Molecular Biology And Evolution[JOURNAL]
Sun
200 papers
Replicated hybrid zones reveal genomic patterns of local adaptation and introgression in spruce.
Nocchi G, Sendrowski J, Shi A … +4 more , Boufford B, Lamothe M, Isabel N, Yeaman S
Mol Biol Evol · 2026 Apr · PMID 41886597 · Full text
Hybridization between species can occur along repeated zones of contact, providing a natural laboratory for studying the interplay between migration and selection, and identifying loci involved in adaptation and reproduc...
Hybridization between species can occur along repeated zones of contact, providing a natural laboratory for studying the interplay between migration and selection, and identifying loci involved in adaptation and reproductive isolation. However, interpreting how evolutionary processes shape genomic patterns can be challenging: repeatability of genotype-environment association alone is not strong evidence for selection, as hybrid zones derived from the same parental species are not evolutionarily independent. Conversely, processes that operate within the middle of each hybrid zone, such as selection driving directional introgression, may be more evolutionarily independent, and therefore provide stronger evidence of selection. Here, we compared hybridization and local adaptation patterns between 2 replicated regions within the western Canada interior spruce hybrid zone: a broad latitudinal transect with gradual environmental variation and a narrow elevational transect with substantial topographical and environmental variation. We discovered a complex pattern of introgression, with strong differences in ancestry maintained even across small spatial scales at several locations along the elevational transect. Despite differences in their spatial scales, the elevational and latitudinal transects revealed strikingly similar genome-wide patterns of differentiation and adaptation, and consistent patterns of directional introgression. We explore the extent to which the evolutionary nonindependence of these hybrid zones allows inferences about the role of natural selection and drift in shaping these patterns. Consistent with theory, we found longer genomic tracts in the elevational transect, likely because the steeper environmental gradients over shorter distances limit the rate of mixing by migration and recombination relative to drift and selection.
Age-dependent Phylodynamics with Application to Single-cell Lineage Trees.
Mulberry N, Pilarski J, Dinger J … +1 more , Stadler T
Mol Biol Evol · 2026 Apr · PMID 41883176 · Full text
As novel technologies for single-cell lineage tracing emerge, phylogenetic and phylodynamic tools are increasingly being used to study developmental processes. However, traditional phylodynamic methods rely on assumption...
As novel technologies for single-cell lineage tracing emerge, phylogenetic and phylodynamic tools are increasingly being used to study developmental processes. However, traditional phylodynamic methods rely on assumptions that are difficult to justify in developmental contexts. We present a generalization of the birth-death phylodynamic model to an age-dependent phylodynamic model. This method captures a key feature of development: due to cells dividing after characteristic generation times rather than after exponential waiting times, empirical cell lineage trees deviate from phylogenies generated under a birth-death model. By applying our method to a public dataset of stem cell colonies, we show how previous estimates of the underlying population-dynamic parameters were biased by the choice of a birth-death tree prior. We additionally showcase our method on embryonic lineage trees of an arthropod limb, demonstrating that age-dependence appears to be a common feature of development. Beyond developmental biology, our framework provides an approach for analyzing systems where classical birth-death assumptions may be violated or where empirical tree shapes are poorly captured by those expected under standard phylodynamic models. Our method is available as a BEAST2 package.
Genomic erosion across avian lineages in the context of their evolutionary history.
Wang X, Fontsere C, Alva Caballero LX … +6 more , Nielsen SD, Groombridge JJ, Hansson B, van Oosterhout C, Pacheco C, Morales HE
Mol Biol Evol · 2026 Apr · PMID 41877660 · Full text
Loss of genetic diversity threatens species survival, yet its dynamics and impacts can vary widely across species depending on their evolutionary histories, life-history traits, and demographic trajectories. To investiga...
Loss of genetic diversity threatens species survival, yet its dynamics and impacts can vary widely across species depending on their evolutionary histories, life-history traits, and demographic trajectories. To investigate these differences, we analyzed the genomes of 3 species that experienced extreme and well-documented population bottlenecks, the Mauritius parakeet, the Mauritius kestrel, and the pink pigeon, and compared them to 36 species spanning the avian phylogeny with varied IUCN Red List statuses. For each species, we assessed nucleotide diversity, genetic load, and inbreeding coefficients based on runs of homozygosity (FROH). We found a negative correlation between nucleotide diversity and FROH, but neither metric was a good predictor of the species' Red List status. Rather, the effective population size to census size ratio (Ne/Nc) showed a strong correlation to Red List status. Species with larger historical effective population sizes showed greater heterozygosity but carried a higher heterozygous load, highlighting the importance of historical demography for contextualizing species' vulnerability to genomic erosion. We also found significant differences in genetic load between taxonomic groups (parrots, pigeons, and falcons), possibly due to differences in life-history traits and demographic histories, underscoring the importance of interpreting genomic erosion dynamics in an evolutionary context. By anchoring our study on 3 evolutionarily divergent endangered species from Mauritius, we show how multispecies comparisons can contextualize extreme bottlenecks within a broader evolutionary framework, thereby identifying both general patterns of genomic erosion and species-specific vulnerabilities.
