Genome Biology And Evolution[JOURNAL]
Sun
200 papers
Genome Skimming Illuminates Hidden Species Diversity and Symbiodiniaceae Associations in East Pacific Pocillopora Corals.
Connelly MT, Glynn VM, Cornejo A … +10 more , Villalobos-Cubero T, Kleypas J, Alvarado JJ, Brandt M, Logan CA, Palacio-Castro AM, Flot JF, Leray M, Connolly SR, Quattrini AM
Genome Biol Evol · 2026 Jan · PMID 41339007 · Full text
Biodiversity conservation relies upon accurate species taxonomy to support decision-making. Stony corals in the genus Pocillopora are critical ecosystem engineers in the Eastern Tropical Pacific (ETP); however, Pocillopo...
Biodiversity conservation relies upon accurate species taxonomy to support decision-making. Stony corals in the genus Pocillopora are critical ecosystem engineers in the Eastern Tropical Pacific (ETP); however, Pocillopora species diversity in the region is still unresolved due to high phenotypic plasticity, lack of diagnostic morphological characters, and low-resolution genetic markers used in previous studies. To address this gap, we leveraged low-coverage whole-genome sequencing for 342 Pocillopora coral samples collected from Panamá, Costa Rica, Colombia, Ecuador, and Clipperton Atoll (France). Sequence data were used to recover mitochondrial genomes and barcode loci, ultraconserved elements, and genome-wide single-nucleotide polymorphisms (SNPs) for species delimitation. Together, our data revealed the existence of four distinct Pocillopora species in the ETP, corresponding to the nominal species P. effusa (Veron, 2000), P. meandrina Dana, 1846, P. capitata Verrill, 1864, and P. lacera Verrill, 1869. Two P. capitata population subclusters with moderate genetic differentiation were separated between offshore islands and continental sites, and individual colonies with signatures of admixture between P. effusa and P. lacera were identified at Isla del Coco, Costa Rica. Additionally, Pocillopora-associated algal symbiont community profiling identified Cladocopium and Durusdinium as dominant genera that varied according to the host species, with P. lacera demonstrating higher specificity for associations with Cladocopium. This study highlights the power of genome skimming as an affordable, high-resolution approach to rapidly assess coral species diversity and algal symbiont associations, thereby empowering marine conservation.
A Chromosome-Level Reference Assembly and Annotation for the White-Faced Plover (Charadrius dealbatus) Genome.
Zeng Y, Tu J, Ho H … +6 more , Niu X, Lin H, Cheng Y, Song Z, Zheng C, Liu Y
Genome Biol Evol · 2025 Nov · PMID 41332310 · Full text
The Charadrius genus encompasses 36 species, each exhibiting a wide array of life histories and behaviors. Conspecific variations in mating systems and migratory behavior also exist in widely distributed species, such as...
The Charadrius genus encompasses 36 species, each exhibiting a wide array of life histories and behaviors. Conspecific variations in mating systems and migratory behavior also exist in widely distributed species, such as the Kentish plover (Charadrius alexandrinus). Recent years have witnessed the establishment of new species from distinct populations, such as the identification of the snowy plover (C. nivosus) and the white-faced plover (C. dealbatus) as separate species from the Kentish plover (C. alexandrinus) species complex. Studies on the phylogenetic relationships across the entire genus, as well as population genetics and adaptation to various climatic conditions, necessitate the support of a high-quality reference genome. Here, we successfully assembled the first high-quality genome for the white-faced plover. The genome size is 1.25 Gb, anchored on 31 chromosomes, with a contig-level N50 size of 23.62 Mb and a scaffold-level N50 of 84.07 Mb. The completeness of the C. dealbatus genome assembly is supported by the 97.3% completeness (BUSCO) and ultraconserved element (UCE) (4,889/5,041; 97.0%) loci retrieved. A total of 17,641 protein-coding genes were predicted among 19,648 pseudogenes, and the completeness of the genome annotation is 94.7% (BUSCO). The chromosome-level genome provides the availability of permanent genomic resources for advancing evolutionary and conservation genomic studies on the genus Charadrius.
