2.5 Evolution and Development

We usually say that species evolve, but what actually changes over evolutionary time is a life cycle, and every life cycle has to be rebuilt through development in each generation. If each generation must develop rather than simply reproduce a form already specified in advance, then changes in developmental processes can alter the forms that become possible. Evolutionary change can therefore be approached partly as historical change in the processes through which life cycles are reconstructed.

Heterochrony: The Life Cycle Evolves

One way that development enters into evolution is through heterochrony, which refers to evolutionary changes in the timing, rate, or duration of developmental processes. This does not mean that an organism develops according to a single clock that simply speeds up or slows down. Different processes can change in different ways, so that the timing of one part of development shifts in relation to another.

Stephen Jay Gould’s Ontogeny and Phylogeny (1977) helped bring heterochrony back into discussions of evolution and development. The axolotl provides a striking example. It becomes reproductively mature while retaining characteristics that, in related salamanders, belong to an earlier phase of development. What has changed is the relation among developmental processes that were already there, with no entirely new structure required.

The giraffe shows the same general principle in a different way. Like most mammals, giraffes have seven cervical vertebrae. Their long neck did not evolve through the addition of more cervical segments. Instead, the vertebrae themselves follow an altered growth trajectory, with much of their disproportionate elongation occurring after birth (van Sittert et al., 2010).

Snakes reached an elongated form through a rather different developmental change. Vertebrae arise from embryonic structures called somites, which are produced rhythmically along the developing body axis. Gomez and colleagues (2008) found that in corn snakes, the molecular process regulating this segmentation runs much faster relative to the overall rate of embryonic development than it does in other amniotes. More, smaller somites are produced, and these give rise to a much larger number of vertebrae. Timing matters for brains as well. Humans have far more cortical neurons than other primates, and much of the difference appears to come from neural progenitor cells dividing for longer, a shift in the timing of processes that were already in place (Rakic, 1995).

Changes in the course of development alter the resulting form. Giraffes and snakes did not arrive at elongated bodies by the same route, and neither case requires us to imagine a finished form appearing first and development subsequently carrying it out. Evolutionary change occurs partly through changes in the developmental processes from which form emerges.

Evo Devo

Heterochrony is one way that changes in development can alter the forms produced over evolutionary time. Evolutionary developmental biology, or Evo Devo, broadened this connection by showing that many of the molecular resources involved in building animal bodies are themselves deeply conserved. Hox genes, for example, help organize the body along its head-to-tail axis across a remarkably wide range of animals. Much evolutionary change in animal form therefore involves not the appearance of entirely new genes, but changes in when, where, and how existing developmental resources are used (Carroll et al., 2005).

This led to the idea of a developmental genetic toolkit: genes, regulatory elements, and signaling pathways that have been retained across long stretches of evolutionary history and repeatedly used in different developmental contexts. Changes in the regulation of these resources can alter developmental processes and, through them, the form that develops. Evolution and development are connected here quite directly: a change inherited across generations has its effects by changing what happens during development. Existing structures can also be put to new uses. As Neil Shubin (2008) puts it, mammals hear with bones that reptiles eat with.

But the toolkit account leaves open the question of where possibilities for those forms come from in the first place. Earlier we encountered Stuart Newman’s argument that the material properties and organization of cells and tissues can themselves contribute to the generation of form. Cells adhere, move, change shape, exert forces on one another, and organize into tissues with particular geometries and mechanical properties. The evolutionary implication is that developing bodies may generate new forms through these interactions, with genetic and regulatory changes subsequently contributing to the stabilization and reliable reconstruction of some of those forms over evolutionary time (Newman & Bhat, 2008; Newman & Müller, 2000).

From this perspective, the close relationship we now see between genes and bodily form is partly an outcome of evolutionary history rather than its starting point. Evolution becomes “recorded” in relatively stable changes to developmental systems, including changes in DNA and its regulation. DNA is an especially durable part of that record, but it does not by itself contain the history of how a form first became possible. What persists is a developmental organization that has itself been altered and stabilized over time.

