About

Sarah Kocher is an Associate Professor in the Department of Ecology & Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics at Princeton University. She is also a Freeman Hrabowski Scholar and a researcher affiliated with the Howard Hughes Medical Institute. Her research focuses on behavioral and evolutionary genomics, with particular interest in social polymorphisms and social evolution in bees. Kocher has contributed to understanding the genetic basis of social behavior, as evidenced by her publications on the genetics of social polymorphisms in halictid bees and the genomic analysis of socially polymorphic species. Her work explores the transitions in social complexity along environmental gradients and the evolutionary mechanisms underlying social behavior in insects.

Research topics

• Artificial Intelligence
• Computer Science
• Computer vision
• Biology
• Machine Learning
• Psychology
• Genetics
• Human–computer interaction
• Evolutionary biology
• Zoology
• Computational biology
• Ecology

Selected publications

• Nature-inspired neuroscience

  Current Opinion in Neurobiology · 2026-04-18

  articleOpen accessSenior author

  The early decades of neuroscience drew inspiration from the rich diversity of animal life, but in recent years, the field has converged on a narrow set of canonical models. These organisms provide access to a wealth of scientific tools, a large community, and the ability to rapidly build on existing knowledge, but they represent only a small sample of the neural architectures and behaviors found in the animal kingdom. Here, we highlight the value of harnessing a more diverse panel of organisms to study the neural basis of behavior using the sensory systems as an example. From moths navigating using the Milky Way, to deep-sea dragonfish detecting far-red bioluminescence via a chlorophyll-derived photosensitizer, and octopuses tasting by touch through chemoreceptors in their suckers, studies of diverse systems reveal novel mechanisms for solving sensory challenges, as well as striking examples of convergence. Developments in species-agnostic scientific tools like behavioral tracking, gene editing, and electrophysiology are making it possible to study a broader array of organisms, enabling neurobiological comparisons inspired by the vast variation found in nature. We argue that a nature-inspired approach to neuroscience that considers the full diversity of brains in the animal kingdom will lead to new and unexpected biological discoveries, help reveal general principles of nervous system organization, and expand the breadth of biological phenomena that can be uncovered.

  PublisherDOI

• Bumble bee workers adopt novel behavioral roles and reshape their social networks in the absence of a queen

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-07 · 2 citations

  preprintOpen accessSenior author

  Abstract Dominant individuals often structure group organization, but less is known about how social networks reorganize in their absence and how variation among subordinates contributes to collective outcomes. Bumble bees ( Bombus impatiens ) provide an ideal system to study these dynamics: queens typically monopolize reproduction, but in some contexts individual workers can adopt queenlike social roles. Using multi-animal pose tracking, we compared matched queenright and queenless partitions from the same source colonies, quantifying over 80 million social interactions. Queen-less colonies exhibited increased behavioral variation and contained a subset of highly influential workers with elevated movement, spatial centrality, and reproductive activity that was absent in queen-right conditions. The emergence of these individuals coincided with a shift from centralized to decentralized, efficient network architectures. These results demonstrate that queen presence constrains latent worker variation, revealing how individual behavioral differences can scale up to reshape collective social organization in hierarchical societies.

  PublisherDOI

• The Fire Ant Social Chromosome Exerts a Major Influence on Genome Regulation

  Molecular Biology and Evolution · 2025-05-23 · 2 citations

  articleOpen access

  Supergenes underlying complex trait polymorphisms ensure that sets of coadapted alleles remain genetically linked. Despite their prevalence in nature, the mechanisms of supergene effects on genome regulation are poorly understood. In the fire ant Solenopsis invicta, a supergene containing over 500 individual genes influences trait variation in multiple castes to collectively underpin a colony level social polymorphism. Here, we present results of an integrative investigation of supergene effects on gene regulation. We present analyses of ATAC-seq data to investigate variation in chromatin accessibility by supergene genotype and STARR-seq data to characterize enhancer activity by supergene haplotype. Integration with gene co-expression analyses, newly mapped intact transposable elements (TEs), and previously identified copy number variants (CNVs) collectively reveals widespread effects of the supergene on chromatin structure, gene transcription, and regulatory element activity, with a genome-wide bias for open chromatin and increased expression in the presence of the derived supergene haplotype, particularly in regions that harbor intact TEs. Integrated consideration of CNVs and regulatory element divergence suggests each evolved in concert to shape the expression of supergene encoded factors, including several transcription factors that may directly contribute to the trans-regulatory footprint of a heteromorphic social chromosome. Overall, we show how genome structure in the form of a supergene has wide-reaching effects on gene regulation and gene expression.

  PublisherOA PDFDOI

• The fire ant social chromosome exerts a major influence on genome regulation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-18

  preprintOpen access

  Abstract Supergenes underlying complex trait polymorphisms ensure sets of coadapted alleles remain genetically linked. Despite their prevalence in nature, the mechanisms of supergene effects on genome regulation are poorly understood. In the fire ant Solenopsis invicta , a supergene containing over 500 individual genes influences trait variation in multiple castes to collectively underpin a colony level social polymorphism. Here, we present results of an integrative investigation of supergene effects on gene regulation. We present analyses of ATAC-seq data to investigate variation in chromatin accessibility by supergene genotype and STARR-seq data to characterize enhancer activity by supergene haplotype. Integration with gene coexpression analyses, newly mapped intact TEs, and previously identified CNVs, collectively reveal widespread effects of the supergene on chromatin structure, gene transcription, and regulatory element activity, with a genome-wide bias for open chromatin and increased expression in the presence of the derived supergene haplotype, particularly in regions that harbor intact TEs. Integrated consideration of CNVs and regulatory element divergence suggests each evolved in concert to shape the expression of supergene encoded factors, including several transcription factors that may directly contribute to the trans -regulatory footprint of a heteromorphic social chromosome. Overall, we show how genome structure in the form of a supergene has wide-reaching effects on gene regulation and gene expression.

  PublisherOA PDFDOI

• The distribution of fitness effects varies phylogenetically across animals

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-13 · 2 citations

  preprintOpen access

  1 Abstract The distribution of fitness effects (DFE) describes the selection coefficients ( s ) of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila , and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (Pagel’s λ = 0.84, P = 0.01). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (PGLS λ , P = 0.03), and the proportion of new beneficial mutations ( , P < 0.001). These findings align with Fisher’s Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGM’s predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals. 2 Significance Statement Understanding how mutations affect fitness is fundamental in evolution, but little is known about how and why the distribution of fitness effects (DFE) varies across species. In this study, we examine the DFE in diverse animal populations and show that closely related species exhibit similar patterns of mutation effects, with new mutations being more deleterious in mammals compared with birds and insects. Our findings corroborate Fisher’s Geometric Model, which explains the variation in the DFE across species as a function of organismal complexity and long-term population size. By connecting organismal complexity and population size with the DFE, we offer a phylogenetic view into the selective forces shaping species adaptation and evolution.

  PublisherOA PDFDOI

• Integrating computer vision and molecular neurobiology to bridge the gap between behavior and the brain

  Current Opinion in Insect Science · 2024-09-06 · 6 citations

  reviewOpen accessSenior author

  The past decade of social insect research has seen rapid development in automated behavioral tracking and molecular profiling of the nervous system, two distinct but complementary lines of inquiry into phenotypic variation across individuals, colonies, populations, and species. These experimental strategies have developed largely in parallel, as automated tracking generates a continuous stream of behavioral data, while, in contrast, 'omics-based profiling provides a single 'snapshot' of the brain. Better integration of these approaches applied to studying variation in social behavior will reveal the underlying genetic and neurobiological mechanisms that shape the evolution and diversification of social life. In this review, we discuss relevant advances in both fields and propose new strategies to better elucidate the molecular and behavioral innovations that generate social life.

  PublisherDOI

• Variation in season length and development time is sufficient to drive the emergence and coexistence of social and solitary behavioural strategies

  Proceedings of the Royal Society B Biological Sciences · 2024-10-01 · 3 citations

  articleOpen accessSenior authorCorresponding

  Season length and its associated variables can influence the expression of social behaviours, including the occurrence of eusociality in insects. Eusociality can vary widely across environmental gradients, both within and between different species. Numerous theoretical models have been developed to examine the life history traits that underlie the emergence and maintenance of eusociality, yet the impact of seasonality on this process is largely uncharacterized. Here, we present a theoretical model that incorporates season length and offspring development time into a single, individual-focused model to examine how these factors can shape the costs and benefits of social living. We find that longer season lengths and faster brood development times are sufficient to favour the emergence and maintenance of a social strategy, while shorter seasons favour a solitary one. We also identify a range of season lengths where social and solitary strategies can coexist. Moreover, our theoretical predictions are well matched to the natural history and behaviour of two flexibly eusocial bee species, suggesting that our model can make realistic predictions about the evolution of different social strategies. Broadly, this work reveals the crucial role that environmental conditions can have in shaping social behaviour and its evolution and it underscores the need for further models that explicitly incorporate such variation to study the evolutionary trajectories of eusociality.

