Molecular Biology And Evolution[JOURNAL]
Sun
200 papers
Social Stratification Without Genetic Differentiation at the Xisima Site in the Late Shang Dynasty.
Tang J, Wang R, Wei Q … +12 more , He H, Deng C, Tao L, Mao X, Ma H, Wang X, Zou X, Yang X, Zhang Q, Wu Q, Guo Y, Wang CC
Mol Biol Evol · 2026 Jan · PMID 41313720 · Full text
Ancient DNA and archaeological studies indicate the Central Plain's pivotal role in the cultural and genetic evolution of ancient China. However, limited genome-wide data have constrained our understanding of this region...
Ancient DNA and archaeological studies indicate the Central Plain's pivotal role in the cultural and genetic evolution of ancient China. However, limited genome-wide data have constrained our understanding of this region's population history during the Bronze Age Shang Dynasty (around 1600 to 1046 BCE). Here, we present genome-wide data from 11 individuals from the Xisima Cemetery in Central Plain, a site exhibiting clear burial evidence of social stratification dating to the Late Shang Dynasty (around 1300 to 1046 BCE). Genetic analyses reveal that all Xisima individuals can be modeled as direct, unadmixed descendants of Late Neolithic Central Plain-related people. We found no systematic genetic differentiation between individuals buried in high-grade (south-to-north) and low-grade (east-to-west) tombs, indicating genetic homogeneity across social strata. These results demonstrate that social stratification at Xisima occurred without corresponding genetic distinction, supporting the decoupling of social hierarchy from significant genetic differentiation in this Shang community.
Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.
Cheng Q, Sohail MS, McKay MR
Mol Biol Evol · 2025 Nov · PMID 41311308 · Full text
Estimating selection from genetic time-series data is fundamental to understanding evolutionary dynamics. Accurate selection inference is confounded by multiple noise sources, including limited sampling of populations an...
Estimating selection from genetic time-series data is fundamental to understanding evolutionary dynamics. Accurate selection inference is confounded by multiple noise sources, including limited sampling of populations and genetic drift. To characterize how these uncertainties collectively affect estimator performance, we analyze a mathematically tractable selection coefficient estimator derived under the marginal path likelihood (MPL) framework. We identify a parameter, the integrated mutant allele variance, as a key quantity determining estimator precision. Our analysis reveals that variance integration mitigates sampling and genetic drift errors at different rates, with drift typically becoming the dominant source of error in longer trajectories. The increased robustness of MPL-based estimation to sampling is surprising, since MPL is derived from a model that neglects this effect. Our findings offer insights into how incorporating temporal information reduces multiple sources of noise when estimating selection coefficients.
Ancestral Chaperonins Provide the First Structural Glimpse into Early Multimeric Protein Evolution.
Severino R, Cuéllar J, Gutiérrez-Seijo J … +6 more , Maestro-López M, Sánchez-Pulido L, Santiago C, Moreno-Paz M, Valpuesta JM, Parro V
Mol Biol Evol · 2025 Nov · PMID 41310978 · Full text
Chaperonins are essential protein-folding machines, classified into three structural and phylogenetic groups: Group I (bacterial GroEL), Group II (archaeal thermosome and eukaryotic CCT), and Group III (bacterial thermos...
Chaperonins are essential protein-folding machines, classified into three structural and phylogenetic groups: Group I (bacterial GroEL), Group II (archaeal thermosome and eukaryotic CCT), and Group III (bacterial thermosome-like). Using ancestral sequence reconstruction (ASR) and protein resurrection, we inferred and experimentally characterized the last common ancestors of these groups (ancestral chaperonins ACI, ACII, and ACIII). The resurrected proteins exhibited ATPase activity (except ACII) and protected client proteins from heat-induced inactivation. Structural analyses by electron microscopy and Cryo-EM revealed that ACI forms single 7-mer rings, whereas ACII adopts a mixed population of single/double 8-mer rings, representing the first experimental observation of intermediate oligomeric states. ACII also features a unique cochaperonin-independent closure mechanism, distinct from modern Group I and II chaperonins. Together, these findings provide the experimental structural reconstruction of the most ancient and complex multimeric proteins so far, uncover novel intermediate states in chaperonin evolution, and offer a direct empirical framework for studying the emergence of multimeric complexity in early cellular life.
