Genome Biology And Evolution[JOURNAL]
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200 papers
SCPP Gene Repertoires in Teleosts and Evolutionary Changes in Bone, Teeth, and Scales.
Kawasaki K
Genome Biol Evol · 2026 Jun · PMID 42324611 · Publisher ↗
Secretory calcium-binding phosphoprotein (SCPP) genes are involved in bone, tooth, and scale formation in bony vertebrates, including teleosts. Various studies have investigated teleost SCPP genes to pinpoint genetic cha...
Secretory calcium-binding phosphoprotein (SCPP) genes are involved in bone, tooth, and scale formation in bony vertebrates, including teleosts. Various studies have investigated teleost SCPP genes to pinpoint genetic changes associated with phenotypic changes in mineralized skeletal elements. However, no comprehensive studies have been described to date. Here, SCPP genes were searched in 63 teleost genome sequences. The chromosomal distribution of individual SCPP genes suggests that all SCPP genes, except one, originally formed four clusters after the teleost genome duplication. Subsequently, various SCPP genes were apparently lost in different lineages, and scpp1 and spp1 were the only SCPP genes identified in all investigated teleosts. These 63 teleosts include 10 species with reduced scales, 11 scaleless species, and 2 toothless species. Among them, either scpp7 or gsp37 was missing or non-functional in 9 species with reduced scales, and both scpp7 and gsp37 in all 11 scaleless species. In seahorse and pipefish, which have bone but lost teeth and scales, scpp1, spp1, and only two other SCPP genes were found, while in closely related scaleless but toothed cornetfish, scpp5, scpp3, and odam were additionally identified. These findings suggest vital roles of scpp1 and spp1 in bone, scpp7 and gsp37 in scale, and scpp5, scpp3, and odam in tooth formation. However, many other SCPP genes are also involved in the formation of mineralized tissues and are likely important for some specific features of teeth or scales. It appears that the repertoire of SCPP genes in teleost species underlies diverse conditions of mineralized skeletal elements.
OrthoGuide: A Database for Rooting Inference of Orthologous Genes.
Cavalcante JVF, de Azevedo GM, Imparato DO … +3 more , Marques-Coelho D, Castro MAA, Dalmolin RJS
Genome Biol Evol · 2026 Jun · PMID 42319894 · Full text
Orthology provides a powerful framework for investigating the evolutionary history of biological systems, as genes within the same orthologous group typically share a common ancestry. By tracing their distribution across...
Orthology provides a powerful framework for investigating the evolutionary history of biological systems, as genes within the same orthologous group typically share a common ancestry. By tracing their distribution across species, it is possible to infer the evolutionary origin of genes and reconstruct the stepwise assembly of molecular pathways and regulatory networks. However, performing such analyses at scale often requires specialized computational tools and expertise, limiting their accessibility to a broader community. Here, we introduce OrthoGuide, a database and web application that provides precomputed evolutionary rooting information for orthologous groups across 360 eukaryotic species. The platform enables users to query gene sets and rapidly explore their evolutionary origins through an intuitive interface, without the need for local computational workflows. In addition to tabular outputs, OrthoGuide offers interactive visualizations that facilitate the interpretation of evolutionary patterns and the identification of key events in the emergence of biological systems. By removing technical barriers and standardizing large-scale evolutionary inferences, OrthoGuide enables researchers to translate gene lists into biologically meaningful hypotheses. This resource democratizes access to orthology-based evolutionary analyses and supports the investigation of system-level evolutionary processes across a wide range of organisms. The web application and the database are hosted at https://dalmolingroup.imd.ufrn.br/orthoguide/.
Correction to: Molecular Complexity Constrained Early Amino Acid Recruitment into the Genetic Code.
Genome Biol Evol · 2026 Jun · PMID 42308552 · Full text
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The Effects of Rapid Mitochondrial Gene Loss on Organellar Proteomes.