In both evolution and development, we need to ask how history is carried forward. Across an individual life, earlier development is retained in the organism’s current organization and in the relations through which it acts. Across generations, evolutionary history is carried forward in developmental resources and organizations that are reconstructed rather than begun anew. The two histories are different, but they meet in the developing organism: phylogenetic history helps structure the possibilities with which development begins, while developmental activity can alter the variation and conditions that are carried forward over evolutionary time.

Changes in bodily development also alter the conditions under which the nervous system develops, because a brain takes shape in relation to the body whose activity it coordinates. Krubitzer and Prescott (2018) explore this connection through the evolution and development of bodies and cortical organization. Mammalian forelimbs provide a particularly revealing example.

Mouse Paws and Bat Wings

Mice and bats share the same basic mammalian forelimb organization, but development carries that organization along very different trajectories. Mouse paws and bat wings are not independent designs but transformations of a common developmental organization.

One part of this evolutionary difference involves Prx1, a gene involved in the development and elongation of the limb skeleton. Mice and bats both possess Prx1, but they differ in regulatory DNA that affects when and how strongly the gene is expressed during limb development.

Cretekos and colleagues (2008) tested the significance of this difference by replacing the mouse Prx1 limb enhancer with the bat version. Prx1 expression increased in the developing forelimb bones, and just before birth the mice had forelimbs about 6 percent longer than those of controls, after accounting for body mass. The difference was no longer present in the adults measured at six weeks of age. A change in a regulatory sequence can therefore alter the developmental process through which limb form is produced.

But this does not make Prx1 a “wing gene,” nor does the experiment explain the evolution of the bat wing. The regulatory sequence altered growth within a limb that was already developing. Its effects depended on the other processes involved in building that limb.

When the researchers deleted the mouse Prx1 limb enhancer entirely, rather than replacing it with the bat version, the mice developed forelimbs of normal length and showed normal Prx1 expression. Other regulatory elements could sustain Prx1 expression in its absence. Even an enhancer capable of changing limb growth therefore works within a regulatory system in which its effects depend on what else is present.

The mouse and bat comparison will return in Brain, Body, World, where differences in developing bodies can be followed into differences in the developing nervous system.

These examples raise a historical question: why did development sit so far from the center of twentieth-century evolutionary theory?

The Modern Synthesis and the Extended Evolutionary Synthesis

The Modern Synthesis emerged during the early and middle decades of the twentieth century by bringing Darwinian natural selection together with Mendelian genetics and population biology. It provided a powerful account of evolution in terms of changes in the genetic composition of populations through mutation, natural selection, genetic drift, and gene flow, and it remains fundamental to evolutionary biology.

Development was not excluded from this framework, but it was usually not where the main explanatory work was being done. Population genetics could describe the transmission and changing frequencies of genetic variants without needing to explain in detail how those variants participated in the construction of a phenotype. In simplified versions of the story, mutations therefore appear to introduce traits and natural selection then sorts among them.

What becomes compressed is the development that occurs between genetic variation and the organism on which selection acts. A mutation does not produce a finished characteristic by itself, and whether its consequences matter depends on what develops and on the conditions in which the organism lives.

This compression has another consequence. If a form is characteristic of a species and reliably appears across generations, it is natural to say that the form evolved. From there it is only a short step to saying that the form must therefore be genetically specified. But these are different claims. An evolutionary explanation can help explain why a lineage repeatedly reconstructs a developmental system with particular resources and constraints. It does not by itself explain how those resources produce the form in an individual.

DNA is an especially tempting place to locate that explanation because it is transmitted with remarkable stability across generations. A trait is evolutionarily conserved, DNA is inherited, and so the conserved part of the phenotype can begin to look like the part that is “in the genes,” with development supplying only later modification or fine-tuning. But stable transmission is not the same thing as developmental specification. Genes can be indispensable to a developmental process without containing a description of the outcome that process produces.

This distinction is important because otherwise two different questions become folded together. One question is historical: why does this developmental system, with these resources and constraints, recur in this lineage? Another is developmental: how do those resources and constraints interact through time to generate this organism? Evolutionary history bears directly on the first question. Genetics is part of the answer to the second, but it does not make the second question disappear.

