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PubMed2006

Plant-plant interactions and environmental change.

Natural systems are being subjected to unprecedented rates of change and unique pressures from a combination of anthropogenic environmental change drivers. Plant-plant interactions are an important part of the mechanisms governing the response of plant species and communities to these drivers. For example, competition plays a central role in mediating the impacts of atmospheric nitrogen deposition, increased atmospheric carbon dioxide concentrations, climate change and invasive nonnative species. Other plant-plant interaction processes are also being recognized as important factors in determining the impacts of environmental change, including facilitation and evolutionary processes associated with plant-plant interactions. However, plant-plant interactions are not the only factors determining the response of species and communities to environmental change drivers - their activity must be placed within the context of the wide range of factors that regulate species, communities and ecosystems. A major research challenge is to understand when plant-plant interactions play a key role in regulating the impact of environmental change drivers, and the type of role that plant-plant interactions play. Although this is a considerable challenge, some areas of current research may provide the starting point to achieving these goals, and should be pursued through large-scale, integrated, multisite experiments.

Biological Evolution↗

PubMed2025

Evolutionary dynamics and genetic diversity of transposable elements revealed by resequencing data in maize population.

Zea mays (maize) is a globally significant crop with a complex genome enriched with transposable elements (TEs), which are crucial drivers of genomic diversity and plant evolution. In this study, we identified the TE insertion loci (TILs) from resequencing data of 103 maize accessions with the developed pipeline, and 64 293 non-redundant unique TILs were obtained in 82 maize accessions after filtering; approximately 80% (51 361) of loci showed insertion polymorphisms within the population. All TE superfamilies have low frequency in the maize population except for short interspersed nuclear elements, while some TE families have high fixed TE insertions, revealing distinct evolutionary dynamics among TE superfamilies and families. Genetic analysis using the transposon insertion polymorphism information from the maize population showed that the TE polymorphism loci can reflect their geographical origin and evolutionary relationships. Furthermore, TE insertions could also significantly impact gene expression, implying functional consequences for maize phenotypes and adaptation. These findings provide valuable insights into the evolutionary dynamics and genetic diversity of maize genomes, offering a valuable resource for molecular markers and association studies.

Zea mays↗

PubMed2006

Systems biology as a foundation for genome-scale synthetic biology.

As the ambitions of synthetic biology approach genome-scale engineering, comprehensive characterization of cellular systems is required, as well as a means to accurately model cell-scale molecular interactions. These requirements are coincident with the goals of systems biology and, thus, systems biology will become the foundation for genome-scale synthetic biology. Systems biology will form this foundation through its efforts to reconstruct and integrate cellular systems, develop the mathematics, theory and software tools for the accurate modeling of these integrated systems, and through evolutionary mechanisms. As genome-scale synthetic biology is so enabled, it will prove to be a positive feedback driver of systems biology by exposing and forcing researchers to confront those aspects of systems biology which are inadequately understood.

Biology↗

PubMed2026

Pangenome of Streptomyces sampsonii and Relatives Highlights Horizontal Gene Transfer and Secondary Metabolism in Environmental Adaptation and Ecological Significance.

Streptomyces sampsonii is a promising biocontrol bacterium, but its genomic basis of adaptation and secondary metabolism remains unclear. Here, we present a chromosome-level genome assembly of S. sampsonii (7.20 Mb, 6015 protein-coding genes) and perform comparative analyses with 95 related Streptomyces species. Phylogenomic and synteny analyses revealed its closest relationship with S. albidoflavus, while extensive structural variations distinguished more distant lineages. Pangenome analysis uncovered 84,178 gene clusters, with pan_shell and pan_cloud genes predominantly enriched in xenobiotic biodegradation, metabolism, and antibiotic biosynthesis, highlighting their roles in ecological adaptation and biocontrol potential. Biosynthetic gene cluster (BGC) analysis identified numerous NRPS, PKS, and terpene pathways, many of which belong to pan_shell and pan_cloud regions, suggesting dynamic evolutionary origins. We further detected 66,260 horizontally transferred (HGT) genes, including 438 in BGCs, underscoring HGT as a major driver of metabolic innovation. Together, these findings provide novel insights into the genomic diversity, adaptive capacity, and secondary metabolic potential of S. sampsonii and its close relatives.

BGCs↗

PubMed2025

Genomic insights into karyotype evolution and adaptive mechanisms in Polygonaceae species.

Polygonaceae, with ecological versatility and global distribution, is an ideal system for investigating plant adaptation. However, the genomic mechanisms underlying its karyotype evolution and environmental resilience remain unclear. We herein present chromosome-level genomes of 11 species from 10 Polygonaceae genera. Our analyses reveal that Gypsy retrotransposons are key drivers of genome size variations in Polygonaceae. We reconstructed a Polygonaceae ancestral karyotype comprising 28 proto-chromosomes and elucidated evolutionary trajectories via extensive chromosomal rearrangements. Furthermore, we constructed a cross-genus super pan-genome for Polygonaceae, identifying 80,055 gene families, of which 9,845 (12.30%) are core gene families. Private genes are found to contribute significantly to interspecific differences in adaptability. Notably, gene copy number variations are identified as a critical factor influencing adaptations to diverse niches involving species-specific increases in metabolic pathways. This study provides a genomic framework for Polygonaceae karyotype plasticity and adaptive innovation, offering insights into plant evolution under environmental challenges.

Karyotype↗

PubMed2000

Evolution of cortical lamination: the reelin/Dab1 pathway.

The mammalian cortical plate is characterized by its radial organization and its inside-outside developmental gradient. Observations on reelin and Dab1-deficient mice show that reelin and Dab1 are both required to develop radial cortical organization and a normal maturation gradient. In the reptilian cortex, radial organization varies among species; it is the most rudimentary in turtles and the most elaborate in lizards, and can be described as intermediate in other species such as crocodilians and Sphenodon. On the other hand, the gradient of corticogenesis is directed from outside to inside in all reptiles studied, as well as in mice that are deficient in reelin, Dab1, as well as cyclin-dependent kinase 5 (Cdk5) and p35. All reptiles, even turtles, have reelin-expressing cells in the embryonic marginal zone. Mammals are characterized by a drastic increase in the number of reelin-positive cells (Cajal-Retzius cells) as well as by an amplification of reelin expression per cell. In lizards, the pattern of reelin expression is different, as reelin-expressing cells are also present below the cortical plate. In all mammalian and reptilian species, Dab1 is expressed in cortical plate cells. These data suggest that the reelin/Dab1 pathway was a driver of cortical evolution on the synapsid lineage and that similarities in radial cortical organization between squamates and mammals result from evolutionary convergence.

Animals↗

PubMed2026

Megamimivirus double-stranded DNA linear genomes flanked by highly diverse terminal inverted repeats.

UNLABELLED: Giant viruses have fundamentally expanded our understanding of virology by challenging the conventional boundaries of both virion size and genome complexity. However, the scarcity of isolates has left many of their unique biological features unexplored. Here, we report the isolation and characterization of four new giant virus species belonging to the subfamily Megamimivirinae, sampled from distinct environments across China. Among these, Megavirus daqingense is the first giant virus isolated from an oil reservoir; it exhibits virion stability under high salinity, chloroform exposure, and elevated temperatures, suggesting fitness adaptations to subsurface conditions. Using a hybrid sequencing approach that integrates short- and long-read technologies, we assembled complete linear genomes for all four isolates, each flanked by long terminal inverted repeats (TIRs). Comparative genomic and synteny analyses identified 29 distinct TIRs from 46 megamimivirus genomes. Gene content within these TIRs was highly diverse, with no orthologous proteins conserved across all repeats. Furthermore, TIR genes experienced weaker purifying selection than those in non-TIR regions (i.e., the genomic regions excluding the TIRs), consistent with their role as drivers of genome plasticity. Notably, we discovered for the first time that identical tRNA genes are shared between TIRs and non-TIR regions of eukaryotic viruses. Collectively, our work provides insights into the structural and evolutionary complexity of megamimiviruses, revealing TIRs as reservoirs of genetic diversity and hotspots for gene transfer, thereby playing a pivotal role in shaping the dynamic architecture of giant virus genomes. IMPORTANCE: Terminal inverted repeats (TIRs) are critical structural elements at the termini of linear genomes essential for fundamental processes such as recombination, replication, and integration across diverse organisms. However, the inherent limitations of short-read sequencing technologies have left the complete structure, diversity, and evolutionary significance of long TIRs in giant viruses unexplored. In this study, we leverage hybrid sequencing and comparative genomic analyses to unveil the complexity of TIRs across the subfamily Megamimivirinae. We demonstrate that TIRs are dynamic genomic hotspots characterized by remarkable gene diversity and unexpected conservation of specific tRNA genes. These findings establish TIRs as key drivers of genome plasticity, serving as hotspots for horizontal gene transfer and genetic innovation. By resolving the long-hidden terminal structures of megamimivirus genomes, this work provides a foundational framework for understanding how TIRs shape the evolution of giant viruses and, more broadly, advances our understanding of genome architecture in large DNA viruses.

Megavirus↗

PubMed2005

Confounding factors in the detection of species responses to habitat fragmentation.

Habitat loss has pervasive and disruptive impacts on biodiversity in habitat remnants. The magnitude of the ecological impacts of habitat loss can be exacerbated by the spatial arrangement -- or fragmentation -- of remaining habitat. Fragmentation per se is a landscape-level phenomenon in which species that survive in habitat remnants are confronted with a modified environment of reduced area, increased isolation and novel ecological boundaries. The implications of this for individual organisms are many and varied, because species with differing life history strategies are differentially affected by habitat fragmentation. Here, we review the extensive literature on species responses to habitat fragmentation, and detail the numerous ways in which confounding factors have either masked the detection, or prevented the manifestation, of predicted fragmentation effects. Large numbers of empirical studies continue to document changes in species richness with decreasing habitat area, with positive, negative and no relationships regularly reported. The debate surrounding such widely contrasting results is beginning to be resolved by findings that the expected positive species-area relationship can be masked by matrix-derived spatial subsidies of resources to fragment-dwelling species and by the invasion of matrix-dwelling species into habitat edges. Significant advances have been made recently in our understanding of how species interactions are altered at habitat edges as a result of these changes. Interestingly, changes in biotic and abiotic parameters at edges also make ecological processes more variable than in habitat interiors. Individuals are more likely to encounter habitat edges in fragments with convoluted shapes, leading to increased turnover and variability in population size than in fragments that are compact in shape. Habitat isolation in both space and time disrupts species distribution patterns, with consequent effects on metapopulation dynamics and the genetic structure of fragment-dwelling populations. Again, the matrix habitat is a strong determinant of fragmentation effects within remnants because of its role in regulating dispersal and dispersal-related mortality, the provision of spatial subsidies and the potential mediation of edge-related microclimatic gradients. We show that confounding factors can mask many fragmentation effects. For instance, there are multiple ways in which species traits like trophic level, dispersal ability and degree of habitat specialisation influence species-level responses. The temporal scale of investigation may have a strong influence on the results of a study, with short-term crowding effects eventually giving way to long-term extinction debts. Moreover, many fragmentation effects like changes in genetic, morphological or behavioural traits of species require time to appear. By contrast, synergistic interactions of fragmentation with climate change, human-altered disturbance regimes, species interactions and other drivers of population decline may magnify the impacts of fragmentation. To conclude, we emphasise that anthropogenic fragmentation is a recent phenomenon in evolutionary time and suggest that the final, long-term impacts of habitat fragmentation may not yet have shown themselves.

Animals↗

PubMed2025

Adaptive Evolution for Freshwater Adaptation in Coilia nasus by Directional Selection on Osmoregulation Genes.

The molecular mechanisms underlying the adaptation to freshwater habitats in fish of marine origin remain unclear. Grenadier anchovies, such as Coilia nasus, originate from marine environments and include both anadromous and freshwater-resident conspecifics, making them ideal for studying adaptive evolution from marine to freshwater habitats. We conducted a comparative population genomic and transcriptome analysis of two distinct C. nasus lineages, one anadromous and the other freshwater-resident, collected from mainstream and estuarine regions of the Yangtze River, China. By genome-wide genotyping of the anadromous and the freshwater-resident populations, we observed significant divergence in osmoregulation, energy metabolism, and immune response pathways associated with ecological adaptation and energy expenditure for migration. Some ion transport genes such as CAMK1, ATP1α3, KCNJ1 and SLC30A2 were identified that may contribute to freshwater adaptation. Notably, numerous mineralocorticoid signalling genes (e.g., NR3C2, SGK1, ATP1α3, KCNJ1) exhibit dynamic change between the anadromous and freshwater populations, suggesting an important role for the hormone cortisol in regulating salinity acclimation in euryhaline fish. Among these genes, the ion channel ATP1α3 experienced adaptive amino acid substitutions (Val317Ile and Thr329Ser), which appear to be evolutionary hotspots across migratory species based on ortholog comparisons. These variants may facilitate sodium/potassium transport and highlight salinity tolerance as a key driver of divergence in anadromous fish transitioning to freshwater. These results enhance our understanding of the genetic basis underlying freshwater adaptation for an anadromous fish across osmotic boundaries.

Animals↗

PubMed2025

The landscape of structural variation in pediatric cancer.

Structural variants (SVs) account for over 60% of the driver variants in pediatric cancer, and in many cases act as the cancer initiating event. To study SVs from a pan-cancer perspective, we analyzed 1,616 pediatric cancer genomes in 16 major cancer types of hematological malignancies (n = 908), brain tumors (n = 183), and solid tumors (n = 525) and compared their profiles to those of 2,203 adult cancers. The SV burden varied ~100-fold across pediatric cancer types and demonstrated an 8- to 16-fold reduction compared to adult brain and solid tumors but was comparable in pediatric versus adult hematological malignancies. Recurrent SV hotspots occurred uniquely in pediatric acute lymphoblastic leukemias (ALLs) in proximity to RAG-mediated recombination signal sequences (RSS) and disrupted multiple immune-related loci as well as 69 genes, which often involved cryptic RSS sites. By contrast, such hotspots affected only immune-related loci but not driver genes in adult lymphoid cancers. Eight SV signatures extracted from the cohort had varying distributions across cancer types, with clustered translocations reflecting templated insertions in osteosarcoma, and medium-sized deletions (10 kb to 1 Mb) enriched in cancers with RAG-mediated deletions. Intra-patient evolutionary analysis in 13 patients with multiple spatiotemporally distinct samples revealed that RAG-mediated recombination in leukemia and complex rearrangements in solid tumors occurred both early in disease initiation and continuously during later diversification, contributing to clonal heterogeneity. Finally, we found that both driver genes and fragile sites were the two genomic regions most frequently disrupted by SVs. The unique and diverse SV landscapes that emerged from this comprehensive analysis expand the scope of RSS-mediated mutagenesis in pediatric ALL and will be a valuable resource for guiding future functional studies and the design of clinical genomic testing in pediatric cancer.

Journal Article↗

PubMed2005

Horizontally acquired genes for purine salvage in Borrelia spp. causing relapsing fever.

Unlike Borrelia burgdorferi, the relapsing fever agent Borrelia hermsii and the related Borrelia miyamotoi had purA and purB genes of the purine salvage pathway. These were located among the rRNA genes. Phylogenetic analysis indicated that these genes had a different evolutionary history than those of orthologs in other spirochetes.

Adenylosuccinate Lyase↗

PubMed1981

Evolutionary distances in Hawaiian Drosophila measured by DNA reassociation.

Comparisons of the sequence divergence of three species of Hawaiian Drosophila have been made by hybridization of single-copy tracer DNA of each of the species with driver DNA from each species, and measurement of the average melting temperature (Tma) in a chaotropic solvent (2.4 M tetraethylammonium chloride) which minimizes differences due to base composition. Correction was made for the length of hybrid duplex regions to obtain the reduction in thermal stability due to divergence. An accuracy of +/- 0.2 degrees C was achieved and the mean reduction in Tm for hybridization between D. heteroneura and D. silvestris (found only on the island of Hawaii) was 0.55 degrees C and between D. picticornis, found only on the island of Kauai, and the other two species was 2.13 degrees C. The rate of DNA change is estimated to be between 0.2 and 0.4%/My by assuming that the D. heteroneura-D. silvestris divergence occurred 0.8 My ago and the divergence between these species and D. picticornis between 4 and 6 My ago. The general single copy DNA sequence divergence appears to be very much greater than the minimal coding region sequence divergence previously estimated from allozyme studies.

Animals↗

PubMed2025

Comparative analysis of DREB gene family in buckwheat: the role of FtDREB02 in the delphinidin biosynthesis and drought stress response.

Dehydration response element binding (DREB) transcription factors play a pivotal role in plant abiotic stress responses, but its evolutionary and functional characterization in buckwheat remains unexplored. Here, we conducted a comprehensive analysis of the DREB gene family across three buckwheat species, revealing segmental duplication as the primary driver of family expansion and potential purifying selection during evolution. A FtDREB02 gene, classified as group A2, was identified through genome-wide association analysis (GWAS) on drought tolerance and delphinidin content. Functional validation in Arabidopsis thaliana and the hairy root of Tartary buckwheat (Fagopyrum tataricum) demonstrated that overexpression of this gene promotes delphinidin biosynthesis and enhances plant resistance to water scarcity. Through the integration of DAP-seq and PEG transcriptome cluster analysis, a FtANS candidate was screened. Functional studies showed that FtDREB02 regulates delphinidin content by binding directly to DRE elements of the FtANS promoter. This research identifies and comprehensively analyzes the DREB family within buckwheat species, elucidating the regulatory mechanisms of FtDREB02 in controlling flavonoid biosynthesis and drought resistance, providing potential genetic resources for breeding buckwheat varieties with excellent agronomic traits.

Anthocyanins↗

PubMed2005

Consumer driven healthcare: strategic, operational, and information technology implications for today's healthcare CIO.

This article explores the phenomenon of consumerism in healthcare from an evolutionary perspective and with a view to understanding its implications on the future of our industry. Drawing from the perspectives of leading industry thought leaders and CIOs, it explores the strategic drivers moving our industry toward consumerism and the operational and information technology implications of that trend. By blending real-life examples with potential scenarios, the article is designed to provoke thinking regarding the challenges and opportunities presented by consumerism, thereby informing strategic planning efforts. By doing so, the authors seek to initiate a dialog with readers on this emerging topic while sharing their insights and perspectives with those entrusted with developing consumer-driven healthcare strategies and action plans.

Consumer Behavior↗

PubMed2024

Extreme elevational migration spurred cryptic speciation in giant hummingbirds.

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.

Animals↗

PubMed2026

Evolution and heterogeneity of lethal metastatic bladder cancer subtypes.

Histological variation is a prognostic feature of metastatic urothelial cancer1-3, but its evolutionary trajectory remains poorly defined. We developed a metastatic bladder cancer rapid autopsy programme enriched in histological subtypes4 to profile individuals with terminal disease. Here by reconstructing the evolutionary histories of patient tumours, we show that metastasis-to-metastasis seeding is the dominant pattern of cancer spread and that increased polyclonal migration predicts poor prognosis. The burden, heterogeneity and timing of genomic alterations differ markedly among histological subtypes. Plasmacytoid and neuroendocrine variants develop early driver alterations associated with shorter survival. Mutational signature analyses and experimental models demonstrated that plasmacytoid tumours uniquely use the Fanconi anaemia pathway to mitigate chemotherapy-induced genomic scarring. Single-nucleus profiling revealed mixed cell states in histological subtypes and an association between transcriptional heterogeneity and patient survival. Characterization of the tumour microenvironment uncovered distinct immune states across subtypes, with plasmacytoid tumours exhibiting immune-inflamed profiles, whereas squamous tumours are predominantly immunosuppressive. Last, we demonstrate that post-mortem cell-free DNA captures genomic and transcriptional heterogeneity of the subtypes, which provides a potential strategy for noninvasive assessment of tumour identity and aggressiveness. Our results provide new insights into how tumour heterogeneity shapes the evolutionary history of disease progression in bladder cancer histological subtypes.

Journal Article↗

PubMed2026

The genomic landscape of HER2 negative metastatic breast cancer with loss of estrogen and progesterone receptors.

INTRODUCTION: Loss of estrogen receptor (ER) and/or progesterone receptor (PR) might occur during the metastatic progression of ER positive and HER2 negative (ER+/HER2-) breast cancer (BC), but the underpinning molecular alterations remain elusive. We explored the genomic context of HER2- tumors with ER and/or PR loss to investigate potential drivers and actionable alterations that might help personalize treatment of ER+/HER2- BC. METHODS: We accessed data from metastatic HER2- BC included in the MSK-2018 dataset to compare outcome, tumor characteristics and genomic alterations of BC with loss of ER (ER+/-, n = 66) to those maintaining ER positivity (ER+/+, n = 364) or ER negativity (ER-/-, n = 50). We also compared metastatic ER+/+ BC with loss of PR (PR+/-, n = 111) to those maintaining PR positivity (PR+/+, n = 192) or PR negativity (PR-/-, n = 41). RESULTS: In line with previous reports, ER+/- BC was associated with aggressive clinico-pathological characteristics and poor outcome. ER+/- BC showed significantly higher frequency of TP53 and RB1 mutations and lower frequency of PIK3CA and GATA3 mutations compared to ER+/+. ER+/- or PR+/- status was mutually exclusive with ESR1 mutations and was associated with a significantly higher tumor mutational burden. Moreover, ER+/- BC were enriched in driver alterations in the genes of the Notch and Retinoblastoma pathways and showed a significantly lower frequency of level 1 actionable alterations according to OncoKB. CONCLUSIONS: Loss of ER and/or PR may identify a distinct evolutionary trajectory of ER+/HER2- metastatic progression, largely non-overlapping with ESR1-mutant endocrine resistance. Further studies on matched primary and metastatic samples are warranted.

Humans↗

PubMed2025

Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae).

Allopolyploidization, resulting from hybridization and subsequent whole-genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized deep genome skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS-Tree2GD) tailored explicitly for accurately detecting WGD events. Additionally, we introduced two methods to evaluate the contribution of incomplete lineage sorting (ILS) to lineage diversification. Phylogenomic discordance analyses revealed that allopolyploidization, rather than ILS, played a dominant role in the origin and dynamics of polyploid Prunus. Moreover, we inferred that the uplift of the Himalayas from the Middle to Late Miocene was a key driver in the rapid diversification of the Maddenia clade, an endemic group in East Asia. This geological event facilitated extensive hybridization and allopolyploidization, particularly the introgression between the Himalayas-Hengduan and Central-Eastern China clades. This case study demonstrates the robustness and efficacy of our analytical approach in precisely identifying WGD events and elucidating the evolutionary mechanisms underlying allopolyploidization in polyploid Prunus.

Polyploidy↗