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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↗
PubMed2003

From local interactions to population dynamics in site-based models of ecology.

A central problem in ecology is relating the interactions of individuals-described in terms of competition, predation, interference, etc.-to the dynamics of the populations of these individuals-in terms of change in numbers of individuals over time. Here, we address this problem for a class of site-based ecological models, where local interactions between individuals take place at a finite number of discrete resource sites over non-overlapping generations and, between generations, individuals move randomly between sites over the entire system. Such site-based models have previously been applied to a wide range of ecological systems: from those involving contest or scramble competition for resources to host-parasite interactions and meta-populations. We show how the population dynamics of site-based models can be accurately approximated by and understood through deterministic and stochastic difference equations. Conversely, we use the inverse of this approximation to show what implicit assumptions are made about individual interactions by modelling of population dynamics in terms of difference equations. To this end, we prove a useful and general theorem: that any model in our class of site-based models has a corresponding stochastic difference equation population model, by which it can be approximated. This theorem allows us to calculate long-term population dynamics, evolutionary stable strategies and, by extending our theory to account for large deviations, extinction probabilities for a wide range of site-based systems. Our methodology is then illustrated to various examples of between species competition, predator-prey interactions and co-operation.

Competitive Behavior↗
PubMed2001

Molecular evolution of the wound-induced serine protease inhibitor wip1 in Zea and related genera.

Plant defense mechanisms have been the subject of intensive investigation. However, little is known about their long-term evolutionary dynamics. We investigated the molecular diversity of a wound-induced serine protease inhibitor, wip1, in the genus Zea, as well as the divergence of wip1 among four genera, Zea, Tripsacum, Sorghum, and Oryza, in order to gain insight into the long-term evolution of plant defense. The specific objectives of this study were to determine (1) whether wip1 has a history of positive or balancing selection, as has been shown for genes involved in plant defense against pathogens, and (2) if the evolutionary histories of wip1 inhibitory loops, which come into closest contact with proteases, differ from the evolutionary history of other parts of this gene. The Zea polymorphism data are consistent with a neutral evolutionary history. In contrast, relative-rate tests suggest a nonneutral evolutionary history. This inconsistency may indicate that selection acting on wip1 is episodic or that wip1 evolves in response to selection favoring novel alleles. We also detected significant heterogeneity in the evolutionary rates of the two inhibitory loops of wip1-one inhibitory loop is highly conserved, whereas the second has diverged rapidly. Because these two inhibitory loops are predicted to have very similar biochemical functions, the significantly different evolutionary histories suggest that these loops have different ecological functions.

Evolution, Molecular↗
PubMed1998

The neuro-immunological interface in an evolutionary perspective: the dynamic relationship between effector and recognition systems.

The evolutionary perspective indicates that an immune-neuroendocrine effector system integrating innate immunity, stress and inflammation is present in invertebrates. This defense network, centered on the macrophage and exerting primitive and highly promiscuous recognition units, is very effective, ancestral and appears to have been conserved throughout evolution from invertebrates to higher vertebrates. It would seem that there was a "big bang" in the recognition system of lower vertebrates, and T and B cell repertoires, MHC and antibodies suddenly appeared. We argue that this phenomenon is the counterpart of the increasing complexity of the internal circuitry and recognition units in the effector system. The immediate consequences were a progressive enlargement of the pathogen repertoire and new problems regarding self/not-self discrimination. Probably not by chance, a new organ appeared, capable of purging cells able of excessive self recognition. This organ, the thymus, appears to be the result of a well known evolutionary strategy of re-using pre-existing material (neuroendocrine cells and mediators constituting the thymic microenvironment). This bricolage at an organ level is similar to the effect we have already described at the level of molecules and functions of the defense network, and has a general counterpart at genetic level. Thus, in vertebrates, the conserved immune-neuroendocrine effector system remains of fundamental importance in defense against pathogens, while its efficiency has increased through synergy with the new, clonotipical recognition repertoire.

Animals↗
PubMed1986

Nonequilibrium thermodynamics and different axioms of evolution.

