Radiations and Extonctions

What percentage of species that ever existed are extinct?

~99.9% (Raup, 1991).

What is the background extinction rate?

0.1-1 extinction per million species per year (E/MSY); accounts for 95% of extinctions.

How long do species typically survive?

1-4 million years; Homo sapiens at 200,000 years.

What is a key difference between background and mass extinctions?

Background: Slow, multigenerational, driven by competition/habitat loss; Mass: Rapid, stochastic, non-selective.

Name a cause of the Permian mass extinction (~252 MYA).

Volcanic activity, deep ocean anoxia (“Great Dying”).

What triggered the mammalian radiation in the Tertiary?

Cretaceous-Tertiary (K-Pg) mass extinction (~66 MYA) from asteroid impact; ~70% species lost.

What are the three steps of adaptive radiation (Schluter, 2000)?

1. Rapid diversification into niches; 2. Competition drives specialization; 3. Specialization causes reproductive isolation/speciation

How does Pseudomonas fluorescens demonstrate adaptive radiation?

Static culture creates niches (top, middle, bottom) → three phenotypes (fuzzy, wrinkly, smooth) emerge from clonal founder.

What are three paleontological drivers of adaptive radiation?

Ecological release, ecological opportunity, key innovations/major transitions.

Why are background extinction rates important today?

Benchmark current extinction crisis; rates post-1500 AD far exceed 0.1-1 E/MSY.

How does life avoid thermodynamic equilibrium?

Creates local negative entropy via energy dissipation (e.g., sunlight, food → metabolism → waste heat).

What is an example of a non-linear chemical reaction in early life?

Belousov-Zhabotinsky reaction; creates local order via energy dissipation.

When did multicellular life emerge, and what evidence supports this?

~600 MYA; Ediacaran microfossils show germ-soma separation, cell differentiation.

What are two trade-offs of multicellularity?

Benefits: Cell specialization, resilience. Costs: Inter-cellular conflict, nutrient demands.

Name a model organism for studying multicellularity.

Volvocine algae (Chlamydomonas → Volvox) or slime moulds (Dictyosteliomycetes).

What are three synapomorphies of Animalia?

Blastula development, conserved HOX genes, eggs from one Meiosis II daughter cell.

How do animals compare to prokaryotes in biomass?

Animals: <1,000 Mt C (invertebrates), <120 Mt C (vertebrates); Prokaryotes: 15,000–303,000 Mt C.

What is the holobiont concept?

Animals are communities; bacterial cells outnumber host cells 10:1, with 150x more genes.

What embryonic layers do all animals share?

Endoderm (digestive system) and ectoderm (CNS, skin); Bilateria add mesoderm (muscles, organs).

How are Bilateria classified based on embryology?

Protostomes (mouth-first blastopore) vs. Deuterostomes (anus-first blastopore).

What do HOX genes do in animals?

Transcription factors controlling body plan along head-tail axis; highly conserved.

Where are HOX genes absent in basal animals?

Ctenophora (box jellies) and Porifera (sponges).

What is the Cambrian Explosion, and when did it occur?

Rapid diversification of animal phyla ~541 MYA, post-Ediacaran extinction.

Name two drivers of the Cambrian Explosion.

Increased oxygen/predation (ecological); HOX gene evolution (genetic).

How many modern animal phyla exist, and what are the main groups?

~35 phyla; Radiata (Cnidaria), Bilateria (Protostomes: Lophotrochozoans, Ecdysozoans; Deuterostomes: Echinoderms, Chordates).

What is the main source of dog breed diversity?

Domestication from grey wolves; founder events and hybridization.

What drives dog breed divergence?

Genetic drift (non-adaptive) and selection (adaptive: morphology, behavior).

What is modularity in the context of dog skulls?

Independence of trait groups (e.g., jaws separate from cranium).

How does modularity affect dog skull evolution?

Allows jaw length changes without cranium/brain trade-offs, speeding evolution.

What is the main cranial variation in dogs?

Jaw length (brachycephalic: short, e.g., Pug; dolichocephalic: long, e.g., Collie).

How many genetic loci drive dog skull differences?

Five loci, identified via GWAS.

What is the key gene mutation for brachycephaly?

BMP3F452L, nearly fixed in short-faced breeds.

How was BMP3’s role in brachycephaly confirmed?

Morpholino knockdown in zebrafish caused shorter, flatter face.

What does evo-devo study in dog evolution?

How developmental changes (e.g., modularity, BMP3) drive morphological variation.