Whole-Genome Duplication Reshapes Adaptation: Autotetraploid Arabidopsis arenosa Leverages its High Genetic Variation to Compensate for Selection Constraints.
Celestini S, Lipánová V, Vlček J … +1 more , Kolář F
Mol Biol Evol · 2025 Nov · PMID 41306061 · Full text
Whole-genome duplication (WGD), a widespread macromutation across eukaryotes, is predicted to affect the tempo and modes of evolutionary processes. By theory, the additional set(s) of chromosomes present in polyploid org...
Whole-genome duplication (WGD), a widespread macromutation across eukaryotes, is predicted to affect the tempo and modes of evolutionary processes. By theory, the additional set(s) of chromosomes present in polyploid organisms may reduce the efficiency of selection while, simultaneously, increasing heterozygosity and buffering deleterious mutations. Despite the theoretical significance of WGD, empirical genomic evidence from natural polyploid populations is scarce and direct comparisons of selection footprints between autopolyploids and closely related diploids remains completely unexplored. We therefore combined locally sampled soil data with resequenced genomes of 76 populations of diploid-autotetraploid Arabidopsis arenosa and tested whether the genomic signatures of adaptation to distinct siliceous and calcareous soils differ between the ploidies. Leveraging multiple independent transitions between these soil types in each ploidy, we identified a set of genes associated with ion transport and homeostasis that were repeatedly selected for across the species' range. Notably, polyploid populations have consistently retained greater variation at candidate loci compared with diploids, reflecting lower fixation rates. In tetraploids, positive selection predominantly acts on such a large pool of standing genetic variation, rather than targeting de novo mutations. Finally, selection in tetraploids targets genes that are more central within the protein-protein interaction network, potentially impacting a greater number of downstream fitness-related traits. In conclusion, both ploidies thrive across a broad gradient of substrate conditions, but WGD fundamentally alters the ploidies adaptive strategies: tetraploids leverage their greater genetic variation and redundancy to compensate for the predicted constraints on the efficacy of positive selection.
Evolutionary dampening of Wnt signaling may contribute to naturally ascrotal testes in mammals.
Chai S, Zhong C, Zhang Z … +4 more , Yin D, Xu S, Ren W, Yang G
Mol Biol Evol · 2025 Nov · PMID 41294232 · Publisher ↗
The testicular descent leading to the exteriorization of male gonads is a complex sexual dimorphic process observed in numerous mammals, whereas some species, such as elephants and cetaceans, retain the lifelong ascrotal...
The testicular descent leading to the exteriorization of male gonads is a complex sexual dimorphic process observed in numerous mammals, whereas some species, such as elephants and cetaceans, retain the lifelong ascrotal testes. Despite the implication of Wnt signaling in testicular development and descent, the evolutionary mechanisms underlying ascrotal testes have not been adequately addressed. Here, we examined selection signatures and unique amino-acid substitutions in genes of the Wnt signaling pathway. We identified an ascrotal mammal-specific substitution (S406G) in ZNRF3 located within the DVL-interaction region. Functional assays showed that this substitution enhances the affinity of ascrotal ZNRF3 for DVLs and suppresses Wnt3a-induced Wnt signaling. Comparative transcriptomics of the gubernaculum between male fetal rats from wild-type and spontaneous cryptorchid (orl) strains revealed upregulation of Ctnnb1 and Gsk3b in orl rats, along with ascrotal-specific evolutionary changes in regulatory elements. Collectively, these findings suggest that Wnt signaling may be dampened in ascrotal mammals. This study provides insights into the pathogenesis of cryptorchidism in humans and domestic animals.
Evolutionary dampening of Wnt signaling may contribute to naturally ascrotal testes in mammals: Dampened Wnt pathway under ascrotal testes.
Chai S, Zhong C, Zhang Z … +4 more , Yin D, Xu S, Ren W, Yang G
Mol Biol Evol · 2025 Nov · PMID 41293833 · Publisher ↗
The testicular descent leading to the exteriorization of male gonads is a complex sexual dimorphic process observed in numerous mammals, whereas some species, such as elephants and cetaceans, retain the lifelong ascrotal...