Proponents of two axioms of biological evolutionary theory have attempted to find justification by reference to nonequilibrium thermodynamics. One states that biological systems and their evolutionary diversification are physically improbable states and transitions, resulting from a selective process; the other asserts that there is an historically constrained inherent directionality in evolutionary dynamics, independent of natural selection, which exerts a self-organizing influence. The first, the Axiom of Improbability, is shown to be nonhistorical and thus, for a theory of change through time, acausal. Its perception of the improbability of living states is at least partially an artifact of closed system thinking. The second, the Axiom of Historically Determined Inherent Directionality, is supported evidentially and has an explicit historical component. Historically constrained dynamic populations are inherently nonequilibrium systems. It is argued that living, evolving systems, when considered to be historically constrained nonequilibrium systems, do not appear improbable at all. Thus, the two axioms are not compatible. Instead, the Axiom of Improbability is considered to result from an unjustified attempt to extend the contingent proximal actions of natural selection into the area of historical, causal explanations. It is thus denied axiomatic status, and the effects of natural selection are subsumed as an additional level of constraint in an evolutionary theory derived from the Axiom of Historically Determined Inherent Directionality.

Biological Evolution↗
PubMed1998

System-dependent Selection, Ecological Feedback and the Emergence of Functional Structure in Ecosystems.

Most models of natural selection assume either that the material environment remains constant or that it fluctuates in ways unrelated to changes in gene frequencies (and therefore changes in the distribution of phenotypes) of the organism undergoing selection. In this paper, we consider what happens when this assumption does not hold, that is, when ecological feedback between organism and environment is included in the evolutionary process. Specifically, we examine the unusual evolutionary dynamics that occur when changes in the distribution of phenotypes (resulting from selection) alter an environmental parameter in ways that, in turn, modify selection pressures. This process, which we term "system-dependent selection", can produce stable phenotypic diversity which functions to regulate the relevant environmental parameter within a much narrower range would occur in the absence of ecological feedback. This environmental regulation raises the mean fitness of the population and reduces variance in fitness among different phenotypes. Thus, system-dependent selection produces functional organization at the level of the system, as a whole, rather than at the level of the individual organism. We use James Lovelock's model of the imaginary planet Daisyworld to describe the unusual dynamics of this selective process and then use a similar model to examine the structure of an ancient system of wet-rice farming on the Indonesian island of Bali. This model accurately predicts the actual structure of functional organization along two Balinese rivers. We investigate the stability of such systems by exploring the conditions under which mutant phenotypes can invade Daisyworld. The results suggest that the phenotypic diversity and functional organization produced by system-dependent selection may be maintained when there exists variation, over evolutionary time, in the environmental parameters underlying system-dependent dynamics.Copyright 1998 Academic Press Limited

Journal Article↗
PubMed2000

Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup.

In this study, a comparative genomics approach is employed to investigate the forces that shape evolutionary change in the mitochondrial DNA (mtDNA) of members of the Drosophila melanogaster subgroup. This approach facilitates differentiation of the patterns of variation resulting from processes acting at a higher level from those acting on a single gene. The mitochondrial genomes of three isofemale lines of D. simulans (siI, -II, and -III), two of D. melanogaster (Oregon R and a line from Zimbabwe), and D. mauritiana (maI and -II), and one of D. sechellia were sequenced and compared with that derived from D. yakuba. Data presented here indicate that at least three broad mechanisms shape the evolutionary dynamics of mtDNA in these taxa. The first set of mechanisms is intrinsic to the molecule. Dominant processes may be interpreted as selection for an increased rate of replication of the mtDNA molecule, biases in DNA repair, and differences in the pattern of nucleotide substitution among strands. In the genes encoded on the major strand (62% of the coding DNA) changes to or from C predominate, whereas on the minor changes to or from G predominate. The second set of mechanisms affects distinct lineages. There are evolutionary rate differences among lineages, possibly owing to population demographic changes or changes in mutational biases. This is supported by the heterogeneity found in synonymous, nonsynonymous, and silent substitutions. The third set of mechanisms differentially affects distinct genes. A maximum-likelihood sliding-window analysis detected four disjunct regions that have a significantly different nucleotide substitution process from that derived from the complete sequence. These data show the potential for comparative genomics to tease apart subtle forces that shape the evolution of DNA.

Animals↗
PubMed2025

Single-cell mutational burden distributions in birth-death processes.