Warren JM, Broz AK, Stikeleather R … +1 more , Sloan DB
Genome Biol Evol · 2026 Jun · PMID 42308339 · Full text
Mitochondrial genomes retain only a tiny number of genes from their bacterial progenitors, including key components of protein translation machinery. The set of mitochondrially encoded tRNAs and ribosomal subunits is hig...
Mitochondrial genomes retain only a tiny number of genes from their bacterial progenitors, including key components of protein translation machinery. The set of mitochondrially encoded tRNAs and ribosomal subunits is highly variable across angiosperms, with many examples of mitochondrial gene loss, replacement, and/or transfer to the nucleus. This dynamic history suggests large-scale remodeling of mitochondrial translation machinery in some lineages, but such conclusions are largely inferred from genomic sequence and protein targeting predictions. Here, we use proteomic (LC-MS/MS) analysis of purified mitochondria and chloroplasts from angiosperm species with major differences in mitochondrial gene content (Arabidopsis thaliana and Silene conica). Our analysis largely confirms the current understanding of subcellular localization for nuclear-encoded proteins involved in tRNA metabolism and ribosome function in A. thaliana, although some aminoacyl-tRNA synthetases (aaRSs) may have more specialized subcellular roles than previously thought. In contrast, S. conica has undergone extensive mitochondrial gene loss and numerous associated changes in the composition of its mitochondrial proteome, including apparent retargeting of aaRSs, replacement of ribosomal subunits, and loss of the glutamine amidotransferase (GatCAB) complex. Overall, this analysis illustrates how the complex network of molecular interactions necessary for mitochondrial translation are perturbed by gene loss, transfer, and replacement.
No Evidence Supports the Presence of SRF-type MADS-Box Genes in Land Plants.
Qiu Y, Li Z, Köhler C
Genome Biol Evol · 2026 Jun · PMID 42301153 · Full text
MADS-box transcription factors are a key gene family central to understanding the evolutionary success of land plants. Land plant MADS-box genes are divided into Type I and Type II. They were initially considered ortholo...
MADS-box transcription factors are a key gene family central to understanding the evolutionary success of land plants. Land plant MADS-box genes are divided into Type I and Type II. They were initially considered orthologous to SRF and MEF2 genes in animals and fungi, respectively, which originated by an ancient duplication before the diversification of extant eukaryotes. However, using updated phylogenetic analyses and AI-based protein structure prediction, we showed that both Type I and Type II genes are plant-specific duplicates derived from MEF2-type ancestors, while ancestral SRF genes were lost before the divergence of the plant lineage. A recent study proposed instead a polyphyletic origin for plant Type I genes. While this study also found that the majority of Type I MADS-box genes in land plants cluster with MEF2 genes, a few genes were grouped as Type I and considered related to SRF genes. By reanalyzing the original data from that study, we do not find supporting evidence for this hypothesis. Moreover, using phylogeny, sequence similarity, and structural evidence, we demonstrate that there is no evidence of SRF-derived genes in land plants.
Genomic evolution of Francisella: metabolic innovation, endosymbiotic transitions to ticks, and biogeographic history.
Echeverry-Pérez JS, Castelli M, Muñoz-Leal S … +6 more , Nava S, Sassera D, Sánchez-Vialas A, Olmeda AS, Valcárcel F, Uribe JE
Genome Biol Evol · 2026 Jun · PMID 42301021 · Publisher ↗
Ticks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. Beyond vector roles, they maintain mutualistic associations with bacteria, including endosymbionts that provi...