The testicular descent leading to the exteriorization of male gonads is a complex sexual dimorphic process observed in numerous mammals, whereas some species, such as elephants and cetaceans, retain the lifelong ascrotal testes. Despite the implication of Wnt signaling in testicular development and descent, the evolutionary mechanisms underlying ascrotal testes have not been adequately addressed. Here, we examined selection signatures and unique amino-acid substitutions in genes of the Wnt signaling pathway. We identified an ascrotal mammal-specific substitution (S406G) in ZNRF3 located within the DVL-interaction region. Functional assays showed that this substitution enhances the affinity of ascrotal ZNRF3 for DVLs and suppresses Wnt3a-induced Wnt signaling. Comparative transcriptomics of the gubernaculum between male fetal rats from wild-type and spontaneous cryptorchid (orl) strains revealed upregulation of Ctnnb1 and Gsk3b in orl rats, along with ascrotal-specific evolutionary changes in regulatory elements. Collectively, these findings suggest that Wnt signaling may be dampened in ascrotal mammals. This study provides insights into the pathogenesis of cryptorchidism in humans and domestic animals.
SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes.
Haller BC, Ralph PL, Messer PW
Mol Biol Evol · 2026 Jan · PMID 41292177 · Full text
Evolutionary simulations of multiple chromosomes, even up to the scale of full-genome simulations, are becoming increasingly important in population genetics and evolutionary ecology. Unfortunately, the popular simulatio...
Evolutionary simulations of multiple chromosomes, even up to the scale of full-genome simulations, are becoming increasingly important in population genetics and evolutionary ecology. Unfortunately, the popular simulation framework SLiM has always been intrinsically limited to simulations of a single diploid chromosome. Modeling multiple chromosomes of different types, such as sex chromosomes, has always been cumbersome, even with scripting, presenting a substantial barrier to the development of full-genome simulations. Here we present SLiM 5, a major extension of SLiM's capabilities for simulating multiple chromosomes. Modeling up to 256 chromosomes is now possible, and each chromosome may belong to any of a wide variety of types-not just autosomes (diploid and haploid), but also sex chromosomes (X, Y, Z, and W), haploid mitochondrial and chloroplast DNA, and more. This new functionality is integrated across all of SLiM, including not only the mechanics of reproduction and inheritance, but also input and output of multi-chromosome data in formats like VCF, and tree-sequence recording across multiple chromosomes. New recipes in the SLiM manual demonstrate these new features, and SLiM's graphical modeling environment, SLiMgui, has been extended in many ways for the visualization of multi-chromosome models. These new features will open new horizons and enable a heightened level of realism for full-genome simulations.
Quick Analysis of Sedimentary Ancient DNA Using quicksand.
Szymanski M, Visagie J, Romagné F … +2 more , Meyer M, Kelso J
Mol Biol Evol · 2025 Nov · PMID 41287599 · Full text
Ancient DNA extracted from the sediments of archaeological sites (sedaDNA) can provide fine-grained information about the composition of past ecosystems and human site use, even in the absence of visible remains. However...
Ancient DNA extracted from the sediments of archaeological sites (sedaDNA) can provide fine-grained information about the composition of past ecosystems and human site use, even in the absence of visible remains. However, the growing amount of available sequencing data and the nature of the data obtained from archaeological sediments pose several computational challenges; among these, the rapid and accurate taxonomic classification of sequences. While alignment-based taxonomic classifiers remain the standard in sedaDNA analysis pipelines, they are too computationally expensive for the processing of large numbers of sedaDNA sequences. In contrast, alignment-free methods offer fast classification but suffer from higher false-positive rates. To address these limits, we developed quicksand, an open-source Nextflow pipeline designed for rapid and accurate taxonomic classification of mammalian mitochondrial DNA in sedaDNA samples. quicksand combines fast alignment-free classification using KrakenUniq with post-classification mapping, filtering, and ancient DNA authentication. Based on simulations and reanalyses of published datasets, we demonstrate that quicksand achieves accuracy and sensitivity comparable to or better than existing methods, while significantly reducing runtime. quicksand offers an easy workflow for large-scale screening of sedaDNA samples for archaeological research and is freely available at https://github.com/mpieva/quicksand.