Ancient origin and dynamic evolution of bivalent spider toxins.
Araya RA, Maurstad MF, Wilson DT … +4 more , Rash LD, Mobli M, Jakobsen KS, Undheim EAB
Mol Biol Evol · 2026 May · PMID 41877653 · Full text
Bivalent peptide toxins comprising 2 cysteine-rich domains have evolved from single-domain precursors on multiple occasions in animal venoms, resulting in enhanced molecular target selectivity and avidity. Although bival...
Bivalent peptide toxins comprising 2 cysteine-rich domains have evolved from single-domain precursors on multiple occasions in animal venoms, resulting in enhanced molecular target selectivity and avidity. Although bivalent toxins are emerging as prevalent in animal venoms, the genomic and evolutionary processes driving the transitions between single- and multi-domain architectures remain poorly understood. Here, we investigated the evolution of bivalent inhibitor cystine knot (ICK) toxins in spider venom. We first generated a genome assembly of the tree-dwelling funnel-web spider Hadronyche cerberea, revealing a massive expansion of ICK toxin-encoding genes, including the bivalent π-hexatoxin-Hc1a. All ICK toxin genes share a conserved 3-exon structure, flanked by transposable elements (TEs) that may have facilitated gene expansion. This gene structure is shared by the Hc1a subfamily, where the entire mature bivalent toxin is encoded by the third exon. Leveraging de novo transcriptome assemblies from 86 spider species along with venom proteomic data, we show that bivalency in the Hc1a subfamily is of ancient origin and evolved via intra-exonic duplication not involving introns. This was followed by domain expansion and recurrent domain losses mediated by point mutations, deletions, and unequal crossing-over facilitated by high interdomain sequence similarity. In contrast, the bivalent toxin DkTx from Cyriopagopus schmidti is confined to a small group of tarantulas, where it appears to have evolved once, with subsequent domain losses potentially linked to TE activity. Our findings reveal that singular events of domain duplication can give rise to complex, asymmetrical evolutionary trajectories shaped by gene instability and selective retention of functional domains.
Evolutionary trajectories, early diversification, and species-specific amplification of the metazoan inhibitor of apoptosis (IAP) repertoire.
Ribeiro Lopes M, Parisot N, Peignier S … +7 more , Renoz F, Baa-Puyoulet P, Jousselin E, Charles H, Callaerts P, Brochier-Armanet C, Calevro F
Mol Biol Evol · 2026 May · PMID 41876750 · Full text
IAP proteins play central roles in regulating apoptosis and diverse cellular processes, influencing cancer biology, or stress resistance in economically important species, highlighting their major biomedical and ecologic...
IAP proteins play central roles in regulating apoptosis and diverse cellular processes, influencing cancer biology, or stress resistance in economically important species, highlighting their major biomedical and ecological relevance. Despite this importance, IAP evolutionary diversity and history remain largely unexplored. Here, we present a large-scale comparative analysis of 2,843 IAP proteins from 312 species spanning all major animal lineages, revealing striking variation in IAP repertoire size and exceptional architectural diversity. We show that IAP expansion has repeatedly emerged through lineage-specific duplication events, seemingly shaped by different duplication dynamics with more recent gene family expansions in arthropods compared with mollusks and chordates. Expression data show that IAP expansion supports distinct strategies. Bivalves and gastropods mobilize multiple IAP subfamilies in response to biotic and abiotic stress, whereas aphids exhibit differential IAP expression associated with polyphenism. These contrasting patterns indicate that heterogeneous selective pressures have recurrently reshaped IAP repertoires, promoting lineage- and species-specific functional diversification. Despite this diversification, phylogenetic analyses reveal the maintenance of a core set of three IAP types. Survivin/Deterin-like and Bruce-like IAPs emerged early in metazoans and remained structurally conserved, although Bruce-like IAPs were independently lost in chelicerates, most nematodes, and some hemipteran insects. RING-containing IAPs also originated early but followed more dynamic evolutionary trajectories, being lost in nematodes and platyhelminthes while expanding in other lineages through domain acquisition (eg gnathostomes) or repeated domain duplication and loss (eg mollusks and insects). Our findings establish a comprehensive evolutionary framework for metazoan IAPs, linking lineage-specific diversification to structural innovation and functional specialization.
