Relative High Fitness and Genome-wide Diversity May Facilitate Plastic and Active Foragers’ Diversification

Dylan Padilla
Martha Muñoz, David Skelly

June 22, 2025
Yale Institute for Biospheric Studies
New Haven, Connecticut

Outline

Introduction

• Overview of the ways by which organisms forage in nature
• Fitness landscapes and the link between foraging behaviors and diversification rates

Methods

• State-dependent diversification framework
• Ancestral state reconstruction
• Patterns of genomic variation

Results and Discussion

• Explain variation in diversification rates across the Tree of Life
• Elucidate a potential answer to the question of how fitness variation through different foraging behaviors can lead to species diversification

Introduction

Foraging behaviors lie along a continuum

Foraging behaviors may influence fitness

Foraging behaviors may influence fitness

Foraging behaviors may influence fitness

Foraging behaviors may influence fitness

Predictions based on fitness landscapes

Predictions based on fitness landscapes

Predictions based on fitness landscapes

1. Active and plastic foraging may lead to high diversification if populations exploit new fitness peaks
2. A plastic response may come at the cost of carrying around additional genetic machinery
3. Restricted locomotion could lead to low diversification via stochastic processes such as drift

Methods

Data source

• Physiological, behavioral, and life history data
• Foraging behaviors: Active foragers, Plastic foragers, and Sit-and-wait foragers
• Reproductive effort: Average clutch size x Average # clutches per year

Data source

• Maximum body mass (g)
• 997 species distributed among 56 families

State-dependent diversification framework

• We relied on state-dependent speciation and extinction models

• We started with a null model

• Next, we fitted a model in which all rates of speciation and extinction depended on the character state for our multi-state character

• We fitted models varying (\(\lambda\)) between states, only (\(\mu\)), and neither \(\lambda\) nor \(\mu\)

• We compared the models’ goodness of fit based on \(AIC_{c}\)

Genome size and genetic diversity

• 99 squamate species distributed among 29 families

• Association between genome size and the foraging behavior of species
• We fitted a set of PGLS models
• We compared the models’ goodness of fit based on \(AIC_{c}\)
• We compared \(\pi\) of an active forager (Podarcis muralis) vs sit-and-wait forager (Anolis carolinensis)

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Ancestral state reconstruction

• Fitted discrete-state Markov chain models
• An equal-rates (ER) model, an all-rates-different model (ARD), a symmetrical model (SYM)
• We compared the models’ goodness of fit based on \(AIC_{c}\)

Results and Discussion

Plastic foraging and active foraging are associated with higher diversification rates

Active foraging appears to be the ancestral state of all reptiles (0.639)

Sit-and-wait -> active foraging (\(\sim64\)), succeeded by Sit-and-wait -> plastic foraging (\(\sim57\))

Active foragers and sit-and-wait foragers may be stabilizing in the present but plastic-foraging lineages grow almost monotonically

Not only was the net diversification of plastic foragers high, but they also evolved high reproductive effort

Plastic foragers’ large genomes potentially contain more genes, more and longer introns, and more transposable elements

A high genome-wide nucleotide diversity among active foragers could compensate for the small size of active foragers’ genomes

Summary

• Plastic foragers and active foragers not only have high diversification rates but may also have higher fitness compared to sit-and-wait foragers

• Plastic foragers could accelerate the pace of evolution by exposing cryptic genetic variation to selection

• A higher genome-wide nucleotide diversity among active foragers could make up for the small size of their genomes

• Restricted locomotion among sit-and-wait foragers potentially led to relatively low diversification via stochastic processes such as population bottlenecks

For a preprint of the study, check out the qrcode 👉🏼