Why is dog skull evolution considered an adaptive radiation?

Rapid cranial variation from standing wolf variation, driven by selection, fills functional niches.

What is speciation?

The evolution of reproductive isolation within an ancestral species, resulting in two or more descendant species.

How has the idea of species evolved since Darwin?

Darwin saw species as arbitrary groups; now defined by genetic differentiation and reproductive isolation (Biological Species Concept).

What is the Biological Species Concept?

Groups of interbreeding populations unable to exchange genes with others in the same area (Mayr).

Name the three geographic modes of speciation.

Allopatric, Parapatric, Sympatric.

What is Allopatric speciation?

Speciation due to a geographic barrier (e.g., mountains, oceans) with no gene flow; includes vicariance (large populations) and peripatric (small).

What is Parapatric speciation?

Speciation with restricted gene flow between adjacent populations due to environmental differences (e.g., clines).

What is Sympatric speciation?

Speciation without geographic barriers, driven by disruptive selection and assortative mating in the same area.

Name three genetic/causal bases of speciation.

What is Ecological speciation?

Barriers to gene flow evolve due to ecologically-based divergent selection, not just geography.

What is Dobzhansky-Mueller incompatibility?

Genetic incompatibility causing reproductive isolation when alleles from divergent populations mix incorrectly.

Example of Allopatric speciation?

Appalachian salamanders, diversified by topographic isolation.

Example of Sympatric speciation?

Nicaragua crater lake cichlids, diverged within the same lake via disruptive selection.

What is an adaptive radiation?

The evolution of ecological and phenotypic diversity within a rapidly multiplying lineage.

What three factors influence the speed of speciation?

Time (neutral divergence), geography (selection), and lineage effects (varies across groups).

How does prezygotic isolation compare to postzygotic isolation?

Prezygotic isolation arises faster than postzygotic, except in polyploid speciation.

How does geography affect speciation speed?

Prezygotic isolation develops faster in sympatric populations than allopatric due to reinforcement.

What is reinforcement in speciation?

Natural selection enhances prezygotic isolation in sympatric populations to prevent hybridization.

Name the four criteria of adaptive radiations.

Common ancestry, phenotype-environment correlation, trait utility, rapid speciation.

What is phenotype-environment correlation?

Traits of species match their environment, e.g., stickleback body shape suits benthic or limnetic habitats.

What is trait utility in adaptive radiations?

Traits enhance fitness for specific niches, e.g., cichlid jaw shapes improve feeding efficiency.

Example of adaptive radiation in fish?

African cichlids (e.g., Lake Malawi: >1000 species) diversified via ecological and sexual selection.

Example of adaptive radiation in sticklebacks?

Threespine sticklebacks evolved benthic and limnetic forms in lakes, differing in size and shape.

What drives adaptive radiations?

Ecological speciation from divergent selection, resource competition, and new niches, often in “island” habitats.

How to test for adaptive radiations?

Use the comparative method, considering phylogeny, to test adaptation (e.g., convergent evolution vs. shared ancestry).

What are the defining features of mammals?

Hair, sweat glands, three middle ear bones, single jaw bone, diphyodonty, red blood cells without nuclei, and a neocortex.

What are the three living groups of mammals?

Monotremes, Marsupials (Metatheria), and Placentals (Eutheria).

What is diphyodonty?

The condition of having two successive sets of teeth — one deciduous and one permanent.

What structure is thought to have evolved into mammary glands?

Apocrine-like sweat glands.

What are the two types of placenta in mammals?

Chorio-allantoic (placentals) and chorio-vitelline (marsupials).

Which mammals lay eggs and lack nipples?

Monotremes (e.g., platypus and echidnas).

What are the functions of mammalian hair?

Insulation, communication, camouflage, waterproofing, protection, touch sensitivity (vibrissae), and filter feeding.

What are amniotes?

Tetrapods with embryos enclosed in membranes (amnion, chorion, allantois), enabling reproduction on land.

What skeletal trait separates mammals from reptiles?

Mammals have a single lower jaw bone (dentary) and differentiated teeth.

What is the evolutionary origin of mammal middle ear bones?

Derived from reptilian jaw bones (e.g., articular and quadrate).

What is the "nocturnal bottleneck" hypothesis?

Suggests early mammals were nocturnal to avoid dinosaurs, leading to enhanced smell, hearing, and endothermy.

What are the main placental mammal clades?

Afrotheria, Xenarthra, and Boreoeutheria (which includes Euarchontaglires & Laurasiatheria).

What are the five theories about placental mammal evolution post-KPg extinction?

Explosive, Soft Explosive, Trans-KPg, Long Fuse, and Short Fuse models.

What is a “ghost lineage”?

A predicted evolutionary lineage with no fossil record but inferred from genetic or other fossil data.

What role did the K-Pg extinction play in mammalian radiation?

It wiped out non-avian dinosaurs, allowing mammals to diversify and dominate terrestrial ecosystems.

What is the key difference between anamniotes and amniotes regarding egg-laying?

• Anamniotes (fishes, amphibians) typically lay eggs in water.

• Amniotes (reptiles, birds, mammals) can lay eggs on land (or retain them internally) due to the amniotic egg.

What is the key innovation of amniotes that allowed for true colonisation of land away from water for reproduction?

The amniotic egg (with its protective membranes like the amnion).

During which geological periods did early tetrapod lineages (early "amphibians") diversify?

The Devonian and Carboniferous periods.

When did the lineages leading to modern amphibians and amniotes diverge?

Approximately 370 million years ago (MYA).

What are the three main groups of modern amphibians, collectively known as Lissamphibia?

1. Anura (frogs and toads)

2. Caudata (salamanders and newts)

3. Gymnophiona (caecilians)

Name an important transitional fossil from the Early Permian, considered an ancestor of frogs and salamanders (a "frogamander").

Gerobatrachus

Key characteristics of Anura (frogs and toads):

Short body, no tail (as adults), long muscular hind limbs (for jumping), shortened vertebral column, mostly external fertilisation.

Key characteristics of Caudata (salamanders and newts):

Well-developed tail, cylindrical bodies, reduced skulls, internal fertilisation (via spermatophore) or external, some lungless.

Key characteristics of Gymnophiona (caecilians)

Legless, fossorial (burrowing), often with dermal scales, sensory tentacles, vestigial eyes, internal fertilisation.

What major geological event is linked to the significant radiation of neobatrachian frogs (which constitute ~88% of extant frogs)?

The K-Pg (Cretaceous-Paleogene) extinction event (~66 MYA), which opened new ecological niches.

 Define a "key innovation" in evolutionary terms.

A novel phenotypic trait that allows a taxonomic group to diversify and achieve subsequent radiation and success.

Give two examples of key innovations seen in modern amphibians.

1. Diverse reproductive strategies (e.g., parental care, direct development).

2. Production of defensive toxins

What is direct development in amphibians, and which group exemplifies it as the most species-rich vertebrate genus?

Development where eggs (often terrestrial) hatch directly into miniature adults ('froglets'), bypassing the free-living aquatic tadpole stage. Exemplified by Pristimantis frogs.

How can different reproductive modes, like brook breeding vs. pond breeding in Boophis treefrogs, contribute to speciation?

 By leading to spatial segregation and adaptation to different microhabitats, potentially reducing gene flow and promoting divergence.

 What does the study on Salamandra toxins and colour patterns suggest about the primary driver of toxin profile differences?

Toxin profiles differ more significantly across species than between different colour morphs within the same species, suggesting species-level evolutionary pressures are more critical for toxin composition than colour pattern alone.

What defines a mass extinction event?

A rapid and widespread decrease in biodiversity, often identified by major collapses in marine fauna.

How many mass extinctions are widely accepted since the Cambrian?

Five.

What was the most severe mass extinction event?

The End-Permian extinction (~251 mya), also known as "The Great Dying".

Which mass extinction event marked the end of dinosaurs (except birds)?

The Cretaceous–Paleogene (K-Pg) extinction (~66 mya).

What is the likely cause of the K-Pg extinction?

A massive asteroid impact, supported by the iridium layer and Chicxulub crater.

What geological features are used to trace past extinction events?

Fossil records, shale colour, isotope ratios, LIPs (Large Igneous Provinces), and climate models.

What are conodonts, and why are they important?

Tiny tooth-like fossils used as ideal index fossils due to their wide distribution and rapid evolution.

Which extinction is linked to the eruption of the Siberian Traps?

The End-Permian extinction.

What caused the two extinction pulses in the End-Ordovician event?

First by glaciation (sea level drop), second by anoxic sea conditions as sea levels rose again.

What is the term for the significant diversification during the Ordovician period?

The Great Ordovician Biodiversification Event (GOBE).

What were the main environmental impacts of the Late Devonian extinction?

Anoxia in oceans, global cooling, collapse of reefs, and loss of placoderms and ammonites.