Molecular Biology And Evolution[JOURNAL]
Sun
200 papers
Amhy/Amhr2y-mediated sex determination in two distantly related teleosts relies on the conserved Alk3-Smad5 axis.
Zhou L, Zhang L, Qu Z … +5 more , Jian H, Zheng S, Li M, Wang D, Liu X
Mol Biol Evol · 2026 Feb · PMID 41656994 · Full text
In teleosts, homologs of Anti-Müllerian Hormone (Amhy) and its type II receptor (Amhr2/Amhr2y) have been independently recruited as master sex-determination genes in about 50% of known cases. However, it remains unknown...
In teleosts, homologs of Anti-Müllerian Hormone (Amhy) and its type II receptor (Amhr2/Amhr2y) have been independently recruited as master sex-determination genes in about 50% of known cases. However, it remains unknown whether a conserved transducer pair exists, as the requisite type I receptors and R-Smad effectors remain unidentified amidst their diversity and potential redundancy. In this study, we employed an in vitro reporter assay to screen five type I receptors (Alk2a, Alk2b, Alk3, Alk6a, Alk6b) and three R-Smads (Smad1, Smad5, Smad8), discovering that only Alk3, Alk6a, or Alk6b, in combination with Smad5, significantly activated Amhy/Amhr2 signaling. In Nile tilapia, levels of phosphorylated Smad5 (p-Smad5) were notably elevated in XY gonads compared with XX gonads during the critical sex-determination window (8 to 15 dpf), while total Alk3 and Smad5 expression did not exhibit sexual dimorphism. The inhibition of type I receptors in XY fish resulted in feminization or complete sex reversal. Similarly, CRISPR/Cas9 mutagenesis of alk3 or smad5 led to male-to-female sex reversal in F0 mosaic mutants. Importantly, homozygous mutations in alk3 or smad5 resulted in embryonic lethality at the gastrula stage, whereas mutations in other type I receptors or R-Smads were viable and demonstrated normal sexual development. The conservation of this pathway was further substantiated in Southern catfish, where mutations in alk3a or smad5 also induced sex reversal in XY individuals. Collectively, our findings establish Alk3 and Smad5 as essential and specific transducers of the Amhy/Amhr2-mediated sex-determination pathway, revealing a potentially conserved signaling axis across teleosts.
The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability.
Deng R, Guo F, Fan F … +5 more , Wei W, Pfrender ME, Dudycha JL, Lynch M, Ye Z
Mol Biol Evol · 2026 Feb · PMID 41656912 · Full text
Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutational dynamics in Daphnia obtusa, we generated a chromosome-level genome as...
Spontaneous mutations are the primary source of genetic variation and play a central role in shaping evolutionary processes. To investigate mutational dynamics in Daphnia obtusa, we generated a chromosome-level genome assembly spanning 129.4 Mb across 12 chromosomes, encompassing 15,321 predicted protein-coding genes. Leveraging whole-genome sequencing of eight mutation-accumulation (MA) lines propagated for an average of 482 generations (spanning over 20 years), we estimated a spontaneous single-nucleotide mutation (SNM) rate of 2.45 × 10-9 and an indel mutation rate of 3.34 × 10-10 per site per generation. The SNM spectrum was strongly biased toward C:G > T:A transitions. Despite the design of MA experiments to minimize selection, nonsynonymous mutations were strongly underrepresented, providing rare evidence that purifying selection can act detectably even during mutation accumulation. Comparative analyses with natural population data revealed that exonic mutations observed in the MA lines were significantly less likely to be present in standing variation than intronic or intergenic mutations, suggesting that purifying selection in natural populations acts to remove deleterious alleles. We also identified 48 loss-of-heterozygosity (LOH) events, comprising 8 heterozygous deletions and 40 gene-conversion events, yet found no evidence of GC-biased gene conversion. Instead, while mutation predicts a substantially lower equilibrium GC content, the observed GC level is maintained at higher values, implicating natural selection as the primary force stabilizing base composition. Together, these results provide one of the most comprehensive assessments of the interplay among mutation, selection, and genome stability in an ecologically important species.
Evolutionary remodeling of the FXR binding pocket drove functional divergence and ligand discrimination.
