Secretly Lamarckian?

Olivia Mathieson, Erin McKenney, Aram Mikaelyan, Autumn Sylvestri, Aurora Toennisson

(Author names listed alphabetically)

The modern synthesis of evolutionary biology rests on a clear separation of concepts: acquired traits are not inherited, inheritance flows through the germline, and adaptation proceeds through random mutation followed by natural selection. Yet, advances in microbiome research, epigenetics, and horizontal gene transfer (HGT) have begun to challenge the strictness of these boundaries - without violating Darwinian principles, but by complicating how inheritance and adaptation are understood in host-associated systems.

Microbiomes, in particular, occupy a conceptual gray zone. While microbial genomes evolve under classical Darwinian mechanisms - mutation, selection, and drift - they do so at rates and through mechanisms (e.g., HGT) that vastly outpace their multicellular hosts. This time-scale mismatch creates the appearance that microbiomes confer rapid, environmentally induced traits that persist across generations. When microbial community shifts influence host digestion, immunity, behavior, or stress tolerance, and when these changes are reliably passed down via maternal behavior, coprophagy, or egg-smearing, the result can resemble a form of functional inheritance - even in the absence of host genomic change.

This resemblance to Lamarckian logic has led to increasing interest in whether host-microbe systems enable the persistence of acquired traits through non-genetic, yet heritable channels. While classical Lamarckism invoked use and disuse as drivers of heritable change within an individual's lifetime, many of the mechanisms now observed - particularly microbial acquisition and epigenetic modulation - achieve similar outcomes through different routes. If a microbe acquires a novel function via HGT (e.g., fiber degradation) and is consistently passed to host offspring, or reliably reacquired from the environment due to host traits, this constitutes a form of inheritance of an environmentally induced trait - not through the host genome, but through stable symbiosis.

Furthermore, epigenetic modifications in hosts (e.g., changes to intestinal pH, mucus secretion, or root exudates) can regulate microbial assembly and persistence. If such modifications are themselves heritable, this introduces another layer through which acquired environmental responses can be transmitted.

These processes do not overturn Darwinian principles. Rather, they operate alongside them, with selection still acting on variation. But they do suggest that evolutionary theory may need to accommodate distributed inheritance systems, where the unit of selection includes microbial partners and where phenotypic plasticity is mediated not only by host genes, but by symbiont communities.

In this view, host–microbe systems can be seen as Lamarckian scaffolds supporting Darwinian stabilization: traits may originate through non-genetic means but become embedded through selection over time. This hybrid logic - fast microbial innovation filtered through slower host evolution- offers a powerful model for understanding evolvability, ecological flexibility, and even speciation.

The challenge now is not whether these systems are “Lamarckian,” but whether evolutionary biology has the conceptual language to fully describe them.

Note: This post was developed as a pedagogical exercise in collaborative synthesis and argument literacy, emerging from a discussion among three students and two faculty members in the lab's chat group, exploring how microbiomes challenge conventional views of inheritance and evolution.