Ticks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. Beyond vector roles, they maintain mutualistic associations with bacteria, including endosymbionts that provide essential B vitamins lacking in their blood-based diet. The most extensively studied endosymbionts belong to the genera Coxiella, Midichloria, and Francisella. The genus Francisella encompasses endosymbionts (FE), pathogens (FP), opportunistic pathogens (FO) and free-living environmental strains (FL), making it a powerful system for evolutionary and comparative genomic analyses. In this study, total DNA from six adult female ticks of the genera Hyalomma and Amblyomma was sequenced to generate new FE genomes. Seven deeply sequenced public metagenomes were also assembled, yielding 71 Francisella and three Allofrancisella strains. This dataset supported phylogenomic reconstruction and comparison of genomic features, including vitamin biosynthesis and virulence pathways, with a focus on transitions to tick endosymbiosis. A densely sampled MLST phylogeny was constructed to explore biogeographic patterns. Our results show that, except for FE, no ecological trait is monophyletic, supporting an origin of Francisella diversity from free-living ancestors. Biogeography suggests Palearctic and Afrotropical FE strains are derived and may involve horizontal transfers. Francisella comparative genomics reveals two contrasting profiles: environmental generalists and host-restricted specialists. These findings reinforce the role of tick FEs as nutritional mutualists, retaining key pathways such as riboflavin, shikimate, and biotin biosynthesis. In contrast, virulence is not ancestrally conserved but an innovation in pathogenic lineages, largely degraded in tick FEs. These results advance understanding of endosymbiont evolution and provide genomic insights with potential for disease control.
Silent Erosion: Impact of Forest Logging on Genetic Diversity in Tropical Understorey Birds.
Messina S, Edwards DP, Tomassi S … +4 more , Benedick S, Sin YCK, Rheindt FE, Costantini D
Genome Biol Evol · 2026 Jun · PMID 42287228 · Full text
Anthropogenic habitat disturbance can erode genetic diversity long before population declines become apparent, potentially contributing to extinction debt. However, empirical assessments of genetic erosion following anth...
Anthropogenic habitat disturbance can erode genetic diversity long before population declines become apparent, potentially contributing to extinction debt. However, empirical assessments of genetic erosion following anthropogenic habitat degradation remain scarce. Here, we investigated whether selective logging, the most pervasive anthropogenic disturbance in tropical forests, affects genetic diversity in tropical forest biota. We resequenced whole genomes of 99 understorey songbirds from ten forest specialist species captured in both primary and selectively logged forests of Borneo. The study species are all sedentary and weak flyers but differ in their susceptibility to forest logging. The within-species comparisons of whole genomes between primary and selectively logged forests showed reduced nucleotide diversity and higher levels of inbreeding in disturbed versus undisturbed habitat for a common understorey rainforest inhabitant, Malacocincla sepiaria. We also found a substantial amount of homozygosity in the local population of that same species as well as in another, Malacopteron cinereum, regardless of forest type, indicating reduced standing genetic diversity due to historical bottlenecks. Nine out of ten species, including those considered more sensitive to the environmental conditions of selectively logged forests, showed no reduction in genetic diversity, indicating that selectively logged forests retain substantial conservation value for many rainforest birds. Nonetheless, our findings indicate that genetic erosion can occur within a few decades of habitat disturbance even in apparently common tropical bird species, raising concerns about silent population-genetic processes that might threaten the long-term persistence of seemingly abundant species in selectively logged forests.
Genomic Insights Into the Evolution of Parental Care in Weevils.
Rinke S, Biedermann P, Schebeck M … +1 more , Harrison MC
Genome Biol Evol · 2026 Jun · PMID 42284453 · Full text
Parental care, a key step in the evolution of sociality, has evolved multiple times in insects, yet the molecular mechanisms underlying its emergence remain poorly understood. Weevils (Curculionidae) exhibit diverse pare...