Yamamoto N, Sudhakar N, Khan SH … +5 more , Biswas A, Mooney EJ, Hoshino Y, Gaucher EA, Okafor CD
Mol Biol Evol · 2026 Feb · PMID 41656862 · Full text
Nuclear receptor subfamilies are comprised of members that can have markedly different ligand preferences. The NR1H subfamily contains the farnesoid X receptor (FXR) and liver X receptors (LXR), which regulate myriad met...
Nuclear receptor subfamilies are comprised of members that can have markedly different ligand preferences. The NR1H subfamily contains the farnesoid X receptor (FXR) and liver X receptors (LXR), which regulate myriad metabolic processes, often in a coordinated fashion. As sensors for bile acids and oxysterols, respectively, it is not known what ligand(s) activated the precursor of FXR and LXR. We reconstruct the common FXR/LXR vertebrate ancestor and determine that it responds to neither class of ligands for the extant receptors. Using structural and functional analysis, we identify the set of evolutionary substitutions that recapitulate the shift in ligand preference from the FXR/LXR ancestor to the ancestral vertebrate FXR. We show that the substitutions reshaped the ligand binding pocket to drive this functional shift. Subsequent evolutionary mutations altered the secondary structure of FXR to scaffold the binding pocket and support functional specialization.
Invasion preferences suggest a possible role for Plasmodium falciparum parasites in the expansion of Duffy negativity in West and Central Africa.
Manneh B, Introini V, Reed J … +6 more , Rotariu M, Antrobus R, Cicuta P, Weekes MP, Penman BS, Rayner JC
Mol Biol Evol · 2026 Feb · PMID 41634932 · Full text
Duffy antigen receptor for chemokines (DARC) is the primary red blood cell (RBC) receptor for invasion of human RBCs by Plasmodium vivax and Plasmodium knowlesi parasites. By contrast, Plasmodium falciparum parasites use...
Duffy antigen receptor for chemokines (DARC) is the primary red blood cell (RBC) receptor for invasion of human RBCs by Plasmodium vivax and Plasmodium knowlesi parasites. By contrast, Plasmodium falciparum parasites use multiple RBC receptors for invasion. Whether DARC is one of these receptors has never been systematically explored. We used flow cytometry and microscopy-based approaches to investigate whether P. falciparum parasites preferentially invade specific Duffy RBC phenotypes and explored 2 potential explanations for invasion preference-differences in RBC biophysical properties and surface protein composition. P. falciparum parasites showed a consistent preference for Duffy-positive RBCs, and some biophysical properties and surface protein expression varied between Duffy-positive and Duffy-negative RBCs. We then used our in vitro invasion data to parametrize an evolutionary-epidemiological model of the relationship between P. falciparum and the FYBES allele. Our model accounts for immunity against P. falciparum virulence, gained through exposure, and thus mutations that impede infection are not always advantageous. The inhibition of P. falciparum invasion that we observed in vitro leads to FYBES frequencies increasing at low levels of P. falciparum transmission but decreasing at high levels of transmission. The impact of P. falciparum on the prevalence of Duffy negativity may therefore be most apparent in lower transmission settings. Our findings show a link between Duffy negativity and P. falciparum and suggest that DARC may directly or indirectly be involved in P. falciparum invasion of human RBCs which could, together with P. vivax, explain the distribution of Duffy negativity in sub-Saharan Africa.
Genetic formation and regional disparities of Kra-Dai and Hmong-Mien speakers inferred from ancient genomes of cave burial populations in southwest China.
Tao L, Xie Y, He H … +7 more , Bai T, Guo J, Zhu K, Wang B, Xie G, Lin Q, Wang CC
Mol Biol Evol · 2026 Feb · PMID 41632808 · Full text
Cave burial is a funerary practice believed to be associated with modern Kra-Dai (KD) and Hmong-Mien (HM) speakers for thousands of years. However, the extent to which these ancient cave burial practitioners contributed...
Cave burial is a funerary practice believed to be associated with modern Kra-Dai (KD) and Hmong-Mien (HM) speakers for thousands of years. However, the extent to which these ancient cave burial practitioners contributed to the formation of modern ethnic minority groups remains poorly understood due to the limited ancient genomic data. We generated 14 newly sequenced ancient human genomes from cave burial sites in Guangxi. The findings reveal continuous gene flow from northern lineages into ancient cave burial populations, shaping their genetic profiles over time. We observed a significant genetic distinction in HM populations: Southeast Asian HM groups derive 74.8% to 100% of their ancestry from cave burials, preserving a robust ancient southern genetic signature, while Chinese HM populations exhibit only 11.1% to 37.2% ancient cave burial ancestry, but heavily admixed with Yellow River-related populations (14.7% to 52.1%), reflecting differential historical interactions with northern migrants. In contrast, most KD speakers maintain tight genetic clustering with Guangxi ancestors (28.5% to 100% contribution from cave burials). The HM formation involved admixture between ancient cave burials, northern farmers, and local KD-related groups, which is evident in the genetic cline of She and Miao populations.