Phage toxin variants are linked to protection specificity in a defensive symbiont.
Panossian B, McLean AHC, Patel V … +4 more , Wu T, Haider MB, Oliver KM, Henry LM
Mol Biol Evol · 2026 May · PMID 41873149 · Full text
Insects often depend on symbiotic bacteria for protection; however, the mechanisms by which these microbes target specific natural enemies remain poorly understood. In aphids, different strains of the facultative symbion...
Insects often depend on symbiotic bacteria for protection; however, the mechanisms by which these microbes target specific natural enemies remain poorly understood. In aphids, different strains of the facultative symbiont Hamiltonella defensa provide highly specific protection against particular species of parasitoid wasps. To uncover the genetic basis of this specificity, we analyzed 26 Hamiltonella genomes and their toxin-encoding APSE bacteriophages with distinct protective phenotypes. Our analyses revealed that Hamiltonella strains share a conserved core genome but differ significantly in accessory gene content, reflecting their distinct evolutionary origins. Strikingly, we show that variation in toxin types is the key distinguishing feature of APSE phages in Hamiltonella strains that protect against different parasitoid species. These toxin repertoires include several novel candidates, such as variants with MAC/perforin domains and leucine-rich repeat (LRR) proteins previously unreported in insect defensive symbionts. We also reveal cases of multiple cointegrated APSE phages carrying different toxins within a single genomic locus. These findings suggest phage-borne toxins are important determinants of enemy-specific defense and point to phage-driven toxin diversification as a major force shaping the functional evolution of this symbiosis. This work highlights how mobile genetic elements influence the ecological roles and diversification of protective symbionts.
WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads.
Zhang C, Nielsen R
Mol Biol Evol · 2026 Apr · PMID 41870206 · Full text
The advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree of life, yet achieving a complete species-level phylogeny remains a distant goal due to significant c...
The advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree of life, yet achieving a complete species-level phylogeny remains a distant goal due to significant costs and computational demands. Traditional species tree inference methods, though effective, are hampered by the need for high-coverage sequencing, high-quality genomic alignments, and extensive computational resources. To address these challenges, this study introduces WASTER, a novel de novo tool for inferring shallow phylogenies directly from short-read sequences. WASTER employs a k-mer based approach for identifying variable sites, circumventing the need for genome assembly and alignment. Using simulations, we demonstrate that WASTER achieves accuracy comparable to that of traditional alignment-based methods, even for low sequencing depth, and has substantially higher accuracy than other alignment-free methods. We validate WASTER's efficacy on real data, where it accurately reconstructs phylogenies of eukaryotic species with as low depth as 1.5X. WASTER provides a fast and efficient solution for phylogeny estimation in cases where genome assembly and/or alignment may bias analyses or is challenging, for example due to low sequencing depth. It also provides a method for generating guide trees for tree-based alignment algorithms. WASTER's ability to accurately estimate shallow phylogenies from low-coverage sequencing data without relying on assembly and alignment will lead to substantially reduced sequencing and computational costs in phylogenomic projects.
Reshaping organellar translation and tRNA metabolism: the consequences of photosynthesis loss and massive horizontal gene transfer.
Ceriotti LF, Gatica-Soria LM, Prasad KVSK … +9 more , DeTar RA, Warren JM, Eichler E, Chustecki JM, Elowsky C, Christensen AC, Zhou R, Sloan DB, Sanchez-Puerta MV
Mol Biol Evol · 2026 Apr · PMID 41866796 · Full text
The transition to holoparasitism in plants precipitates the loss of photosynthesis, fundamentally altering the selective landscape acting on organellar genomes. These changes raise questions about the mechanisms by which...
