Gene Flow and Recent Lineage Colonization Constrain Genetic Differentiation Despite Local Adaptation

Dylan Padilla, Lisa Brady,
and David Skelly

June 21, 2026
Yale Institute for Biospheric Studies
New Haven, Connecticut

Outline

Introduction

Factors facilitating population structure and those maintaining genetic cohesion
Compelling system to examine the forces that shape genomic and phenotypic evolution among populations

Methods

Population structure and genetic differentiation
Demographic modeling
Outlier test of selection and phenotypic test for selection

Results and Discussion

Elucidate a potential answer to the question of why populations remain genetically similar in the presence of strong selection

Introduction

Polymorphism is widespread in nature

Common patterns of genetic structure

Does the lack of genetic structure reflect absence of divergent selection?

Selection-migration balance

Colonization to new environments

Compelling system to examine these hypotheses

Skelly, 2000. Ecology Letters.

Range of wood frog

Methods

Genetic analysis

In 2018, we assembled a comprehensive dataset of ddRAD samples collected from wood frog populations distributed across 19 wetlands at Yale-Myers forest
We processed the raw reads with ipyrad v.0.9.107 pipeline, using the wood frog reference genome and its annotation
To understand how individuals were genetically related, we estimated admixture proportions and the fixation index (Fst) across our samples.

Demographic inference

We inferred the demographic history of the wood frog by employing a composite likelihood approach using fastsimcoal2

Demographic inference

We inferred the demographic history of the wood frog by employing a composite likelihood approach using fastsimcoal2

Selection signatures across the genome

To detect signatures of local adaptation across the genome of the wood frog, we performed a genotype\(\times\)environment association analysis based on a latent factor mixed model
We used the anottation file generated from the wood frog genome annotation described above to extract gene names associated with the candidate loci under selection

Selection on phenotypes

We compared the divergence of a phenotypic trait such as embryonic development with the total genetic differentiation observed across populations of the wood frog (overall \(F_{st}\))

Selection on phenotypes

This experimental designed enabled us to partition the total genetic variance for embryonic development into two main components: the variance among populations and the variance within populations

Selection on phenotypes

Where \(\sigma^2_{GB}\) represents the genetic variance among populations and \(\sigma^2_{GW}\) the additive genetic variance within populations

Results

Populations of the wood frog are genetically homogeneous

Recent divergence populations from a common ancestor approximately 24 generations ago

The genotype\(\times\)environment association analysis reveals two outlier loci:

Significant signature of divergent selection

Concluding remarks

This genomic signature of selection together with a remarkable phenotypic differentiation strongly suggests that natural selection overcomes the power of genetic drift, even in a landscape characterized by a recent colonization and significant connectivity