Evolutionary Flexibility of Ribosome Biogenesis in Bacteria.
Amikura K, Ishii SI, Shimizu Y … +1 more , Suzuki S
Mol Biol Evol · 2025 Oct · PMID 41277349 · Full text
Ribosomes are essential for protein synthesis and require ribosome biogenesis factors for assembly. To uncover the evolutionary diversity of ribosome biogenesis, we analyzed over 30,000 bacterial genomes and revealed tha...
Ribosomes are essential for protein synthesis and require ribosome biogenesis factors for assembly. To uncover the evolutionary diversity of ribosome biogenesis, we analyzed over 30,000 bacterial genomes and revealed that Candidate Phyla Radiation, also known as the phylum Patescibacteria, characterized by reduced genomes and smaller ribosomes, has about half the average number of ribosome biogenesis factors compared with non-Candidate Phyla Radiation bacteria. Notably, key ribosome biogenesis factors such as der, obgE, and rbfA, considered indispensable, are conserved in only around 20%-70% of Candidate Phyla Radiation genomes. Since such repertoires were not observed in reduced genomes of other phyla, Candidate Phyla Radiation presumably diverged early in bacterial evolution. We further confirmed that ribosomal structural changes correlate with reduced ribosome biogenesis factor, evidencing co-evolution between ribosome biogenesis factor and the ribosome. These findings suggest that ribosomal biogenesis is more flexible than recognized, and the small cell and genome sizes of Candidate Phyla Radiation bacteria and their early divergence may influence the unusual repertoires of ribosome biogenesis factors.
Accelerated Mitochondrial Genome Evolution in Parasitic Barnacles Driven by Adaptive and Non-adaptive Responses.
Jung J, Song S, Kim MY … +5 more , Kwak H, Chan BKK, Cha SS, Hwang UW, Park JK
Mol Biol Evol · 2025 Nov · PMID 41277223 · Full text
Parasitic lifestyles often impose profound evolutionary pressures, affecting molecular evolution through both adaptive and non-adaptive mechanisms. Among barnacles (subclass Cirripedia), the obligate parasitic Rhizocepha...
Parasitic lifestyles often impose profound evolutionary pressures, affecting molecular evolution through both adaptive and non-adaptive mechanisms. Among barnacles (subclass Cirripedia), the obligate parasitic Rhizocephala differ markedly from their filter-feeding thoracican relatives in morphology, ecology, and life history. However, how the shift to parasitism has shaped mitochondrial genome evolution within Cirripedia remains unclear. Here, we present the first comprehensive comparative analysis of mitochondrial genomes between parasitic and non-parasitic barnacles, including three newly sequenced and one unpublished species of parasitic Rhizocephala, a clade whose mitochondrial genomes had not been characterized until now. Phylogenomic and molecular evolutionary analyses reveal that Rhizocephala species exhibit extremely long branches likely attributed to the clade-specific tempo (high substitution rate) and mode (selection pressure) of mtDNA sequence evolution associated with their parasitic lifestyle. A two-cluster molecular clock test reveals significantly elevated substitution rates across rhizocephalans, consistent with reduced effective population sizes (Ne) linked to their opportunistic, host-dependent life cycles. We also detect signatures of positive selection in protein-coding genes encoding key components of the electron transport chain complexes III and IV. Structural modeling highlights amino acid substitutions at functionally critical sites for electron transfer and proton pumping, suggesting adaptive modifications to mitochondrial bioenergetics under hypoxic conditions within host tissues. Together, our findings underscore that both non-adaptive (genetic drift, relaxed selection) and adaptive (positive selection) processes have driven the rapid sequence divergence of mitochondrial genomes in parasitic Rhizocephala. Further experimental study is needed to elucidate how mitochondrial and nuclear-encoded subunits of oxidative phosphorylation coevolve in this specialized parasitic group.
Ancestral Sequence Reconstruction Provides Insights into the Structural Diversification and Neofunctionalization of T-superfamily Conotoxins in Conus.