The transition to holoparasitism in plants precipitates the loss of photosynthesis, fundamentally altering the selective landscape acting on organellar genomes. These changes raise questions about the mechanisms by which the essential, coevolved machinery of translation responds to extreme genomic erosion and metabolic dependency. Integrating comparative genomics, tRNA sequencing, and subcellular localization assays, we elucidate the extensive rewiring of organellar translation systems and the tRNA-dependent tetrapyrrole biosynthesis pathway in the holoparasitic angiosperm family Balanophoraceae, which exhibits extreme reduction of tRNA content in plastid and mitochondrial genomes. We identified a rare evolutionary event: the putative intracellular transfer of the plastid initiator tRNA (tRNA-iMet) to the nucleus, which compensates for its loss from the plastid genome. We also demonstrate that the unusual UAG-to-Trp reassignment in the Balanophora plastid genetic code is driven by the loss of release factor pRF1 and the recruitment of a mutated nuclear tRNA-Trp. Furthermore, we reveal that the retention of organellar nuclear-encoded aminoacyl-tRNA synthetases is dictated by the presence/absence of cognate organellar tRNAs, which appear to be functional regardless of their foreign (horizontal transfer from the host plant) or native origins. Finally, we uncover a striking evolutionary asymmetry in nuclear-encoded ribosomal proteins: while plastid subunits exhibit elevated substitution rates consistent with relaxed selection and compensatory coevolution, mitochondrial subunits display high sequence conservation, likely maintaining compatibility with the extensive horizontal gene transfer observed in this lineage. Collectively, these findings represent some of the most extreme changes ever identified in the anciently conserved machinery of plant organellar translation.
Forecasting Multitrait Resistance Evolution under Antibiotic Stress.
Roy S, Libby E, Lind PA
Mol Biol Evol · 2026 Apr · PMID 41821518 · Full text
Many bacteria rely on efflux pumps to survive antibiotic stress and exposure to antibiotics often leads to mutations in pump genes or their regulators that increase pump expression. Predicting the spectrum of these mutat...
Many bacteria rely on efflux pumps to survive antibiotic stress and exposure to antibiotics often leads to mutations in pump genes or their regulators that increase pump expression. Predicting the spectrum of these mutations is important for designing effective antibiotic treatments, but the underlying regulatory networks are large and complex, making them difficult to map experimentally. To address this challenge, we developed a mathematical framework that integrates dynamical equations for efflux pump regulation with a genetic algorithm for parameter estimation and evolutionary simulations. Using this framework, we simulated in silico evolution of Pseudomonas aeruginosa under exposure to the antibiotics meropenem, tobramycin, and ciprofloxacin. The simulations revealed mutational spectra affecting the expression of four Resistance-Nodulation-Division efflux pumps and their shared regulatory network. The most frequently mutated genes were single-target regulators that matched well with previous observations in clinical and in vitro studies. The model also showed that the shared use of the OprM protein by two pumps is a key factor shaping their distinct mutational patterns. Mutations often produced multitrait phenotypes, manifesting as collateral sensitivity or cross-resistance to antibiotics not used for selection. While cross-resistance evolved readily, its extent depended on initial pump expression levels and thus may vary between strains. Finally, simulations of changing environments showed that efflux pump genes tend to be lost in the absence of antibiotics, suggesting a potential strategy to steer bacterial evolution toward reduced capacity to re-evolve resistance.
Comparing Neanderthal Introgression Maps Reveals Core Agreement But Substantial Heterogeneity.
Chen Y, Velazquez-Arcelay K, Capra JA
Mol Biol Evol · 2026 Mar · PMID 41821294 · Full text
Statistical methods to identify Neanderthal ancestry in modern human genomes rest on varying assumptions and inputs. Nonetheless, most studies of introgression use only a single method to define Neanderthal ancestry. Due...
Statistical methods to identify Neanderthal ancestry in modern human genomes rest on varying assumptions and inputs. Nonetheless, most studies of introgression use only a single method to define Neanderthal ancestry. Due to a lack of "ground truth," we have a limited understanding of the accuracy, comparative strengths and weaknesses, and the sensitivity of downstream conclusions for these methods. Here, we performed large-scale comparisons of 14 genome-wide introgression maps computed by 11 representative Neanderthal introgression detection algorithms: admixfrog, ArchaicSeeker2, ArchIE, ARGweaver-D, CRF, DICAL-ADMIX, hmmix, IBDmix, SARGE, Sprime, and S*. These algorithms span statistical approaches based on summary statistics, probabilistic modeling, and machine learning, and vary in their use of archaic, modern, and simulated genomes as input. Our results highlight a core set of regions predicted by nearly all methods, as well as substantial heterogeneity in commonly used Neanderthal introgression maps, especially at the individual genome level. Furthermore, we find that downstream analyses may result in different conclusions depending on the map used. Thus, we recommend careful consideration of map(s) chosen for downstream analysis and support the use of multiple maps to ensure robustness of conclusions. We make integrated prediction sets available, enabling further understanding of Neanderthal introgression's legacy on modern humans.
