History of Life and Macroevolution

Rocks about 3.48 billion years old in the Dresser Formation of the Pilbara, Western Australia, preserve layered mounds and microbial fabrics that a 2017 study read as traces of life in hot springs. That date tells you life existed by then. It cannot tell you when life began, because older traces could have been destroyed, never formed or not yet found. Every date in the history of life has this shape: a measured age, a method, an uncertainty, and a direction in which the truth could lie.

Macroevolution is evolution above the species level, built from the processes in speciation and molecular evolution read over hundreds of millions of years. Below, Ma means millions of years ago and Ga billions of years ago.

The idea: dating deep time

Fossils are rarely dated directly; minerals in the rocks around them are. Radiometric dating compares how much of a radioactive parent isotope remains in a mineral with how much of its daughter has built up. The half-life is the time for half of the parent atoms in a sample to decay. It is constant for each isotope, so the mineral works like an hourglass: the sand in the bottom bulb tells you the time since it was turned over.

Zircon, common in volcanic ash, takes up uranium as it crystallizes but almost no lead, so its lead comes from later decay.

Worked problem. A hypothetical zircon from an ash bed has stayed closed since it crystallized: no parent or daughter has entered or left, and it started with no radiogenic lead. Treat uranium-235 decaying to lead-207 as one parent and one daughter, with the rounded teaching half-life of 704 million years that the US Geological Survey uses. You measure a daughter-to-parent ratio D/P = 3.

1. Recover the starting parent. Every daughter atom was once a parent atom, so P0 = P + D = P + 3P = 4P. The fraction of parent left is P/P0 = 0.25.
2. Count half-lives. After n half-lives the fraction left is (1/2)^n. Since 0.25 = (1/2)^2, n = 2.
3. Convert to years. Age = 2 x 704 million years = 1,408 million years, or 1.408 billion years.
4. Check. After one half-life 50% of the parent remains; after two, 25%. Then 75% is daughter, and 75 / 25 = 3, the measured ratio.
5. Date the fossils. The ash lies above a fossil bed, and a second ash below the bed is dated to 1,450 million years. The fossils are younger than 1,450 and older than 1,408 million years. The answer is a bracket, not a point.

fraction of parent left = P / (P + D) = (1/2)^n, age = n x half-life

Real geochronology uses exact decay constants, both uranium chains and corrections for initial lead; this exercise is a model, only as good as its assumptions. The clock must also match the age. Carbon-14 has a half-life of about 5,730 years, so after roughly 50,000 years too little remains to measure. Dinosaur bones are not carbon-dated.

Molecular clocks convert sequence differences among living species into divergence times, with fossils calibrating particular nodes (see reading phylogenetic trees). Parham and colleagues (2012) argued that each calibration needs an explicit justification of the fossil’s place on the tree and the age of its rock, because a misplaced or misdated fossil carries its error into the dates.

A timeline of firsts, each a minimum

Read each entry as “by this time, at the latest”, with the place and method beside it.

• About 3.48 Ga, Dresser Formation, Western Australia. Djokic and colleagues (2017) reported stromatolites, microbial palisade fabric and geyserite, a mineral deposit of hot springs, in rocks they interpreted as hot springs on land. Older claims need care: Allwood and colleagues (2018) reinterpreted supposed stromatolites in 3.7-billion-year-old rocks at Isua, Greenland, as more plausibly deformation structures.
• Onset of the Great Oxidation Event, about 2,460 to 2,426 Ma. The GOE is the first significant buildup of oxygen in the atmosphere. Gumsley and colleagues (2017) bracketed its onset using successions in southern Africa anchored by dated volcanic rocks, and inferred that oxygen rose and fell rather than climbing once. The GOE is not the origin of oxygenic photosynthesis, which the light reactions lesson explains; it marks when oxygen accumulated.
• 1.047 Ga, Bylot Supergroup, Baffin Island, Canada. Gibson and colleagues (2018) used rhenium-osmium dates of sedimentary rocks above and below the fossil red alga Bangiomorpha pubescens to revise its age to 1.047 billion years (plus 0.013, minus 0.017). Using that age as a calibration, their molecular clocks put the origin of the primary plastid, the chloroplast that began as an engulfed cyanobacterium (see organelles as environments), at about 1.25 Ga. That figure is a model estimate conditional on the calibration, not an observed event.
• Ediacaran, which that study places at 571 to 541 Ma. Bobrovskiy and colleagues (2018) extracted cholesteroid molecules, the steroid family that animals make, from organically preserved Dickinsonia. The result supported an animal affinity for Dickinsonia and its close relatives, though not for every Ediacaran fossil.
• About 473 to 471 Ma, Argentina. Rubinstein and colleagues (2010) recovered cryptospores, spores attributed to early land plants, from Middle Ordovician rocks.