Gastrulation makes the distinction fairly obvious. Gastrulation evolved, and genes are indispensable to it. But saying either of those things does not explain how gastrulation happens. To answer that question we still have to trace the signaling, cell movements, mechanical relations, changes in gene expression, and earlier organization through which a new form is produced. The same logic applies more generally to development.

Laland and colleagues (2015) set out the Extended Evolutionary Synthesis, or EES, as one attempt to give greater explanatory weight to processes that tend to disappear inside that compressed step. Its proponents retain mutation, inheritance, differential reproduction, and natural selection, but argue that developmental processes also influence what kinds of phenotypic variation are produced and therefore what becomes available for evolutionary change.

One part of this argument concerns developmental bias. Development does not generate every imaginable form with equal probability. Because developmental systems already have a particular organization and history, some variations are relatively easy to produce, others are difficult, and many are not possible at all. Development can therefore channel evolutionary change by shaping the range and organization of the variation that selection encounters.

Developmental plasticity opens another possibility. A change in developmental conditions can sometimes produce a different phenotype without a new mutation having initiated that difference. If the altered phenotype affects survival or reproduction, natural selection can then act on existing heritable differences in how individuals produce that developmental response. Over generations, the response itself may change, becoming easier to produce, more reliable, or less dependent on the conditions that originally elicited it. West-Eberhard (2003) calls this general process genetic accommodation.

This is related to the Baldwin effect: a plastic response can allow organisms to persist or function under new conditions, which changes the circumstances in which later natural selection occurs. The response acquired during development is not copied into DNA. Selection acts on heritable variation affecting the developmental processes that produce it. If the phenotype eventually becomes relatively independent of the environmental condition that first elicited it, this is called genetic assimilation, one possible outcome of genetic accommodation (Crispo, 2007).

Other arguments associated with the EES concern inheritance and the activity of organisms themselves. The developmental resources reconstructed across generations include more than DNA, while organisms also modify some of the environments in which they and their descendants develop. These claims connect directly with the account of heredity developed in the Developmental Systems Theory reading. The evolutionary consequence is that development, inheritance, and selection occur within changing organism–environment relations rather than as separate stages in a linear sequence. Laland and colleagues call this reciprocal causation: organisms and their environments shape each other over both developmental and evolutionary time.

Reciprocal causation still allows causal explanation, and some causes can matter more than others. Their importance depends on what we are trying to explain. A regulatory change may carry much of the explanatory weight in one case, while the organization of a tissue, the activity of an organism, or some feature of its environment may matter more in another.

Not all evolutionary biologists agree that these ideas require a distinct synthesis. Futuyma (2017), for example, argues that developmental plasticity, developmental bias, non-genetic inheritance, and niche construction can be incorporated within an expanded version of existing evolutionary theory. The disagreement is less about whether these processes occur than about how much explanatory weight they should carry.

In an overview coauthored with Jan Baedke, the developmental biologist Scott Gilbert puts the development-first view this way: “Development is the artist; natural selection is the curator” (Baedke & Gilbert, 2024, section 3). Selection is still important, but it can only act on forms that development has produced. Elsewhere Gilbert puts it another way: “We do not inherit a text to be decoded. Rather, we inherit a composition to be interpreted” (Gilbert, 2016, p. 428).

None of this replaces genes or natural selection with some other master cause. Development generates and organizes variation; selection changes which forms persist. What gets carried across evolutionary time is the capacity to rebuild a viable life cycle, generation after generation. Knowing that something evolved doesn’t explain how it developed.

Sources

Baedke, J., & Gilbert, S. F. (2024). Evolution and development. In E. N. Zalta & U. Nodelman (Eds.), The Stanford Encyclopedia of Philosophy. https://plato.stanford.edu/entries/evolution-development/

Carroll, S. B., Grenier, J. K., & Weatherbee, S. D. (2005). From DNA to diversity: Molecular genetics and the evolution of animal design (2nd ed.). Blackwell.