Espino SS, Koch TL, Gajewiak J … +4 more , Giglio ML, Watkins M, Safavi-Hemami H, Olivera BM
Mol Biol Evol · 2025 Nov · PMID 41275382 · Full text
Due to their remarkable diversity and rapid evolution, conotoxins-peptide toxins from predatory marine cone snails-provide a powerful system for exploring how gene diversification may contribute to the development of lin...
Due to their remarkable diversity and rapid evolution, conotoxins-peptide toxins from predatory marine cone snails-provide a powerful system for exploring how gene diversification may contribute to the development of lineage-specific adaptations. We previously demonstrated that 2-loop Tau conotoxins represent an evolutionary innovation associated with mollusk-hunting behaviors in cone snails. Here, we investigate the evolutionary history of these toxins as a model to understand the mechanism of ancestral gene neofunctionalization, which may have contributed to the emergence of mollusk-hunting in cone snails. Using ancestral sequence reconstruction, we present a model in which ancestral T-superfamily conotoxins neofunctionalized into the 2-loop Tau conotoxins. Predicted ancestral sequences reveal an intermediate structure between the classic T-superfamily conotoxins and the derived 2-loop Tau forms. Notably, these ancestral intermediates acquired a new cysteine scaffold that facilitated a structural transition from a globular to a ribbon fold. This conformational shift was followed by sequence-level changes that presumably enhanced activity against molecular targets in mollusks. We propose that the emergence of 2-loop Tau conotoxins may have been one factor that contributed to the emergence of molluscivory, providing insight into how gene innovation may underlie ecological diversification.
Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More).
Mirchandani C, Enbody E, Sackton TB … +1 more , Corbett-Detig R
Mol Biol Evol · 2025 Nov · PMID 41275381 · Full text
The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversity (π) and divergence (dxy). Accurate estimates of diversity require knowle...
The increasing scale of population genomic datasets presents computational challenges in estimating summary statistics such as nucleotide diversity (π) and divergence (dxy). Accurate estimates of diversity require knowledge of missing data, and existing tools require all-site VCFs. However, generating these files is computationally expensive for large datasets. Here, we introduce Callable Loci And More (clam), a tool that leverages callable loci-determined from depth information-to estimate population genetic statistics using a variant-only VCF. This approach offers improvements in storage footprint and computational performance compared to contemporary methods. We validate clam's accuracy using simulated data, demonstrating that it produces estimates of π, dxy, and fixation index (FST) identical to those from all-site VCF approaches. We then benchmark clam using a large muskox dataset and demonstrate that it produces accurate estimates of π while substantially reducing runtime requirements compared to current best-practice methods. clam provides an efficient and scalable alternative for population genomic analyses, facilitating the study of increasingly large and diverse datasets. clam is available as a standalone program and integrated into snpArcher for efficient reproducible population genomic analysis.
Bayesian Model Averaging of Parametric Coalescent Models for Phylodynamic Inference.
Xu Y, Chen K, Xie D … +1 more , Drummond AJ
Mol Biol Evol · 2025 Nov · PMID 41272398 · Full text
Bayesian phylodynamic models have become essential for reconstructing population history from genetic data, yet their accuracy depends crucially on choosing appropriate demographic models. To address uncertainty in model...
Bayesian phylodynamic models have become essential for reconstructing population history from genetic data, yet their accuracy depends crucially on choosing appropriate demographic models. To address uncertainty in model choice, we introduce a Bayesian model averaging (BMA) framework that integrates multiple parametric coalescent models-including constant, exponential, logistic, and Gompertz growth-along with their "expansion" variants that account for non-zero ancestral populations. Implemented in a Bayesian setting with Metropolis-coupled Markov chain Monte Carlo, this approach allows the sampler to switch among candidate growth functions, thereby capturing demographic histories without having to pre-specify a single model. Simulation studies verify that the logistic and Gompertz models may require specialized sampling strategies such as adaptive multivariate proposals to achieve robust mixing. We demonstrate the performance of these models on datasets simulated under different substitution models, and show that joint inference of genealogy and population parameters is well-calibrated when properly incorporating correlated-move operators and BMA. We then apply this method to two real-world datasets. Analysis of Egyptian Hepatitis C virus sequences indicates that models with a founder population followed by a rapid expansion are well supported, with a slight preference for Gompertz-like expansions. Our analysis of a metastatic colorectal cancer single-cell dataset suggests that exponential-like growth is plausible even for an advanced stage cancer patient. We believe this highlights that tumor subclones may retain substantial proliferative capacity into the later stages of the disease. Overall, our unified BMA framework reduces the need for restrictive model selection procedures and can also provide deeper biological insights into epidemic spread and tumor evolution. By systematically integrating multiple growth hypotheses within a standard Bayesian setting, this approach naturally avoids overfitting and offers a powerful tool for inferring population histories across diverse biological domains.
