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PubMed2026

Pathogen local adaptation shapes Pierce's disease of grapevines outcomes under field conditions.

Climate change is broadly expected to increase the range of many plant diseases, yet the current status of local thermal adaptation in many pathogens is poorly understood. Xylella fastidiosa (Xf) is a global bacterial plant pathogen that causes Pierce's disease (PD) of grapevines and infects over 700 other host plant species, impacting both agricultural and natural ecosystems. In a common garden experiment with 477 vines in the field, we compared PD outcomes from a local (colder climate in CA) vs non-local (warmer climate in CA) bacterial strain in 13 Mediterranean grapevine varieties over 3 years. Relative to the local strain, there was 77% lower overwinter survival in the non-local strain from a warmer climate, strongly indicating local adaptation in these CA Xf populations. Host genotype also had a significant effect on pathogen winter survival, and grapevine varieties differed in PD susceptibility. Additionally, we assessed in planta evolution of the two pathogen strains over 3 years by whole-genome sequencing 58 field-derived isolates. There were convergent loss-of-function mutations in genes encoding minor Type IV pilin (T4P) proteins, which control twitching motility and other virulence phenotypes, suggesting rapid adaptive evolution. Our results suggest local adaptation to cold temperatures in a bacterial plant pathogen and a possible role for minor Type IV pilins in thermal adaptation. These findings demonstrate the urgent need to incorporate X. fastidiosa evolution and local thermal adaptation into global models of PD spread. Differentiating pathotypes with distinct thermal adaptations will improve disease forecasting and inform quarantine decisions.IMPORTANCEForecasting the movement of plant pathogens is a critical issue under global warming to effectively manage future plant disease outbreaks. Yet, current plant pathogen local thermal adaptation is often unaccounted for, especially in bacterial pathogens. Our study examines local adaptation to temperature in a bacterial plant pathogen, Xylella fastidiosa, that causes disease in grapevines in addition to infecting 700 other plant species. In a large-scale field experiment across 13 grapevine varieties, we demonstrate local adaptation in pathogen winter survival in distinct Xylella fastidiosa strains. Additionally, we found evidence of adaptive evolution in just 3 years, as we observed convergent mutations after resequencing strains that evolved in the field. Our results suggest that X. fastidiosa populations-even within a small geographic area-have distinct adaptations to winter temperatures and may exhibit differential responses to warming winters.

Type IV pili↗
PubMed2000

Sex-limited mutations and the evolution of sexual dimorphism.

Although the developmental and genetic mechanisms underlying sex differences are being elucidated in great detail in a number of species, there remains a breach between proximate and evolutionary studies of sexual dimorphism. More precisely, the evolution of sex-limited gene expression at autosomal loci has not been well reasoned using either theoretical or empirical methods. Here, I show that a Mendelian genetic model including elementary details of sexual differentiation provides novel insight into the evolution of sex differences via sex limitation. This model indicates that the nature of allelic effects and the pattern of selection must be known in both sexes to predict the evolution of sex differences. That is, selection interacts with genetic variation for sexual dimorphism to produce unanticipated patterns of trait divergence or convergence between the sexes. Ultimately, this model may explain why previous models for the evolution of sexual dimorphism do not predict the erratic behavior of the sex difference during artificial selection experiments.

Alleles↗
PubMed2007

The biological standard of living (and its convergence) in Colombia, 1870-2003. A tropical success story.

During the 20th century, the evolution of the biological standard of living in Colombia was a tropical success story from the point of view of the secular increase in height as well as the reduction of inequality. During the period 1905-1985 the average height of females and males increased by nearly 9 cm on the basis of 9 million records examined from National Identification Cards. We also study the evolution of height of Colombians on the basis of passport records. The elite group of passport holders was much taller than average, and remained stable for the birth cohorts of 1870-1919. In the early 20th century the height of passport recipients was 168.7 cm (men) and 158 cm (women) compared with 162 cm and 150 cm for heights in the national ID cards. The results also show that Colombians experienced significant regional and intrapersonal convergence in height.