  PublisherDOI

• The Molecular Substrates of Insect Eusociality

  Annual Review of Genetics · 2024-08-15 · 19 citations

  reviewOpen access1st authorCorresponding

  The evolution of eusociality in Hymenoptera-encompassing bees, ants, and wasps-is characterized by multiple gains and losses of social living, making this group a prime model to understand the mechanisms that underlie social behavior and social complexity. Our review synthesizes insights into the evolutionary history and molecular basis of eusociality. We examine new evidence for key evolutionary hypotheses and molecular pathways that regulate social behaviors, highlighting convergent evolution on a shared molecular toolkit that includes the insulin/insulin-like growth factor signaling (IIS) and target of rapamycin (TOR) pathways, juvenile hormone and ecdysteroid signaling, and epigenetic regulation. We emphasize how the crosstalk among these nutrient-sensing and endocrine signaling pathways enables social insects to integrate external environmental stimuli, including social cues, with internal physiology and behavior. We argue that examining these pathways as an integrated regulatory circuit and exploring how the regulatory architecture of this circuit evolves alongside eusociality can open the door to understanding the origin of the complex life histories and behaviors of this group.

  PublisherDOI

• Chromosomal fusion drives sex chromosome evolution in treehoppers despite long-term X chromosome conservation

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-07-15

  preprintOpen access

  Abstract Sex chromosomes follow distinct evolutionary trajectories compared to the rest of the genome. In many cases, sex chromosomes (X and Y, or Z and W) significantly differentiate from one another resulting in heteromorphic sex chromosome systems. Such heteromorphic systems are thought to act as an evolutionary trap that prevents subsequent turnover of the sex chromosome system. For old, degenerated sex chromosome systems in which turnover is unlikely, chromosomal fusion with an autosome may be one way that sex chromosomes can ‘refresh’ their sequence content. We investigated these dynamics using treehoppers (hemipteran insects of the family Membracidae), which ancestrally have XX/X0 sex chromosomes. We assembled the first chromosome-level treehopper genome from Umbonia crassicornis and employed comparative genomic analyses of 12 additional treehopper species to analyze X chromosome variation across different evolutionary timescales. We find that the X chromosome is largely conserved, with one exception being an X-autosome fusion in Calloconophora caliginosa . We also compare the ancestral treehopper X with other X chromosomes in Auchenorrhyncha (the clade containing treehoppers, leafhoppers, spittlebugs, cicadas, and planthoppers), revealing X conservation across more than 300 million years. These findings shed light on chromosomal evolution dynamics in treehoppers and the role of chromosomal rearrangements in sex chromosome evolution. Significance The evolutionary forces underlying sex chromosome stability versus turnover have been challenging to disentangle. We present the first chromosome-level treehopper genome and find evidence of long-term X chromosome conservation within treehoppers – and among treehoppers and other hemipteran insects. A key exception is the evolution of neo-XX/XY sex chromosomes via an X-autosome fusion. Sex chromosome-autosome fusions may play an important role in the evolution of otherwise ‘trapped’ (i.e., old and degenerated) sex chromosome systems.

  PublisherOA PDFDOI

• Neo-Sex Chromosome Evolution in Treehoppers Despite Long-Term X Chromosome Conservation

  Genome Biology and Evolution · 2024-12-01 · 4 citations

  articleOpen access

  Sex chromosomes follow distinct evolutionary trajectories compared to the rest of the genome. In many cases, sex chromosomes (X and Y or Z and W) significantly differentiate from one another resulting in heteromorphic sex chromosome systems. Such heteromorphic systems are thought to act as an evolutionary trap that prevents subsequent turnover of the sex chromosome system. For old, degenerated sex chromosome systems, chromosomal fusion with an autosome may be one way that sex chromosomes can "refresh" their sequence content. We investigated these dynamics using treehoppers (hemipteran insects of the family Membracidae), which ancestrally have XX/X0 sex chromosomes. We assembled the most complete reference assembly for treehoppers to date for Umbonia crassicornis and employed comparative genomic analyses of 12 additional treehopper species to analyze X chromosome variation across different evolutionary timescales. We find that the X chromosome is largely conserved, with one exception being an X-autosome fusion in Calloconophora caliginosa. We also compare the ancestral treehopper X with other X chromosomes in Auchenorrhyncha (the clade containing treehoppers, leafhoppers, spittlebugs, cicadas, and planthoppers), revealing X conservation across more than 300 million years. These findings shed light on chromosomal evolution dynamics in treehoppers and the role of chromosomal rearrangements in sex chromosome evolution.

  PublisherDOI

Recent grants

• Is sociality driven by an increased capacity for gene regulation?

  NSF · $1.1M · 2018–2024

Frequent coauthors

• Naomi E. Pierce

  Harvard University

  22 shared

• Benjamin E. R. Rubin

  Princeton University

  21 shared

• Jon G. Sanders

  Cornell University

  19 shared

• Kyle M. Turner

  Harvard University

  19 shared

• Andrew E. Webb

  Princeton University

  18 shared

• Christina M. Grozinger

  Pennsylvania State University

  14 shared

• Beryl M. Jones

  Princeton University

  13 shared

• Rena M. Schweizer

  Agricultural Research Service

  12 shared

Labs

• Kocher LabPI

Awards & honors

• Freeman Hrabowski Scholar, Howard Hughes Medical Institute