Modeling the Evolution of Ultraconserved Elements by Indels.
Biller P
Mol Biol Evol · 2025 Nov · PMID 41272394 · Full text
Ultraconserved elements are segments of DNA that are identical or nearly identical in distantly related species. Finding 100% identity over long evolutionary times is unexpected, but pioneering research in human-mouse pa...
Ultraconserved elements are segments of DNA that are identical or nearly identical in distantly related species. Finding 100% identity over long evolutionary times is unexpected, but pioneering research in human-mouse pairwise alignment uncovered something even more puzzling: these elements are not as rare as previously suspected. Furthermore, their sizes are distributed as a power-law, a feature that cannot be explained by standard models of genome evolution where conservation is expected to decay exponentially. Despite the power-law behavior having been reported and investigated in a wide variety of biological and physical contexts, from cell-division to protein family evolution, why it appears in the size distribution of ultraconserved elements remains elusive. To address this question, I propose a model of DNA sequence evolution by mutations of arbitrary length based on a classical integro-differential equation that arises in various applications in biology. The model captures the ultraconserved size distribution observed in pairwise alignments between human and 40 other vertebrates, encompassing more than 400 million years of evolution, from chimpanzee to zebrafish. I also show that the model can be used to predict other important aspects of genome evolution, such as indel rates and conservation in functional classes.
Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage.
Kwun MJ, Ion AV, Apagyi KJ … +1 more , Croucher NJ
Mol Biol Evol · 2025 Oct · PMID 41269752 · Full text
Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recombination (HR). This process may provide an evolutionary advantage to cells...
Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recombination (HR). This process may provide an evolutionary advantage to cells through enabling "chromosomal curing": the deletion of integrative mobile genetic elements (MGEs). However, many such MGEs are sensitive to RecA-DNA filaments, triggering activation of a lifecycle that may enable them to evade HR-mediated deletion. Despite >40% of isolates containing prophage integrated at a site that inhibits transformation, 3 representative prophages were identified in naturally competent pneumococci to test this hypothesis. These encompassed representatives with C1-type and ImmAR-type regulatory systems, found in almost all pneumococcal prophages. All 3 prophages were deleted by HR with an efficiency similar to the transfer of base substitutions. Mutations that impaired a C1-regulated prophage increased this deletion rate, reflecting this element being activated by RecA-DNA filaments imported during transformation, likely preferentially killing cells that induce competence. ImmAR-regulated prophage instead responded to transient stimuli by excising as deletion-resistant pseudolysogens, only driving cell lysis in response to sustained stimuli. This was likely a consequence of these prophages reacting to multiple signals, as they differed in their response to both RecA and the DNA-binding protein and competence repressor DprA. One prophage constitutively elevated host DprA levels, thereby reducing transformation by preventing induction of the competence machinery. Hence, these data are consistent with an evolutionary arms race between prophage and the competence machinery, resulting in bacterial diversification though HR being impeded by MGEs preventing their own elimination from the chromosome.
SAI: A Python Package for Statistics for Adaptive Introgression.
Huang X, Chen S, Hackl J … +1 more , Kuhlwilm M
Mol Biol Evol · 2025 Nov · PMID 41258824 · Full text
Adaptive introgression is an important evolutionary process, which can be identified with widely used summary statistics, such as the number of uniquely shared sites and the quantile of the derived allele frequencies in...