Parental care, a key step in the evolution of sociality, has evolved multiple times in insects, yet the molecular mechanisms underlying its emergence remain poorly understood. Weevils (Curculionidae) exhibit diverse parental care behaviors, from nest building to egg and larval attendance, making them an ideal system to investigate genomic changes associated with social behavior. We analyzed 13 high-quality weevil genomes, encompassing independent origins of egg and larval attendance, to test two predictions: (i) the sheltering hypothesis, where parental care relaxes selection on traits critical for independent larval survival and (2) the regulatory hypothesis, where behavioral shifts are driven by changes in transcriptional regulation. In support of hypothesis 1, we identified over 400 genes with evidence of significantly relaxed selection on the branches where egg and larval attendance evolved. In further support, we uncovered a significant number of convergent gene losses that coincided with both origins of larval attendance, particularly in genes linked to transcriptional regulation, metabolism and development. In contrast, positive selection and intensified selection were rare but contained multiple genes regulating gene expression, consistent with hypothesis 2. Together, these results suggest that parental care in weevils drives both simplification of larval traits through relaxed selection and convergent gene loss, and innovation in caregiving behaviors via adaptive changes in gene regulation.
PolyAdapt: Characterizing Polygenic Adaptive Architectures in the Presence of Strong Linkage Disequilibrium.
Mazzucco R, Schlötterer C
Genome Biol Evol · 2026 Jun · PMID 42262278 · Full text
Characterizing the genetic architecture of adaptation remains a central challenge in population genetics, particularly when multiple loci contribute to selected phenotypes. Two-genotype experimental evolution studies off...
Characterizing the genetic architecture of adaptation remains a central challenge in population genetics, particularly when multiple loci contribute to selected phenotypes. Two-genotype experimental evolution studies offer a powerful framework for this purpose, yet existing methods lack the capacity for genome-wide inference of selection targets and their coefficients under linkage. Here, we introduce polyAdapt, a novel iterative algorithm that identifies selected haplotype blocks and estimates the associated selection coefficients from Pool-Seq data in two-genotype experiments. Rather than exploring all possible combinations of selection targets simultaneously, polyAdapt sequentially incorporates targets of decreasing effect, accounting for linked selection at each step and optimizing both selection coefficients and effective population size through comparison of empirical and simulated replicate allele frequency trajectories. Using simulated data sets, we demonstrate that polyAdapt accurately recovers selection targets and coefficients for oligogenic architectures (5 and 13 targets) and provides a lower bound on the number of contributing loci for polygenic architectures (50 targets). Applied to yeast experimental evolution data, polyAdapt infers a highly polygenic architecture with at least 20 selected haplotype blocks per chromosome, consistent with independent estimates from the literature. polyAdapt thus represents a flexible and powerful tool for dissecting the genetic architecture of adaptation in experimental evolution studies.
Ancient Species Diversity and Niche Adaptation in Tannerella and Porphyromonas Revealed Through Pangenomics.
Galtier A, Warinner C, Velsko IM
Genome Biol Evol · 2026 Jun · PMID 42252506 · Full text
De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to perio...
De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n = 238) and Porphyromonas (n = 976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.
Early Evolution of the Prokaryotic Transcription Factor Repertoire.
Singh IR, Dubey A, Seshasayee ASN
Genome Biol Evol · 2026 Jun · PMID 42252092 · Full text
Transcription initiation is regulated by transcription factors (TFs). Though TFs determine phenotype, they are nonessential for minimal cellular life. Given this and the idea that it is a certain level of organism "compl...
Transcription initiation is regulated by transcription factors (TFs). Though TFs determine phenotype, they are nonessential for minimal cellular life. Given this and the idea that it is a certain level of organism "complexity" that calls for transcription regulation, we traced the evolution of TF repertoire on a bacterio-archaeal phylogeny using a dataset of ∼500,000 TFs. The most ancestral prokaryotes probably encoded multiple TFs. These, based on functions of extant relatives, possibly regulated sugar-fermentation metabolism, sensed overall metabolic state and redox, responded to DNA damage or bound metals; many of which are consistent with some reconstructions of ancestral gene pools and physiologies. The number of TFs and their superfamily-level diversity, through evolutionary history, are similar to those in extant bacteria. These suggest pre-LUCA diversification of TF families. Emergence of new TFs along the phylogeny shows innovation early in prokaryote evolution, in contrast to eukaryotes, in which many TF families emerged in bursts at multicellular lineages. Gains of TFs late in prokaryotic evolution appear to be products of horizontal acquisition of proteins discovered earlier along some other lineage. We speculate on the difference between the evolutionary trajectory of prokaryotic and eukaryotic TF repertoire and how this might be explained by how complexity is envisioned in these two different kingdoms.