Genetic mutations are footprints of cancer evolution and reveal critical dynamic parameters of tumour growth, which otherwise are hard to measure in vivo. The mutation accumulation in tumour cell populations has been described by various statistics, such as site frequency spectra (SFS), single-cell division distributions (DD) and mutational burden distributions (MBD). While DD and SFS have been intensively studied in phylogenetics especially after the development of whole genome sequencing technology of bulk samples, MBD has drawn attention more recently with the single-cell sequencing data. Although those statistics all arise from the same somatic evolutionary process, an integrated understanding of these distributions is missing and requires novel mathematical tools to better inform the ecological and evolutionary dynamics of tumours. Here we introduce dynamical matrices to analyse and unite the SFS, DD and MBD and derive recurrence relations for the expectations of these three distributions. While we successfully recover classic exact results in pure-birth cases for the SFS and the DD through our new framework, we derive a new expression for the MBD and approximate all three distributions when death is introduced. We demonstrate a natural link between the SFS and the single-cell MBD, and show that the MBD can be regenerated through the DD. Counter-intuitively, the single-cell MBD is mainly driven by the stochasticity arising in the DD, rather than the extra stochasticity in the number of mutations at each cell division.

Single-Cell Analysis↗
PubMed1989

Antagonistic co-evolution and the evolution of genotypic randomization.

Antagonistic co-evolution, such as the pursuit and flight of host-parasite co-evolution, easily generates cyclical co-evolutionary dynamics. It is well known that a fluctuating, contrary environment may favour the evolution of recombination, but previous analyses have shown that the optimal rate of recombination declines as the period of the environmental fluctuations gets longer. It is here shown that the direction of selection for recombination (for higher or lower rates) may only be sensitive to fluctuation period if the fluctuations are generated by non-co-evolving features of the environment, such as changes in climate. In the simple model of this paper, co-evolutionary cycling provides an advantage for recombination that is independent of period length. This independence of period length necessitates a new framework for understanding the advantage of recombination in the context of co-evolution. In the model studied in this paper it is the phase difference of the host and parasite trajectories that is the relevant feature, and phase relationships are independent of the co-evolutionary cycle time. That is, the phase difference of the oscillations is independent of their frequency.

Biological Evolution↗
PubMed2003

The population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae): avoidance of mating constraints imposed by low S-allele number.

Senecio squalidus L. (Asteraceae) has been the subject of several ecological and population genetic studies due to its well-documented history of introduction, establishment and spread throughout Britain in the past 300 years. Our recent studies have focused on identifying and quantifying factors associated with the sporophytic self-incompatibility (SSI) system of S. squalidus that may have contributed to its success as a colonist. These findings are of general biological interest because they provide important insights into the short-term evolutionary dynamics of a plant mating system. The number of S-alleles in populations and their dominance interactions were investigated in eight wild British populations using cross-diallel studies. The numbers of S-alleles in British S. squalidus populations are typically low (average of 5.3 S-alleles) and the entire British population is estimated to possess no more than 7-11 S-alleles. Such low numbers of S-alleles are most probably a consequence of population bottlenecks associated with introduction and colonization. Potential evolutionary impacts on SSI caused by a paucity of S-alleles, such as restricted mate availability, are discussed, and we suggest that increased dominance interactions between S-alleles may be an important short-term means of increasing mate availability when S-allele numbers are low.

Alleles↗
PubMed2004

Evolution of 4-coumarate:coenzyme A ligase (4CL) gene and divergence of Larix (Pinaceae).

The evolutionary dynamics of the 4CL gene encoding 4-coumarate:coenzyme A ligase was investigated in the genus Larix (Pinaceae) by comparing copy number, GC content and codon usage, sequence divergence, and phylogenetic analysis. All 4CL clones of Larix formed a strongly supported monophyletic group, in which two robust clades (4clA and 4clB) derived from an ancient gene duplication event in the common ancestor of Larix were identified. Further gene duplication in the 4clA clade gave rise to two subclades 4clA(1) and 4clA(2). Frequent duplication/deletion appears to be a common evolutionary phenomenon in the 4CL gene family and paralogous genes differ greatly in their evolution rate. The existence of L. speciosa in subclades 4clA(1) and 4clA(2) suggests that this species may represent a primitive form of Larix or the closest relative of the common ancestor of the Eurasian Sect. Multiserialis. In addition, cpDNA and nrDNA ITS analyses support the hypothesis of an early separation of Larix into a North American and a Eurasian clade, which is congruent with the results of previous allozyme and very recent AFLP analyses. The unexpected close relationship between North American larches and the short-bracted species L. gmelinii in East Asia, based on the 4CL gene tree, may stem from lineage sorting.

Base Composition↗
PubMed1997

Phylogenetic analysis of a retrotransposon with implications for strong evolutionary constraints on reverse transcriptase.

This study examines the evolutionary dynamics of a retrotransposon in a group of parasitoid wasps. A region containing the reverse transcriptase (RT) domain was sequenced for 43 elements from the genomes of nine different wasp species. Phylogenetic analysis of the elements revealed concordance with taxonomic classification of the host species, and the pattern was consistent with that expected for vertical transmission of a multicopy element during differentiation of the species. Twenty-three of the 43 elements had comparable intact open reading frames in the amplified region, and these were used in an analysis of evolutionary constraint on the amino acid sequence. As previously documented for retroelements, closely related elements exhibited nearly equal substitution rates at nonsynonymous and synonymous sites, but relative nonsynonymous substitution rates decreased as increasingly divergent elements were compared. A statistical test indicated that the decrease was not due to saturation of weakly selected sites. The pattern is most likely caused by a "pseudogene effect." Individual elements are not subject to purifying selection, and therefore, synonymous and nonsynonymous substitutions accumulate at equal rates. Comparisons among closely related elements are influenced strongly by this pseudogene evolution, whereas comparisons among distantly related elements reveal selection on the actively replicating lineages connecting the elements. These distant comparisons more accurately reflect the constraints on the amino acid sequence, and the comparisons among elements in this study indicated strong constraints on RT.

Amino Acid Sequence↗
PubMed2004

An obligate brood parasite trapped in the intraspecific arms race of its hosts.

Reciprocal selection pressures often lead to close and adaptive matching of traits in coevolved species. A failure of one species to match the evolutionary trajectories of another is often attributed to evolutionary lags or to differing selection pressures across a geographic mosaic. Here we show that mismatches in adaptation of interacting species--an obligate brood parasitic duck and each of its two main hosts--are best explained by the evolutionary dynamics within the host species. Rejection of the brood parasite's eggs was common by both hosts, despite a lack of detectable cost of parasitism to the hosts. Egg rejection markedly reduced parasite fitness, but egg mimicry experiments revealed no phenotypic natural selection for more mimetic parasitic eggs. These paradoxical results were resolved by the discovery of intraspecific brood parasitism and conspecific egg rejection within the hosts themselves. The apparent arms race between species seems instead to be an incidental by-product of within-species conflict, with little recourse for evolutionary response by the parasite.

Adaptation, Physiological↗
PubMed1998

Instability of signaling resolution models of parent-offspring conflict.

Recent signaling resolution models of parent-offspring conflict have provided an important framework for theoretical and empirical studies of communication and parental care. According to these models, signaling of need is stabilized by its cost. However, our computer simulations of the evolutionary dynamics of chick begging and parental investment show that in Godfray's model the signaling equilibrium is evolutionarily unstable: populations that start at the signaling equilibrium quickly depart from it. Furthermore, the signaling and nonsignaling equilibria are linked by a continuum of equilibria where chicks above a certain condition do not signal and we show that, contrary to intuition, fitness increases monotonically as the proportion of young that signal decreases. This result forces us to reconsider much of the current literature on signaling of need and highlights the need to investigate the evolutionary stability of signaling equilibria based on the handicap principle.

Animals↗
PubMed2025

Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.

BACKGROUND: Centromeres are crucial for precise chromosome segregation and maintaining genome stability during cell division. However, their evolutionary dynamics, particularly in polyploid organisms with complex genomic architectures, remain largely enigmatic. Allopolyploid wheat, with its well-defined hierarchical ploidy series and recent polyploidization history, serves as an excellent model to explore centromere evolution. RESULTS: In this study, we perform a systematic comparative analysis of centromeres in common wheat and its corresponding ancestral species, utilizing the latest comprehensive reference genome assembly available. Our findings reveal that wheat centromeres predominantly consist of five types of centromeric-specific retrotransposon elements (CRWs), with CRW1 and CRW2 being the most prevalent. We identify distinct evolutionary trajectories in the functional centromeres of each subgenome, characterized by variations in copy number, insertion age, and CRW composition. By utilizing CENH3-ChIP data across various ploidy levels, we uncover a series of CRW invasion events that have shaped the evolution of AA subgenome centromeres. Conversely, the evolutionary process of the DD subgenome centromeres involves their expansion from diploid to hexaploid wheat, facilitating adaptation to a larger genomic context. Integration of complete einkorn centromere assemblies and Aegilops tauschii pan-genomes further revealed subgenome-specific centromere evolutionary trajectories. By inclusion of synthetic hexaploid from S2-S3 generations, alongside 2x/6 × natural accessions, we demonstrate that DD subgenome centromere expansion represents a gradual evolutionary process rather than an immediate response to polyploidization. CONCLUSIONS: Our study provides a comprehensive landscape of centromere adaptation, evolution, and maturation, along with insights into how retrotransposon invasions drive centromere evolution in polyploid wheat.

Centromere↗
PubMed1997

A phylogenetic perspective on P transposable element evolution in Drosophila.

The P element, originally described in Drosophila melanogaster, is one of the best-studied eukaryotic transposable elements. In an attempt to understand the evolutionary dynamics of the P element family, an extensive phylogenetic analysis of 239 partial P element sequences has been completed. These sequences were obtained from 40 species in the Drosophila subgenus Sophophora. The phylogeny of the P element family is examined in the context of a phylogeny of the species in which these elements are found. An interesting feature of many of the species examined is the coexistence in the same genome of P sequences belonging to two or more divergent subfamilies. In general, P elements in Drosophila have been transmitted vertically from generation to generation over evolutionary time. However, four unequivocal cases of horizontal transfer, in which the element was transferred between species, have been identified. In addition, the P element phylogeny is best explained in numerous instances by horizontal transfer at various times in the past. These observations suggest that, as with some other transposable elements, horizontal transfer may play an important role in the maintenance of P elements in natural populations.

Animals↗
PubMed2004

Evolution of multihost parasites.

Multihost parasites can infect different types of hosts or even different host species. Epidemiological models have shown the importance of the diversity of potential hosts for understanding the dynamics of infectious disease (e.g., the importance of reservoirs), but the consequences of this diversity for virulence and transmission evolution remain largely overlooked. Here, I present a general theoretical framework for the study of life-history evolution of multihost parasites. This analysis highlights the importance of epidemiology (the relative quality and quantity of different types of infected hosts) and between-trait constraints (both within and between different hosts) to parasite evolution. I illustrate these effects in different transmission scenarios under the simplifying assumption that parasites can infect only two types of hosts. These simple but contrasted evolutionary scenarios yield new insights into virulence evolution and the evolution of transmission routes among different hosts. Because many of the pathogens that have large public-health and agricultural impacts have complex life cycles, an understanding of their evolutionary dynamics could hold substantial benefits for management.

Animals↗
PubMed2005

The evolution of host resistance: tolerance and control as distinct strategies.

In response to parasitic infection, hosts may evolve defences that reduce the deleterious effects on survivorship. This may be interpreted as a form of resistance, as long as infected hosts are able to either recover or reproduce. Here we distinguish two important routes to this form of resistance. An infected host may either: (1) tolerate pathogen damage, or (2) control the pathogen by inhibiting its growth. A model is constructed to examine the evolutionary dynamics of tolerance and control to a free-living microparasite, where both forms of resistance are costly in terms of other life-history traits. We do not observe polymorphism of tolerant genotypes. In contrast, the evolution of control may lead to disruptive selection, and ultimately dimorphism of extreme strains. The optimal host genotype also varies with the type of resistance-individuals invest more in tolerance and pay a greater cost. The free-living framework used makes the distinction between tolerance and control explicit but the distinction applies equally to directly transmitted parasites. Due to the evolutionary differences exhibited, it is important to design experiments that distinguish between the two forms of resistance.

Animals↗