Adaptive introgression is an important evolutionary process, which can be identified with widely used summary statistics, such as the number of uniquely shared sites and the quantile of the derived allele frequencies in such sites. However, these as well as more recently developed statistics such as D+ and Danc, still lack accessible implementations. Here, we present SAI, a Python package for computing these statistics along with a new statistic, DD, and demonstrate its application on 2 datasets. First, using the 1000 Genomes Project data, we replicated previously reported candidate regions and identified additional ones, including a region detected by studies using supervised deep learning. Second, we investigated bonobo introgression into central chimpanzees and identified candidate genes, finding one region that overlaps a high-frequency Denisovan-introgressed haplotype block reported in modern Papuans. This is an intriguing co-occurrence across divergent lineages, underscoring the role of adaptive introgression in evolution.
Robust and Efficient Confidence Limits for Phylogenomic Inference of Organismal Relationships.
Sharma S, Kumar S
Mol Biol Evol · 2025 Nov · PMID 41250902 · Full text
Phylogenomic data are indispensable for establishing reliable relationships needed to build a robust Tree of Life. The superalignment approach concatenates hundreds or thousands of genomic segments, providing a straightf...
Phylogenomic data are indispensable for establishing reliable relationships needed to build a robust Tree of Life. The superalignment approach concatenates hundreds or thousands of genomic segments, providing a straightforward, computationally efficient, and effective means of inferring phylogenies. However, the standard bootstrap method can produce overly confident support for incorrect inferences based on superalignments. It fails to account for the heterogeneity in phylogenetic signals across the data, which is caused by incomplete lineage sorting (ILS), data errors, and other biological processes. To detect such erroneous inferences, researchers need to produce and deliberate on the concordance of inferences derived from many complex and computationally demanding analyses that require knowledge of data partitions. This study demonstrates that analyzing phylogenomic subsamples with bootstrap upsampling overcomes the overconfidence drawback of the superalignment approach. We found that bootstrapping multiple small, randomly selected site subsets can detect the presence of phylogeny variation signals across the dataset, similar to that detected using data partitions. We present the Net Bootstrap Support (NBS) approach that accounts for this phylogenetic variation in the estimates of bootstrap confidence. NBS values showed comparable performance to multispecies coalescent analyses in the presence of ILS and surpassed it for datasets simulated with gene tree estimation errors. NBS analyses of phylogenomic data from rodents, fungi, and carnivorous plants corroborated the performance observed in simulated datasets and even mitigated overconfidence resulting from some data errors. NBS calculations are computationally efficient, with low memory consumption and high computational time savings, making the NBS approach well suited for big data molecular phylogenetics on both desktops and high-performance computing systems.
Human Population Genetic History and Evolutionary Dynamics on the Eastern Tibetan Plateau.
He G, Duan S, Chen G … +10 more , Wang CC, Yuan H, Li X, Sun Q, Bu F, Cheng J, Lu Y, Liu C, Yuan H, Wang M
Mol Biol Evol · 2025 Oct · PMID 41243841 · Full text
The origins of Tibeto-Burman populations on the eastern Tibetan Plateau (TP), especially within the Tibetan-Yi Corridor, remain unresolved. We sequenced whole genomes of 293 individuals from 21 Tibeto-Burman-speaking gro...
The origins of Tibeto-Burman populations on the eastern Tibetan Plateau (TP), especially within the Tibetan-Yi Corridor, remain unresolved. We sequenced whole genomes of 293 individuals from 21 Tibeto-Burman-speaking groups and genotyped 799 individuals from 60 Sino-Tibetan-speaking groups to reconstruct regional population history. Our analyses reveal fine-scale substructure and extensive admixture along the underrepresented Tibetan-Yi and Hexi corridors, driven by gene flow from Eastern Eurasian rice/millet farmers and Western Eurasian steppe pastoralists. We estimate that Tibetans diverged from their common ancestors with Han Chinese in the early Neolithic (∼9.9 kya), followed by differentiation among Tibetan-Yi Corridor populations in the middle Neolithic (∼4.6 kya). These splits coincide with distinct cultural trajectories that produced a pronounced north-south genetic structure among Tibeto-Burman groups. QpAdm modeling indicates that northern Tibeto-Burman speakers derive most of their ancestry from Neolithic millet farmers. Along the Hexi Corridor, an essential axis of Eurasian connectivity, fine-scale analyses show a dominant legacy of millet-farming populations with additional ancestry from incoming Eurasian herders. Together, these findings clarify the settlement history of eastern TP populations and underscore the role of geographic and cultural corridors in structuring ancient intercontinental gene flow across Eurasia.
