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PubMed2006

Data depth, data completeness, and their influence on quantitative genetic estimation in two contrasting bird populations.

Evolutionary biologists increasingly use pedigree-based quantitative genetic methods to address questions about the evolutionary dynamics of traits in wild populations. In many cases, phenotypic data may have been collected only for recent parts of the study. How does this influence the performance of the models used to analyse these data? Here we explore how data depth (number of years) and completeness (number of observations) influence estimates of genetic variance and covariance within the context of an existing pedigree. Using long-term data from the great tit Parus major and the mute swan Cygnus olor, species with different life-histories, we examined the effect of manipulating the amount of data included on quantitative genetic parameter estimates. Manipulating data depth and completeness had little influence on estimated genetic variances, heritabilities, or genetic correlations, but (as expected) did influence confidence in these estimates. Estimated breeding values in the great tit were not influenced by data depth but were in the mute swan, probably because of differences in pedigree structure. Our analyses suggest the 'rule of thumb' that data from 3 years and a minimum of 100 individuals per year are needed to estimate genetic parameters with acceptable confidence, and that using pedigree data is worthwhile, even if phenotypes are only available toward the tips of the pedigree.

Animals↗
PubMed2006

A broad-scale analysis of population differentiation for Zn tolerance in an emerging model species for tolerance study: Arabidopsis halleri (Brassicaceae).

Although current knowledge about the overall distribution of zinc (Zn) tolerance in Arabidopsis halleri populations is scarce, the species is an emerging model for the study of heavy metal tolerance in plants. We attempted to improve this knowledge by testing the Zn tolerance of scattered European metallicolous (M) and nonmetallicolous (NM) populations of A. h. subsp. halleri and A. h. subsp. ovirensis in hydroponic culture. The occurrence of constitutive tolerance was unconditionally established in A. h. halleri and tolerance was extended to the subspecies ovirensis. M populations were the most tolerant but there was a continuous range of variation in tolerance from NM to M populations. Finally, relatively high levels of tolerance were detected in some NM populations, suggesting that enhanced tolerance could be present at high frequency in populations that have not experienced metal exposure. We used our results to argue the evolutionary dynamics and origin of Zn tolerance in A. halleri.

Arabidopsis↗
PubMedDate not supplied

Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster.

To further understand the evolutionary dynamics of the regulatory interactions underlying development, we expand on our previous analysis of hunchback and compare the structure and function of the tailless enhancer between Musca domestica and Drosophila melanogaster. Our analysis shows that although the expression patterns and functional protein domains of tll are conserved between Musca and Drosophila, the enhancer sequences are unalignable. Upon closer investigation, we find that these highly diverged enhancer sequences encode the same regulatory information necessary for Bicoid, Dorsal, and the terminal system to drive tll expression. The binding sites for these transcription factors differ in the sequence, number, spacing, and position between the Drosophila and Musca tll enhancers, and we were unable to establish homology between binding sites from each species. This implies that the Musca and Drosophila Bcd-binding sites have evolved de novo in the 100 million years since these species diverged. However, in transgenic Drosophila embryos the Musca tll enhancer is able to drive the same expression pattern as endogenous Drosophila tll. Therefore, during the rapid evolution of enhancer sequences individual binding sites are continually lost and gained, but the transcriptional output is maintained by compensatory mutations in cis and in trans.

Amino Acid Sequence↗
PubMed2025

Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.

Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.

Animals↗
PubMed2026

Unraveling epigenetic and genetic variations in response to cold stress in two lotus ecotypes.

Genetic variations accumulate over long evolutionary timescales, whereas epigenetic modifications can arise rapidly and be inherited across generations. However, the interplay between genetic and epigenetic variations in shaping ecotype-specific phenotypic plasticity remains elusive. Focusing on two lotus ecotypes that evolved under distinct winter temperature regions and display divergent annual growth cycles under cold stress, we generated DNA methylation landscapes across three sequence contexts (CG, CHG, and CHH, where H = A, T, or C) and identified single-cytosine methylation polymorphisms (SMPs) and single-nucleotide polymorphisms (SNPs). Interestingly, only CG methylation patterns mirror population-level genetic variations. Using epigenetic genome-wide association analysis, we identified differentially methylated CG sites that are either cis- or trans-regulated by SNP. Notably, we constructed a multifactorial regulatory network centered on the NnMKK4-NnCYCD5 module, linking cold response with cell cycle regulation. Temperature stress experiments conducted on lotus ecotypes and transgenic Arabidopsis (OE-NnMKK4 and OE-NnCYCD5) confirmed that NnMKK4 acts as a cold receptor and that NnCYCD5 promotes cell cycle progression and growth under cold conditions. Collectively, our findings provide novel insights into the co-evolutionary dynamics of epigenetic and genetic variations that are associated with different growth cycles of lotus ecotypes in response to cold stress.

DNA methylation↗
PubMed2025

The evolutionary trajectories and gene regulatory roles of nuclear-integrated plastid DNA: clues for enhancing environmental adaptation in Caryophyllales.

Environmental stimuli can induce the transfer of chloroplast DNA to the nuclear genome, resulting in nuclear-integrated plastid DNAs (NUPTs). However, their role in plant adaptability remains unclear. Species within the Caryophyllales order, known for their adaptation to extreme environments, provide an ideal model for studying the evolutionary dynamics and functions of NUPTs. In this study, we analyzed NUPTs in 24 Caryophyllales species to investigate their evolution and regulatory roles in gene expression, particularly in response to environmental stimuli. We found significant interspecies variation in NUPT abundance, ranging from 566 insertions in Amaranthus cruentus to 3585 in Beta vulgaris, with sizes spanning from 100 bp to over 100 kb. Approximately 62% of NUPTs were inserted within the last 20 million years, while some species exhibit insertion peaks dating back 49 million years. NUPT presence/absence polymorphisms in six related species suggest that NUPT insertions and deletions are dynamic processes influenced by phylogeny. NUPTs predominantly integrate into intergenic regions but also insert into genes and promoters, with certain regions acting as hotspots. Notably, NUPTs introduce numerous environmental-responsive cis-acting elements in promoter regions. Genes with NUPT insertions in their promoters are significantly enriched for functions related to environmental response. Further luciferase assays in Spinacia oleracea demonstrated that NUPT insertions can regulate the expression of genes related to environmental responses, indicating their potential role in adaptive evolution. Overall, our study provides insights into NUPT evolution and their influence on gene function and plant adaptability to environmental stimuli.

Plastids↗
PubMed2025

Subgenomic divergence and functional innovation following whole-genome duplication in Maleae species of Rosaceae.

Whole-genome duplication (WGD) drives plant evolution by inducing karyotype rearrangements and gene loss through subgenome fractionation. In this study, we investigate post-WGD evolutionary dynamics in Rosaceae, focusing on Maleae species, which uniquely experienced an additional WGD. Using phylogenetic and synteny analyses, we reveal that chromosomal breakpoints act as hotspots for localized fractionation, contributing to blurred homoeologous origins and influencing gene retention patterns. Here, we reconstruct karyotype evolution across Rosaceae subfamilies, highlighting chromosome reductions and lineage-specific rearrangements in Dryadoideae, Rosoideae, and Amygdaloideae. We also identify a bias for retaining transcription factors and hormone-related genes from older WGDs in subsequent polyploidy events. Transcriptome analysis classifies WGD-derived genes in Maleae species, such as apple and loquat, into three expression groups, with hormone-enriched genes playing roles in lignification and fruit-related innovations. These findings demonstrate the interplay between chromosomal breakpoints, biased retention, and functional divergence, revealing their contributions to genomic and phenotypic evolution in Maleae and their adaptive success within Rosaceae.

Genome, Plant↗
PubMed2025

Haplotype-resolved telomere-to-telomere genome assembly of Populus lasiocarpa unveils retrotransposon-driven centromere evolution.