Inference and Visualization of Complex Genotype-Phenotype Maps.
Martí-Gómez C, Zhou J, Chen WC … +3 more , Stoltzfus A, Kinney JB, McCandlish DM
Mol Biol Evol · 2026 Feb · PMID 41631708 · Full text
Understanding how biological sequences give rise to observable traits, that is, how genotype maps to phenotype, is a central goal in biology. Yet, our knowledge of genotype-phenotype maps in natural systems remains limit...
Understanding how biological sequences give rise to observable traits, that is, how genotype maps to phenotype, is a central goal in biology. Yet, our knowledge of genotype-phenotype maps in natural systems remains limited by the high dimensionality of sequence space and the context-dependent effects of mutations. The emergence of Multiplex assays of variant effect (MAVEs) and the availability of ever growing collections of natural sequences offer new opportunities to characterize these maps at an unprecedented scale. However, tools for statistical and exploratory analyses of such high-dimensional data are still needed. To address this gap, we developed gpmap-tools (https://github.com/cmarti/gpmap-tools), a python library integrating models for inference, phenotypic imputation, and error estimation from MAVE data or natural sequences in the presence of genetic interactions of any order. gpmap-tools also provides methods for summarizing patterns of epistasis across sites and visualization of genotype-phenotype maps with millions of genotypes. We demonstrate its utility by inferring genotype-phenotype maps containing 262,144 variants of the Shine-Dalgarno sequence, a key motif for mRNA translation in bacteria, from both genomic 5 'UTR sequences and MAVE data. Visualization of the inferred landscapes consistently revealed high-fitness ridges that link core motifs at different distances from the start codon, motivating a new, highly interpretable thermodynamic model for this system. In summary, gpmap-tools provides a flexible, interpretable framework for studying complex genotype-phenotype maps, offering new insights into the architecture of genetic interactions and their evolutionary consequences.
Genomic insights into chromosomal fusion and its evolutionary implications for zokors.
Kuang Z, Yang X, Wan N … +9 more , Chen J, Duan Q, Li B, Liu X, Liang X, Liu X, Liu W, Nevo E, Li K
Mol Biol Evol · 2026 Feb · PMID 41630659 · Full text
Chromosomal fusion and fission are widespread across species, yet the underlying genomic mechanisms and their evolutionary implications remain poorly understood. Here, we present high-quality chromosome-level genome asse...
Chromosomal fusion and fission are widespread across species, yet the underlying genomic mechanisms and their evolutionary implications remain poorly understood. Here, we present high-quality chromosome-level genome assemblies for two closely related subterranean rodent species, Eospalax rufescens and E. rothschildi. Through comparative genomic and synteny analyses, we identified two species-specific chromosomal fusions in E. rothschildi, likely mediated by ectopic recombination through repetitive elements and by mutations affecting genome stability. Despite minimal changes in base-level genomic features, the fused chromosomes are associated with altered three-dimensional (3D) chromatin architecture, including increased chromatin entropy, topologically associating domain (TAD) rearrangement, and compartment switching. Reduced gene flow on the fused chromosomes suggests a role in reproductive isolation. Additionally, molecular signals of relaxed selection and adaptive evolution in pathways related to DNA repair, chromatin dynamics, and environmental sensing highlight the interplay between structural and ecological factors in shaping divergence. Together, our findings provide a mechanistic and evolutionary framework linking chromosomal fusions with genome architecture remodeling, epigenetic changes, and barriers to gene flow in mammals, offering a valuable resource for future evolutionary genomics studies.
Holostean genomes reveal evolutionary novelty in the vertebrate immunoproteasome that have implications for MHCI function.