Pan-Angiosperm Analysis of the CLE Signaling Peptide Gene Family Unveils Paths, Patterns, and Predictions of Paralog Diversification.
Gentile I, Santo Domingo M, Zebell SG … +2 more , Fitzgerald B, Lippman ZB
Mol Biol Evol · 2025 Oct · PMID 41231740 · Full text
The compositions of conserved gene families often vary widely between species, complicating predictions and experimental tests of shared versus distinct functions, especially in families shaped by extensive duplication,...
The compositions of conserved gene families often vary widely between species, complicating predictions and experimental tests of shared versus distinct functions, especially in families shaped by extensive duplication, redundancy, and paralog diversification. The plant CLV3/EMBRYO-SURROUNDING REGION (CLE) small signaling peptide family exemplifies these challenges. Although genetic studies in model systems have identified shared roles for a few CLE genes and species-specific redundancies, an evolutionary analysis of the entire family over deep time could empower predictive and experimental dissections of functions obscured by redundancy. We developed a scanning pipeline that de novo annotated CLE genes from 2,000 genomes representing 1,000 species, uncovering thousands of previously undetected family members and producing a comprehensive view of the family's evolution and sequence diversification over 140 million years. Computational modeling of coding and cis-regulatory regions predicted lineage-specific asymmetries in paralog redundancy, stemming from ancestral amino acids in the functional core of the dodecapeptide and partial conservation of promoter elements. We tested these predictions using two genome-editing strategies in Solanaceae. Base-editing of deeply conserved residues in the CLV3 dodecapeptide and its paralogs across three species confirmed their critical roles in repressing stem cell proliferation, and multiplex CRISPR knockouts of the 52 tomato CLE genes resolved simple and complex redundancies, revealing previously uncharacterized regulators of shoot architecture and plant size. These findings show how both peptide and cis-regulatory erosion shape CLE redundancy and provide a framework for detecting and translating deep evolutionary signals into testable genetic hypotheses across compositionally complex gene families.
Tandem Duplication of Serpin Genes Yields Functional Variation and Snake Venom Inhibitors.
Ward MS, Holding ML, Haynes LM … +3 more , Margres MJ, Matocq MD, Ginsburg D
Mol Biol Evol · 2025 Oct · PMID 41218074 · Full text
Tandem duplication of genes can play a critical role in the evolution of functional novelty, yet our understanding is limited concerning the role of gene duplication in coevolution between species. Much is known about th...
Tandem duplication of genes can play a critical role in the evolution of functional novelty, yet our understanding is limited concerning the role of gene duplication in coevolution between species. Much is known about the evolution and function of tandemly duplicated snake venom genes, however, the potential of gene duplication to fuel venom resistance within prey species is poorly understood. The SERPINA subfamily of genes produces globular serine protease inhibitors and carrier molecules, and SERPINA1 has previously been shown to inhibit snake venom serine proteases. In this study, we characterize patterns of duplication within the tandem array of SERPINA, documenting trends in copy number evolution between species. We find the hallmarks of rapid birth-death evolution of SERPINA1-like and SERPINA3-like genes within and between rodent lineages, and evidence for diversifying selection acting on rodent genes. To explore the functional significance of copy number evolution, we recombinantly expressed the full set of 12 paralogous duplicates of SERPINA3 found in the genome of the Big-eared woodrat (Neotoma macrotis), a species known for resistance to protease-rich rattlesnake venoms. Two SERPINA3 paralogs inhibited venom serine proteases, indicating that these proteins may serve as resistance factors. In addition, functional variation is apparent among paralogs, including neofunctionalization to inhibit both chymotrypsin-like and trypsin-like proteases simultaneously for one venom-inhibiting paralog. Our results provide further evidence that the rapid evolution of SERPINA1 and SERPINA3 gene copy number across rodents has adaptive potential by producing functionally diverse venom inhibitors.
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