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them.
Brault M, Brazier T, Mackintosh A … +3 more , Paupe A, Lascoux M, Glémin S
Genome Biol Evol · 2026 Jun · PMID 42246341 · Full text
Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomic data being generated. In the context of questioning the utility of produc...
Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomic data being generated. In the context of questioning the utility of producing such a large amount of genomic data, whether for ecological or economic reasons, we argue that data publication should be standardized to ensure long-term reusability. Based on a literature review and key examples, we emphasize that despite the growing volume of available data, the lack of methodological documentation and the absence of metadata make most published polymorphism datasets incomparable, preventing the calculation of meaningful statistics and the application of FAIR (Findable, Accessible, Interoperable, Reusable) principles. We stress that the Variant Calling Format (VCF) as it is used and published today is insufficient, as it does not report the number of monomorphic sites, which are required to compute basic statistics such as pairwise nucleotide diversity (π) or Watterson's θ. We further propose guidelines and best practices to provide sufficient information to allow the proper calculation of these statistics while accounting for sources of bias and misestimation frequently observed in the literature. Finally, we underscore the need for the systematic reporting of standardized statistics, coupled with transparent documentation of data processing steps, to ensure the reproducibility and comparability of population genomic research.
A High-quality Reference Genome and Tissue Expression Atlas for the European Lobster (Homarus gammarus).
Paris JR, Jenkins TL, Ferrer Obiol J … +23 more , Gundappa MK, Regan T, Campbell L, Maslen GL, Alvarez-Jarreta J, Dyer S, Jeffries AR, Murray G, Farbos A, Bickley LK, Verbruggen B, Bateman KS, Daniels CL, Ellis CD, Ashton TJ, Tyler CR, Stentiford GD, Houston RD, Bean TP, van Aerle R, Macqueen DJ, Stevens JR, Santos EM
Genome Biol Evol · 2026 Jun · PMID 42244022 · Full text
Homarid lobsters are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster (Homarus americanus), but not for the...
Homarid lobsters are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster (Homarus americanus), but not for the European lobster (H. gammarus), despite its ecological significance and importance to fisheries and aquaculture. Here, we present a high-quality genome assembly and annotation for the European lobster. The assembly spans 1.76 Gb, with a scaffold N50 of 1.82 Mb and a BUSCO completeness of 97.6% (96.8% single-copy, 0.8% duplicated). As observed in the American lobster, the total assembly span is substantially smaller than genome size estimates derived from flow cytometry (3.18 to 3.42 Gb). This discrepancy may reflect the highly repetitive nature of decapod genomes, with 51.8% of the European lobster assembly consisting of repetitive elements. Leveraging a comprehensive multi-tissue RNA-seq dataset, we annotated 23,223 protein-coding genes and characterized gene expression across ten tissues to generate a tissue gene expression atlas, available at www.LobsterGeneX.com. Using single-copy orthologues, we estimated a divergence time of 26 Mya between H. gammarus and H. americanus, corresponding to the Oligocene-Miocene boundary. We also identified lobster-specific gene duplications with roles in immunity and longevity, including telomere maintenance. These genomic resources will facilitate future research into lobster biology, supporting sustainable fisheries and aquaculture, while enabling investigations of homarid evolutionary adaptations.
Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.
Bonar M, Elliott TA, Ahmadi MAM … +2 more , Cottenie K, Linquist S
Genome Biol Evol · 2026 Jun · PMID 42243990 · Full text
Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TEs) to their genomic architecture. We leveraged a robust repeat annotation p...
Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TEs) to their genomic architecture. We leveraged a robust repeat annotation pipeline, in combination with manual and automated curatorial techniques, to produce a more comprehensive repeat annotation of Octopus vulgaris. This revealed that ∼66% of the genome are repeats, in contrast to previous estimates of 43% to 50% in closely related octopus species. Whereas previous studies of TE expansion in Octopus bimaculoides identified two bursts of activity, 25 and 56 MYA, our re-annotation revealed four such expansions at 18, 25, 33, and 56 MYA. We further identified a landscape of TE hot- and cold spots. This refined TE timescape and landscape will serve as a useful basis for understanding TE contributions to O. vulgaris evolution, also for identifying factors contributing to variation in the TE community across genomic space and evolutionary time.
Evolutionary Rate Variation at Predicted PTM Sites Reveals Localized Host-Associated Patterns in Influenza A Virus.
Teufel AI, Hasan MI, Smyth DS
Genome Biol Evol · 2026 Jun · PMID 42240086 · Full text
Influenza A viruses (IAVs) represent a persistent threat to global public health because of their capacity to cross species barriers and rapidly adapt to new hosts. Posttranslational modifications (PTMs) are known to reg...
Influenza A viruses (IAVs) represent a persistent threat to global public health because of their capacity to cross species barriers and rapidly adapt to new hosts. Posttranslational modifications (PTMs) are known to regulate viral protein function, yet the evolutionary dynamics of PTM sites across influenza strains remain largely uncharacterized. In this study, we employed MusiteDeep to computationally predict potential PTM sites across influenza A virus proteins from H1N1, H5N1, and H7N9. We modeled predicted PTM states as discrete evolutionary traits using Bayesian phylogenetic methods to examine patterns of evolutionary rate variation at these computationally identified sites. Our analysis identified 34 positions at predicted PTM sites showing either significantly elevated (11 sites) or reduced (23 sites) evolutionary rates relative to other PTM-associated positions within each protein. Fast-evolving sites were enriched in polymerase proteins and surface glycoproteins, where slowly evolving sites were more broadly distributed, with notable concentrations in PB1 polymerase and NS1 protein. A subset of these sites showed potential host-associated rate differences, suggesting that selective pressures on PTM sites may differ across host lineages.
Conservation of Human IgSF Proteins Throughout Eukaryotic Evolution.
Grudman S, Fiser A
Genome Biol Evol · 2026 Jun · PMID 42230317 · Full text
The human immunoglobulin superfamily (IgSF) encompasses hundreds of proteins involved in cell-cell adhesion, neural connectivity, junctional organization, and immune regulation, with many serving as key checkpoint protei...
The human immunoglobulin superfamily (IgSF) encompasses hundreds of proteins involved in cell-cell adhesion, neural connectivity, junctional organization, and immune regulation, with many serving as key checkpoint proteins. To elucidate the evolutionary history of human IgSF members, we systematically analyzed all available eukaryotic reference genomes to determine when each IgSF subfamily first appeared. The human IgSF was partitioned into six major evolutionary timeframes: Metazoa, Vertebrata, Gnathostomata, Tetrapoda, Amniota, and Mammalia. Although proteins were grouped solely by their conservation across eukaryotes, their biological functions clustered naturally, reflecting how new physiological systems create selective pressures that drive the appearance, retention, and diversification of protein architectures suited to those functions. Conservation and functional analyses indicate that human IgSF members arising in tetrapods and amniotes primary regulate the strength and duration of immune responses and form many of the critical components of the immune synapse, while IgSF genes that appear first in mammals have evolved to fine-tune immune activation thresholds to support maternal-fetal tolerance. Case studies are provided to illustrate three key evolutionary themes: (i) highly conserved yet catalytically inactive proteins retain essential regulatory functions, (ii) functional convergence among evolutionarily distinct IgSF families, and (iii) compensatory evolution within adaptive immunity following a lineage-specific loss of an IgSF member. Together, these findings establish an evolutionary framework for organizing the human IgSF by both ancestry and function, providing a foundation for assessing IgSF importance. Notably, this study facilitates the identification of conserved but understudied proteins that emerged alongside the development of the adaptive immune system, highlighting them as promising candidates for future experimental investigation.