Barker AV, Carlson KB, Wcisel DJ … +5 more , Birchler De Allende I, Braasch I, Fisk M, Dornburg A, Yoder JA
Mol Biol Evol · 2026 Mar · PMID 41628657 · Full text
Holosteans (gars and bowfins) have emerged as valuable models for understanding early vertebrate evolution, offering insights into diverse topics ranging from genomic architecture to molecular processes. These lineages a...
Holosteans (gars and bowfins) have emerged as valuable models for understanding early vertebrate evolution, offering insights into diverse topics ranging from genomic architecture to molecular processes. These lineages also exhibit unusual features in their immune response, combining molecular elements seen in both tetrapods and ray-finned fishes. However, the immune repertoire of holosteans remains relatively unexplored. Here, we investigate the evolution of PSMB8, a core component of the immunoproteasome responsible for cleaving intracellular proteins into peptides for presentation by MHC class I molecules. We identify two holostean PSMB8 types-S type and K type-that are unique among vertebrates. These types likely cause significant biochemical changes to the S1 binding pocket involved in antigen cleavage which could result in the presentation of novel peptides by MHC class I. Integrating comparative analyses across major ray-finned fish lineages demonstrates that bowfins and gars independently evolved the PSMB8 S type within separate PSMB8 paralog lineages, while the PSMB8-K type is an evolutionary novelty found only in gars. Our results provide new perspectives into PSMB8 haplotypes and their role in peptide antigen processing, offering unique insights into the molecular evolution of the vertebrate immunity and antigen presentation.
Genomic adaptations for tail-length evolution in arboreal snakes.
Wang Z, Wu W, Shen F … +5 more , Ren JL, Yan C, Tang CY, Zhang X, Li JT
Mol Biol Evol · 2026 Feb · PMID 41622621 · Full text
Adaptation to arboreal environments requires overcoming gravitational constraints, driving repeated morphological innovations across snake lineages. Among these, elongated tails represent a key adaptation that enhances b...
Adaptation to arboreal environments requires overcoming gravitational constraints, driving repeated morphological innovations across snake lineages. Among these, elongated tails represent a key adaptation that enhances branch-gripping ability, yet the genomic changes underlying this trait remain poorly understood. Here, ancestral state reconstruction revealed that arboreality evolved independently in multiple snake clades, with tail elongation as a recurrent morphological adaptation. To investigate its genetic underpinnings, we generated a high-quality, chromosome-level genome assembly for the green cat snake (Boiga cyanea) and performed comparative analyses with the Asian vine snake (Ahaetulla prasina). We identified accelerated evolution in genes associated with somite specification, a critical process for axial elongation, and detected positive selection in key somitogenesis regulators, including HES7 and TBX18. Notably, LOXL3, which contributes to somite boundary formation, exhibited a conserved amino acid substitution in both arboreal lineages. In addition, convergent divergence of conserved nonexonic elements (CNEs) was observed in genomic regions linked to the GDF11-LIN28-HOX13 pathway, which governs the axial-to-tail transition. Functional assays confirmed that divergence in these CNEs alters regulatory activity, potentially modulating gene expression within critical developmental pathways. Collectively, our findings establish a genomic framework for snake axial elongation, highlighting how arboreal specialization shaped tail length evolution.
Dynamic regulation of spermatogenesis and hybrid sterility revealed by single-cell analysis in yak and cattle.
Wu SX, Wang GW, Wan RD … +7 more , Yan RG, Gao X, Zhang RN, Yang QL, Fang YG, Jia GX, Yang QE
Mol Biol Evol · 2026 Feb · PMID 41622528 · Full text
Spermatogenesis is a highly orchestrated germ cell differentiation process involving the dynamic regulation of cell fate transitions. Dissecting the molecular landscapes of spermatogenic cell types is crucial for identif...
Spermatogenesis is a highly orchestrated germ cell differentiation process involving the dynamic regulation of cell fate transitions. Dissecting the molecular landscapes of spermatogenic cell types is crucial for identifying fertility-related problems and improving the reproductive performance of farm animals. Here, we conducted transcriptomic and chromosome spreading across meiotic stages of testicular cells from taurine cattle (Bos taurus), yak (Bos grunniens), and their hybrid progenies to describe the transcriptional landscape of normal spermatogenesis and identify potential regulators that are involved in hybrid sterility. The results revealed seven types of spermatogonia, ten spermatocytes and ten types of spermatids in the cattle or yak testes. In sharp contrast, the testes of the cattle-yak hybrids contained only seven spermatogonial subtypes and six types of spermatocytes. Notably, the arrest of spermatocytes at the diplotene-to-diakinesis transition was accompanied by defects in double-strand break repair. In the testes of backcrossed offspring, spermatogenic arrest was partially rescued, and round spermatozoa were produced. By performing joint analysis, we identified 115 genes that exhibited differential protein abundance in spermatocytes of cattle-yak. Among them, 24 genes carrying genomic structural variations were differentially expressed in spermatocytes of cattle-yak but recovered in those of backcrossed offspring. This work provides important insights into spermatogenesis in large animals and serves as a valuable resource for identifying the factors determining reproductive isolation.
Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection.
Ochsner N, Bouman J, Vaughan T … +3 more , Stadler T, Bonhoeffer S, Regoes R
Mol Biol Evol · 2026 Feb · PMID 41622429 · Full text
Phylodynamic methods are widely used to infer the population dynamics of viruses between and within hosts. For HIV-1, these methods have been used to estimate migration rates between different anatomical compartments wit...
Phylodynamic methods are widely used to infer the population dynamics of viruses between and within hosts. For HIV-1, these methods have been used to estimate migration rates between different anatomical compartments within a host. These methods typically assume that the genomic regions used for reconstruction are evolving without selective pressure, even though other parts of the viral genome are known to experience strong selection. In this study, we investigate how selection affects phylodynamic migration rate estimates. To this end, we developed a novel agent-based simulation tool, virolution, to simulate the evolution of virus within two anatomical compartments of a host. Using this tool, we generated viral sequences and genealogies assuming both, neutral evolution and selection governed by an empirically-supported distribution of fitness effects that is concordant in both compartments. We found that, under the selection regime, migration rates are significantly overestimated with a stochastic mixture model and a structured coalescent model in the Bayesian inference framework BEAST2. Our results reveal that commonly used phylogeographic methods, which assume neutral evolution, can significantly bias migration rate estimates in selective regimes. This study underscores the need for assessing the robustness of phylodynamic analysis with respect to more realistic selection regimes.
TreeProfiler: large-scale metadata profiling along gene and species trees.
Deng Z, Sanchis-López C, Hernández-Plaza A … +2 more , Davín AA, Huerta-Cepas J
Mol Biol Evol · 2026 Feb · PMID 41622108 · Full text
Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infer gene function from co-evolutionary patterns (phylogenetic profiling), rec...
Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infer gene function from co-evolutionary patterns (phylogenetic profiling), reconstruct ancestral states, and uncover ecological associations. However, existing profiling tools are typically tailored to specific use cases, have limited scalability for large datasets, and lack robust methods to aggregate or summarize traits at internal tree nodes. Here, we present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes. TreeProfiler supports the profiling of custom continuous and discrete traits, as well as ancestral character reconstruction and phylogenetic signal tests. It also integrates commonly used genomic features, including multiple sequence alignments, protein domain architectures, and functional annotations. We demonstrate TreeProfiler's utility beyond traditional phylogenetic profiling, as well as its ability to efficiently handle massive datasets, by analyzing the functional diversification of the methyl-accepting chemotaxis protein family comprising over 400,000 genomic and metagenomic sequences and by profiling the relative abundance of 124,295 bacterial and archaeal species across 51 biomes. TreeProfiler is open-source and freely available at https://github.com/compgenomicslab/TreeProfiler.
Genomic consequences of domestication and the diversification of body coloration and morphology in ornamental medaka strains.
Kon T, Tang R, Kon-Nanjo K … +9 more , Tomihara S, Fushiki S, Fujii W, Sera M, Takehana Y, Noguchi H, Toyoda A, Naruse K, Omori Y
Mol Biol Evol · 2026 Feb · PMID 41612673 · Full text
Ornamental medaka strains derived from wild Japanese medaka (Oryzias latipes species complex) are bred worldwide. Over 200 years of selective breeding have produced over 700 strains with a wide variety of phenotypes, inc...
