Fishapods
10.1 Tempo, level, and co-option #
10.1.1 Punctuated equilibrium and phyletic gradualism #
Phyletic gradualism is Darwin’s default pattern: a lineage changes more or less continuously, and a complete rock record would show the intermediates. Punctuated equilibrium, Eldredge and Gould’s term from 1972, is the pattern they argued is common. A species appears already differentiated, over a geologically short interval, and then shows stasis until it disappears. The claim is about where in a species’ history morphological change is concentrated.
A punctuation of a few thousand to a few tens of thousands of years is abrupt in a rock section and ordinary on the timescale of Chapters 4 to 6. Selection of a strength Haldane calculated, or drift in a small isolate, can shift a mean in that many generations. Punctuated equilibrium does not require macromutations, does not reject selection, and does not say that a bird hatches from a reptile’s egg. Eldredge and Gould’s mechanism was allopatric speciation, poorly sampled if one collects a widespread species, followed by stasis. One can accept the pattern and dispute that mechanism.
Both patterns occur. Some planktonic foraminifera in deep-sea cores change gradually. Many shelly invertebrates show stasis, with change concentrated near speciation. A gap in the rocks is not a punctuation. Punctuation is evidence of rapid change bracketed by stasis. The distinction is a description of rates, compatible with ordinary population genetics.
10.1.2 Species selection #
Species selection is the proposal that species differ in speciation or extinction rate because of species-level traits, and that this differential sorts those traits through time. Geographic range is a property of the species, not of one member, and wide-ranging marine species sometimes survive extinctions that remove narrow-ranging relatives.
The debate is species selection versus species sorting. Species can differ in extinction rate because of traits of their individuals — body size, diet, generation time — in which case the tally at species level is still organismal selection and ecology. Strict species selection needs an effect of an emergent species-level trait, or a claim that the species is the unit whose birth and death rates respond. Some fossil patterns fit the strict reading. Many are explained as well by sorting. Species selection is a proposed process, not an established force coordinate with natural selection, and it is not “for the good of the species” in the sense Chapter 3 rejected.
10.1.3 Exaptation #
Exaptation, Gould and Vrba’s term, is a trait whose current use is not the use for which selection originally built it, or a trait not built by selection for a function and later co-opted. An adaptation, in the strict sense of Chapter 3, was shaped for the function now under study. Present utility does not decide which word applies. The test is the order: the trait, or its precursor, present before the current function.
Feathers are the large-scale case. Feathered theropods that were not flying birds are known as fossils. Insulation, display, or brooding are the candidate early functions, and they are not all settled. The order is settled. Feathers precede flight. The flight surface of a bird wing is, at its origin, an exaptation, followed by further adaptation of the wing for aerodynamic work. “Feathers evolved for flight” collapses the history. “Feathers cannot be adaptations” collapses the later refinement. A spandrel can be co-opted and then modified. The vocabulary exists so that a story about current benefit is not mistaken for a story about origin.
10.2 The evolution of development #
10.2.1 A shared anterior–posterior toolkit #
Bilaterian animals share genes that lay out the anterior–posterior axis. Hox genes encode homeodomain transcription factors and lie in clusters. In many animals the order of genes in the cluster matches the order of expression along the body: spatial colinearity. Vertebrate clusters also tend to be activated in temporal order along the axis. Drosophila has eight Hox genes that pattern the trunk, split between the Antennapedia and Bithorax complexes. Mammals have four clusters, from ancient whole-genome duplications, and humans have 39 Hox genes. The numbers are a trace of duplication.
How a fly builds stripes — maternal gradients, gap genes, pair-rule genes, segment-polarity genes, and only then Hox genes assigning segment identity — is Developmental Biology. It is not repeated here. The evolutionary point is what remains when that mechanism is set aside. The common ancestor of bilaterians already distinguished anterior from posterior with a Hox system. Body plans have diverged largely by changing where and when these genes are expressed, and which genes they regulate, not by inventing a new axis system in each phylum. Shifts in Hox domains track some anatomical differences, including an expanded trunk in snakes and a difference between feeding and locomotory appendages in crustaceans. A match between expression and anatomy is a hypothesis precise enough to test, not already a proof of cause.
Other toolkit genes need the same caution. Pax6 is required for eye development in flies and in vertebrates. That shared regulator does not mean the compound eye and the camera eye are one organ inherited intact. The gene is older than either modern eye and has been recruited into both. Deep homology is shared genetic machinery. It is a weaker claim than homology of the organ. Chapter 2’s analogy between insect and vertebrate wings survives the discovery that some of the same outgrowth genes are used in both.
10.2.2 Gene duplication and new genes #
Duplication is the main way genomes gain genes that start similar to genes they already have. Ohno’s point was that a second copy can diverge while the first keeps the old job, so selection need not break a necessary function to gain a new one. Most duplicates become pseudogenes and are lost.
Neofunctionalisation is a new function in one copy, the other keeping the old one. Subfunctionalisation splits the ancestral job. Under duplication–degeneration–complementation, the ancestor did two things, each copy loses a different thing, and both copies become necessary to cover the original work. Neither has a new function. Dose can also favour keeping both copies. A pair of duplicates is not evidence of neofunctionalisation merely because two copies exist. The tests are where each copy is expressed and what happens when one is removed.
Whole-genome duplications scale the same logic up. Vertebrates had two early rounds, which is why Hox clusters come in families. Teleosts had another. Flowering plants have repeated episodes, some of them the polyploid speciations of Chapter 7. Most extra copies are still lost. Survivors are often enriched for regulators. Enrichment is a pattern after loss, not a plan at the moment of doubling.
New genes also arise by exon shuffling, fusion, fission, and birth from non-coding sequence. Horizontal transfer, important in bacteria, adds genes that are new to the recipient. Duplication remains the route that explains families of similar genes. The molecular errors that duplicate DNA belong to Molecular Biology. Loss, split, or novelty are the evolutionary fates.
10.2.3 Heterochrony #
Heterochrony is an evolutionary change in the timing or rate of development, so that a descendant adult resembles a different stage of the ancestor. The terms need a comparison. Without an ancestor, or a reasoned stand-in, “earlier” and “slower” have nothing to mean.
Paedomorphosis leaves ancestral juvenile features in the adult. In neoteny, somatic development slows relative to sexual maturation. In progenesis, maturation is accelerated and development is truncated at a juvenile stage. Peramorphosis runs development further than in the ancestor: hypermorphosis extends the growth period, acceleration raises the somatic rate.
| Pattern | What shifted | Adult, relative to the ancestor |
|---|---|---|
| Neoteny | Somatic rate slowed | Juvenile traits retained |
| Progenesis | Maturation earlier | Stopped at a juvenile stage |
| Hypermorphosis | Growth period extended | Ancestral adult trait carried further |
| Acceleration | Somatic rate increased | Ancestral adult trait carried further |
The axolotl, Ambystoma mexicanum, is the classic neotene. It breeds while keeping external gills and an aquatic larval body, where metamorphosing relatives of the genus transform into a terrestrial adult. Thyroid hormone induces metamorphosis in salamanders, and experimental hormone can still push an axolotl through that transition. The adult programme is largely present and untriggered, not deleted. The basis is a changed hormonal schedule, not a single switch these notes should pretend to name. Retaining a larval trait is a new phylogenetic state, even though the morphology looks ancestral. It is not evolution running backwards. A shift in Hox timing is itself a heterochrony of expression, and a duplicate can diverge in when it is switched on. The words name levels that often act together.
10.3 Key terms, summary, and self-check #
Key terms. Phyletic gradualism; punctuated equilibrium; stasis; species selection; species sorting; exaptation; Hox gene; colinearity; deep homology; neofunctionalisation; subfunctionalisation; heterochrony; neoteny; peramorphosis.
Summary. Punctuated equilibrium and phyletic gradualism are patterns of rate. A punctuation of thousands of years does not reject selection or require macromutation. Species selection is a debated sorting by speciation and extinction, and it must be distinguished from organismal selection tallied by species. Exaptation is co-option; feathers precede flight. Hox genes are a shared anterior–posterior toolkit — eight trunk genes in Drosophila, 39 in four clusters in humans — whose fly-embryo mechanics belong elsewhere and whose comparative fact is that body plans diverge by redeploying the toolkit. Duplicates are usually lost, and otherwise split an old function or gain a new one. The axolotl is neotenic: somatic development slowed relative to reproduction, still inducible by thyroid hormone, and not a reversal of evolution.
Self-check.
1. Why is punctuated equilibrium not a claim that selection is too weak to change morphology inside a species?
2. What extra finding would turn a difference in extinction rate into species selection rather than species sorting?
3. Why do feathers in non-flying theropods make flight an exaptation of feathers at its origin, without denying later adaptation of the wing?
4. Which facts about Hox genes belong here, and which description of the fly embryo is left to Developmental Biology?
5. Distinguish neoteny from progenesis. Which fits the axolotl, and what does the thyroid-hormone result show?