Centromeres, essential for chromosome segregation, exhibit remarkable evolutionary dynamism in sequence composition and structural organization. Here, we report the first haplotype-resolved, telomere-to-telomere genome assembly of Populus lasiocarpa (PLAS) and precisely map all 38 functional centromeres through CENH3 ChIP-Seq. Unlike classical satellite-rich centromeres in model plants, PLAS centromeres lack abundant satellite arrays but are dominated by retrotransposons, particularly RLG and RIL elements, which form intricate nested TE arrays within the functional centromeric regions, disrupting their structural integrity and driving their evolution. Comparative analysis with P. trichocarpa reveals a conserved retrotransposon-dominated architecture, despite minimal sequence conservation. We propose a cyclic model of centromere evolution in which autonomous retrotransposons destabilize functional centromeres through epigenetic erosion, triggering neocentromere formation at pericentromeric sites enriched in transposable elements (TEs) and tandem repeats (TRs). These neocentromeres either succumb to recurrent retrotransposon invasions or stabilize through KARMA-mediated TR expansion, ultimately giving rise to satellite-rich centromeres. Our work redefines centromeres as dynamic, epigenetically plastic domains shaped by retrotransposon-TR antagonism, challenging the satellite-centric paradigm and offering novel insights into plant genome evolution.

Retroelements↗
PubMed2004

Large shifts in pathogen virulence relate to host population structure.

Theory on the evolution of virulence generally predicts selection for an optimal level of virulence determined by trade-offs with transmission and/or recovery. Here we consider the evolution of pathogen virulence in hosts who acquire long-lived immunity and live in a spatially structured population. We show theoretically that large shifts in virulence may occur in pathogen populations as a result of a bistability in evolutionary dynamics caused by the local contact or social population structure of the host. This model provides an explanation for the rapid emergence of the highly virulent strains of rabbit hemorrhagic disease virus.

Animals↗
PubMed2006

An equivalence principle for the incorporation of favorable mutations in asexual populations.

Rapid evolution of asexual populations, such as that of cancer cells or of microorganisms developing drug resistance, can include the simultaneous spread of distinct beneficial mutations. We demonstrate that evolution in such cases is driven by the fitness effects and appearance times of only a small minority of favorable mutations. The complexity of the mutation-selection process is thereby greatly reduced, and much of the evolutionary dynamics can be encapsulated in two parameters-an effective selection coefficient and effective rate of beneficial mutations. We confirm this theoretical finding and estimate the effective parameters for evolving populations of fluorescently labeled Escherichia coli. The effective parameters constitute a simple description and provide a natural standard for comparing adaptation between species and across environments.

Adaptation, Biological↗
PubMed1996

Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection.

The rate of progression to disease varies considerably among individuals infected with human immunodeficiency virus-type 1 (HIV-1). Analyses of semiannual blood samples obtained from six infected men showed that a rapid rate of CD4 T cell loss was associated with relative evolutionary stasis of the HIV-1 quasispecies virus population. More moderate rates of CD4 T cell loss correlated with genetic evolution within three of four subjects. Consistent with selection by the immune constraints of these subjects, amino acid changes were apparent within the appropriate epitopes of human leukocyte antigen class I-restricted cytotoxic T lymphocytes. Thus, the evolutionary dynamics exhibited by the HIV-1 quasispecies virus populations under natural selection are compatible with adaptive evolution.

Acquired Immunodeficiency Syndrome↗
PubMed2000

The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies.

The mechanisms by which hepatitis C virus (HCV) induces chronic infection in the vast majority of infected individuals are unknown. Sequences within the HCV E1 and E2 envelope genes were analyzed during the acute phase of hepatitis C in 12 patients with different clinical outcomes. Acute resolving hepatitis was associated with relative evolutionary stasis of the heterogeneous viral population (quasispecies), whereas progressing hepatitis correlated with genetic evolution of HCV. Consistent with the hypothesis of selective pressure by the host immune system, the sequence changes occurred almost exclusively within the hypervariable region 1 of the E2 gene and were temporally correlated with antibody seroconversion. These data indicate that the evolutionary dynamics of the HCV quasispecies during the acute phase of hepatitis C predict whether the infection will resolve or become chronic.

Acute Disease↗
PubMed2001

Evolution of universal grammar.

Universal grammar specifies the mechanism of language acquisition. It determines the range of grammatical hypothesis that children entertain during language learning and the procedure they use for evaluating input sentences. How universal grammar arose is a major challenge for evolutionary biology. We present a mathematical framework for the evolutionary dynamics of grammar learning. The central result is a coherence threshold, which specifies the condition for a universal grammar to induce coherent communication within a population. We study selection of grammars within the same universal grammar and competition between different universal grammars. We calculate the condition under which natural selection favors the emergence of rule-based, generative grammars that underlie complex language.

Algorithms↗
PubMed2006

From fluctuations to phenotypes: the physiology of noise.

There are fundamental physical reasons why biochemical processes might be subject to noise and stochastic fluctuations. Indeed, it has long been understood that random molecular-scale mechanisms, such as those that drive genetic mutation, lie at the heart of population-scale evolutionary dynamics. What we can now appreciate is how stochastic fluctuations inherent in biochemical processes contribute to cellular and organismal phenotypes. Advancements in techniques for empirically measuring single cells and in corresponding theoretical methods have enabled the rigorous design and interpretation of experiments that provide incontrovertible proof that there are important endogenous sources of stochasticity that drive biological processes at the scale of individual organisms. Recently, some studies have progressed beyond merely ascertaining the presence of noise in biological systems; they trace its role in cellular physiology as it is passed through and processed by the biomolecular pathways-from the underlying origins of stochastic fluctuations in random biomolecular interactions to their ultimate manifestations in characteristic species phenotypes. These emerging results suggest new biological network design principles that account for a constructive role played by noise in defining the structure, function, and fitness of biological systems. They further show that stochastic mechanisms open novel classes of regulatory, signaling, and organizational choices that can serve as efficient and effective biological solutions to problems that are more complex, less robust, or otherwise suboptimal to deal with in the context of purely deterministic systems. Research in Drosophila melanogaster eye color-vision development and Bacillus subtilis competence induction has elegantly traced the role of noise in vital physiological processes from fluctuations to phenotypes, and is used here to highlight these developments.

Animals↗
PubMed2026

Repeated emergence and fitness heterogeneity of KPC-33 in ST11 Klebsiella pneumoniae under ceftazidime-avibactam pressure.

Ceftazidime-avibactam (CZA) is an important therapeutic option for infections caused by Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae. However, CZA exposure also selects for emergent KPC variants. Their in vivo evolutionary patterns, fitness consequences, and underlying molecular mechanisms remain unclear. We performed a longitudinal multiomics analysis of 35 clonally related ST11 KPC-producing K. pneumoniae isolates collected from eight hospitalized patients during clinical follow-up, most of whom had received CZA therapy. Whole-genome sequencing, antimicrobial susceptibility testing, in vitro competition assays, enzyme kinetic analysis, and transcriptomic sequencing were used to systematically characterize the within-host evolutionary dynamics of KPC variants and the fitness heterogeneity of KPC-33. Multiple KPC variants were identified during longitudinal follow-up, among which KPC-33 was the most frequently detected. Among the seven patients who received CZA treatment, KPC-33 was detected in longitudinal isolates from four patients. It was also identified in patient P3, who had not received CZA, whereas other variants were only sporadically identified. Biochemical analysis showed that KPC-33 exhibited an altered kinetic profile relative to KPC-2, characterized by reduced catalytic turnover and altered substrate affinity. KPC-33 did not exhibit a uniform and pronounced fitness defect but instead showed marked strain-dependent heterogeneity. Strains with higher competitive fitness generally showed only limited transcriptional changes, whereas those with lower fitness were accompanied by broader transcriptional remodeling. In this longitudinal cohort, KPC-33 was repeatedly detected, predominantly under CZA-associated selective conditions. Its fitness consequences were clearly strain background dependent and may be associated with the extent of transcriptional remodeling. These findings provide new evidence for understanding the in vivo evolution of CZA resistance.

KPC-33↗
PubMed1999

Host-specific modulation of the selective constraints driving human immunodeficiency virus type 1 env gene evolution.

To address the evolution of human immunodeficiency virus type 1 (HIV-1) within a single host, we analyzed the HIV-1 C2-V5 env regions of both cell-free genomic-RNA- and proviral-DNA-derived clones. Sequential samples were collected over a period of 3 years from six untreated subjects (three typical progressors [TPs] and three slow progressors [SPs], all with a comparable length of infection except one. The evolutionary analysis of the C2-V5 env sequences performed on 506 molecular clones (253 RNA- and 253 DNA-derived sequences) highlighted a series of differences between TPs and SPs. In particular, (i) clonal sequences from SPs (DNA and RNA) showed lower nucleotide similarity than those from TPs (P = 0. 0001), (ii) DNA clones from SPs showed higher intra- and intersample nucleotide divergence than those from TPs (P < 0.05), (iii) higher host-selective pressure was generally detectable in SPs (DNA and RNA sequences), and (iv) the increase in the genetic distance of DNA and RNA sequences over time was paralleled by an increase in both synonymous (Ks) and nonsynonymous (Ka) substitutions in TPs but only in nonsynonymous substitutions in SPs. Several individual peculiarities of the HIV-1 evolutionary dynamics emerged when the V3, V4, and V5 env regions of both TPs and SPs were evaluated separately. These peculiarities, probably reflecting host-specific features of selective constraints and their continuous modulation, are documented by the dynamics of Ka/Ks ratios of hypervariable env domains.

Base Sequence↗
PubMed1999

Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts.

dUTPase is a ubiquitous and essential enzyme responsible for regulating cellular levels of dUTP. The dut gene exists as single, tandemly duplicated, and tandemly triplicated copies. Crystallized single-copy dUTPases have been shown to assemble as homotrimers. dUTPase is encoded as an auxiliary gene in a number of virus genomes. The origin of viral dut genes has remained unresolved since their initial discovery. A comprehensive analysis of dUTPase amino acid sequence relationships was performed to explore the evolutionary dynamics of dut in viruses and their hosts. Our data set, comprised of 24 host and 51 viral sequences, includes representative sequences from available eukaryotes, archaea, eubacteria cells, and viruses, including herpesviruses. These amino acid sequences were aligned by using a hidden Markov model approach developed to align divergent data. Known secondary structures from single-copy crystals were mapped onto the aligned duplicate and triplicate sequences. We show how duplicated dUTPases might fold into a monomer, and we hypothesize that triplicated dUTPases also assemble as monomers. Phylogenetic analysis revealed at least five viral dUTPase sequence lineages in well-supported monophyletic clusters with eukaryotic, eubacterial, and archaeal hosts. We have identified all five as strong examples of horizontal transfer as well as additional potential transfer of dut genes among eubacteria, between eubacteria and viruses, and between retroviruses. The evidence for horizontal transfers is particularly interesting since eukaryotic dut genes have introns, while DNA virus dut genes do not. This implies that an intermediary retroid agent facilitated the horizontal transfer process between host mRNA and DNA viruses.

Amino Acid Sequence↗
PubMed2002

LTR retrotransposons in the dioecious plant Silene latifolia.

Conserved domains of two types of LTR retrotransposons, Tyl-copia- and Ty3-gypsy-like retrotransposons, were isolated from the dioecious plant Silene latifolia, whose sex is determined by X and Y chromosomes. Southern hybridization analyses using these retrotransposons as probes resulted in identical patterns from male and female genomes. Fluorescence in situ hybridization indicated that these retrotransposons do not accumulate specifically in the sex chromosomes. These results suggest that recombination between the sex chromosomes of S. latifolia has not been severely reduced. Conserved reverse transcriptase regions of Ty1-copia-like retrotransposons were isolated from 13 different Silene species and classified into two major families. Their categorization suggests that parallel divergence of the Ty1-copia-like retrotransposons occurred during the differentiation of Silene species. Most functional retrotransposons from three dioecious species, S. latifolia, S. dioica, and S. diclinis, fell into two clusters. The evolutionary dynamics of retrotransposons implies that, in the genus Silene, dioecious species evolved recently from gynodioecious species.

Amino Acid Sequence↗