Ornamental medaka strains derived from wild Japanese medaka (Oryzias latipes species complex) are bred worldwide. Over 200 years of selective breeding have produced over 700 strains with a wide variety of phenotypes, including diverse body coloration, scales, eyeball morphology, and fin and body shapes. In this study, we first identified and described 34 phenotypes in ornamental medaka strains. To understand the genomic basis of this phenotypic diversity and the domestication process, we performed whole-genome sequencing on 181 individuals of 86 ornamental Japanese medaka strains. Population genomic analyses revealed that modern ornamental medaka strains are genetically closer to the wild Southern Japan population of the Kansai-Setouchi regions, suggesting the origin of ornamental strains. In addition, the gene loci poc1a, tyr, nme2a, and gabrr2b have undergone selection during domestication. We performed genome-wide association studies analysis for 29 phenotypes observed in ornamental medaka strains and identified strong candidate genes for some phenotypes, including kcnq5a for hirenaga and swallow, bmp5 for deme, adcy5 for orochi, and kitlga for aurora, respectively. We found that loss of exon 8 of adcy5 caused melanism, a dark body color phenotype, in medaka, providing a molecular insight into this phenomenon in vertebrates and human familial dyskinesia. In addition, we uncovered the predominant candidate peaks of genome-wide association studies, including a total of 3,328 genes associated with 26 phenotypes. Our findings highlight the potential of population genomics to explore genotype-phenotype correlations and the genomic basis of body coloration and morphogenesis in medaka.
Estimates of molecular convergence reveal multiple genes with adaptive variation across teleost fish.
Barua A, Srivastava M, Beinsteiner B … +2 more , Laudet V, Robinson-Rechavi M
Mol Biol Evol · 2026 Jan · PMID 41604226 · Full text
Molecular convergence, where specific nonsynonymous changes in protein-coding genes lead to identical amino acid substitutions across multiple lineages, provides strong evidence of adaptive evolution. Detecting this sign...
Molecular convergence, where specific nonsynonymous changes in protein-coding genes lead to identical amino acid substitutions across multiple lineages, provides strong evidence of adaptive evolution. Detecting this signal across diverse taxa can reveal adaptive variation that may not be apparent when studying individual lineages. In this study, we search for convergent substitutions in the most speciose group of vertebrates, teleost fishes. Using an unsupervised approach, we detected convergence in 89 protein-coding gene families across 143 chromosomal-level genomes. To assess their functional implications, we integrate data on protein properties, gene expression across species and tissues, single-cell RNA sequencing of zebrafish embryonic development, and gene perturbation experiments in zebrafish. We found that, on average, the convergent genes had more gene copies as compared to background sets of genes. The convergent genes were associated with diverse processes including embryonic development, tissue morphogenesis, metabolism, and heat stress response. We found evidence that convergent substitutions were more radical than nonconvergent substitutions. When analyzing the expression of the convergent genes, we found that only one-third of them were tissue-specific, while the majority were expressed across multiple tissues and cell types. Genetic perturbation data further showed that the convergent genes can affect multiple structures across diverse tissues. These results highlight the important functional roles of the convergent genes, their potential pleiotropic nature, and suggest that they may underlie the evolution of lineage-specific adaptations in teleost fishes.
Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics.
Ruckman SN, Long AD
Mol Biol Evol · 2026 Feb · PMID 41593459 · Full text
The genetics of complex traits has been fundamentally transformed by the dramatic reduction in short-read sequencing costs, leading to a dramatic reversal in the relative costs of genotyping versus phenotyping. We explor...
The genetics of complex traits has been fundamentally transformed by the dramatic reduction in short-read sequencing costs, leading to a dramatic reversal in the relative costs of genotyping versus phenotyping. We explore this new scientific landscape by examining key experimental strategies that leverage inexpensive sequencing, including low-coverage whole-genome sequencing with imputation (lcWGS + I) for genotyping large cohorts. Although somewhat limited in outbred populations, lcWGS + I can be extremely effective in multiparent populations and in founder-unknown closed colonies, where imputation accuracy can exceed 98%. We further explore pooled-sequencing approaches for dissecting complex traits, such as Evolve and Resequence for tracking adaptive changes in allele frequency over several generations, and extreme quantitative trait loci mapping that identifies loci by contrasting pooled samples from phenotypic extremes. We show that extreme quantitative trait loci mapping in multiparent populations, by testing for shifts in founder haplotype frequencies across small genomic windows, can be extremely powerful and cost-effective. Finally, we discuss methods where sequencing reads serve as the phenotype itself. DNA barcoding enables massive-scale fitness assays, while the "*-seq" toolkit (e.g. RNA-seq, ATAC-seq) allows for mapping molecular quantitative trait loci, though this introduces a significant multiple testing burden. Systems leveraging certain breeding designs in concert with low cost sequencing can greatly accelerate progress toward a mechanistic understanding of the genotype-phenotype relationship.
The evolutionary genomics of meiotic drive.
Presgraves DC, Dawe RK, Dyer KA … +22 more , Fishman L, Bhide SA, Bradshaw SL, Brady MJ, Burga A, Courret C, Fagen BL, Machado Ferretti ABS, Kelemen RK, Kitano J, Liu Y, Martí E, Erlenbach T, Reinhardt JA, Ross L, Runge JN, Swanepoel CM, Vicoso B, Vogan AA, Lindholm AK, Larracuente AM, Unckless RL
Mol Biol Evol · 2026 Feb · PMID 41589062 · Full text
Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologists have considered meiotic drivers as interesting, albeit esoteric, case stu...
Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologists have considered meiotic drivers as interesting, albeit esoteric, case studies. It is now clear, however, that meiotic drive is more common and phylogenetically widespread than previously supposed. Indeed, intensive study of a few well-known cases has begun to reveal the evolutionary genomic consequences of meiotic drive. We argue here that many features of genome evolution, content, and organization that are seemingly inexplicable by organismal adaptation or nearly neutral processes are instead best accounted for by recurrent histories of meiotic drive. We review how meiotic drive can affect the evolution of sequences, gene copy numbers, genes with functions in meiosis and gametogenesis, signatures of "selection," chromosome rearrangements, and karyotype evolution. We also explore the interactions of meiotic drive elements with other classes of selfish genetic elements, including satellite DNAs, transposable elements, and with the endogenous host genes involved in drive suppression. Finally, we argue that some aspects of drive-mediated genome evolution are now sufficiently well established that we might reverse the direction of discovery-rather than ask how drive affects genome evolution, we can use genome data to discover new putative drive elements.
Two independent origins of XY sex chromosomes in Asparagus.
Bentz PC, Carey SB, Mercati F … +5 more , Hale H, Ricciardi V, Sunseri F, Harkess A, Leebens-Mack JH
Mol Biol Evol · 2026 Feb · PMID 41581085 · Full text
The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enables the investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two...
The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enables the investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy, Asparagus is a model genus for studying the genetics of sex-determination and sex chromosome evolution. Dioecy first evolved in Asparagus ∼3 to 4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade including garden asparagus (Asparagus officinalis). A second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade, including Asparagus horridus. New haplotype-resolved reference genomes for garden asparagus and A. horridus, elucidate contrasting first steps in the origin of the sex chromosomes of the Eurasian and Mediterranean Basin clade ancestors. Analysis of the A. horridus genome revealed an XY system derived from a different ancestral pair of autosomes with different sex-determining genes than have been characterized for garden asparagus. We estimate that proto-XY chromosomes evolved 1 to 2 Ma in the Mediterranean Basin clade, following a ∼2.1-megabase inversion that now distinguishes the X and Y chromosomes. Recombination suppression and LTR retrotransposon accumulation drove the expansion of the male-specific region on the Y (MSY) that reaches ∼9.6-megabases in A. horridus. The garden asparagus genome revealed an MSY spanning ∼1.9-megabases. A segmental duplication and neofunctionalization of one duplicated gene (SOFF) drove the origin of dioecy in the Eurasian clade. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy in Asparagus and establish the genus as a model for investigating sex chromosome evolution.
PharaohFUN: phylogenomic analysis for plant protein history and function elucidation.
Ramos-González M, Ramos-González V, Serrano-Pérez E … +4 more , Arvanitidou C, Hernández-García J, García-González M, Romero-Campero FJ
Mol Biol Evol · 2026 Feb · PMID 41570082 · Full text
Since DNA sequencing has become commonplace, the development of efficient methods and tools to explore gene sequences has become indispensable. In particular, despite photosynthetic eukaryotes constituting the largest pe...
