Cameron K. Ghalambor

Transposable elements (TEs) are ubiquitous repetitive DNA sequences that can mobilise within genomes and may modulate gene expression in an environment-dependent manner. TEs and the safeguarding epigenetic machinery targeting them, can be tuned by environmental fluctuations to influence gene expression by inducing genomic, epigenetic, and transcriptomic changes. Yet, the degree to which TE-driven molecular diversity translate into inter-individual phenotypic variation vs accumulating without any phenotypic consequences remains unclear. Here, we used five populations of genetically engineered Drosophila melanogaster flies that carry variable TE content but share an otherwise identical genetic background to test the phenotypic consequences of the early stages of TE accumulation. Phenotypic screenings across 17 traits (fertility-related traits, life-history traits and stress resistance tests) revealed significant differences between the populations (e.g. reduced hatchability). We also observed a notable increase in intra-population phenotypic variation for the heavily TE-burdened populations across a wide panel of traits. These results suggest considerable TE-driven inter- and intra-population phenotypic variation. Further investigation revealed that variable TE contents can influence the response to environmental changes, positioning TEs as drivers of environmentally-induced phenotypic variation in a system deprived of other sources of genetic variation. These results provide empirical evidence that TEs contribute to the heterogeneity of the environmental response and therefore represent an underlying mechanism of phenotypic variation. Significant statement: The molecular mechanisms underlying phenotypic variation and variation in the environmental response continue to be a central question in evolutionary biology. Leveraging a biological system composed of Drosophila melanogaster populations containing varying levels of transposable elements (TEs), which are repetitive and widespread genomic elements, within an otherwise identical genetic background, we demonstrate the influence of TEs in generating phenotypic variation. By employing this innovative system to isolate the specific contributions of TEs, we provide evidence for their role as drivers of both phenotypic variability and divergence of the environmental response. Such results show that, rather than being largely neutral or silenced through epigenetic mechanisms, TE accumulation can contribute to measurable phenotypic diversity and thus provide heritable variation that selection can act upon.

Temperature fundamentally shapes ectotherm biology, from continuous changes in sublethal performance to acute functional failure at upper thermal limits. Sublethal performance is commonly characterized using thermal performance curves (TPCs), which describe continuous changes in performance across temperatures, whereas acute heat tolerance is often quantified by the critical thermal maximum (CT _max ), the temperature marking organism-level functional failure. Whether these dimensions of thermal physiology vary independently or covary as components of a coordinated warm-end thermal phenotype remains unclear. Synthesizing data from more than 100 ectotherm species, we tested how CT _max scales with two key warm-end TPC traits: the thermal optimum (T _opt ) and the upper limit of performance (TPC _max ). Across diverse taxa, both T _opt and TPC _max scaled approximately 1:1 with CT _max , and these relationships were broadly consistent across the biological, experimental, and environmental contexts represented in our dataset. Although both slopes were individually consistent with 1:1 scaling, when T _opt and TPC _max were compared directly, TPC _max increased more steeply with CT _max than did T _opt , such that the declining portion of the TPC widened as CT _max increased. Species with greater acute heat tolerance therefore tended to retain positive performance across a broader range of supra-optimal temperatures before reaching the upper performance limit. Together, these relationships show that sublethal warm-end performance and acute heat tolerance covary systematically across species, supporting their interpretation as broadly coordinated components of the thermal phenotype rather than independent axes of thermal biology. Significance: As climate warming pushes temperatures beyond the conditions species have previously experienced, predicting ectotherm vulnerability requires understanding how measures of thermal biology relate. Heat tolerance measures the maximum temperature organisms can survive, whereas temperature-dependent performance measures how they function across temperatures. Whether these measures capture related aspects of thermal biology has remained unclear. We synthesized thermal trait data from more than 100 ectotherm species to test how heat tolerance relates to temperature-dependent performance. We show that species with higher heat tolerance also reach peak performance and maintain function at higher temperatures, with these traits scaling approximately 1:1 across diverse contexts. This relationship links two major approaches to thermal biology and provides a quantitative basis for understanding ectotherm responses to warming.

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs among three closely related species of North American jays ( Aphelocoma , scrub-jays) displaying a 55-fold range in effective population size. We find rapid evolution of genome architecture, including ~100-megabase decreases in genome size driven by shifts in complex satellite landscapes. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with consistent evidence of adaptive fixation only in the largest population. Gene copy number variants exhibit an inverse relationship with population size, indicating strongly deleterious dynamics, with consequences for gene expression. Our long-read dataset and pangenome analysis demonstrate how population size shapes genome complexity.

Whether the same genes underlie parallel adaptive trait evolution remains an open question in biology. The degree of genetic parallelism is expected to increase at higher genetic hierarchical levels (i.e., single nucleotide polymorphisms [SNPs] to genes to pathways to phenotype) due to the hierarchical nature of the genetic basis of traits, which genomic approaches can help elucidate. Previous research shows a large degree of variation in the extent to which phenotypic parallelism shares the same genetic mechanisms in nature. Here, we analyzed the degree of genetic parallelism underlying repeated divergence in bill morphology of island scrub-jays (Aphelocoma insularis), across three naturally replicated pine–oak ecotones on Santa Cruz Island, California, US. We analyzed 66,503 SNPs generated using restriction site-associated DNA sequencing in 161 island scrub-jays to identify candidate SNPs associated with environmental variation and divergence in bill morphology. We then examined signatures of parallelism in genomic regions containing candidate SNPs and the associated genetic pathways. We found little evidence for parallelism at the SNP or gene level, but substantial parallelism at the pathway level. Our results support the view that the degree of genetic parallelism underlying repeated phenotypes depends on the genetic level of organization being analyzed.

Las diferencias individuales entre las poblaciones tienen importantes implicaciones ecológicas y evolutivas a la hora de entender las respuestas a nivel de población a la variación ambiental. Encontramos evidencia de diferencias relacionadas con el hábitat en la composición isotópica estable de las plumas y el comportamiento de forrajeo de las urracas de Santa Cruz (Aphelocoma insularis), endémicas de la isla Santa Cruz, California, EE. UU., que muestran divergencia fenotípica paralela en la forma del pico entre los hábitats de pino y roble. Usamos isótopos estables de hidrógeno (δD), carbono (δ13C) y nitrógeno (δ15N) de las plumas y observamos directamente el comportamiento de alimentación para inferir la variación de la dieta específica del hábitat entre las urracas de Santa Cruz. Si bien, la composición de isótopos de hidrógeno de las plumas no difirió entre hábitats como esperábamos, las urracas muestreadas en hábitats de pinos mostraron mayor contenido de 13C, mientras que, las urracas encontradas en hábitats de robles presentaron mayor contenido de 15N en sus plumas. Las observaciones de alimentación indicaron que las dietas fueron prácticamente las mismas en ambos hábitats, no obstante, las urracas localizadas en hábitats de pinos tuvieron más probabilidades de consumir artrópodos. Además, estas urracas usaban relativamente más maniobras de búsqueda de alimentos, tales como sondeo, salidas y picoteo para capturar a sus presas. Estos hallazgos sugieren nuevas vías de investigación para comprender cómo la divergencia fenotípica vinculada al hábitat moldea el comportamiento y la dieta de la urraca omnívora de Santa Cruz.

Phenotypic expression is often constrained by functional conflicts between traits, and the resulting trade-offs impose limits on phenotypic and taxonomic diversity. However, the underlying mechanisms that maintain trade-offs or allow organisms to resolve them via phenotypic plasticity are often challenging to detect. The trade-off between gas exchange and water loss across respiratory surfaces represents a fundamental trade-off that constrains phenotypic diversity in terrestrial life. Here, we investigate plastic mechanisms that mitigate this trade-off in lungless salamanders that breathe exclusively across their skin. Our field and laboratory experiments identified plastic responses to environmental variation in water loss and oxygen uptake, and gene expression analyses identified putative pathways that regulate this trade-off. Although the trade-off was generally strong, its strength covaried with environmental conditions. At the molecular level, antagonistic pleiotropy in multiple biological pathways (e.g., vasoconstriction and upregulation of aerobic respiration) putatively produce the trade-off, while other pathways mitigate the trade-off by affecting a single trait (e.g., oxygen binding affinity, melanin synthesis). However, organisms are likely to encounter novel trade-offs in the process of bypassing another. Our study provides evidence that alternative pathways allow organisms to mitigate pleiotropic conflicts, which ultimately may allow greater phenotypic diversity and persistence in novel environments.

Predator reintroductions are an important tool for conserving vulnerable species and restoring natural communities but can lead to unintended consequences if prey have lost appropriate anti-predator behaviors. We provide experimental evidence that 11 bird species on Santa Rosa Island, California retain anti-predator behavior toward a locally extirpated nest predator, Aphelocoma insularis (Island Scrub-Jay) that has been extinct for >100 yr and has been proposed for reintroduction. Our experimental test of prey naivete compared the species’ behavioral responses within and across islands to taxidermic models and vocalizations of Aphelocoma jays, a familiar nest predator (Corvus corax, common raven), a novel species, (Scolopax minor, American woodcock) and a control (Haemorhous mexicanus, house finch). We show that anti-predator behavior toward jays was similar to behaviors directed toward the familiar nest predator. Moreover, anti-predator behavior toward jays did not differ between Santa Rosa Island and Santa Cruz Island, where the jay is currently a single-island endemic. Species with lower annual fecundity were more likely to respond to all experimental treatments. Our results demonstrate the retention of anti-predator behavior on Santa Rosa Island for at least a century after the extinction of a native predator and highlight a cost-effective approach for evaluating prey naivete and the risk of predator translocations in other contexts.

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ∼100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.

Species interactions can contribute to species turnover when the outcomes of the interactions are context dependent (e.g., change along environmental gradients). Plasticity may change this dynamic by altering the environmental tolerances of the species interacting. Here, we explored how the competitive interaction between two euryhaline fish, Poecilia reticulata and Poecilia picta, is influenced by acute and developmental responses to salinity. In Trinidad, P. reticulata is confined to freshwater despite being tolerant of brackish water. P. reticulata may fail to occupy brackish water because of reduced tolerance to salinity or because P. picta competitively excludes them, and developing in brackish water could alter the dynamics of either scenario. To test this, we compared the salinity tolerances of both species in the absence of competition, reared P. reticulata individuals in freshwater or brackish water, and tested the consequences of developmental plasticity in experiments in which P. reticulata competed against conspecifics or P. picta during acute exposure to freshwater or brackish water. We found that (1) P. reticulata has a weaker salinity tolerance than P. picta; (2) P. reticulata that developed in freshwater perform best when competing against P. picta in freshwater but perform poorly when competing against P. picta in brackish water, suggesting the species interaction is context dependent; and (3) developing in brackish water did not benefit P. reticulata in brackish water. Our results suggest that P. reticulata's freshwater range limit is in part a product of a lower salinity tolerance leading to a decrease in competitive performance in brackish water. Adaptive plasticity has been suggested to be a crucial part of the colonization process, yet nonadaptive plastic responses as found here can limit range expansion and reinforce range limits.

Interactions with competitors and predators can generate strong selection and favour the evolution of novel strategies for mitigating fitness costs. Adaptations to mitigate competition and predation risk often involve evolution of traits which directly reduce costs. Simultaneously, the evolution of behaviours that co‐opt the functional traits of non‐interacting, third‐party species have also been observed but remain poorly studied (e.g. anointing behaviour, tri‐trophic interactions). Here we investigate if the novel behavioural co‐option of conifer resin in a cavity‐nesting bird can ameliorate interactions with nest predators and nest site competitors. Red‐breasted nuthatches (Sitta canadensis) collect resin from live trees and apply it around the entrances of their nest cavities in dead trees. Using paired nest boxes, we mimicked the nuthatch behaviour by apply resin around the hole of one and not the paired box in two field experiments to test a priori hypotheses about the evolution and adaptive value of this behaviour. The first experiment baited the paired boxes with food to attract mammalian predators (e.g. red squirrels Tamiasciurus hudsonicus). The second experiment left boxes available for breeding by cavity‐nesting birds that compete with nuthatches for nest sites (e.g. house wrens Troglodytes aedon). We also used ancestral trait reconstruction to test whether resin use is a non‐adaptive derivation of mud‐plastering behaviour observed in numerous congeners. Experimental nest boxes with resin applied to the entrance were less likely to have bait removed and less likely to have nests built or initiated than paired nest boxes without resin. Ancestral trait reconstruction suggested that resin use was more likely (>77%) to have evolved in ancestors that did not exhibit mud‐plastering behaviour. Our results do not support a major role of phylogenetic inertia and provide experimental evidence that application of conifer resin to nest cavities ameliorates interference competition from other cavity‐nesting species and reduces nest predation risk. Overall, our results showcase the ecological function of behavioural co‐option and its important consequences for fitness in nature. Read the free Plain Language Summary for this article on the Journal blog.