Evolutionary Biology: Chapter 2 — Evidence for evolution

2.1 Homology, analogy, and vestiges #

The study of Homology, analogy, and vestiges provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.

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2.1.1 Nested hierarchy and homology #

A tree of descent predicts nesting. Species that share a recent ancestor should share features that more distant relatives lack, and the same clusters should appear in bones, development, and sequences. Mammals share hair, milk, and a particular jaw–ear arrangement. Primates share a further subset. The groups sit inside one another.

A homologue is a structure, gene, or behaviour whose similarity comes from a common ancestor. Owen defined homology as the same organ under every variety of form and function. Darwin supplied the cause: the ancestor had it, and the functions diverged. The tetrapod forelimb is the standard case. Human, horse, bat, bird, and whale share one upper-limb bone, two lower-limb bones, wrist or ankle bones, and digits. The jobs differ. The pattern of the bones does not. Insect legs solve locomotion with a different construction.

Homology is a hypothesis, tested by detail and by agreement with other characters. A similarity that fights the rest of the evidence is probably not homology. Chapter 8 makes that test phylogenetic.

2.1.2 Analogy and convergence #

An analogue is a similarity not inherited from an ancestor that already had the trait. Wings of bats, birds, and insects are analogous as wings. The bat wing and the bird wing are also homologous as forelimbs: the bones correspond, the flight surfaces do not. A bird’s surface is feathers; a bat’s is skin stretched on elongated digits. An insect wing is not a modified tetrapod limb. Independent arrival at a similar function is convergence.

Convergence is evidence that similar conditions can build similar solutions, and it is the main trap in classification. Grouping by “has wings” unites bats, birds, and insects, which never were one branch. Chapter 8 calls the misleading similarity homoplasy. A few convergences do not scramble a hierarchy built from thousands of characters. A single shared feature, however striking, is weak evidence until other characters are scored.

2.1.3 Vestigial structures #

A vestigial structure is a reduced homologue of an organ better developed in relatives. Reduced does not mean functionless. It means diminished relative to the ancestral condition, often with a smaller remaining job. The pelvis of a modern whale does not support a hind limb. It is the reduced homologue of the pelvis of terrestrial artiodactyl relatives, and in some whales it still anchors reproductive muscles. That secondary job does not make it a limb girdle. Hind-limb remnants in boas and pythons, and reduced eyes in many cave fishes, are the same kind of fact.

The human appendix is a bad example if it is called useless. It contains lymphoid tissue. Whether it is also a reduced fermenting caecum is a narrower claim than “vestige, therefore worthless”. Vestiges are evidence of ancestry because a remnant sits where a relative has a working organ. Present function and origin by reduction are separate questions. Chapter 3 returns to that split.

2.2 Fossils and biogeography #

2.2.1 Transitional forms, not a ladder #

A transitional fossil preserves a combination of traits that no living species has, sitting in character space between groups that are distinct today. It is not a rung on a ladder, and it is not a certified ancestor of a named living species. Most fossils are side branches. The evidence is the intermediate combination, which a branching history predicts and which separate origin of modern groups does not.

Tiktaalik roseae, from Ellesmere Island, is Late Devonian, about 375 million years old. It has scales and fin rays, and also a flat head, a neck, and fin bones in a wrist-like pattern. It is a stem tetrapod that still lived in water, not “the ancestor of amphibians”. Acanthostega and Ichthyostega, also Late Devonian, carry digits further and were still largely aquatic. Limbs appear in animals that were not yet living on dry land.

Archaeopteryx, from the Late Jurassic Solnhofen limestone, is about 150 million years old. It has feathers and a wishbone, and also teeth, a long bony tail, and clawed fingers. It is a bird-line dinosaur, not the ancestor of the robin. Living birds sit inside theropod dinosaurs. Feathered non-flying theropods show that feathers precede flight (Chapter 10). Treating Archaeopteryx as the single plank between “reptiles” and “birds” is the ladder mistake. One group sits inside the other.

Whales are a grade of early Cenozoic fossils, not a single file. Pakicetus, early Eocene, about 50 million years ago, is a terrestrial or semi-aquatic artiodactyl relative with a cetacean ear region. Ambulocetus and Rodhocetus are more aquatic. By the middle Eocene, Dorudon and Basilosaurus are fully aquatic, with tiny hind limbs that could not bear the body. Modern whales keep a vestigial pelvis. Molecular trees place whales inside the artiodactyls, with hippos as the closest living relatives. Neither the fossils nor the molecules say “hippo begat Pakicetus begat blue whale”. They document an aquatic body built from a terrestrial artiodactyl ancestor over a few tens of millions of years. Each of those animals was a finished organism in its own environment. Transitional describes characters, not a provisional life.

2.2.2 Islands and Wallace’s line #

Evolution predicts that distribution depends on where lineages arose, where they could disperse, and where barriers stood. It does not predict that every suitable climate contains the same body.