Each is a minimum age: the oldest fossil sets a floor, and the lineage may be older. Holland (2016) stressed a second point: preservation is uneven in space and time, so a gap in the record is not a gap in life.

Radiations: ecological opportunity in a flask and in the record

An adaptive radiation is the rapid diversification of one lineage into types adapted to different ecological niches. A niche, here, is the set of conditions and resources a type uses. The fossil record cannot be rerun. Bacteria can.

Paul Rainey and Michael Travisano (1998) grew Pseudomonas fluorescens from a single genotype in microcosms of broth. Left unshaken, where conditions differ from the surface down, new heritable types arose beside the ancestral smooth type, including a “wrinkly spreader” that forms a mat at the surface. Shaken to keep the broth uniform, they did not diversify. Spatial structure supplied ecological opportunity, and competition among the niche specialists kept them all present. Kassen, Llewellyn and Rainey (2004) then varied productivity and disturbance in the same system, and diversity peaked at intermediate levels of both.

Keep the scope: these are heritable morphs of an asexual bacterium, not new species, and nothing here says every fossil radiation had the same cause. The flask shows the logic: unoccupied niches plus heritable variation gave repeatable diversification.

In the rock record, mammals diversified after the end-Cretaceous losses. That sequence is consistent with release from competitors but does not test it; a coincident change in climate is one alternative.

Mass extinctions and the evidence for their causes

A widely used benchmark (Barnosky and colleagues, 2011) defines a mass extinction as the loss of more than three-quarters of species in a geologically short interval. In 1982 David Raup and J. John Sepkoski analysed a compilation of fossil marine families and found four extinction events statistically distinct from the background rate: the end of the Ordovician, the Late Permian, the Late Triassic and the end of the Cretaceous. A Devonian event was conspicuous but not statistically significant in those data. The “Big Five” is later usage that adds it.

End-Cretaceous, about 66 Ma. Luis Alvarez, Walter Alvarez, Frank Asaro and Helen Michel (1980) measured iridium, scarce in Earth’s crust but more abundant in many meteorites, in deep-sea limestones at the Cretaceous-Tertiary boundary. They found enrichments of about 30-fold in Italy, 160-fold in Denmark and 20-fold in New Zealand. They proposed, as a hypothesis, that an asteroid struck Earth and that dust darkened the sky and suppressed photosynthesis. Independent evidence followed: a buried impact crater, Chicxulub, on Mexico’s Yucatán Peninsula, and argon-argon dating by Renne and colleagues (2013) that placed the impact and the extinction within 32,000 years of each other. That figure is synchrony, not how long the dying took.

End-Permian, about 252 Ma. Burgess, Bowring and Shen (2014) dated zircons from five volcanic ash beds at Meishan, China, and placed the extinction between 251.941 ± 0.037 and 251.880 ± 0.031 Ma. Check their duration yourself: 251.941 − 251.880 = 0.061 million years, about 61,000 years, in line with the 60 ± 48 thousand years they estimated. That is one section. It constrains timing there, not the kill mechanism and not worldwide synchrony.

How much died? A figure of 96% “of all life” circulates. Stanley (2016) estimated about 81% of marine species for the terminal Permian crisis, inferred from data on higher taxa, and argued that larger figures merged separate Permian crises. Another bias runs the other way: because the record is incomplete, a species’ last fossil usually lies below where it actually vanished, smearing a sudden extinction backwards. This is the Signor-Lipps effect.

What rates the record can and cannot give

A clade’s net diversification rate is speciation minus extinction:

r = λ − μ (each in events per lineage per million years)

where λ is the speciation rate and μ the extinction rate. A time tree of living species records when surviving lineages split. Lineages that went extinct leave no tips, and recent lineages have had less time to die out, so a tree of survivors shows a “pull of the present”: the number of lineages climbs steeply near today even when rates were constant.

Louca and Pennell (2020) showed that, under a general birth-death model in which both rates may change through time, infinitely many histories are equally likely to have produced the same tree of living species, and that adding living species does not fix this even with unlimited data. A constrained hypothesis can still be tested, but the constraint must be justified from outside the tree.

Fossils supply that outside information. Silvestro and colleagues (2014) built a method, PyRate, that estimates speciation and extinction from fossil occurrences while modelling preservation and sampling explicitly, and lets the two rates vary independently through time. Applied to fossil rhinoceroses, it inferred repeated shifts in both rates.

Design problem

The living species of a clade form a time tree in which the number of lineages rises steeply toward the present. A student concludes that speciation sped up recently. What else could produce this pattern, and what data would decide between the explanations?