Chromosomal Rearrangements and Transposable Elements in Locally Adapted Island Drosophila.
Turner BA, Erlenbach TR, Stewart NB … +3 more , Reid RW, Moore CC, Rogers RL
Genome Biol Evol · 2026 Jan · PMID 41332251 · Full text
Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes, inducing de novo gene formation, or altering gene expression. Here, we inve...
Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes, inducing de novo gene formation, or altering gene expression. Here, we investigate rearrangements evolutionary role during habitat shifts in two locally adapted populations, D. santomea and D. yakuba, who have inhabited the island São Tomè for 500,000 and 10,000 years, respectively. Using the D. yakuba-D. santomea species complex, we identified 16,480 rearrangements in the two island populations and the ancestral mainland African population of D. yakuba. We find a disproportionate association with TEs, with 83.5% of rearrangements linked to TE insertions or TE-facilitated ectopic recombination. Using significance thresholds based on neutral expectations, we identify 383 and 468 significantly differentiated rearrangements in island D. yakuba and D. santomea, respectively, relative to the mainland population. Of these, 99 and 145 rearrangements also showed significant differential gene expression, highlighting the potential for adaptive solutions from rearrangements and TEs. Within and between island populations, we find significantly different proportions of rearrangements originating from new mutations versus standing variation depending on TE association, potentially suggesting adaptive genetic mechanisms differ based on the timing of habitat shifts. Functional analyses of rearrangements most likely driving local adaptation revealed enrichment for stress response pathways, including UV tolerance and DNA repair, in high-altitude D. santomea. These findings suggest that chromosomal rearrangements may act as a source of genetic innovation, and provides insight into evolutionary processes that SNP-based analyses might overlook.
DNA Circles as Vehicles for Genes to Evade Chromosomal Discipline.
Rojas-Triana M, Boomsma JJ, Regenberg B
Genome Biol Evol · 2025 Nov · PMID 41330888 · Full text
In this Perspective article, we follow the journey of a gene that breaks free from its stringent chromosomal transmission dynamics to become an independently multiplying agent on so-called extrachromosomal circular DNA (...
In this Perspective article, we follow the journey of a gene that breaks free from its stringent chromosomal transmission dynamics to become an independently multiplying agent on so-called extrachromosomal circular DNA (ecDNA/eccDNA). We discuss how the release of a gene from its chromosomal anchor can affect its dosage, regulatory context, and potential evolutionary trajectory before examining the phenotypic implications for unicellular and multicellular eukaryotes that transmit genes on circular DNA. We also briefly explore the fundamental difference between circularized genes in flowering plants (angiosperms) and mammals (primarily cancer) concerning somatic and germline inheritance.
Comparative Genomics of the Testacea Group of Drosophila Reveals Introgression and Variation in Chromosome Size and Structure.
Erlenbach T, Gawryluk RMR, Perlman SJ … +2 more , Unckless RL, Dyer KA
Genome Biol Evol · 2025 Nov · PMID 41327877 · Full text
Comparative genomic analyses among closely related species provide an opportunity to assess their evolutionary history. The relatedness between species can depend on a variety of factors, including reproductive isolation...
Comparative genomic analyses among closely related species provide an opportunity to assess their evolutionary history. The relatedness between species can depend on a variety of factors, including reproductive isolation, introgression, and incomplete lineage sorting, and this can impact divergence across the genome. Here, we use a combination of long- and short-read sequencing and HI-C scaffolding to assemble genomes for each of the four species in the testacea species group of Drosophila, including D. testacea, D. orientacea, D. neotestacea, and D. putrida, and its outgroup, D. bizonata. First, among species, we find many structural rearrangements across the genome as well as a large size difference in the dot chromosome that we infer is due to the expansion of repetitive elements. Second, we assess phylogenetic discordance and uncover a difference in the phylogeny inferred from genes on Muller E and the mitogenome relative to the rest of the genome, which may be due to recent hybridization. Lastly, we assess the rate of molecular evolution of genes shared across all species and identify genes evolving at different rates across the phylogeny. Our results present genomic resources for this species group and begin to probe into some of the evolutionary characteristics that contribute to variation in genome structure, while highlighting the need for high-quality genome resources to fully capture and understand the evolutionary history among closely related species.
A Draft Genome Assembly of the Antarctic Springtail Cryptopygus antarcticus and Diversity of Glycoside Hydrolase Genes.
Jeon D, Song CU, Choi H … +5 more , Youn J, Jung H, Lee YH, Lee SH, Eyun SI
Genome Biol Evol · 2025 Nov · PMID 41321109 · Full text
The Antarctic springtail Cryptopygus antarcticus Willem (family Isotomidae) is a representative arthropod species of the maritime Antarctic environment that could be used as an important organism for further study of ani...
The Antarctic springtail Cryptopygus antarcticus Willem (family Isotomidae) is a representative arthropod species of the maritime Antarctic environment that could be used as an important organism for further study of animal evolution and adaptation. Despite the biological and ecological peculiarities that distinguish them from the majority of collembolan species, our understanding of the genetic background behind their success in an extreme habitat remains unclear. We present the first high-quality draft genome of C. antarcticus assembled from in-depth whole genome and transcriptome sequencing data obtained from both long-read and short-read sequencing platforms. The genome was 103.6 Mb in size with 81 scaffolds and a scaffold N50 of 3.4 Mb, appearing to have a smaller genome than that of hitherto known collembolan genomes. Following protein-coding gene prediction and annotation analyses, 19,808 non-redundant genes were identified, representing 97.0% Benchmarking Universal Single-Copy Ortholog (BUSCO) gene coverage. Subsequent Gene Ontology (GO) functional enrichment analyses revealed that significantly expanded gene families were mainly associated with cell cycle regulation and changes in cell states or activities, while contracted gene families were related to the inhibition of germ cell proliferation. Several glycoside hydrolase family genes were identified in C. antarcticus, some of which may have evolved to facilitate their survival in the extreme environment. These findings suggest that the evolution of these gene families is related to their adaptation to the habitat's extreme conditions.
Comparative Genomics Reveals Multipartite Genomes Undergoing Loss in the Fungal Endosymbiotic Genus Mycetohabitans.
Abbot B, Field S, Carneal L … +5 more , White RA, Buchan A, West C, Lee L, Carter ME
Genome Biol Evol · 2025 Nov · PMID 41320831 · Full text
Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding the trajectory of su...
Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding the trajectory of such a genome has largely been done through the study of animal-associated bacteria, especially insect endosymbionts. Yet, endofungal bacteria provide another natural experimental model for investigating how microbial genomes change when living inside of a host cell. Mycetohabitans spp. are culturable bacterial endosymbionts of the Mucoromycota fungus Rhizopus microsporus. To investigate the genome dynamics resulting from the endohyphal nature of this emerging model genus, we long-read sequenced and assembled new complete genomes to combine with previous assemblies, creating a global dataset of 28 complete Mycetohabitans genomes. All genomes were between 3.3 and 3.9 Mbp in size and were multipartite, structured into two conserved replicons with some strains having an additional plasmid. Based on evolutionary rate and gene content analysis of the different replicons, we termed the two major ones a chromosome and chromid. The differential presence of a third, mobilome-rich plasmid in some strains and the proliferation of transposable elements provide putative mechanisms for recombination or gene loss. The conservation of intact prophage and putative toxin-antitoxin systems and extensive enrichment of secondary metabolite clusters in the Mycetohabitans genomes highlight the dynamic nature of this reducing genome. With fungal-bacterial symbioses becoming increasingly apparent phenomena, lessons learned from this symbiosis will inform our understanding of bacterial adaptation to novel hosts and the process of microbe-microbe coevolution.
