2026-07-23
Abstract Horizontal Gene Transfer (HGT) is the movement of genetic material across species. In Saccharomyces cerevisiae , a DNA segment known as Region B was acquired horizontally from a distant yeast species. This region (∼17 Kb) encodes 5 genes and is present in the genomes of yeast strains from different phylogenetic clades. Interestingly, the presence of Region B is not restricted to yeast strains isolated from fermentative environments, leaving its contribution to yeast niche-specific adaptation remains unclear. In this work, the genomic structure of Region B was analyzed in yeast strains from the ScRAP ( Saccharomyces cerevisiae Reference Assembly Panel) collection, identifying 10 structural variants that maintain a circular continuity. To assess the role of Region B in yeast adaptation, we performed a high-throughput phenotyping of the ScRAP collection under different growth conditions, identifying that Region B is associated with higher tolerance to oxidative stress. Then, we characterized the transcriptional activity of each gene within Region B using a fluorescent reporter. The results revealed that gene expression depends on the host’s genetic background and transcription factors encoded within Region B. To identify the genetic determinants involved in Region B expression within different genetic backgrounds, three expression Quantitative Trait Loci (eQTLs) were mapped and validated. Finally, by performing the deletion of Region B in two different strains, we determined a background-dependent contribution of this region to various fermentative phenotypes. Altogether, our results suggest a complex regulatory interaction between the horizontally acquired genes and the host genome that contributes to yeast adaptation under fermentation conditions.
DOI: 10.1093/molbev/msag1872026-07-21
Abstract A-to-I RNA editing enzymatically converts adenosine (A) to inosine (I) in RNA molecules. During sexual reproduction in several filamentous ascomycete fungi, hundreds to tens of thousands of protein-coding sites are edited from A to I, mostly read as guanine (G) by ribosomes. A previous study reported a higher frequency of nonsynonymous than synonymous editing and inferred that A-to-I editing is adaptive in these fungi. However, this inference was based on ∼1% of all editing sites due to methodological limitations, and an alternative nonadaptive explanation—the harm-permitting model—was not considered. Here, we develop a method to test the adaptive hypothesis of RNA editing while accounting for sequence motifs associated with editing, thereby enabling the inclusion of all detected editing events. We apply this method to genomic and transcriptomic data from Fusarium graminearum , Neurospora crassa , and N. tetrasperma . Our analyses suggest that nonsynonymous A-to-I RNA editing in these species is frequently adaptive and that, for at least some nonsynonymous editing events, the benefit primarily arises from the production of multiple distinct proteins from a single gene. Nonetheless, not all nonsynonymous editing is adaptive. Sequence motifs prone to nonsynonymous editing have been selectively depleted at specific genomic locations in genes expressed in sexual reproduction, and a subset of editing events exhibits patterns consistent with the harm-permitting model. In summary, both adaptive and nonadaptive nonsynonymous editing exist in filamentous ascomycetes.
DOI: 10.1093/molbev/msag1792026-07-17
Abstract Hypotheses concerning eukaryogenesis, the evolution of eukaryotic cells, differ in the relative timing of mitochondrial acquisition. Recently, a serial endosymbiotic hypothesis proposed that hydrogenosomes and mitosomes (MROs) in Metamonada originated from an independent endosymbiosis, later replaced by Alphaproteobacteria-related mitochondria, contradicting the paradigm of mitochondrial presence in the last eukaryotic common ancestor. This serial endosymbiotic hypothesis implicitly predicts the scarcity of alphaproteobacterial genes from Metamonada genomes, because they never contained this endosymbiont. We tested this prediction using a set of 1,399 and 97 proteins inferred for the Metamonada ancestor and confined to their MROs, respectively. We detected five and 14 orthologous groups (OGs) with alphaproteobacterial affiliation in the respective datasets. None of these OGs was present in oxymonads, a Metamonada subgroup lacking MROs, thus serving as blank references. Our data are therefore consistent with the ruling paradigm that mitochondria and MROs originated from an Alphaproteobacterium during a single common endosymbiosis.
DOI: 10.1093/molbev/msag1752026-07-09
Abstract Hybridization may offer a form of genetic rescue from warming temperatures through the introgression of heat-adapted alleles from a high-tolerance population into a low-tolerance population. However, the success of adaptive introgression can be impeded by hybrid incompatibility at other loci, especially those that participate in coadapted gene complexes that could lead to unfavorable combinations in hybrids. We tested the success of introgression of heat-adapted alleles in the face of potential fitness tradeoffs associated with hybridized mitonuclear gene complexes in the crustacean Tigriopus californicus . We created reciprocal hybrid crosses of the San Diego (SD) and Strawberry Hill (SH) populations, which show divergence in both thermal tolerance and mitochondrial genomes, then subjected hybrid populations to 10 generations of either selection for thermal tolerance or to control conditions. Lines under selection in both crosses evolved higher thermal tolerance. Moreover, both crosses showed substantial increases in nuclear SD allele frequencies, with the SH♀xSD♂ cross having as much SD introgression as the reciprocal cross despite having higher risk of mitonuclear incompatibilities with its SH mtDNA. This suggests that introgression of warm-adapted alleles was largely successful despite the risk of introducing mitonuclear incompatibilities that could result from genome-wide shifts towards the paternal allele. This outcome was likely made possible by strong Mito nuclear matching being maintained in a few genomic regions on different chromosomes, exclusive of those responding to thermal selection, pointing to components of cytochrome c oxidase, in particular COX6A1 , as potentially having a disproportionate impact in mitonuclear coadaptation.
DOI: 10.1093/molbev/msag1582026-07-09
Abstract RNA editing, a post-transcriptional modification in plant mitochondria and plastids, is essential for environmental adaptation and diverse physiological processes. Despite extensive identification of RNA editing factors, primarily including pentatricopeptide repeat (PPR), multiple organelle RNA editing factor (MORF), organelle RNA recognition motif-containing (ORRM), and organelle zinc finger (OZ) proteins, their evolutionary history remains poorly understood. Here, we perform kingdom-wide evolutionary analyses across 364 high-quality Archaeplastida genomes and find massive PPR gene expansions in early-diverging land plants, predominantly driven by dispersed duplication associated with retroposition. Furthermore, integrative analyses imply that DYW subgroup PPR genes have been horizontally transferred from plants to bdelloid rotifers. MORF proteins, accessory partners of PPRs, possess MORF hallmark domains structurally similar to protein-folding peptidase S8 propeptide/proteinase inhibitor I9 domains, suggesting a role in protein folding during RNA editing. Considering diverse domain compositions, we reclassify MORF, ORRM, and OZ proteins and uncover prevalent hallmark domain fusions. Together, these findings illuminate the kingdom-wide evolution of plant RNA editing machinery.
DOI: 10.1093/molbev/msag1682026-07-07
<span class="paragraphSection"><div class="boxTitle">Abstract</div>Plastids, the photosynthetic organelles of eukaryotes, arose via endosymbiosis of cyanobacteria by a eukaryotic host and were subsequently spread across eukaryotic diversity by additional endosymbioses. The process of plastid endosymbiosis is poorly understood, as most endosymbiotic events happened long ago. One group of microbial eukaryotes, the dinoflagellates, are characterized by their highly convoluted plastid evolution, particularly the family Kareniaceae, who have replaced their ancestral dinoflagellate plastid in most members with haptophyte plastids. To further explore the evolutionary history of kareniacean plastids, we obtained transcriptomic data from two representatives: <span style="font-style:italic;">Gertia stigmatica</span> and <span style="font-style:italic;">Karlodinium ballantinum</span>. We determined that <span style="font-style:italic;">Gt. stigmatica</span> retained its ancestral plastid and that it is nested deep within the Kareniaceae. Furthermore, the transcriptome shows no evidence of haptophyte plastid ancestry, indicating a haptophyte plastid was likely never present. Conversely, <span style="font-style:italic;">K. ballantinum</span> has abundant gene transfers originating from haptophytes, shared with other Kareniaceae. Surprisingly, <span style="font-style:italic;">K. ballantinum</span>’s plastid genome is nearly identical to that of extant haptophyte <span style="font-style:italic;">Gephyrocapsa huxleyi</span>, but we were unable to identify gene transfers from this current plastid across the transcriptome. We therefore conclude that i) the phylogenomic position of <span style="font-style:italic;">Gt. stigmatica</span> and its retention of the ancestral plastid supports at least two independent plastid replacements in Kareniaceae, and ii) <span style="font-style:italic;">K. ballantinum</span> has replaced its plastid organelle twice, with the second replacement being as yet unaccompanied by endosymbiotic gene transfer. Phylogenomics of plastid genomes suggests that the unusually high plastid replacement rate in Kareniaceae might be caused by accelerated mutation of the plastid genome within the host.</span>
DOI: 10.1093/molbev/msag1662026-06-29
<span class="paragraphSection"><div class="boxTitle">Abstract</div>Ultraconserved elements (UCEs) and BUSCO genes are commonly used markers in reduced-representation phylogenomic studies. They are valued for their evolutionary conservation, ease of alignment, and cost-effectiveness in generating phylogenomic datasets for non-model species. Recombination-aware phylogenomic approaches reveal that, with increased historical and recent gene flow, the species tree may be limited to genomic regions with low recombination rates, whereas introgression-associated alleles are most often found in high-recombining regions. In this study, we aimed to determine whether widely used UCE and BUSCO datasets can reliably recover the species tree in mammalian clades where extensive introgression has previously been documented using recombination-aware methods. Our analyses indicate that UCEs and BUSCO loci are not sampled randomly from the genome and are underrepresented in mammalian sex chromosomes and other low-recombining genomic regions. Concatenation and coalescent-based phylogenomic analyses across 12 clades with varying degrees of gene flow showed that UCEs and BUSCO datasets do not recover the true species topology when introgression is frequent. Although neutral loci are generally preferred for phylogenomic analyses, per-base constraint measures estimated genome-wide show that UCE and BUSCO loci originate from genomic regions under very strong selective constraint. Comparisons of branch lengths and node heights from trees based on accelerated, neutral, and conserved PhyloP datasets revealed that those derived from UCE and BUSCO data are compressed relative to trees from neutral regions. We conclude by proposing mitigation strategies to address some of the issues identified in this study, thereby improving the use of UCE-based or other target-enrichment methods in phylogenomics.</span>
DOI: 10.1093/molbev/msag1552026-06-23
<span class="paragraphSection"><div class="boxTitle">Abstract</div>Intracellular bacteria in the early stages of host adaptation often show extraordinarily disrupted genomes, where up to half of their ancestral genes are found in a pseudogenized state. The mealybug <span style="font-style:italic;">Pseudococcus longispinus</span> hosts two bacterial endosymbionts with high pseudogene loads, <span style="font-style:italic;">Symbiopectobacterium endolongispinus</span> and <span style="font-style:italic;">Sodalis endolongispinus</span>. Here, we measure transcript abundance, ribosome-associated RNA, and protein abundance in these bacterial symbionts to understand how bacteria avoid (or fail to avoid) accumulating large amounts of non-functional RNAs and proteins from these pseudogenes. Consistent with previous work, we show that pseudogene transcripts remain detectable, but at lower levels compared to those from intact and functional genes, and that relatively few pseudogenes yield detectable proteins in proteomic data. However, we find that many pseudogene transcripts still bind to <span style="font-style:italic;">Symbiopectobacterium</span> ribosomes, and uncover a possible role for the tmRNA ribosome rescue system in the targeting of pseudogene proteins for degradation. Our results suggest a possible mechanism by which bacterial endosymbionts remove aberrant pseudogene-derived proteins during the critical time when many pseudogenes have formed but not enough time has passed for sequence evolution to erode ribosome binding sites from pseudogene transcripts.</span>
DOI: 10.1093/molbev/msag1532026-06-16
<span class="paragraphSection"><div class="boxTitle">Abstract</div>The potential for conflict between sexes and life stages while sharing predominantly the same genome has important evolutionary consequences. In dioecious angiosperms, genes beneficial for the haploid pollen stage may reduce the fitness of diploid offspring of both males and females. However, we still lack an understanding of the extent of shared genetic architecture for gene expression between the sexes or life stages in plants, a key component for predicting the potential for conflict. We performed expression quantitative trait loci (eQTL) mapping to test if standing variation affects sexes and life stages differently using a population sample of the dioecious outcrossing plant <span style="font-style:italic;">Rumex hastatulus</span>. We compared effect sizes and allele frequencies of <span style="font-style:italic;">cis</span>-eQTLs in male and female leaf tissues and pollen and tested for genotype-by-sex interactions for gene expression. We found stronger shared genetic architecture between sexes than between life stages, suggesting greater potential for ongoing sexual conflict in leaves, which have been shown to be sexually dimorphic in earlier studies. In contrast, conflict over optimal gene expression between pollen and leaves may be easily resolved due to their distinct genetic architectures. Additionally, our burden of rare allele test suggested a signature of stabilizing selection against extreme gene expression in leaves. Our study highlights the use of eQTLs to investigate selection on gene expression and the evolution of conflict between sexes and life stages in dioecious species.</span>
DOI: 10.1093/molbev/msag1512026-06-15
<span class="paragraphSection"><div class="boxTitle">Abstract</div>The extent to which we can predict evolution is crucial in our era of rapid anthropogenic change. Alewives (<span style="font-style:italic;">Alosa pseudoharengus</span>) in the Atlantic coastal USA are a unique model to test for evolutionary predictability in an anthropogenic context, as multiple, formerly anadromous (migratory from ocean to freshwater) populations have been independently restricted to freshwater (landlocked) by dams built in the last 350 years. Landlocked alewives show parallel changes in life history, feeding morphology, and osmoregulatory physiology. To test if recent freshwater adaptations are repeatable and predictable at the genomic level, we compared whole genomes of four landlocked and one anadromous population representing the ancestor. We determined that repeated positive selection is rare, limited to a single region on a single chromosome. Despite this, candidate analysis revealed that regions of repeatability do occur - in some populations but not others - in genes with putative function in freshwater adaptation, most notably in those involved in osmoregulation. Surprisingly, the strongest signal of selection in the genome was not one of positive selection, but one of conserved, balancing selection in a single gene family known as protocadherins, which play an important role in neural circuit formation and neuron recognition. Our results suggest that constrictive demographic histories and/or a polygenic nature of the complex trait architecture limits parallel selection at the genotypic level despite parallelism of phenotype. This highlights the need to understand both demography and trait architecture when determining the degree to which evolution is predictable.</span>
DOI: 10.1093/molbev/msag1492026-06-11
<span class="paragraphSection"><div class="boxTitle">Abstract</div>Cetaceans tolerate repeated diving bouts. While the extent to which cetaceans experience decompression sickness (DCS) remains debated, this group of fully aquatic mammals must have evolved a tolerance to damaging nitrogen (N<sub>2</sub>) gas bubbles that can form during overly rapid ascents or after prolonged dives. Here, we present the first in-depth molecular evolutionary analysis of the nitric oxide synthase gene family across cetaceans and identify cetacean-specific amino acid substitutions in <span style="font-style:italic;">NOS3</span> (encoding endothelial nitric oxide synthase, eNOS) that likely arose in a stem cetacean ancestor, coincident with the transition to obligate aquatic life. Using <span style="font-style:italic;">in vitro</span> assays, we demonstrate that cetacean eNOS exhibits enhanced enzymatic activity and function, potentially mediated by strengthened binding to its molecular chaperone Hsp90. Our findings provide a molecular foundation for an evolved, more resilient vascular system in cetaceans, offering new insights into their adaptations to a hyperbaric environment.</span>
DOI: 10.1093/molbev/msag1442026-06-03
<span class="paragraphSection"><div class="boxTitle">Abstract</div>Larvae of the caddisfly <span style="font-style:italic;">Arctopsyche grandis</span> BANKS build protective structures and spin silken capture nets in flowing water. Caddisfly H-fibroin, the major protein component of its silk fibers, has a blocky structure with repeating units defined as beginning with a [(SX)<sub>n</sub>E]<sub>m</sub> region followed by a G-rich spacer. Previous observation of H-fibroin allelic variation in haploid-resolved individuals led us to investigate allelic variation within two geographically close but separated natural populations of <span style="font-style:italic;">A. grandis</span>. The genomes of 18 individuals were sequenced, and 34 haploid-resolved H-fibroin sequences were extracted. Twenty-four unique alleles were identified in 18 genomes, revealing the dynamic nature of the <span style="font-style:italic;">H-fibroin</span> gene. H-fibroin length variations of at up to 25% were tolerated. The major source of the length variations were large-scale deletions and insertions of entire [(SX)<sub>n</sub>E]<sub>m</sub> blocks. Small scale indel events were numerous, non-randomly distributed, and constrained to a few types. One, a 44 residue indel comprising two (SX)<sub>n</sub>E motifs changed m ± 2 by splitting direct tandem repeats without disrupting tertiary structure or block boundaries. The G-rich spacers are of two types, the first distinguished by repeating GLGPH pentapeptides. Indels within this spacer type occur as multiples of the GLGPH pentapeptide. The other category of G-rich spacer was confined to a narrow length distribution. Overall, the results demonstrate the rapid evolution of the caddisfly <span style="font-style:italic;">H-fibroin</span> gene and the wide range of H-fibroin structural polymorphism tolerated in functional capture net silk. At the same time, the limited nature of the indels point to the critical structural features of H-fibroin.</span>
DOI: 10.1093/molbev/msag1322026-05-27
<span class="paragraphSection"><div class="boxTitle">Abstract</div>Supergenes are clusters of linked loci that underlie complex alternative phenotypes, such as colony social organization in ants. In many species of the genus <span style="font-style:italic;">Formica,</span> a 30 million-year-old supergene determines whether colonies have one queen (monogyny) or multiple queens (polygyny), yet the detailed architecture of this genetic polymorphism remains poorly known. Here we investigate the structural and functional evolution of the supergene haplotypes controlling alternative social forms in <span style="font-style:italic;">Formica selysi</span>. The comparison of chromosomal-level genome assemblies for each social form reveals a 13.8 Mbp long rearranged supergene comprising three large inversions and a transposition, resulting in reduced recombination and high differentiation between haplotypes. The rearranged, derived polygynous haplotype has accumulated transposable elements (TEs) and gene duplicates. It also exhibits haplotype-specific gene expression and gene specialization. Notably, the <span style="font-style:italic;">Formica</span> genus shows a large expansion of the Ubiquitin Conjugation Factor E4 B gene family, which is significantly enriched in the supergene. Despite its ancient origin, the supergene shows sparse signs of degeneration and little accumulation of deleterious variations. Overall, our results demonstrate that the supergene haplotype associated with multi-queen colonies has undergone enrichment of lineage-specialized single- and multi-copy genes with haplotype-specific expression patterns that likely contribute to the phenotype. A combination of relaxed and purifying selection allowed gene duplicates and TEs to accumulate, but prevented the accumulation of deleterious mutations, which helps to explain the long-term persistence of this large social supergene.</span>
DOI: 10.1093/molbev/msag1272026-05-26
<span class="paragraphSection"><div class="boxTitle">Abstract</div>Understanding why some traits are maintained whereas others are repeatedly lost is a central question in evolutionary biology. Here, we address this question through the evolutionary dynamics of autoregulation of <span style="font-style:italic;">prfB</span>, which encodes peptide-chain release factor 2 (RF2), a factor in bacterial translation termination. RF2 recognizes UGA and UAA stop codons and catalyzes polypeptide release. In many species, <span style="font-style:italic;">prfB</span> contains an internal UGA stop codon that causes premature termination by RF2. Full RF2 synthesis depends on a +1 programmed ribosomal frameshifting (PRF) event at this stop codon, which occurs more frequently when RF2 levels are low, resulting in autoregulation of <span style="font-style:italic;">prfB</span> expression. While widespread, this mechanism has been lost repeatedly across bacteria. We combined phylogenetics, experimental evolution, and molecular genetics to investigate the evolutionary forces underlying this loss. Phylogenetically informed analyses revealed no significant correlation between autoregulation and UGA stop codon usage, and autoregulation elimination in <span style="font-style:italic;">Pseudomonas fluorescens</span> SBW25 had no detectable fitness effect. However, engineered mutations that reduced frameshifting at the <span style="font-style:italic;">prfB</span> autoregulatory site caused fitness defects that were compensated by two classes of mutation: mutations affecting ribosome-associated proteins (RsmA, RsmH, RplI), and single-nucleotide deletions in <span style="font-style:italic;">prfB</span> that adjusted the reading frame to bypass the internal stop codon, eliminating autoregulation. These results suggest that loss of <span style="font-style:italic;">prfB</span> autoregulation can be facilitated by compensatory mutations when frameshifting at the <span style="font-style:italic;">prfB</span> autoregulatory site is compromised and RF2 production is insufficient. Our findings illustrate how compensatory evolution can favor trait loss when the fitness benefit of losing the trait outweighs its cost.</span>
DOI: 10.1093/molbev/msag1252026-05-22
<span class="paragraphSection"><div class="boxTitle">Abstract</div>The Cadherin-Catenin Complex (CCC) is a calcium-dependent assembly that is essential for the organization and function of animal cells and tissues. CCC components form adherens junctions that link cell adhesion to the actin cytoskeleton and important signaling pathways that control processes like gene expression, cell polarity, and growth. While the CCC has been extensively studied and known to be conserved across most metazoan lineages, its occurrence in ctenophores, one of the earliest branching groups, has been questioned, with implications for the origins of multicellularity in animals. Here, we show that the ctenophore <span style="font-style:italic;">Mnemiopsis leidyi</span> possesses a reduced cadherin repertoire yet retains conserved interactions characteristic of the CCC. Phylogenetic analyses identified a novel ctenophore-specific cadherin phylogenetically distant from major cadherin families from other animals. Screening a custom yeast 2-hybrid library, derived from <span style="font-style:italic;">M. leidyi</span> embryo cDNA, with the cytoplasmic tail of this non-canonical cadherin-like protein identified known CCC components β-catenin, p120, and Hakai as interacting proteins. Similarly, a screen using <span style="font-style:italic;">M. leidyi</span> α-catenin as bait identified β-catenin, vinculin, and other known actin cytoskeleton-associated proteins. Directed yeast 2-hybrid assays confirmed key interactions and demonstrated that targeted mutagenesis of conserved residues abolished binding, as is observed in other metazoans. Together, these findings suggest that core molecular interactions underlying the CCC are conserved in <span style="font-style:italic;">M. leidyi</span>, consistent with the hypothesis that a functional CCC was an ancestral trait foundational to the evolution of multicellular animals.</span>
DOI: 10.1093/molbev/msag123