Oceanic islands, never attached to a continent, are poor in terrestrial mammals and amphibians and rich in endemic insects, birds, and plants. Hawaii holds hundreds of drosophilid species found nowhere else, a radiation from colonists, not a sample of every continental fly group. Continental islands, connected at low sea level, carry a fuller sample of the neighbouring fauna. The contrast is historical.

Wallace’s line runs between Bali and Lombok, and between Borneo and Sulawesi. West of it the terrestrial fauna is Asian. East of it the fauna is increasingly Australian, with marsupials rather than the placental groups of the Sunda shelf. During Pleistocene low sea levels the Sunda shelf joined the western islands to Asia, and the Sahul shelf joined New Guinea to Australia. Deep water along the line still separated those land masses. The line is not a wall — Sulawesi is mixed — but it is a real discontinuity with a physical cause.

2.3 Evolution watched, and evolution read from molecules #

2.3.1 Direct observation #

Selection that changes frequencies inside a human lifetime does not, by itself, assemble a phylum. It shows the process the later chapters describe, on a timescale one can watch.

Antibiotic resistance is the clinical case. A drug leaves resistant cells, whether resistance was already present or arose by mutation, and those genotypes increase. If resistance is costly, withdrawing the drug can let susceptibles increase again. Altered targets, drug-destroying enzymes, efflux pumps, and plasmid-borne genes belong to Microbiology. The frequency change is selection. Individuals are resistant or not. The population changes. Mutation is not called up by need. The Luria–Delbrück result, whose design is taught with microbial genetics, showed that resistance mutations can arise before the selective agent is applied.

Industrial melanism needs its caveat. The dark form of the peppered moth, Biston betularia, increased in sooty nineteenth-century Britain and declined after clean-air legislation, as lichens returned. That frequency change is documented in collections and trapping records. The mutation is a transposable-element insertion at cortex. Kettlewell’s mark–recapture experiments of the 1950s, the famous claim that birds eat the mismatched moth, have been criticised: moths were released at unnatural densities and often on trunks, whereas the species more often rests under branches. The criticism damages one study. It does not retract the phenotype or its historical spread. A later predation experiment, designed by Michael Majerus and published after his death, supported differential bird predation. The fair summary is that one classic experiment was imperfect, and that the evolutionary phenomenon is real.

The same class of observation includes the Grants’ measurements of beak size in Darwin’s finches (Chapter 3) and the multi-decade E. coli populations of Lenski and colleagues, in which fitness rose repeatedly under a constant regime and one population gained the ability to use citrate where the ancestor could not. The culture method is not the point. Heritable adaptation has been watched.

2.3.2 Molecular homology #

The genetic code is nearly universal, with a modest list of exceptions, mostly mitochondrial and a few stop-codon reassignments. Chemistry does not force one mapping. The code reduces the damage from misreading, which explains some of its structure, and the exceptions show that it can change. Universality in the face of that freedom is shared ancestry.

Shared losses are often stronger than shared functions, because a flaw is less likely to be rebuilt for a current need. The last enzyme of vitamin C synthesis is a pseudogene in humans and other anthropoid primates, and the damage is shared. Guinea pigs and some bats have lost the pathway independently: that is homoplasy, and the lesions differ.

An endogenous retrovirus that inserts into the germline is inherited as a Mendelian insertion. The same virus landing at the same site in two species after they have split is unlikely. Many orthologous insertions shared by humans and chimpanzees are insertions in the common ancestor, inherited by both. They are shared accidents, not shared needs. The viral life cycle belongs to Molecular Biology. The map of shared sites is the evolutionary evidence.

2.4 Key terms, summary, and self-check #

Key terms. Homology; analogy; convergence; vestigial structure; transitional fossil; Wallace’s line; industrial melanism; endogenous retrovirus; genetic code.

Summary. Common ancestry predicts nested homology, reduced organs where relatives have working ones, intermediate fossil combinations, and distributions that follow barriers. Convergence produces analogous functions and is evidence of repeated selection, not against ancestry. Antibiotic resistance and industrial melanism show selection changing frequencies now; Kettlewell’s experiment was imperfect, and the moth phenotype’s history is not. A shared code, a shared inactivating mutation, and shared retroviral insertions are molecular homology, strongest where the shared feature is not a current need.

Self-check.

1. In what respect are a bat wing and a bird wing homologous, and in what respect analogous? Where does an insect wing fit?

2. Why is Pakicetus → Dorudon → a modern whale not a literal ancestor–descendant ladder?

3. What geographic fact keeps Wallace’s line sharper than a line across continuous land?

4. Which part of industrial melanism was damaged by criticism of Kettlewell, and which part was not?

5. Why is a shared retroviral insertion at the same site stronger evidence of common ancestry than a shared enzyme both species need?