Since DNA sequencing has become commonplace, the development of efficient methods and tools to explore gene sequences has become indispensable. In particular, despite photosynthetic eukaryotes constituting the largest percentage of terrestrial biomass, computational functional characterization of gene sequences in these organisms still predominantly relies on comparisons with Arabidopsis thaliana and other angiosperms. This paper introduces PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships between them. PharaohFUN incorporates a homogeneous representative sampling of key species in this group, bridging clades that have traditionally been studied separately, thus establishing a comprehensive evolutionary framework to draw conclusions about sequence evolution and function. For this purpose, it incorporates modules for exploring gene tree evolutionary history, expansion and contraction events, ancestral states, domain identification, multiple sequence alignments, and diverse functional annotation. It also incorporates different search modes to facilitate its use and increase its reach within the community. Tests were performed on the whole transcription factor toolbox of A. thaliana and on CCA1 protein to assess its utility for both large-scale and fine-grained phylogenetic studies. These exemplify how PharaohFUN accurately traces the corresponding evolutionary histories of these proteins by unifying results for land plants, streptophyte and chlorophyte microalgae. Thus, PharaohFUN democratices access to these kinds of analyses in photosynthetic organisms for every user, independently of their prior training in bioinformatics.
Phylogeny of waterfowl (Anseriformes) constructed using genome sequences provides insights into topological incongruences.
Wang G, Zhu T, Zhang X … +5 more , Ren X, Chen A, Ning Z, van Tuinen M, Qu L
Mol Biol Evol · 2026 Feb · PMID 41560303 · Full text
The evolutionary history of waterfowl (Anseriformes) has long been a focal point of avian research. However, previous phylogenetic investigations have focused primarily on morphology or mitochondrial DNA or have lacked s...
The evolutionary history of waterfowl (Anseriformes) has long been a focal point of avian research. However, previous phylogenetic investigations have focused primarily on morphology or mitochondrial DNA or have lacked sufficient taxon sampling. Accompanied by observed phylogenetic incongruence and incomplete resolution, waterfowl phylogenetic branching patterns remain uncertain at various taxonomic ranks. To further validate phylogenetic relationships among higher waterfowl taxa and assess presence of conflicting signal, we assembled and analyzed 24 waterfowl genomes representing all waterfowl families and several subfamilies. Utilizing both newly acquired and previously obtained genomes, we constructed and analyzed seven DNA data classes, which yielded highly resolved phylogenetic trees including a time-calibrated tree. Most of these trees consistently and completely resolved the phylogenetic relationships of the included waterfowl species. Despite these efforts, our analysis across chromosomes uncovered four instances of phylogenetic incongruous signal. After minimizing tree estimation error through focus on whole-genome alignment dataset and by sequence simulation, analyses revealed that incomplete lineage sorting and gene introgression essentially contributed to all gene-tree discordance. The variable impact of both factors across distinct waterfowl nodes reflects an underlying complexity that warrants further interpretation. This study not only presents a strongly-supported and well-resolved phylogenetic backbone for the major waterfowl lineages, but also provides foundational data for subsequent comparative genomics studies of a more expanded set of waterfowl taxa.
Evolutionary innovation within conserved gene regulatory networks underlying biomineralized skeletons in Bilateria.
Bai Y, Min Y, Liu S … +7 more , Hu Y, Jin S, Yu H, Kong L, Macqueen DJ, Du S, Li Q
Mol Biol Evol · 2026 Feb · PMID 41556888 · Full text
Biomineralized skeletons have evolved convergently across animals and exhibit remarkable diversity in structure and development. However, the evolutionary origins of gene regulatory networks underlying biomineralized ske...
Biomineralized skeletons have evolved convergently across animals and exhibit remarkable diversity in structure and development. However, the evolutionary origins of gene regulatory networks underlying biomineralized skeletons remain elusive. Here, we report comprehensive developmental profiling of transcriptomic and chromatin dynamics in a bivalve mollusc, Crassostrea nippona. We provide evidence for a biphasic regulatory program orchestrating larval and adult shell formation, involving the coordinated activity of ancient transcription factors and dynamic chromatin remodeling. Comparative analyses suggest a conserved developmental toolkit was co-opted for larval exoskeleton formation in the common lophotrochozoan ancestor. In contrast, limited regulatory conservation was observed between lophotrochozoans and echinoderms with regard to the formation of biomineralized skeletons, despite both relying on a heterochronic activation of ancestral regulators. Together, our findings support a hierarchical model in which dynamic chromatin decouples rapidly evolving effectors from deeply conserved regulators, allowing modular innovations within conserved gene regulatory networks. This study highlights how epigenetic dynamics bridge evolutionary conservation and novelty, offering a framework for understanding the independent evolution of biomineralization across Bilateria through combinatorial regulatory evolution.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe