to optimize without constraint, demonstrating how subfunctionalization resolved the conflict through specialization.

Escape from Adaptive Conflict
• Adaptive constraint: multiple functions/genotypes cannot be
optimized simultaneously
• Duplication provides a pathway by which each gene can
specialize to a single function
example: Lycodichthys dearborni

SAS-B protein (from ancestral SAS-A) inhibits ice crystal growth &
changes their shape and catalyzes formation of sialic acid, but when
modified to be antifreeze-like, it loses its original function

Positive selection for altered function
of both genes after duplication

Why do we mostly study large phenotypic effects of single mutations?

It’s really hard to detect small
phenotypic changes
Easier to study the big ones!

Know examples of adaptations arising from new mutations and from existing alleles present @ low freq.

Finding the genotypic changes responsible for phenotypic
innovation = DNA + natural selection!
• Where do the alleles for new adaptations come from? New
mutations, or are they already present @ low frequency?
Adaptation from
new mutation:
Tetrodotoxin
resistance in
garter snakes
Adaptation from
standing variation:
Shared origin of
the stickleback Eda
alleles (plate and
speed phenotypes