Soft Selective Sweeps Predominate in the Yellow Fever Mosquito Aedes aegypti.
Ketchum RN, Matute DR, Schrider DR
Mol Biol Evol · 2026 Apr · PMID 41818228 · Full text
The Aedes aegypti mosquito is a vector for human arboviruses and zoonotic diseases and therefore poses a serious threat to public health. Understanding how Ae. aegypti adapts to environmental pressures-such as insecticid...
The Aedes aegypti mosquito is a vector for human arboviruses and zoonotic diseases and therefore poses a serious threat to public health. Understanding how Ae. aegypti adapts to environmental pressures-such as insecticides-is critical for developing effective mitigation strategies. However, most traditional methods for detecting recent positive selection search for signatures of classic "hard" selective sweeps, and to date no studies have examined soft sweeps in Ae. aegypti. This is a significant limitation as this is vital information for understanding the pace of adaptation-populations that can immediately respond to new selective pressures are expected to adapt more often via standing variation or recurrent adaptive mutations (both of which may produce soft sweeps) than via de novo mutations (which produce hard sweeps). To this end, we used a machine learning method capable of detecting hard and soft sweeps to investigate positive selection in Ae. aegypti population samples from Africa and the Americas. Our results reveal that soft sweeps are significantly more common than hard sweeps, which may imply that this species can respond quickly to environmental stressors. This is a particularly concerning finding for vector control methods that aim to eradicate Ae. aegypti using insecticides. We highlight genes under selection that include both well-characterized and putatively novel insecticide resistance genes. These findings underscore the importance of using methods capable of detecting and distinguishing hard and soft sweeps, implicate soft sweeps as a major selective mode in Ae. aegypti, and highlight genes that may aid in the control of Ae. aegypti populations.
Innovations in Silicon Transport Shaped the Rise of Biosilicification and Skeletal Evolution in Sponges.
Leria L, Maldonado M
Mol Biol Evol · 2026 Mar · PMID 41812157 · Full text
Sponges are the only metazoans capable of making silica skeletons through incorporation of silicic acid (dSi) from seawater, which is polymerized using silicifying proteins. Uptake involves functional cooperation between...
Sponges are the only metazoans capable of making silica skeletons through incorporation of silicic acid (dSi) from seawater, which is polymerized using silicifying proteins. Uptake involves functional cooperation between aquaglyceroporin channels (gAQP) and arsenite efflux pumps (ArsB), a dSi transport system that, surprisingly, also functions in plants. Compared to plants, the silicon selectivity filter of sponge gAQPs is shown here to have replaced hydrophilic residues with hydrophobic ones, reducing water permeation during silicon transport. Phylogenetic analyses of 201 gAQP and 161 ArsB sequences reveal that these transporters, having prokaryotic origins, were already present in ancestral sponges, preceding the emergence of silicifying proteins and fossilized silica skeletons. Through Hexactinellida diversification, the functional interdependence of gAQP and ArsB transporters shaped a remarkable coevolution via synchronized gene duplications. This coevolution was disrupted in Demospongiae, because Heteroscleromorpha demosponges acquired, via horizontal gene transfer, a microbial gAQP that partially displaced ancestral gAQPs. This acquisition and that of an autapomorphic silicifying protein (silicatein) coincided with an exceptional diversification in Heteroscleromorpha. In contrast, sponge lineages that never developed silicifying proteins (Keratosa, Verongimorpha, Calcarea) or acquired them post-Cambrian (Homoscleromorpha, Chondrilla) lost gAQP genes while retaining ArsB homologs, implying selection against a passive dSi influx for sponges lacking dSi polymerization machinery. Thus, the ability to precipitate dSi-ie forming skeleton-likely arose as an adaptive response in early askeletal sponges to the damaging, high dSi concentrations of Precambrian oceans. The evolutionary history of dSi transporters and the fossil record support that such adaptation evolved independently four times within Porifera.
Genomic incompatibilities are persistent barriers when speciation happens with gene flow in Formica ants.
Heidbreder P, Poikela N, Nouhaud P … +3 more , Puukko T, Lohse K, Kulmuni J
Mol Biol Evol · 2026 May · PMID 41810521 · Full text
A current goal of speciation research is identifying loci underlying reproductive barriers between species. Locating barrier loci in population genomic data is difficult due to the often-complex demographic history of di...
A current goal of speciation research is identifying loci underlying reproductive barriers between species. Locating barrier loci in population genomic data is difficult due to the often-complex demographic history of diverged taxa and heterogeneity in evolutionary forces across the genome. We take advantage of natural hybridization between 2 wood ant species (Formica aquilonia and Formica polyctena) to identify regions of reduced long-term gene flow using demographically explicit scans of nonadmixed genomes. In addition, we identify candidate Bateson-Dobzhansky-Muller incompatibilities (BDMIs) through an imbalanced recombinant haplotype frequency analysis using a large sample of natural F. aquilonia × F. polyctena hybrid genomes. These approaches find barriers and BDMIs scattered across the genome. Furthermore, BDMIs significantly overlap with long-term barriers, indicating that some BDMIs have persisted despite divergence with gene flow. Intriguingly, the number of pairwise interactions a BDMI has correlates with its long-term barrier strength: hub-like BDMIs with many interactions reduce gene flow more effectively. Finally, we find that long-term barriers are depleted for both coding sequences (CDS) and transposable elements (TEs), while candidate BDMIs are associated with snRNAs and LTR transposons, specifically Ty1-copia. In contrast, regions where long-term barriers and BDMIs co-locate are significantly associated with introns but not CDS or TEs, implying a potential role of alternative splicing or gene regulation in long-term incompatibilities. Our results highlight the underappreciated impact of BDMI connectivity on the persistence of reproductive barriers over time.
Displacement-Optimized Tanglegrams for Trees and Networks.
Huson DH
Mol Biol Evol · 2026 Mar · PMID 41807123 · Full text
Phylogenetic trees and networks play a central role in biology, bioinformatics, and mathematical biology, and producing clear, informative visualizations of them is an important task. Tanglegrams, which display two phylo...
Phylogenetic trees and networks play a central role in biology, bioinformatics, and mathematical biology, and producing clear, informative visualizations of them is an important task. Tanglegrams, which display two phylogenies side by side with lines connecting shared taxa, are widely used for comparing evolutionary histories, host-parasite associations, and horizontal gene transfer. Existing layout algorithms have largely focused on trees and on minimizing the number of intertaxon edge crossings. We introduce displacement-optimized tanglegrams (DO-tanglegrams), a new approach that applies equally to trees and rooted phylogenetic networks. Our method explicitly minimizes taxon displacement-the vertical misalignment of corresponding taxa across the two sides-and reticulate displacement-the vertical distance spanned by reticulation edges within a network. We formalize one-sided and two-sided optimization problems, show that exact minimization is computationally intractable, and propose a heuristic that combines exhaustive local search with simulated annealing. The algorithm naturally accommodates unresolved nodes (multifurcations or multicombinations) and missing taxa. We have implemented the DO-tanglegram algorithm in SplitsTree. We compare our implementation against the phytools::cophylo R-function on a collection of synthetic trees, and against the NN-tanglegram algorithm in Dendroscope on a collection of synthetic networks. The results indicate that DO-tanglegram performs significantly better than cophylo on trees and then NN-tanglegram on networks.
Ancient genomes uncover dynamic cultural and genetic interplay in the eastern Tianshan.
Yang X, Zou X, Li H … +7 more , Yang X, Wang B, Ma H, Wang Y, Xu Y, Li C, Wang CC
Mol Biol Evol · 2026 Mar · PMID 41806853 · Full text
The eastern Tianshan range in Xinjiang, serving as a crucial link between the East and the West, acts as an important channel for the eastward spread of East Asian millet and painted pottery, as well as the westward diff...
The eastern Tianshan range in Xinjiang, serving as a crucial link between the East and the West, acts as an important channel for the eastward spread of East Asian millet and painted pottery, as well as the westward diffusion of West Asian wheat and barley, bronze wares, and livestock. However, due to the scarcity of ancient genomic data, the history of population interaction and admixture in this region remains unclear. We sequenced 23 ancient individuals from 12 archaeological sites from the Bronze Age to historical periods in Xinjiang. We identified intraregional population interactions, demonstrating that an indigenous local ancestry, represented by Tarim_EMBA1, spread to the Tianshan and persisted into the historical period. The incoming East Asian millet farmers, along with Western Steppe herders characterized by Afanasievo, contributed to the formation of the eastern Tianshan populations during the Iron Age, which is consistent with archaeological findings of painted pottery and pastoral subsistence in this area. The genetic affinity to East Asian millet farmers in the eastern Tianshan increased over time, likely reflecting geographic proximity and geopolitical changes. In contrast, in line with archaeological observations, the Iron Age individuals in the western Tianshan derived their Steppe-related ancestry from populations associated with the Andronovo culture. Our results illustrated the interplay between genetics and culture in the eastern Tianshan.
Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species.
Potapenko E, Shermeister B, Mandel T … +1 more , Hübner S
Mol Biol Evol · 2026 Mar · PMID 41806037 · Full text
A substantial variation in genome size has been observed among individuals of the same species. Theory predicts that increased genome size may confer an advantage in populations with small effective size. However, contra...
A substantial variation in genome size has been observed among individuals of the same species. Theory predicts that increased genome size may confer an advantage in populations with small effective size. However, contradictory evidence for the correlation with environmental variation, and limited understanding of the underlying genetic mechanisms, has cast doubts on the adaptive role of genome size variation. To address this, we studied two Hordeum species which were collected at the same sites along a wide range of environments but differ in life habits (annual/perennial) and mating strategy (self/outcrossing). We detected substantial genome size variation, with differences of up to 10% in both species. While the mating system influenced the distribution of variation within populations, it did not alter the overall range of genome sizes. Drought emerged as the primary environmental factor associated with larger genomes, with past transposable elements (TE) bursts identified as the potential source of genome expansion. Genome-wide association analyses revealed that TE silencing is central to genome size regulation, with selection maintaining smaller genomes among individuals with higher fitness in favorable habitats. Under stressful conditions, silencing becomes less efficient, allowing larger genomes to persist and thereby increasing the reservoir of genetic variation available for selection. Together, these findings provide an integrative view of genome size dynamics in natural populations and underscore its exaptive role in maintenance of genetic variation under environmental stress.
NF-κB: A Diverse and Multifunctional Transcription Factor in Holozoans.
Glass BH, Abraham T, Siggers T … +2 more , Davies SW, Gilmore TD
Mol Biol Evol · 2026 Apr · PMID 41802887 · Full text
Transcription factor nuclear factor-kappa B (NF-κB) and many upstream signaling components have been identified in a diversity of holozoan taxa, including unicellular holozoans (eg Filasterea and Choanoflagellata) and th...
Transcription factor nuclear factor-kappa B (NF-κB) and many upstream signaling components have been identified in a diversity of holozoan taxa, including unicellular holozoans (eg Filasterea and Choanoflagellata) and the metazoan phyla Porifera (sponges), Placozoa, and Cnidaria (eg jellyfishes, sea anemones, corals, and hydra). Herein, we review recent progress made toward characterizing the structure, regulation, activity, and biological functions of NF-κB proteins found in these taxa. We also provide an updated phylogenetic sampling of NF-κB orthologs highlighting their different domain configurations among holozoans, as well as a method for comparing the computationally predicted three-dimensional structures of NF-κB dimers and relating these structures to their amino acid similarities and DNA-binding specificities. This synthesis reveals new insights regarding the evolutionarily conserved and variable domain-dependent activities and regulation of holozoan NF-κBs. Further, we provide an overview of the roles of NF-κB in pathogen responses, stress responses, symbiosis, and development, with a focus on recent findings from sponges and cnidarians. This curation of a growing body of knowledge highlights both conserved and divergent roles of NF-κB in foundational biological processes. Finally, we suggest priorities for future research on the evolution of NF-κB structure and function. Overall, investigations of NF-κB in diverse holozoan taxa will continue to provide information about the origins of this important and pervasive transcriptional regulator and will also contribute to an understanding of the responses of sentinel species to the modern-day stresses associated with changing environmental conditions and novel pathogen-based diseases.
Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths.
Li H, Zhang Y, Tian X … +5 more , Xu X, Wang M, Wang H, Liang D, Zhang P
Mol Biol Evol · 2026 Mar · PMID 41802886 · Full text
Mimicry is a manifestation of natural selection that provides a key system for exploring the evolution of complex adaptive traits. Epicopeiidae moths are strikingly diverse morphologically, having evolved resemblance to...
Mimicry is a manifestation of natural selection that provides a key system for exploring the evolution of complex adaptive traits. Epicopeiidae moths are strikingly diverse morphologically, having evolved resemblance to multiple butterfly and moth models despite their recent origin. To uncover the genomic basis of this rapid morphological diversification, we sequenced high-quality genomes for eight Epicopeiidae species (three at the chromosome level) and conducted comparative genomics, developmental transcriptomics, and chromatin accessibility analyses. We found that genomic structural variations and gene family expansions contributed little to morphological evolution, whereas genes under positive selection in the ancestral Epicopeiidae were enriched for neural and visual functions, likely linked to the shift from nocturnal to diurnal activity of the Epecopeiidae ancestor. In contrast, accelerated conserved noncoding elements and Epicopeiidae-specific accessible chromatin regions (ACRs) were enriched near morphogenetic genes, suggesting that changes in regulatory elements played a key role in morphological innovation. Our analyses also found that Epicopeiidae experienced a pronounced burst of transposable element (TE) activity between 40 and 10 Mya, temporally coinciding with morphological diversification. Approximately two-thirds of ACRs overlapped with TEs, and TE-derived ACRs were enriched near morphogenetic genes. These findings suggest that TE-driven regulatory innovation rewired developmental gene networks of Epicopeiidae and facilitated the emergence of multiple mimetic forms. Epicopeiidae thus provide a compelling example for understanding how TE-mediated regulatory evolution might fuel phenotypic innovation.
piqtree: a python package for seamless phylogenetic inference with IQ-TREE.
McArthur RN, Wong TK, Lang Y … +5 more , Morris RA, Caley K, Mallawaarachchi V, Minh BQ, Huttley G
Mol Biol Evol · 2026 Mar · PMID 41802268 · Full text
piqtree (pronounced pie-cue-tree) is an easy to use, open-source Python package that provides Python script based control of IQ-TREE's phylogenetic inference engine. piqtree builds IQ-TREE as a Python package, presenting...
piqtree (pronounced pie-cue-tree) is an easy to use, open-source Python package that provides Python script based control of IQ-TREE's phylogenetic inference engine. piqtree builds IQ-TREE as a Python package, presenting a library of Python functions for performing many of IQ-TREE's capabilities including phylogenetic reconstruction, ultrafast bootstrapping, branch length optimization, model selection, rapid neighbor-joining, alignment simulation, and more. As piqtree explicitly uses IQ-TREE's phylogenetic algorithms, the computational and statistical performance of piqtree equal that of IQ-TREE. Modestly higher memory usage may be expected owing to the Python runtime and the need to load the alignment in Python. By exposing IQ-TREE's algorithms within Python, piqtree offers users a greatly simplified experience in development of phylogenetic workflows through seamless interoperability with other Python libraries and tools mediated by the cogent3 package. It enables users to perform interactive phylogenetic analyses and visualization using, for instance, Jupyter notebooks. We present the key features available in the piqtree library and a small case study that showcases its interoperability and highlight its potential for linking a high performance phylogenetic inference engine with more user friendly interfaces. piqtree is distributed for use as a standard Python package at https://pypi.org/project/piqtree/, documentation is available at https://piqtree.readthedocs.io, user contributed solutions at https://github.com/cogent3/c3codeshare, help forums at https://github.com/iqtree/piqtree/discussions, and source code at https://github.com/iqtree/piqtree.
Stoichiometry-induced differential selection on codon optimization among ribosomal protein genes in bacterial species.
Xia X
Mol Biol Evol · 2026 Mar · PMID 41794051 · Full text
While it is well established that highly expressed genes in bacteria exhibit stronger codon optimization than lowly expressed ones, whether codon-anticodon adaptation shows fine-scale differentiation among highly express...
While it is well established that highly expressed genes in bacteria exhibit stronger codon optimization than lowly expressed ones, whether codon-anticodon adaptation shows fine-scale differentiation among highly expressed genes themselves remains unexplored. Ribosomal proteins, which are expressed in stoichiometric amounts and often cotranscribed in polycistronic operons, provide an ideal system for testing such differential selection. Here, I demonstrate that in Escherichia coli, Bacillus subtilis, and Vibrio natriegens, codon usage is more optimized in long ribosomal protein genes compared to short ones. This pattern persists even among genes within individual operons, such as S10, spc, and α operons. A ribosome in E. coli or B. subtilis needs four copies of L7/L12 (encoded by rplL) but only one copy each of the other ribosomal proteins. This high demand for L7/L12 leads to my prediction that the rplL gene should be translated more actively than its operonic partner, rplJ, encoding L10. This prediction is also strongly supported by empirical evidence from representative bacterial species. Actively translated mRNAs are protected from endonucleolytic cleavage and degradation. If rplL mRNA is more actively translated than rplJ mRNA, then rplL mRNA would be degraded less and become more abundant than rplJ mRNA, which is true. These results demonstrate that translation optimization reflects functional stoichiometry and protein length constraints. This is the first demonstration of natural selection operating predictably and precisely among ribosomal protein genes in the same operon, fine-tuning translational output to achieve efficient ribosomal assembly.
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