Evolutionary Phenomics: Constraints, Convergence, Extinction Risk

The speaker, an evolutionary phenomics researcher, explores the fundamental question of why life appears the way it does, focusing on the intrinsic and extrinsic factors influencing the tempo and mode of evolution of organismal form. This involves examining an organism's internal aspects (ecology, development) and environmental factors (interactions with other species) over vast timescales.

Dominant Patterns in Evolution

Several dominant patterns emerge when observing species and evolution:

• Uneven Distribution of Diversity: Species variation is not uniformly distributed globally. The tropics, for instance, exhibit significantly higher species diversity than the poles.
• Rapid Changes Over Deep Time: Over millions and billions of years, there have been rapid changes in species numbers and forms. Periods of rapid evolution of new forms are punctuated by sharp declines, known as mass extinctions.
• Varying Diversity Across the Tree of Life: Some groups, like insects (millions of species) and fish (tens of thousands), are hugely diverse, while others remain largely unchanged and undiverse for extended periods. For example, birds boast 10,000 species, whereas their closest living relatives, crocodiles, are far less diverse and show less morphological variation, having remained largely the same for tens of millions of years.

These observations lead to core questions: Why do species diversify differently? Why do different regions of the world exhibit varying diversity? Why do rapid changes occur throughout life's history?

Approaches to Studying Evolution

Various scientific disciplines offer different lenses to answer these questions:

• Molecular Evolution/Genetics: Focuses on how genome evolution influences life's evolution.
• Development: Examines how an organism's developmental stages, from early life to adulthood, impact its evolution.
• Life History: Studies factors like lifespan, lifestyle, and metamorphosis.
• Biomechanics and Physiology: Investigates the physical and chemical functions of organisms.
• Sensory Interactions: Explores how organisms perceive and interact with their environment, including the influence of brain size.
• Environmental Factors: Considers how the environment and its changes influence evolution.

Crucially, all species are influenced by their evolutionary history and lineage; the past significantly shapes present-day life forms.

Evolutionary Phenomics: Quantifying the Shape of Life

The speaker's approach is evolutionary phenomics (or biodiversity phenomics), which aims to quantify the shape of life. Phenomics is defined as the high-dimensional, organism-wide extension of the study of phenotype—the observable traits and characteristics of an organism. These traits are vital because they mediate interactions within and between species, and with the environment. They are also observable in the fossil record, allowing for the integration of evolutionary history.

The Enigma of Cats: An Evolutionary Outlier

To illustrate complex evolutionary concepts, the speaker uses the example of cats. Cats are considered an enigma because, unlike most other vertebrate groups, they exhibit remarkable evolutionary conservatism. They are the only land vertebrates that can exceed 50 kilograms while maintaining a crouched posture; other large mammals tend to become straight-legged. This suggests cats might occupy an "evolutionary optimum," having perfected a niche so effectively that they face little competitive pressure to vary.

Developmental Constraints: Cats vs. Dogs

A key factor influencing adult organismal form is developmental change. While humans and many other species change shape significantly during development (e.g., babies have proportionally larger heads), cats maintain a largely isometric growth pattern—their head shape remains consistent as they grow.

Dogs, in contrast, exhibit allometric growth, meaning their shape changes as they get older, particularly in snout length. This developmental plasticity in dogs allows for greater variation, as breeders can select for different developmental stages, leading to diverse breeds with varying snout-to-braincase proportions. Cats, due to their isometric growth, offer far less developmental "play" for evolution or artificial selection, resulting in less morphological diversity across breeds. The most significant human-induced variation in cats often involves fur characteristics rather than fundamental body plan changes.

Ecological Constraints: Hypercarnivory

Cats' evolutionary inflexibility is also linked to their ecology. Early in their evolution, cats lost most of their teeth except for the carnassials—a specialized slicing pair common to carnivorans (cats, dogs, bears, etc.). Unlike dogs, which retain molars for grinding, cats cannot grind food. This specialization locked them into a hypercarnivorous diet, limiting their ecological niche. Hypercarnivores, like cats, tend to evolve more slowly and exhibit less morphological diversity than their less restricted relatives.