Body Height↗
PubMed1999

Homology--history of a concept.

The concept of homology is traceable to Aristotle, but Belon's comparison in 1555 of a human skeleton with that of a bird expressed it overtly. Before the late 18th century, the dominant view of the pattern of organisms was the scala naturae--even Linnaeus with his divergent hierarchical classification did not necessarily see the resulting taxonomic pattern as a natural phenomenon. The divergent hierarchy, rather than the acceptance of phylogeny, was the necessary spur to discussion of homology and the concept of analogy. Lamarck, despite his proposal of evolution, attributed homology to his escalator naturae and analogy to convergent acquired characters. Significantly, it was the concept of serial homology that emerged at the end of the 18th century, although comparison between organisms became popular soon after, and was boosted by the famous Cuvier/Geoffroy Saint-Hilaire debate of the 1830s. The concepts of homology and analogy were well understood by the pre- (or anti-) evolutionary comparative anatomists before the general acceptance of phylogeny, and they were defined by Owen in 1843. The acceptance of evolution led to the idea that homology should be defined by common ancestry, and to the confusion between definition and explanation. The term 'homoplasy', introduced by Lankester in 1870, also arose from a phylogenetic explanation of homology.

Adaptation, Biological↗
PubMed1990

Morphological evolution of subterranean mammals: integrating structural, functional, and ecological perspectives.

The widely recognized convergence of subterranean mammals offers unique opportunities for the study of patterns, causes and consequences of morphological integration. For example, behavioral and biomechanical observations have revealed a diversity of digging modes among subterranean mammals. In rodents, scratch-digging and chisel-tooth digging, alone or combined, are widespread. This dual nature of the digging apparatus must be understood to avoid erroneous assessments of specializations based on forelimb modifications only. Additionally, bulldozing and disposal of loose soil is performed by head-lifting, by means of the forelimbs, or with the hindlimbs. Insectivores are known to resort to scratch-digging, sand-swimming, or to a unique system known as humeral rotation. Semi-fossorial species among rodents and insectivores are scratch-diggers. In contrast, fully subterranean taxa show further specializations for scratch-digging and/or resort to some of the other digging modes. The ecological correlates of these morphological trends are still poorly known; work in geomyids suggests that scratch-digging specializations are efficient in friable soils, whereas tooth-digging allows the utilization of a much broader spectrum of soil types. This indicates that alternative pathways of morphological specialization are not equivalent in their ecological potentialities. Important morphological features, such as incisor procumbency among tooth-diggers, are shown to be constrained by structural, allometric, and mechanical factors. In geomyids, the same procumbent morphologies may be acquired as a byproduct of size increases, by means of adaptive shifts independent from size, or by a combination of both. Thus, geometric similarity may not be indicative of functional similarity. Further constraints result from the integration of different functions. For instance, it is suggested that mastication imposes limitations upon potential modifications of jaw morphology for tooth-digging. Scratch-digging appears to be less constrained by locomotion, but the effects of integration of various functions in fore- and hind-limbs are largely unexplored. Multiple approaches, combining behavioral, functional, ecological, structural, and phylogenetic data, are necessary for the study of morphological evolution among subterranean mammals.

Animals↗
PubMed1994

Molecular pathways to parallel evolution: I. Gene nexuses and their morphological correlates.

Aspects of the regulatory interactions among genes are probably as old as most genes are themselves. Correspondingly, similar predispositions to changes in such interactions must have existed for long evolutionary periods. Features of the structure and the evolution of the system of gene regulation furnish the background necessary for a molecular understanding of parallel evolution. Patently "unrelated" organs, such as the fat body of a fly and the liver of a mammal, can exhibit fractional homology, a fraction expected to become subject to quantitation. This also seems to hold for different organs in the same organism, such as wings and legs of a fly. In informational macromolecules, on the other hand, homology is indeed all or none. In the quite different case of organs, analogy is expected usually to represent attenuated homology. Many instances of putative convergence are likely to turn out to be predominantly parallel evolution, presumably including the case of the vertebrate and cephalopod eyes. Homology in morphological features reflects a similarity in networks of active genes. Similar nexuses of active genes can be established in cells of different embryological origins. Thus, parallel development can be considered a counterpart to parallel evolution. Specific macromolecular interactions leading to the regulation of the c-fos gene are given as an example of a "controller node" defined as a regulatory unit. Quantitative changes in gene control are distinguished from relational changes, and frequent parallelism in quantitative changes is noted in Drosophila enzymes. Evolutionary reversions in quantitative gene expression are also expected. The evolution of relational patterns is attributed to several distinct mechanisms, notably the shuffling of protein domains. The growth of such patterns may in part be brought about by a particular process of compensation for "controller gene diseases," a process that would spontaneously tend to lead to increased regulatory and organismal complexity. Despite the inferred increase in gene interaction complexity, whose course over evolutionary time is unknown, the number of homology groups for the functional and structural protein units designated as domains has probably remained rather constant, even as, in some of its branches, evolution moved toward "higher" organisms. In connection with this process, the question is raised of parallel evolution within the purview of activating and repressing master switches and in regard to the number of levels into which the hierarchies of genic master switches will eventually be resolved.

Animals↗
PubMed1999

Molecular clock mirages.

The hypothesis of the molecular clock proposes that molecular evolution occurs at rates that persist through time and across lineages, for a given gene. The neutral theory of molecular evolution predicts that the clock will be a Poisson process, with equal mean and variance. Experimental data have shown that the variance is typically larger than the mean. Hypotheses have been advanced to account for the hypervariance of molecular evolution. Four recent papers show that none of the predictive hypotheses that have been proposed can be generally maintained. The conclusion is that molecular evolution is dependent on the fickle process of natural selection. But it is a time-dependent process, so that accumulation of empirical data often yields an approximate clock, as a consequence of the expected convergence of large numbers.

Animals↗
PubMed1999

Laparoscopic microsurgery: current and future status.

The successful introduction of microsuturing and microinstruments for operative laparoscopy has allowed the convergence of laparoscopy and traditional microsurgery, resulting in the evolution of the 'new microsurgery'. This more dynamic approach overcomes the limitations of open microsurgery by providing continuous magnification and the benefits of a closed environment, making laparoscopy a complete surgical tool. The test model for microsurgery is tubal anastomosis, which is very dependent on operative technique to attain well-established pregnancy rates. Our cumulative pregnancy results for laparoscopic microsurgical tubal anastomosis of 76% at 12 months, 70% at 9 months, 67% at 6 months and 44% at 3 months, compares favorably to the best results achieved by traditional open microsurgery. With this validation the technique is now employed as a complete solution for all tubal surgery. The ability to effect microsurgical repair of the ureter, bladder, bowel and vessels has expanded the surgical repertoire, allowing radical excision of deep endometriosis, severe enterolysis, and adhesiolysis.

Anastomosis, Surgical↗
PubMed2004

Repeated evolution of limblessness and digging heads in worm lizards revealed by DNA from old bones.

The evolutionary relationships of the burrowing amphisbaenians ('worm lizards') have long been controversial for several reasons: the rarity of museum specimens available for study, highly derived morphological conditions that can confound comparative studies and difficulty in obtaining tissues for molecular phylogenetic studies because of their secretive habits in the wild. We present a phylogenetic analysis of two nuclear genes obtained from both fresh tissues and museum specimens of worm lizards. We achieved sufficient taxonomic sampling for analysis by extracting DNA from museum specimens using a modified forensics protocol. Results show the limbless Rhineuridae to be the most basal lineage, whereas the limbed Bipedidae occupy a more derived position as the sister-taxon to a Trogonophidae-Amphisbaenidae clade. This pattern of relationships indicates widespread morphological convergence within the group, including three independent incidences of limb loss. Convergence in skull shape and scalation is also prevalent. Mosaic evolution in the skull versus postcranial skeleton parallels that seen in snake evolution.

Animals↗
PubMed2004

The Mozart effect: tracking the evolution of a scientific legend.

Theories of the diffusion of ideas in social psychology converge on the assumption that shared beliefs (e.g., social representations, rumours and legends) propagate because they address the needs or concerns of social groups. But little empirical research exists demonstrating this link. We report three media studies of the diffusion of a scientific legend as a particular kind of shared belief. We studied the Mozart effect (ME), the idea that listening to classical music enhances intelligence. Study 1 showed that the ME elicited more persistent media attention than other science reports and this attention increased when the ME was manifested in events outside of science. Study 2 suggested that diffusion of the ME may have responded to varying levels of collective anxiety. Study 3 demonstrated how the content of the ME evolved during diffusion. The results provide evidence for the functionality of diffusion of ideas and initial elements for a model of the emergence and evolution of scientific legends.

Adolescent↗
PubMed2025

One thousand SARS-CoV-2 antibody structures reveal convergent binding and near-universal immune escape.

Understanding antibody recognition and adaptation to viral evolution is central to vaccine and therapeutic development. Over 1,100 SARS-CoV-2 antibody structures have been resolved, marking the largest structural biology effort for a single pathogen. We present a comprehensive analysis of this landmark dataset to investigate the principles of antibody recognition and immune escape. Human immunoglobulins and camelid single-chain antibodies dominate, collectively mapping 99% of the receptor-binding domain. Despite remarkable sequence and conformational diversity, antibodies exhibit convergence in their paratope structures, revealing evolutionary constraints in epitope selection. Analyses reveal near-universal immune escape of antibodies, including all clinical monoclonals, by advanced variants such as KP3.1.1. On average, over one-third of antibody epitope residues are mutated. These findings support pervasive immune escape, underscoring the need to effectively leverage multi-epitope-targeting strategies to achieve durable immunity. To support community accessibility, we developed an interactive web server for visualization and analysis of antibody-antigen complexes and mutational data.

SARS-CoV-2↗
PubMed2004

Ecological diversification in a group of Indomalayan pitvipers (Trimeresurus): convergence in taxonomically important traits has implications for species identification.

We analyse molecular and phenotypic evolution in a group of taxonomically problematic Indomalayan pitvipers, the Trimeresurus sumatranus group. Mitochondrial DNA sequencing provides a well-resolved phylogeny, with each species representing a distinct lineage. Multivariate morphological analysis reveals a high level of phenotypic differentiation, which is congruent between the sexes but does not reflect phylogenetic history. An adaptive explanation for the observed pattern of differentiation is supported by independent contrasts analysis, which shows significant correlations between current ecology and the characters that most account for the variation between taxa, including those that are presently used to identify the species. Reduced precipitation and altitude, and increased temperature, are correlated with higher numbers of scales on the head, body and tail. It is hypothesized that scale number plays an important role in heat and water exchange by influencing the area of exposed of interstitial skin, and that colour pattern variation reflects selection pressures involving camouflage and thermoregulation. Ecological convergence in traits used for classification is found to have important implications for species identification where taxa are distributed over varying environments.

Animals↗
PubMedDate not supplied

[Evolution of the neocortex. The principle of a double afferent supply in mammalian evolution].

Comparative electrophysiological data are presented on the role of thalamic, hypothalamic and hippocampal structures in organization and activity of different neocortical formations at various steps of evolution. It was shown that higher mammals have double afferent supply of associative zones of the new cortex from the thalamic and hypothalamic nuclei, exhibiting significant increase in the degree of their convergence pattern.

Afferent Pathways↗
PubMed1993

Chaos and the evolution of cooperation.