Genome Assembly of Gangetic Dolphin (Platanista gangetica) Reveals Signature of Regressive Evolution.
Sharma SP, Ghazi MG, Das GC … +3 more , Usmani AA, Badola R, Hussain SA
Genome Biol Evol · 2025 Nov · PMID 41320830 · Full text
The Gangetic dolphin (Platanista gangetica), an endangered freshwater cetacean endemic to the Indian subcontinent, exhibits distinctive morphological and physiological adaptations to riverine habitats. Here, we present a...
The Gangetic dolphin (Platanista gangetica), an endangered freshwater cetacean endemic to the Indian subcontinent, exhibits distinctive morphological and physiological adaptations to riverine habitats. Here, we present a high-quality draft genome assembly of P. gangetica. The assembled genome is 2.53 Gb in size, with a scaffold N50 of 116.1 Mb and a scaffold L50 of 9. Genome completeness assessed using BUSCO against the mammalia_odb10 dataset indicated a genome completeness of 97.73%. We predicted 27,983 protein-coding genes, and 19,616 were confidently mapped to eggNOG ortholog groups. Phylogenetic reconstruction placed the divergence of P. gangetica from the common bottlenose dolphin (Tursiops truncatus) at approximately 30.9 million years ago. Furthermore, we identified 66 positively selected genes in the P. gangetica genome possibly linked to key traits, including sensory adaptations such as vision loss and enhanced hearing, cardiovascular and metabolic regulation, limb modification, and cognitive function. Demographic inference revealed historical fluctuations in effective population size, with a marked decline during the Last Glacial Maximum (∼20 to 30 kya), likely driven by climatic shifts and habitat changes. This assembly represents a substantial improvement over previously available genomes within the Platanista genus and provides an essential resource for advancing our understanding of freshwater cetacean evolution and forms a critical foundation for population genomic studies to inform conservation and management strategies.
Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.
Peede D, Cousins T, Durvasula A … +5 more , Ignatieva A, Kovacs TGL, Nieto A, Puckett EE, Chevy ET
Genome Biol Evol · 2026 Jan · PMID 41315008 · Full text
Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Markovian coalescent (...
Genomes contain the mutational footprint of an organism's evolutionary history, shaped by diverse forces including ecological factors, selective pressures, and life history traits. The sequentially Markovian coalescent (SMC) is a versatile and tractable model for the genetic genealogy of a sample of genomes, which captures this shared history. Methods that utilize the SMC, such as PSMC and MSMC, have been widely used in evolution and ecology to infer demographic histories. However, these methods ignore common biological features, such as gene flow events and structural variation. Recently, there have been several advancements that widen the applicability of SMC-based methods: inclusion of an isolation with migration model, integration with the multi-species coalescent, incorporation of ecological life history traits (such as selfing and dormancy), and many computational advances in applying these models to data. We give an overview of the SMC model and its various recent extensions, discuss examples of biological discoveries through SMC-based inference, and comment on the assumptions, benefits and drawbacks of various methods.
De Novo Genes: Current Status and Future Goals.
Casola C, Luria V, Vakirlis N … +1 more , Zhao L
Genome Biol Evol · 2025 Nov · PMID 41313722 · Full text
The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6 to 9, 2023, represented the first-ever opportunity for scientists studying the...
The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6 to 9, 2023, represented the first-ever opportunity for scientists studying the evolution and biology of de novo genes to gather through a dedicated meeting and discuss about groundbreaking discoveries in this emerging and exciting field of gene evolution. In this perspective, we discuss recent advances and major open questions in de novo gene emergence and evolution that were presented at the SMBE satellite meeting, as well as some of the key recent findings published before or since the conference. These key themes include de novo gene identification, function, and evolution, what we are learning about de novo genes from experimental analyses of random peptides, de novo gene birth and microproteins, and the role of de novo genes in human disease.
Revisiting the Glucose Kinase Superfamily: From Origins to the Evolution of Metabolism.
Jardim-Messeder D, Barzilai L, Sachetto-Martins G
Genome Biol Evol · 2025 Nov · PMID 41313354 · Full text
The glucose kinase superfamily, which includes enzymes such as hexokinases and glucokinases, plays a central role in energy metabolism across all domains of life. This study explores their evolutionary origins, functiona...
The glucose kinase superfamily, which includes enzymes such as hexokinases and glucokinases, plays a central role in energy metabolism across all domains of life. This study explores their evolutionary origins, functional diversity, and adaptation to ecological niches, tracing their journey from early life forms to modern organisms. Recent advances reveal how these enzymes have diversified, with some retaining broad specificity, while others evolved high substrate specificity, reflecting the metabolic demands of their environments. By integrating phylogenetic, structural, and functional analyses, this work sheds light on the evolutionary pressures that shaped these enzymes and their role in metabolic innovation, not only deepening our understanding of life's biochemical evolution but also connecting ancient metabolic pathways to contemporary cellular processes.
Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.
Tabatabaee Y, Zhang C, Arasti S … +1 more , Mirarab S
Genome Biol Evol · 2025 Oct · PMID 41293994 · Full text
Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting,...
Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting, gene duplication and loss, and horizontal gene transfer can complicate the estimation of species tree branch lengths. While several tools exist for estimating the topology of a species tree addressing various causes of gene tree discordance, much less attention has been paid to branch length estimation on multi-locus datasets. For single-copy gene trees, some methods are available that summarize gene tree branch lengths onto a species tree, including coalescent-based methods that account for heterogeneity due to incomplete lineage sorting. However, no such branch length estimation method exists for multi-copy gene family trees that have evolved with gene duplication and loss. To address this gap, we introduce the CASTLES-Pro algorithm for estimating species tree branch lengths while accounting for both gene duplication and loss and incomplete lineage sorting. CASTLES-Pro improves on the existing coalescent-based branch length estimation method CASTLES by increasing its accuracy for single-copy gene trees and extending it to handle multi-copy ones. Our simulation studies show that CASTLES-Pro is generally more accurate than alternatives, eliminating the systematic bias toward overestimating terminal branch lengths often observed when using concatenation. Moreover, while not theoretically designed for horizontal gene transfer, we show that CASTLES-Pro is relatively robust to random horizontal gene transfer, though its accuracy can degrade at the highest levels of horizontal gene transfer.
Haplotype-Resolved Chromatin Conformation Data Reveals Relationship Between Transposable Elements and Chromosomal Pairing.
Genutis LK, Villanueva P, Graze RM … +3 more , AlHaj Abed J, McIntyre LM, Nuzhdin SV
Genome Biol Evol · 2025 Nov · PMID 41293827 · Full text
Chromosomal structural changes happen when genomic stability is compromised, such as in disease or in species hybrids. In these contexts, diminished control of repetitive elements has been reported, but the reasons for t...
Chromosomal structural changes happen when genomic stability is compromised, such as in disease or in species hybrids. In these contexts, diminished control of repetitive elements has been reported, but the reasons for this are not yet well understood. There are causal associations between repetitive elements and phenotypes such as disease progression, leading us to the hypothesis that chromosomal structure may be affected by transposable elements (TEs). In an intraspecific hybrid Drosophila melanogaster cell line (PnM), the degree of pairing among trans homologous chromosomes was affected by the presence of nearby TEs, in particular, LINE and LTR elements, such as Baggins1 or Gypsy. Chromosomal pairing was significantly lower in windows containing TEs than in windows without any TEs. Pairing was also affected by TEs in mouse, which suggests a possible general association between TEs and pairing that is highly conserved.
Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.
Seçkin E, Colinet D, Sarti E … +1 more , Danchin EGJ
Genome Biol Evol · 2025 Nov · PMID 41289037 · Full text
Genes that lack identifiable homologs in other species have been an intriguing and interesting topic of research for many years. These so-called orphan genes were first studied in yeast and since then, they have been fou...
Genes that lack identifiable homologs in other species have been an intriguing and interesting topic of research for many years. These so-called orphan genes were first studied in yeast and since then, they have been found in many other species. This has fostered a whole field of research aiming at tracing back their evolutionary origin and functional significance. Orphan genes represent an important part of protein-coding genes in many species. Their presence was initially mainly hypothesized to result from high divergence from a pre-existing gene, with duplications or horizontal gene transfer facilitating their accelerated evolution. More recently, their possible de novo emergence from nongenic regions has gained particular interest. Several orphan genes are predicted to be involved in reproduction, while others are involved in specific developmental stages, in adaptation mechanisms such as freeze protection or even human disease. However, there is currently no unified resource or synthesis that brings together existing knowledge about how prevalent orphan genes are across different species and what their roles might be. In this review, we focus on orphan genes in animals and fungi. We provide a detailed summary of discoveries over time in terms of orphan gene prevalence in genomes, their origins as well as their roles in different biological contexts.
Contrasting Genomic Trajectories of Bartonellaceae Symbionts of Planthoppers.
Ma M, Michalik A, Deng J … +2 more , Hu Y, Łukasik P
Genome Biol Evol · 2025 Nov · PMID 41261892 · Full text
Symbioses with microorganisms have shaped the nutritional biology and evolution of many insects. For example, several ant clades have adapted to nutrient-poor diets through symbiosis with a specific clade of bacteria in...
Symbioses with microorganisms have shaped the nutritional biology and evolution of many insects. For example, several ant clades have adapted to nutrient-poor diets through symbiosis with a specific clade of bacteria in the family Bartonellaceae (Hyphomicrobiales), notorious for also including virulent vertebrate pathogens. Here we show that Bartonellaceae phylogenetically placed within the clade that has only encompassed ant symbionts to date-Candidatus genus Tokpelaia-have established as symbionts in four different clades of planthoppers (Insecta: Hemiptera: Fulgoromorpha). Genome size and contents indicate different levels of integration of these strains into the planthopper biology and their diverse roles. Symbionts infecting one of the clades have some of the largest genomes among Bartonellaceae, at ca. 2 Mb, two others are under 700 kb, and the fourth is reduced to barely 158 kb. The planthopper-associated Tokpelaia strains with larger genomes, similar to ant symbionts, encode multiple amino acid and vitamin biosynthesis genes, complementing the degraded nutritional capabilities of their hosts' ancient heritable endosymbionts. Strikingly, the smallest Tokpelaia genome lacks any genes linked to essential amino acid biosynthesis, in contrast to all other known insect-associated bacteria with genomes of comparable size. We identified a single vitamin biosynthesis gene and iron-sulfur cluster assembly genes as its only putative contributions to the host biology. Our results broaden the host spectrum of nonpathogenic Bartonellaceae, indicating that they have contributed to nutrition and symbiotic consortium function in diverse diet-restricted host clades. They also highlight an unexpectedly broad range of evolutionary outcomes for this important bacterial group.
Signals of Ancestry-Specific Selection in Gentle Africanized Honey Bees.
Genetti M, Corbett-Detig R
Genome Biol Evol · 2025 Nov · PMID 41250883 · Full text
Understanding the genetic basis of adaptive responses to environmental and human mediated pressures is a central concern in evolutionary biology. Population admixture, a process wherein genetically differentiated populat...
Understanding the genetic basis of adaptive responses to environmental and human mediated pressures is a central concern in evolutionary biology. Population admixture, a process wherein genetically differentiated populations interbreed, is increasingly recognized as a source of genetic material driving rapid evolutionary responses. Honey bees from Puerto Rico are a phenotypically distinct population of Africanized honey bees with demonstrably lower levels of aggression than other Africanized populations. The Puerto Rican honey bee population represents a dynamic system that has experienced both environmental and human-mediated selective pressures over a short period of time marked by a significant influx of genetic variation from mainland Africanized honey bees, which has notably influenced the genetic makeup of the local populations. In this study we detail the current population structure of the Puerto Rican honey bees, how this differs from a mainland population, and regions of the genome that have signals of ancestry-specific selection. To distinguish loci undergoing ancestry-specific selection, we use tools that co-estimate local ancestry and the strength of selection at loci across the genome. We further detail the genes and pathways highlighted through gene ontology (GO) enrichment analysis. Overall, our results suggest that the local pressures on Puerto Rico honey bee behavior may have induced significant changes favoring alleles linked to different ancestries at loci and pathways involved in neuronal development, behavior, and mating among others. Our analysis demonstrates that approaches that explicitly model selection on local ancestry may be valuable tools for understanding evolution in admixture zones.
Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae).
Orzechowski SCM, Doudin D, Shams F … +6 more , Schmitt CJ, Drew A, Wilson C, Joseph L, Ezaz T, Edwards SV
Genome Biol Evol · 2025 Nov · PMID 41239861 · Full text
Mounting discoveries of avian neo-sex chromosomes are providing opportunities to understand the extent of variation in fundamental aspects of avian neo-sex chromosome evolution. We integrated cytogenetic data, long-read...
Mounting discoveries of avian neo-sex chromosomes are providing opportunities to understand the extent of variation in fundamental aspects of avian neo-sex chromosome evolution. We integrated cytogenetic data, long-read assemblies, and whole-genome resequencing to test phylogenetic hypotheses of recombination suppression and to elucidate the phylogenetic distribution of neo-sex chromosomes in honeyeaters (Aves: Meliphagidae). We find that neo-sex chromosomes in honeyeaters evolved through a fusion of the long arm of chromosome 5 and the pseudoautosomal region (PAR) of both ancestral Z and W sex chromosomes. Resequencing data from 11 species of honeyeaters and outgroups supports our cytogenetic evidence that these neo-sex chromosomes are derived within honeyeaters. Phylogenetic analyzes confirm that all tested honeyeaters share the same breakpoint for a new 17.4 Mb PAR at the end of the neo-sex chromosomes and suggest a single, large expansion of recombination suppression, encompassing 44.6 Mb, is most supported in the newly fused region of the neo-W. We also discovered phylogenetic discordance between the mapping of neo-sex chromosomes on the established nuclear and mitochondrial (mtDNA) phylogenies. We conclude that neo-sex chromosomes arose once in honeyeaters because they form a monophyletic clade on the mtDNA tree, which shares the phylogenetic history of the neo-W through matrilineal coinheritance. Overall, our findings provide new insights on recombination suppression dynamics of avian neo-sex chromosomes and demonstrate the value of comparing nuclear and mtDNA trees to determine the phylogenetic distribution of neo-sex chromosomes, especially in the presence of mitonuclear discordance, which is common across the avian tree of life.
Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments.
Sures K, Esser SP, Bornemann TLV … +7 more , Moore CJ, Soares AR, Plewka J, Figueroa-Gonzalez PA, Ruff SE, Moraru C, Probst AJ
Genome Biol Evol · 2025 Oct · PMID 41229344 · Full text
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities against mobile genetic elements, like viruses. In addition, protospacer an...
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities against mobile genetic elements, like viruses. In addition, protospacer analyses revealed a very specific acquisition of CRISPR spacers derived from genomes of related species or from closely interacting episymbiont genomes as recently shown for subsurface archaea. However, the origin of most of the spacers that can be found in CRISPR-Cas systems from natural environments has not been deciphered. Here, by analyzing CRISPR-Cas systems of metagenome-assembled genomes (MAGs) from two subsurface environments spanning more than 1 Tb of sequencing data, we show that a substantial proportion of CRISPR spacers are acquired from DNA of other prokaryotes inhabiting the same environment. As such, we found that the number of respective spacers can be up to three times higher than the number of self-targeting spacers. Statistical analyses demonstrated that the acquisition of CRISPR spacers from other prokaryotic genomes is partly explained by the relative abundance of the MAG containing the protospacer, as well as by other factors, such as the total number of CRISPR arrays present in a MAG with the respective spacers. Further, we found that spacer acquisition from foreign prokaryotic DNA occurs in almost all types of CRISPR-Cas systems, but shows preferences for subtypes of CRISPR-Cas systems that differ across the investigated ecosystems. Taken together, our results shed new light on the diversity of CRISPR spacers in natural microbial communities and provide an explanation for some of the many unmatched spacers in public databases.
Natural Selection in Transcription Factor-DNA Interaction Motifs: A Comparative and Population Genomics Perspective.
Joshi M, Duchen P, Kapopoulou A … +1 more , Laurent S
Genome Biol Evol · 2025 Oct · PMID 41225704 · Full text
Natural selection heavily influences the evolutionary trajectories of species by impacting their genotype-to-phenotype transitions. On the molecular level, these transitions are shaped by the regulatory sequences. In thi...
Natural selection heavily influences the evolutionary trajectories of species by impacting their genotype-to-phenotype transitions. On the molecular level, these transitions are shaped by the regulatory sequences. In this study, we employed a combination of population and comparative genomics to investigate how natural selection affects specific regulatory sequence classes involved in the regulatory transcription factor-DNA interactions. These interactions consist of two motifs, namely: transcription factor-binding domains and transcription factor-binding sites. Using publicly available annotation data for Homo sapiens, Arabidopsis thaliana, and Drosophila melanogaster, we first constructed the species-specific lists of the transcription factor-binding domain regions. On applying some of the commonly used summary statistics, we found signals of purifying selection acting on transcription factor-binding domains, consistent with their functional importance. Next, using the biochemical assay-based annotations, we identified potential transcription factor-binding site regions and used variants within them as nonsynonymous equivalents. Interestingly, we also observed that noncoding transcription factor-binding site regions showed similar levels of constraint to that of coding regions for populations with large Ne. Signals of positive selection were limited. Nevertheless, McDonald-Kreitman estimates revealed that, in both fruit-fly and thale-cress, α for transcription factor-binding domains was consistently higher than for adjacent nonbinding domains, whereas no such difference was apparent in humans. Taken together, our comparative analysis shows that the efficiency of negative-and to a lesser extent positive-selection on transcription factor-DNA interface elements scales with effective population size. The dataset and analysis pipeline provide a baseline for future studies of regulatory evolution across coding and noncoding regions.
Diversification of the Staphylococcal Cassette Chromosome Through Distinct Mechanisms of Horizontal Transfer.
Muller H, Andam CP
Genome Biol Evol · 2025 Oct · PMID 41220211 · Full text
The staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element that carries the mecA gene conferring resistance to beta-lactam antibiotics. While SCCmec is widely disseminated in Staphylococcus aureus, i...
The staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element that carries the mecA gene conferring resistance to beta-lactam antibiotics. While SCCmec is widely disseminated in Staphylococcus aureus, its diversity and evolutionary history across different taxonomic scales have not been investigated in detail. To elucidate the mechanisms governing the diversification of SCCmec, we carried out the largest systematic analysis of SCCmec to date. We focused on the Staphylococcaceae family, which is the primary cellular host of SCCmec. We scanned 2,556 complete genomes, representing 75 species and 8 genera within Staphylococcaceae. For this, we developed SCCeeker, a tailored pipeline to detect SCCmec across a large-scale genomic dataset. We uncovered 1,419 candidate SCCmec regions in 3 of 5 Mammaliicoccus species and 32 of 54 Staphylococcus species. SCCmec-carrying species are not more cladistically related than those without the SCCmec. The present study reveals that the evolution of SCCmec locus is driven by multiple mechanisms of horizontal transfer: transposition of insertion sequences IS1272 and IS6/IS431, transfer of entire cassette or fragments of it, cassettes carried by putative plasmids, formation of chimeric cassettes, and recombination of homologous sequences. The multimodal shuffling of SCCmec elements creates a genetically diverse cassette pool and sheds light on the independent evolution of mobile elements and the origins of SCCmec.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe