Genome Biol Evol
· 2026 May · PMID 42049270
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The subtelomeric regions of eukaryotic chromosomes harbor repeated elements that contribute to genomic plasticity and adaptation. In Saccharomyces cerevisiae, the Y' elements represent a major class of subtelomeric repea...The subtelomeric regions of eukaryotic chromosomes harbor repeated elements that contribute to genomic plasticity and adaptation. In Saccharomyces cerevisiae, the Y' elements represent a major class of subtelomeric repeats; yet, their diversity and evolutionary dynamics remain incompletely characterized. Here, we analyzed Y' elements across 54 S. cerevisiae strains using high-quality telomere-to-telomere genome assemblies. We detected 893 high-confidence Y' elements, which we classified into 12 major clusters, revealing a broader structural diversity than previously described, including canonical short (∼5.2 kb) and long (∼6.7 kb) elements, intermediate-size classes (mid1 and mid2), and a novel family containing CA-rich repeats. Sequence analyses showed that open reading frames, including those encoding the putative Y'-Help1 helicase, are highly conserved within clusters, suggesting selective maintenance of functional sequences. The distribution of Y' elements varied widely across strains and chromosome extremities, with some strains lacking Y' entirely and others, such as the clinical ADI isolate, carrying up to 149 copies. Interstitial telomeric sequences were variably associated with Y' elements and tandem Y' repeats, potentially facilitating recombination and amplification. Analysis of telomere length data further revealed that the presence of long Y' elements, but not Y' elements from other clusters, at the subtelomere is correlated with shorter telomeres at the same chromosome end. Our results provide the most comprehensive catalog of S. cerevisiae Y' elements to date, uncovering unexpected structural and sequence diversity, and a potentially functional role in telomere length regulation.
Hadjipanteli S, Copeland N, Marmolejo Bustamante N
… +3 more, Nweke M, Adhikari B, Kelleher ES
Genome Biol Evol
· 2026 May · PMID 42048570
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Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fitness. Adaptive TE i...Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fitness. Adaptive TE insertions sometimes alter the function of adjacent genes by positively and negatively impacting their expression, or by altering their encoding proteins. Alternatively, individual TE insertions can also be adaptive because they occur in piRNA clusters and lead to piRNA-mediated silencing of transposition. In a recent laboratory evolution experiment, we discovered that the long non-coding RNA CR43651 is an adaptive insertion hot spot for P-element DNA transposons in Drosophila melanogaster. The functional effects of these insertions on P-element repression and CR43651 function were unknown. In this study, we examined the effects of CR43651 insertions on P-element transcriptional regulation, piRNA biogenesis, and viability. We determined that although CR43651 is not a canonical piRNA cluster, chromosomes containing antisense P-element insertions in CR43651 exhibit enhanced piRNA-like silencing in the stage of oogenesis when P-elements transpose, potentially explaining their adaptive benefit. We also discovered that the fitness benefit provided by P-element repression is offset by recessive viability effects of insertion chromosomes, potentially due to disrupted production of mir14, a miRNA produced from CR43651.
Biello R, Iannucci A, Fuselli S
… +5 more, Desiato E, Urban R J, Fossi MC, Panti C, Mancia A
Genome Biol Evol
· 2026 Apr · PMID 42046295
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Whales are key components of marine ecosystems, and several populations are affected by environmental and anthropogenic pressures. Among them, the fin whale, Balaenoptera physalus, from the Mediterranean Sea remains poor...Whales are key components of marine ecosystems, and several populations are affected by environmental and anthropogenic pressures. Among them, the fin whale, Balaenoptera physalus, from the Mediterranean Sea remains poorly characterized at the genomic level despite its classification as Endangered and ongoing population decline driven by human-induced habitat degradation. While bioacoustics and telemetry studies suggest the presence of both resident and migratory subgroups, the extent of genetic isolation in this population remains unclear. Here, we present the first whole-genome analysis of Mediterranean fin whales to assess genomic variability, genetic load, population structure, and adaptive potential of an immunity locus. By comparing genomes from the Mediterranean with those of fin whales from the North Atlantic, North Pacific, and new sequences from Sea of Cortez, we evaluated the degree of genetic isolation and placed the Mediterranean population within a broader evolutionary and conservation context. Our results show that although Mediterranean fin whales form a distinct genetic cluster, they are not fully isolated from North Atlantic populations. We also detected genetic heterogeneity within the Mediterranean basin, with some individuals showing no admixture and others displaying a substantial ancestry component from a different cluster, consistent with previous observations of subgroups exhibiting different migratory tendencies. Despite showing moderate genomic diversity and some adaptive potential compared to other populations, the Mediterranean population remains vulnerable to genomic erosion due to demographic decline, limited connectivity, and growing environmental stress. These findings underscore the importance of conservation actions and long-term genomic monitoring.
Genome Biol Evol
· 2026 May · PMID 42037535
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Oocytes are produced before birth in women and their abundance and quality decrease over time until the loss of ovarian functions at menopause. In contrast, animals such as sea urchins retain stem cells that enable a con...Oocytes are produced before birth in women and their abundance and quality decrease over time until the loss of ovarian functions at menopause. In contrast, animals such as sea urchins retain stem cells that enable a continuous, high fecundity production of quality oocytes throughout their lifespan. We hypothesize that the somatic cells required for these two different adult ovarian functions are distinct. Comparing sea urchin adult ovaries with human fetal ovaries may reveal greater conservation, since they are both in a state of active oocyte production. Here, we present the first integration of the sea urchin adult ovary with the human fetal and adult ovary single-cell RNA-seq datasets. Using SAMap, the resulting integration demonstrates high conservation of cell states and gene expression in both the somatic cells (such as immune and muscle cells) and the germ cells of the ovary. Whereas multiple cell states change over time in the human ovary during its transition from fetal to adult stages, the sea urchin adult ovary instead represents an intermediate state that preserves most of the cell states characteristic of both the fetal and adult human ovary. Comparing reproductive strategies and ovarian function in species separated by 540 million years since their last common ancestor could lead to new approaches to treat human reproductive senescence. Our results highlight the potential of the sea urchin as a powerful comparative model that lacks reproductive senescence to better understand the cellular transitions underlying the aging human ovary.
Flores-Huacuja M, Snow M, Ramos-Madrigal J
… +25 more, Contreras-Cubas C, Barajas-Olmos F, González-Oliver A, Mendoza-Caamal E, Cicerón-Arellano I, Centeno-Cruz F, Córdova EJ, Baca P, Flores-Martínez SE, Ortiz-López R, Reynolds AW, Kostic AD, Villafan-Bernal JR, Galaviz-Hernández C, García-Zapién AG, Miranda-Ortíz H, Lazalde-Ramos BP, Loeza-Becerra F, Carnevale A, Rangel-Villalobos H, Sosa-Macías M, Rojas-Martinez A, Martínez-Hernández A, García-Ortiz H, Orozco L
Genome Biol Evol
· 2026 May · PMID 42030421
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Mitochondrial DNA plays a key role in understanding the demographic history of human populations. Particularly in the Americas#nine widespread Native American specific mitochondrial lineages have been identified. Here we...Mitochondrial DNA plays a key role in understanding the demographic history of human populations. Particularly in the Americas#nine widespread Native American specific mitochondrial lineages have been identified. Here we performed the whole mitogenome sequencing of 572 Indigenous individuals from 60 populations spanning the Mexican territory. To minimize the effects of European and African admixture#we focused on individuals with at least 90% Native American ancestry#estimated by ADMIXTURE. We identified all the five major Native American haplogroups clades#with A2 being the most prevalent (53.9%)#followed by B2 (24.0%)#C1 (17.6%)#D1 (4.3%)#and D4h3a (0.2%). We also identified 82 different subhaplogroup widespread across the country#revealing shared mtDNA haplogroups in populations from distant regions. Moreover#mitochondrial DNA variation in the Mexican Native populations is not structured by geography or linguistic affiliation#suggesting complex gene flow across regions. Demographic reconstructions based on whole mitogenomes showed an exponential increase the maternal Ne around 10 kya in all tested regions. All these findings suggest a mitochondrial genetic persistence through Mexico and possibly the Americas.
Rozenfeld M, Bachar M, Cohen R
… +4 more, Marcos-Hadad E, Milo S, Covo S, Hazkani-Covo E
Genome Biol Evol
· 2026 Apr · PMID 42017484
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Inverted repeats (IRs) are sequences with internal symmetry that can form non-canonical DNA structures. DNA polymerase template switching between imperfect IR arms can homogenize the arms and expand their size. IRs play...Inverted repeats (IRs) are sequences with internal symmetry that can form non-canonical DNA structures. DNA polymerase template switching between imperfect IR arms can homogenize the arms and expand their size. IRs play an important role in the binding of transcription factors (TFs), particularly those that function as dimers. We used comparative genomics to identify recent IR-expansions in the vicinity of promoter regions in the lineage of Saccharomyces cerevisiae. From the thousands of events identified, we further focused on ones with significant expansion, outside of simple repeats and within confirmed binding sites of TFs. These events are located at 107 loci next to 130 genes and could be observed across the phylogenetic tree, with some events that occurred independently several times. We further focused on 2 genes that showed the longest IR expansion and created IR-expanded mutants in the BY4741 lab strain. While the expansion did not change much at the ERT1 gene, the gre2 mutant with IR expansion was very different from BY4741. In the GRE2 IR-expanded mutant, GRE2 expression was higher than in wild-type; the mutant grew more slowly but was relatively more resistant to glycolaldehyde, a substrate of Gre2p. Taken together, we show here that IR-expansion at promoters is frequent and can shape the evolution of transcription regulation.
Genome Biol Evol
· 2026 Apr · PMID 42007690
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Local adaptation drives changes in population phenotypes that confer survival or reproductive success in specific environments. Local adaptation may be hindered or facilitated by pleiotropy, which is the control of multi...Local adaptation drives changes in population phenotypes that confer survival or reproductive success in specific environments. Local adaptation may be hindered or facilitated by pleiotropy, which is the control of multiple traits by a single genetic locus. In this study, we characterized the role of pleiotropy in local adaptation in the Texas endemic silverleaf sunflower, Helianthus argophyllus. Populations of H. argophyllus exhibit a bimodal life history strategy, consisting of tall, late-flowering forms and short, early-flowering forms that occur in close geographic proximity. The expression of life-history traits in H. argophyllus populations is linked to local adaptation and controlled by a highly pleiotropic locus. Still, we do not know how local adaptation and pleiotropy interact at the transcriptomic level. Here, we identify putatively locally adapted genes using whole RNA sequencing data and two selection outlier approaches. We assess transcriptomic pleiotropy by evaluating whether allelic variants within genes regulate the expression of other genes (an eQTL approach) and by assessing gene co-expression network connectivity. Candidate locally adapted genes show a modest enrichment for eQTL, which control the expression of more eGenes than non-candidate eQTL. Candidate locally adapted genes also exhibit significantly higher connectivity in gene co-expression networks, greater genetic differentiation and genetic diversity, and stronger selective sweep signals than the rest of the transcriptome. Gene co-expression networks enriched for candidate locally adapted genes show higher genetic differentiation and stronger signatures of soft selective sweeps than unenriched networks. Our results support a model of ecotypic divergence under gene flow and align with recent revisions of Fisher's geometric theory, wherein large-effect pleiotropic loci can facilitate local adaptation while polygenic soft-sweeps across functional gene networks fine-tune adaptive responses.
Sheinman M, Stentella T, Etheimer P
… +2 more, Massip F, Arndt PF
Genome Biol Evol
· 2026 May · PMID 41999584
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Horizontal gene transfer (HGT) plays a central role in bacterial evolution. Yet, its large-scale dynamics and underlying network structure remain poorly characterized. We present a theoretical framework that models HGT a...Horizontal gene transfer (HGT) plays a central role in bacterial evolution. Yet, its large-scale dynamics and underlying network structure remain poorly characterized. We present a theoretical framework that models HGT as a continuous stochastic process over a network of bacterial genera and analyze its genomic footprint via the distribution of exact sequence matches shared across taxa-the match length distribution (MLD). We show that different evolutionary regimes imprint distinct statistical signatures on the MLD: single episodic gene transfer events yield exponential distributions, while continuous sustained HGT processes lead to power-law tails. The power-law exponent is analytically linked to the topology of the transfer network, distinguishing between intra-clade transfers and hub-mediated dissemination. Empirical MLDs derived from bacterial genomes recapitulate these predicted patterns. Moreover, we find that defining a genus-specific "transferability" parameter that governs pairwise HGT rates, and incorporating a high-transferability hub, accurately reproduces the observed data. Our approach provides a general framework for inferring hidden structure in genomic horizontal transfer processes, enabling quantitative analysis of microbial evolution.
Lo BW, Lin HF, Kong SW
… +5 more, Wu WJ, Peng YL, Wang SC, Lu X, Wang HY
Genome Biol Evol
· 2026 Apr · PMID 41999280
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Figs and fig wasps represent one of the most intimate examples of plant-pollinator coevolution. As figs diversified into geographically isolated populations, both figs and fig wasps underwent selective pressures driven b...Figs and fig wasps represent one of the most intimate examples of plant-pollinator coevolution. As figs diversified into geographically isolated populations, both figs and fig wasps underwent selective pressures driven by local adaptation and coevolution. Ficus pumila comprises two ecologically distinct varieties: the creeping fig (F. pumila var. pumila), which is widely distributed across the lowlands of East Asia, and the jelly fig (F. pumila var. awkeotsang), endemic to Taiwan and found at mid-elevations. To elucidate how codiversification with fig hosts influences the evolutionary trajectories of fig wasps, we analyzed the genomes of Wiebesia sp. 2 and sp. 3, the respective pollinators of creeping fig and jelly fig. Our demographic analysis indicates that vicariance during the Last Glacial Period facilitated ecological differentiation between these two fig-fig wasp pairs. Through comparative and population genomic analyses, we identified selection signals linked to habitat adaptation, with evolutionary rates corresponding to the life history traits of their host figs. Variations in host preference behavior, chemosensory gene expression, and adaptive duplications in olfactory receptors highlight potential mechanisms for adaptation to host floral scents. These findings collectively underscore how the obligate mutualism between figs and their pollinating wasps allows the ecological traits and habitat preferences of fig hosts to shape the evolutionary pathways of their pollinators, leaving distinct molecular imprints in the fig wasp genomes. This study demonstrates the capacity of tightly intertwined life cycles between plants and pollinators to drive adaptation and diversification.
Poikela N, Hoikkala V, Ritchie MG
… +1 more, Kankare M
Genome Biol Evol
· 2026 May · PMID 41992736
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Chromosomal inversions can play a crucial role in population adaptation and divergence by reducing gene flow and preserving adaptive allelic combinations between populations with different arrangements. However, demonstr...Chromosomal inversions can play a crucial role in population adaptation and divergence by reducing gene flow and preserving adaptive allelic combinations between populations with different arrangements. However, demonstrating this empirically is challenging due to numerous interacting processes with similar genomic signatures affecting inversion evolution. In this study, we characterized a large (9.5Mb) polymorphic inversion in the cold-adapted and widely distributed species, Drosophila montana, using long- and short-read sequencing across several populations. The origin of this inversion predates the divergence of North American (NA) and Fennoscandian (North European) populations, suggesting it emerged in the ancestral D. montana population in the Rocky Mountains of NA. Despite the species' expansion across the northern hemisphere, this inversion has remained exclusive to the Rocky Mountains populations, where it is fixed in the southernmost high-elevation population and appears at lower frequencies in the more northern and lower-elevation populations. By independently mapping single nucleotide polymorphisms (SNPs) linked to climate adaptation and barriers to gene flow (barrier loci; identified through reduced migration rates), we found enrichment of both within the inversion, with barrier and adaptive regions partially overlapping. However, the inversion was not enriched for SNPs related to cold tolerance. These findings suggest that inversions may maintain associations between multiple adaptive and barrier loci, effectively coupling them, and that locally adaptive regions may act as barriers to gene flow. Our study provides empirical evidence that inversions can contribute to population adaptation and divergence by reducing gene flow, maintaining adaptive allelic combinations, and facilitating the coupling of different barriers to gene flow.
Hannaford PI, Coff L, Hall RN
… +3 more, Go J, Moody NJG, Lanfear R
Genome Biol Evol
· 2026 May · PMID 41984116
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Megalocytiviruses are pathogens of global significance that can lead to substantial economic losses in aquaculture. Recombination among megalocytiviruses is typically assumed to be rare, although it has been relatively u...Megalocytiviruses are pathogens of global significance that can lead to substantial economic losses in aquaculture. Recombination among megalocytiviruses is typically assumed to be rare, although it has been relatively understudied. Here, we uncover widespread recombination within megalocytiviruses through the detailed analyses of 63 Megalocytivirus genomes, including two that are newly sequenced and assembled. We also identify a number of genes that megalocytiviruses have likely obtained from outside the family Iridoviridae (iridovirids). These results have serious implications for the biosecurity management of megalocytiviruses, as they indicate that Megalocytivirus strains could be misclassified based on traditional approaches, which target individual loci in the genome. We use this new knowledge of recombination to estimate updated phylogenetic trees of megalocytiviruses at the family-, genus-, and species-level. These trees show strong support for the designation of two novel species within the genus Megalocytivirus and highlight the difficulty of placing highly recombinant genomes in a single phylogenetic framework. We discuss the implications of our work for disease management and the importance of genome-wide recombination detection and phylogenomic analysis in the classification and genetic characterization of viruses.
Generalovic TN, Sandrock C, Roberts BJ
… +6 more, Meier JI, Hauser M, Warren IA, Pipan M, Durbin R, Jiggins CD
Genome Biol Evol
· 2026 May · PMID 41984023
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The black soldier fly (Hermetia illucens) is the main species in the developing global industry of insects as food and feed, but little is known about its natural diversity or the genetic basis of its domestication. We o...The black soldier fly (Hermetia illucens) is the main species in the developing global industry of insects as food and feed, but little is known about its natural diversity or the genetic basis of its domestication. We obtained whole-genome sequences for 54 individuals from both wild and captive populations. We identified two major genetic clusters at least 3 million years divergent, revealing cryptic diversity within the species. Our study indicates that the most common populations used for commercial and academic applications are primarily derived from just one of these sampled lineages, likely originating from a wild North American progenitor. We find that captive populations show strong reductions in genetic diversity, consistent with genome-wide effects of population bottlenecks and drift associated with rearing in captivity. Some limited evidence of gene flow between divergent lineages was observed, as well as evidence of hybridization from domesticated populations into the wild. Our study suggests that natural genetic diversity could provide important variation for industrial purposes in this novel agricultural species.
Lorenzo-Fernández L, Bazzicalupo E, Koen EL
… +4 more, Janecka JE, Murphy WJ, Schmidt K, Godoy JA
Genome Biol Evol
· 2026 Apr · PMID 41983803
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Understanding the genetic basis of adaptation is essential for reconstructing evolutionary processes, and this can be accomplished particularly by studying closely related species occupying diverse ecological niches. In...Understanding the genetic basis of adaptation is essential for reconstructing evolutionary processes, and this can be accomplished particularly by studying closely related species occupying diverse ecological niches. In this study, we performed genome-wide scans for recent selective sweeps in the four extant species of the Lynx genus-Lynx canadensis (Canada lynx), Lynx rufus (bobcat), Lynx lynx (Eurasian lynx), and Lynx pardinus (Iberian lynx)-using a composite likelihood ratio test based on genotype frequency spectrum. Analyzing whole-genome sequences from 80 individuals, we identified species-specific selective sweeps and conducted functional enrichment analyses to explore biological processes under selection. Results revealed distinct adaptive mechanisms shaped by ecological specialization and demographic histories of different species. In Canada lynx, enriched functions include olfactory signaling and pigmentation-related processes; the Eurasian lynx showed signals related to cardiac and neural development; the Iberian lynx exhibited enrichment in immune-related pathways, potentially reflecting pathogen-mediated selection under strong genetic drift; and the bobcat displayed functional signals in reproductive and metabolic regulation. Our study revealed the species-specific nature of recent signatures of ecological differentiation in the genomes of closely related species of the genus Lynx, with minimal overlap, illustrating their diverse evolutionary trajectories and shedding light into the mechanism of adaptation among highly specialized carnivores.
Genome Biol Evol
· 2026 May · PMID 41974123
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Biases in synonymous codon use occur in many unicellular and multicellular organisms. Optimal codons, defined as those most commonly used in highly transcribed genes, are thought to arise from selection for cost-efficien...Biases in synonymous codon use occur in many unicellular and multicellular organisms. Optimal codons, defined as those most commonly used in highly transcribed genes, are thought to arise from selection for cost-efficient translation, which would favor codons with abundant matching tRNAs. Such presumed selection is described as optimal codon choice. Non-optimal codons, defined as those least commonly used in highly transcribed genes, may in principle also play important roles, but the dynamics of their use remain understudied. Here, we examine non-optimal codon use using sex-biased genes expressed in the gonads of Drosophila melanogaster as a case study. We show that genes with sex-biased expression exhibit a preference for non-optimal codon use, especially testis-biased genes. Further, we show that the use of non-optimal codons is not random. Instead, specific non-optimal codons are favored, again especially in testis-biased genes. Non-optimal codon use is positively linked to elevated disorder of the encoded proteins. Remarkably, all 18 degenerate amino acids were associated with higher disorder when encoded by the identified primary non-optimal codon, than when encoded by its sister optimal codon. We hypothesize that selection may have promoted non-optimal codon choice for a subset of favored non-optimal codons to regulate translation. We discuss the putative roles of tRNA gene copy numbers, pleiotropy, and sex-biased expression in the evolution of this level of gene regulation.
Buckenmeyer A, Abalde S, Ryan JF
… +1 more, Jondelius U
Genome Biol Evol
· 2026 Apr · PMID 41967470
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The explosion of body forms found in bilaterians is thought to be tied to the diversification of Hox transcription factors, which play a critical role in development along the anterior-posterior axis for most bilaterians...The explosion of body forms found in bilaterians is thought to be tied to the diversification of Hox transcription factors, which play a critical role in development along the anterior-posterior axis for most bilaterians. However, the evolutionary history of Hox genes in Bilateria's early branches remains unclear. Xenacoelomorpha, a clade of marine worms including Xenoturbella and the acoelomorphs Acoela and Nemertodermatida, have a simple Hox complement and are a particular group of interest. Past surveys of Hox in Xenacoelomorpha have been taxonomically limited. To address this, we analyze the homeodomains and surrounding amino acid motifs coded by Hox, ParaHox, and extended Hox genes across 40 xenacoelomorph transcriptomes and four genomes, along with representatives of other major bilaterian groups and the anthozoan Nematostella vectensis. We show that several motif annotations previously proposed to be synapomorphies of Acoela are ubiquitous across both Xenacoelomorpha and the rest of Bilateria and found new Hox content specific to Acoela and Xenoturbella. Our results reveal homology between xenacoelomorph antHox and other bilaterian Hox1 genes, though the relationships of centHox and postHox genes remain unresolved either due to rapid sequence evolution or extensive birth-death processes. Our analyses suggest that diversification of bilaterian Hox involved both extensive retention and loss of ancestral content. Hox variability between xenacoelomorphs and other bilaterians reflects selective retention of ancestral Hox content rather than affinity to either deuterostomes or protostomes and does not remove support from a monophyletic Xenacoelomorpha sister group to all other Bilateria.
Genome Biol Evol
· 2026 Apr · PMID 41967469
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Chemical defense has evolved convergently across multiple lineages and plays a crucial role in shaping ecological communities through selection for toxin resistance. Research on toxin resistance has been pivotal in under...Chemical defense has evolved convergently across multiple lineages and plays a crucial role in shaping ecological communities through selection for toxin resistance. Research on toxin resistance has been pivotal in understanding the genetic basis of trait evolution, as resistance can evolve through mutations in a few target genes, resulting in target-site resistance (TSR). However, in tropical ecosystems, multiple selective pressures from prey with different toxins create complex chemical scenarios for predators that require multiple resistance mechanisms. Royal ground snakes (Erythrolamprus spp.) are significant but understudied predators of poisonous frogs (families Bufonidae and Dendrobatidae), whose toxins affect voltage-gated sodium channels (VGSCs) and other neuromuscular system proteins. In this study, we investigated the evolution of TSR in VGSC genes in relation to toxic frog predation in Erythrolamprus snakes, tracing the phylogenetic origin and geographic distribution of TSR-conferring genotypes across six species in this group. Our findings reveal convergent yet highly heterogeneous TSR evolution in at least two species that evolved to predate poisonous frogs, and possibly in a third one. Amino acid changes at nine resistance-related positions across eight VGSC genes were identified, suggesting a shared evolutionary path across this gene family. Four of these changes are known to provide tetrodotoxin resistance in other animals. We observed polymorphism in resistance-related sites across species and VGSC paralogs, hinting at a complex evolutionary history of alleles at these loci. These findings offer new insights into adaptive mechanisms in predators with complex toxic diets and introduce Erythrolamprus as a model to understand variation in toxin resistance mechanisms.