Chloroplast and Mitochondrial Genomes of the Lichen-Symbiotic Green Alga Trebouxia Illuminate Evolutionary Relationships and Climate Associations and Yield New Phylogenetic Markers.
Wong ELY, Otte J, Schmitt I
Genome Biol Evol · 2026 Jun · PMID 42216275 · Full text
The green-algal genus Trebouxia (Trebouxiophyceae, Chlorophyta) is the most common photosynthetic symbiont of lichens, displaying high phylogenetic diversity, and worldwide distribution across all climate zones. These si...
The green-algal genus Trebouxia (Trebouxiophyceae, Chlorophyta) is the most common photosynthetic symbiont of lichens, displaying high phylogenetic diversity, and worldwide distribution across all climate zones. These single-celled terrestrial algae are valuable systems to study diversification, environmental adaptation and species interactions, yet genomic resources remain limited. We present over 30 new chloroplast and mitochondrial genomes of Trebouxia species, extracted from PacBio metagenomes of diverse Umbilicaria lichens from multiple climate zones. The genomes represent previously identified operational taxonomic units (OTUs) Trebouxia jamesii (A03), T. sp. (A04), T. incrustata (A06), T. vagua (A10), T. sp. (S02), T. sp. (S03), T. sp. (S04), T. suecica (S05), T. sp. (S08), T. angustilobata (S09), T. simplex (S10), T. sp. (S20) and T. barrenoae (S28); a newly designated OTU T. sp. (A57), and several Single-Occurrence Sequences (SOS) from clades A, I, and S. Up to four Trebouxia OTUs were found within a single thallus. Organelle genomes vary considerably in size and structure. The consensus phylogenies from chloroplast (77 genes) and mitochondrial (32 genes) genes are largely congruent with the nuclear ITS tree, differing mainly in the derived clade S sections. All genes are under purifying selection, with mitochondrial genes exhibiting higher nucleotide diversity and hence phylogenetic resolution than chloroplast genes. Certain gene and protein features correlate with temperature variability, and some (such as GC content, arginine, and valine content) mirror findings in mycobiont nuclear genomes from the same samples and highlight shared signatures of environmental adaptation. We designed primers for new, variable phylogenetic markers, including chloroplast genes ftsH and rpoC1, and mitochondrial genes ATP1, ATP6, and ND6. Overall, this study advances our understanding of organelle genome evolution in Trebouxia and provides valuable resources for future ecological and evolutionary research.
Comparative Transcriptomics Suggests that Breast Secretory Epithelium Reuses Gene Repertoires Conserved Across Vertebrates Beyond Mammals.
Saitou M
Genome Biol Evol · 2026 Jun · PMID 42216267 · Full text
The emergence of novel organs is often attributed to lineage-specific innovation; however, accumulating evidence suggests that many complex traits arise through the regulatory redeployment of conserved molecular componen...
The emergence of novel organs is often attributed to lineage-specific innovation; however, accumulating evidence suggests that many complex traits arise through the regulatory redeployment of conserved molecular components. From a molecular evolutionary perspective, an unresolved question is how preexisting gene repertoires are reorganized to generate tissue-specific functions. Here, we examine the molecular evolutionary organization of gene expression programs in human breast tissue by situating its transcriptome within a comparative framework of epithelial tissues with secretory functions. Using bulk RNA-seq data from the GTEx project, combined with co-expression network analysis, single-cell reference integration, and cross-vertebrate orthology assessment, we identify gene expression modules that are broadly shared across epithelial secretory tissues, relatively enriched in breast tissue, or biased toward female breast samples. We show that genes enriched in breast tissue are largely evolutionarily conserved across vertebrates and are embedded within transcriptional modules shared with other epithelial secretory organs. Co-expression analysis revealed partial overlap between breast modules and those of other epithelial secretory tissues, particularly in pathways related to secretion, vesicle trafficking, and extracellular matrix organization. Together, these results support a model in which breast secretory epithelium achieves tissue specialization through integration of conserved vertebrate gene repertoires, rather than through extensive emergence of mammal-specific genes.
Truncated Life History Underlies Rapid Local Adaptation in Island Rattlesnake Venom Expression.
Margres MJ, Hirst SR, Gallinson DG … +8 more , Rautsaw RM, McDonald PJ, Guedouar EG, Nystrom GS, Hogan MP, Ellsworth SA, Wray KP, Rokyta DR
Genome Biol Evol · 2026 Jun · PMID 42216262 · Full text
Rapid adaptive evolution may be more likely to occur not only through standing genetic variation but via existing axes of genetic variation that have previously been exposed to selection. Ontogenetic variation represents...
Rapid adaptive evolution may be more likely to occur not only through standing genetic variation but via existing axes of genetic variation that have previously been exposed to selection. Ontogenetic variation represents one such axis and often evolves under strong selection in snake venoms. Snake venoms are complex cocktails of proteinaceous toxins, and ontogenetic shifts in venom expression are frequent and reflect dietary shifts across life history. Here, we used morphological, proteomic, transcriptomic, epigenomic, and optical genome mapping data to investigate a well-studied island-mainland population pair of eastern diamondback rattlesnakes (Crotalus adamanteus) to determine whether rapid adaptive expression divergence across populations occurred through the co-option of the ontogenetic regulatory network, population-specific changes independent of ontogeny, or a combination thereof. We found that island snakes were significantly smaller than mainland individuals, and venom proteomic data showed that the continuous ontogenetic shift in venom expression in the mainland population was truncated in island snakes. Venom-gland RNA-seq showed that island adults exhibited juvenile-like expression patterns at key transcription factors, and chromatin accessibility was predictive of venom gene differential expression for ontogenetically co-opted venom loci. Overall, rapid adaptation in the island population appears to have predominantly occurred through the co-option and truncation of the ontogenetic venom shift, with spatial differentiation playing a secondary role. Comparative tests in other systems are needed to determine whether rapid adaptation in general is not only biased toward standing genetic variation but toward large pre-existing axes of variation that have or continue to evolve under strong selection.
Evolutionary History and Functional Divergence of Hydroxycarboxylic Acid Receptors in Primates.
Opazo JC, Barros LF, Zavala K … +2 more , Maldonado R, Mardones GA
Genome Biol Evol · 2026 Jun · PMID 42186840 · Full text
Hydroxycarboxylic acid receptors are class A G-protein-coupled receptors that act as metabolic sensors linking cellular metabolic status to physiological and immune responses. This family comprises three members (HCAR1,...
Hydroxycarboxylic acid receptors are class A G-protein-coupled receptors that act as metabolic sensors linking cellular metabolic status to physiological and immune responses. This family comprises three members (HCAR1, HCAR2, and HCAR3), expressed in metabolically active tissues and immune cells. Here, we investigate the evolutionary history of the most recently derived members, HCAR2 and HCAR3, in primates. Phylogenetic analyses reveal a complex duplicative history involving multiple independent duplication events during ape evolution. As a result, most ape lineages harbor independently originated duplicated copies, whereas non-ape primates retain the ancestral single-copy condition (HCAR2/3). Functional inference indicates that this single-copy gene may be functionally similar to HCAR2, suggesting that the major functional innovation in apes is associated with the emergence of HCAR3. Gene expression analyses further show that major divergence in tissue expression occurred early, following the duplication that generated HCAR1 and the HCAR2/3 lineage, while HCAR2 and HCAR3 retain largely overlapping expression profiles. Together, our results suggest that HCAR3 receptors may have evolved repeatedly in apes, potentially contributing to refined lipid-sensing.
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