Trait Linkages and Evolutionary Constraints

Darwin observed that white cats with blue eyes are often deaf, indicating a genetic linkage between these traits. The speaker's research focuses on how such linkages—whether genetic, developmental, or functional—shape evolution. These relationships dramatically constrain how life evolves. Many imaginable organisms, like dragons, have never evolved because developmental constraints, established early in group evolution, make such forms impossible or non-functional.

A study on mollusks demonstrated that despite a vast theoretical "cube" of possible forms, only a tiny fraction have ever evolved due to these trait relationships. The speaker's own simulations, comparing unconstrained evolution (red dots) with evolution under reasonable trait relationships (black dots), showed that most potential evolutionary paths are inaccessible. This concept is termed the "fly in the tube" model: evolution operates within a constrained "tube" of possibilities, rather than an ever-expanding sphere.

While these constraints limit the range of possible forms, they don't necessarily slow down the rate of evolution within the "tube." Organisms can evolve quickly as long as they adhere to these fundamental constraints.

Convergence: A Consequence of Constraints

The "fly in the tube" model also explains the prevalence of convergent evolution, where different groups independently evolve similar forms. This is not a special or unexpected phenomenon but a logical outcome of evolution being channeled into a limited number of viable solutions to similar environmental problems. An example is the striking skull similarity between the extinct marsupial thylacine (Tasmanian tiger) and placental wolves, despite 125 million years of separate evolution. Both are mammals with similar developmental and genetic underpinnings, leading them to converge on similar solutions for a predatory lifestyle.

The Importance of the Fossil Record

Understanding evolution requires looking beyond present-day life. Past life forms, such as Hallucigenia or early dinosaur ancestors of birds, often defy imagination based solely on modern species. Even relatively recent extinctions, like the giant ground sloth (5,000 years ago), highlight how different past ecosystems were. Ignoring this past variation can lead to incomplete or inaccurate explanations of life's diversity.

Advanced Phenomics: High-Resolution 3D Data

The speaker's lab uses evolutionary phenomics to collect vast amounts of 3D scan data to capture the variation of life and model its evolution, integrating intrinsic and extrinsic factors like development, ecology, biomechanics, and brain size.

Traditional methods, like linear measurements, provide only vague descriptions of shape. Geometric morphometrics, using landmarks on 3D models, was an improvement but still limited, especially when comparing highly diverse groups. For instance, only about 12 consistently identifiable landmarks could be found across all vertebrates, yielding limited insight.

To overcome this, the lab developed a semi-landmark approach. Instead of focusing solely on points, they focus on individual structures. A generic 3D template (a hemisphere) is warped to fit the shape of thousands of skulls, mapping points onto them to capture high-resolution 3D detail. This allows for the study of different skull parts and their correlations.

This process is extremely tedious, but recent efforts have focused on automation, moving from manual landmarking to fully automated pipelines using AI models. This has dramatically reduced the time required for analysis from months or years to minutes or hours, enabling unprecedented research.

New Discoveries with Automated Phenomics

This automated pipeline has opened new avenues of research:

• Speciation in Deep Time: A PhD student used the pipeline to analyze CT scans of sediment cores containing thousands of single-celled foraminifera shells. This allowed them to observe speciation events in the fossil record, showing how a single species diversified into two distinct species during periods of climate change. This demonstrates how evolutionary processes, typically studied in labs, can now be examined over deep time, shedding light on how climate change drives evolution.
• Insect Diversity: The pipeline is being used to study insects, which represent the vast majority of Earth's species but have been understudied morphologically. By mass-scanning insects from museum collections, researchers can now quantify their form and understand the evolution of their immense diversity.

Insights into Dinosaur and Mammal Evolution

Birds as "Rubbish Dinosaurs"

Applying the high-dimensional phenomics approach to birds and dinosaurs revealed that while birds are nested within dinosaurs, their skull shapes are quite distinct. Dinosaurs, despite fewer species in the dataset, showed greater morphological diversity in skull shape.

The research also showed that skull parts with tight trait correlations evolve more slowly than those with weaker interactions, reinforcing the idea that trait networks shape evolutionary paths and rates.

Surprisingly, birds were found to be the most slowly evolving group of dinosaurs in terms of skull morphology. While birds are diverse, their skulls are relatively simple (a braincase with a beak). Dinosaurs, in contrast, used their skulls for a wider range of functions, including fighting, diverse feeding, and display structures. This quantitative finding suggests that, in terms of skull evolution, birds are "rubbish dinosaurs."

Mammalian Convergence and Evolutionary Rates

Mammals, when analyzed using principal components analysis, show a strong tendency towards convergence. Most mammals, with the notable exceptions of whales and rodents, tend to evolve towards a "fox-like" average morphology. This convergence is attributed to their shared developmental history.

Analyzing evolutionary rates across the mammalian family tree revealed areas of both fast and slow evolution. Whales, for instance, exhibit extremely fast evolution. Factors influencing these rates include:

• Ecology: Aquatic species (like whales) and herbivores tend to evolve quickly.
• Development and Reproduction: Species with short parental care periods and young that are quickly mobile (like many prey species) evolve faster. Species with long parental care (like humans) evolve more slowly.
• Social Structure: Social species evolve faster than solitary ones.
• Activity Patterns: Species with fixed daily activity patterns evolve more slowly than those with flexible patterns.

Climate Change and Evolution

The research integrates past climate records into evolutionary models to understand how climate change has influenced species evolution. By comparing different climate curves (temperature, rate of temperature change) with evolutionary models, it's clear that climate is a significant driver of evolution.

Different groups respond differently to climate change:

• Temperature-sensitive: Lizards, salamanders, placental mammals, and frogs primarily respond to absolute temperature (hot or cold). Frogs, however, evolve more slowly when it's hot.
• Rate-of-change sensitive: Snakes, marsupials, and birds respond more to the rate of climate change. Marsupials tend to slow down when changes are rapid, while birds and snakes speed up.

Ecological factors further modulate these responses. For example, underground-dwelling frogs are less impacted by temperature changes than those exposed to the surface. Arboreal marsupials are more affected by rapid changes than ground-dwelling ones.

Lessons from the Past for the Future

The Paleocene-Eocene Thermal Maximum (PETM), about 56 million years ago, represents the fastest climate change event since the extinction of non-avian dinosaurs. This event, involving a 5-8 degree Celsius temperature rise over 3,000-20,000 years, serves as a paleontological analogue for future climate change. Current rates of warming are at least 10 times faster than the PETM.

Understanding how species responded to past climate events is crucial because current data, such as the WWF's Living Planet Index, show rapid declines in species populations. These declines are driven by climate change, habitat degradation, pollution, overexploitation, and invasive species.

While current extinction rates (around 0.5-1.5% over the last 100-125 years) are below the 75% threshold for mass extinctions, the number of species currently threatened with extinction pushes us into mass extinction territory. The significant error bars on these estimates reflect our vast data deficiencies regarding species populations and ecologies.

The speaker emphasizes that we are currently on a "ridge" leading towards a mass extinction event, similar to the end-Cretaceous mass extinction boundary. This event, likely caused by a meteor impact, led to a fundamentally different world. The "dead man walking" effect highlights how the loss of some species can cascade, leading to the extinction of others that relied on them.

We have the capacity to make different choices and avoid becoming the "next meteor." Our well-being is intrinsically linked to the health of other species, which provide essential services like water and food. The rate of change, particularly in climate, is a critical factor impacting species evolution. Therefore, we must act quickly to mitigate these changes and prevent a mass extinction event, which would have profound and irreversible impacts on our own survival.