Cretekos, C. J., Wang, Y., Green, E. D., Martin, J. F., Rasweiler, J. J., IV, & Behringer, R. R. (2008). Regulatory divergence modifies limb length between mammals. Genes & Development, 22(2), 141–151. https://doi.org/10.1101/gad.1620408

Crispo, E. (2007). The Baldwin effect and genetic assimilation: Revisiting two mechanisms of evolutionary change mediated by phenotypic plasticity. Evolution, 61(11), 2469–2479. https://doi.org/10.1111/j.1558-5646.2007.00203.x

Futuyma, D. J. (2017). Evolutionary biology today and the call for an extended synthesis. Interface Focus, 7(5), 20160145. https://doi.org/10.1098/rsfs.2016.0145

Gilbert, S. F. (2016). Developmental plasticity and developmental symbiosis: The return of eco-devo. Current Topics in Developmental Biology, 116, 415–433. https://doi.org/10.1016/bs.ctdb.2015.12.006

Gomez, C., Özbudak, E. M., Wunderlich, J., Baumann, D. P., Lewis, J., & Pourquié, O. (2008). Control of segment number in vertebrate embryos. Nature, 454(7202), 335–339. https://doi.org/10.1038/nature07020

Gould, S. J. (1977). Ontogeny and phylogeny. Belknap Press of Harvard University Press.

Krubitzer, L. A., & Prescott, T. J. (2018). The combinatorial creature: Cortical phenotypes within and across lifetimes. Trends in Neurosciences, 41(10), 744–762. https://doi.org/10.1016/j.tins.2018.08.002

Laland, K. N., Uller, T., Feldman, M. W., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., & Odling-Smee, J. (2015). The extended evolutionary synthesis: Its structure, assumptions and predictions. Proceedings of the Royal Society B: Biological Sciences, 282(1813), 20151019. https://doi.org/10.1098/rspb.2015.1019

Newman, S. A., & Bhat, R. (2008). Dynamical patterning modules: Physico-genetic determinants of morphological development and evolution. Physical Biology, 5(1), 015008. https://doi.org/10.1088/1478-3975/5/1/015008

Newman, S. A., & Müller, G. B. (2000). Epigenetic mechanisms of character origination. Journal of Experimental Zoology, 288(4), 304–317. https://doi.org/10.1002/1097-010X(20001215)288:4%3C304::AID-JEZ3%3E3.0.CO;2-G

Rakic, P. (1995). A small step for the cell, a giant leap for mankind: A hypothesis of neocortical expansion during evolution. Trends in Neurosciences, 18(9), 383–388. https://doi.org/10.1016/0166-2236(95)93934-P

Shubin, N. (2008). Your inner fish: A journey into the 3.5-billion-year history of the human body. Pantheon Books.

van Sittert, S. J., Skinner, J. D., & Mitchell, G. (2010). From fetus to adult: An allometric analysis of the giraffe vertebral column. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 314B(6), 469–479. https://doi.org/10.1002/jez.b.21353

West-Eberhard, M. J. (2003). Developmental plasticity and evolution. Oxford University Press.

Explore Further

Laland, K. N., Uller, T., Feldman, M. W., Sterelny, K., Müller, G. B., Moczek, A., Jablonka, E., Odling-Smee, J., Wray, G. A., Hoekstra, H. E., Futuyma, D. J., Lenski, R. E., Mackay, T. F. C., Schluter, D., & Strassmann, J. E. (2014). Does evolutionary theory need a rethink? Nature, 514, 161–164. https://doi.org/10.1038/514161a

A short exchange on whether developmental plasticity, niche construction, non-genetic inheritance, and related findings call for a substantial rethinking of evolutionary theory.

Carroll, S. B. (2005). Endless forms most beautiful: The new science of evo devo and the making of the animal kingdom. W. W. Norton & Company. https://wwnorton.com/books/Endless-Forms-Most-Beautiful/

An accessible introduction to evolutionary developmental biology and the conserved developmental toolkit discussed in this reading.