The "iterated prisoner's dilemma" is the most widely used model for the evolution of cooperation in biological societies. Here we show that a heterogeneous population consisting of simple strategies, whose behavior is totally specified by the outcome of the previous round, can lead to persistent periodic or highly irregular (chaotic) oscillations in the frequencies of the strategies and the overall level of cooperation. The levels of cooperation jump up and down in an apparently unpredictable fashion. Small recurrent and simultaneous invasion attempts (caused by mutation) can change the evolutionary dynamics from converging to an evolutionarily stable strategy to periodic oscillations and chaos. Evolution can be twisted away from defection, toward cooperation. Adding "generous tit-for-tat" greatly increases the overall level of cooperation and can lead to long periods of steady cooperation. Since May's paper [May, R. M. (1976) Nature (London) 261, 459-467], "simple mathematical models with very complicated dynamics" have been found in many biological applications, but here we provide an example of a biologically relevant evolutionary game whose dynamics display deterministic chaos. The simulations bear some resemblance to the irregular cycles displayed by the frequencies of host genotypes and specialized parasites in evolutionary "arms races" [Hamilton, W. D., Axelrod, R. & Tanese, R. (1990) Proc. Natl. Acad. Sci. USA 87, 3566-3573; Seger, J. (1988) Philos. Trans. R. Soc. London B 319, 541-555].

Biological Evolution↗
PubMed1996

A genetic algorithm approach to optimization for the radiological worker allocation problem.

This paper describes a new approach to the radiological worker allocation problem using a multiple objective genetic algorithm. The worker allocation problem in radiological facilities involves various types of constraints and even mutually conflicting ones, such as individual dose limits, working time limits, etc. A major difficulty of this highly working time limits, etc. A major difficulty of this highly constrained problem is the way of finding an optimal solution in the huge search space where a large proportion of solutions are not feasible because some of the constraints cannot be satisfied. The paper proposes a model of evolution to establish an optimal assignment efficiently, based on the biological insights into the evolutionary process and heuristic ideas. The experimental results show a very rapid evolution to produce feasible solutions, and the application of multiple evaluation functions converges the feasible solutions to good ones. The genetic algorithm approach was found to be superior to the goal programming and simplex methods.

Algorithms↗
PubMed2006

Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments.

Extreme conditions in subsurface are suspected to be responsible for morphological convergences, and so to bias biodiversity assessment. Subterranean organisms are also considered as having poor dispersal abilities that in turn generate a large number of endemic species when habitat is fragmented. Here we test these general hypotheses using the subterranean amphipod Niphargus virei. All our phylogenetic analyses (Bayesian, maximum likelihood and distance), based on two independent genes (28S and COI), revealed the same tripartite structure. N. virei populations from Benelux, Jura region and the rest of France appeared as independent evolutionary units. Molecular rates estimated via global or Bayesian relaxed clock suggest that this split is at least 13 million years old and accredit the cryptic diversity hypothesis. Moreover, the geographical distribution of these lineages showed some evidence of recent dispersal through apparent vicariant barrier. In consequence, we argue that future analyses of evolution and biogeography in subsurface, or more generally in extreme environments, should consider dispersal ability as an evolving trait and morphology as a potentially biased marker.

Adaptation, Physiological↗
PubMed2001

Designing fast converging phylogenetic methods.

Absolute fast converging phylogenetic reconstruction methods are provably guaranteed to recover the true tree with high probability from sequences that grow only polynomially in the number of leaves, once the edge lengths are bounded arbitrarily from above and below. Only a few methods have been determined to be absolute fast converging; these have all been developed in just the last few years, and most are polynomial time. In this paper, we compare pre-existing fast converging methods as well as some new polynomial time methods that we have developed. Our study, based upon simulating evolution under a wide range of model conditions, establishes that our new methods outperform both neighbor joining and the previous fast converging methods, returning very accurate large trees, when these other methods do poorly.

Computational Biology↗