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The role of parental age effects on the evolution of aging.

Many studies have found that older parents have shorter-lived offspring. However, the evolutionary significance of these findings is poorly understood. We carried out large-scale demographic experiments to examine the direct effect of maternal age and paternal age on offspring aging in inbred and outbred strains of the fruit fly Drosophila melanogaster. We found that the age of mothers and, to a lesser extent, the age of fathers can have a large influence on both offspring longevity and the shape of the age-specific mortality trajectory. In two independent experiments we found that older mothers generally produced shorter-lived offspring, although the exact effect of maternal age on offspring longevity differed among strains. These results suggest that maternal age effects on progeny aging may influence the evolution of aging.

Aging↗

Macroevolution simulated with autonomously replicating computer programs.

The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. The evolutionary outcome of selection acting on novel variation arising over long periods is therefore difficult to predict. The classical problem of this kind is whether 'replaying the tape of life' would invariably lead to the familiar organisms of the modern biota. Here we study the long-term behaviour of populations of autonomously replicating computer programs and find that the same type, introduced into the same simple environment, evolves on any given occasion along a unique trajectory towards one of many well-adapted end points.

Adaptation, Biological↗

New directions in comparative physiology and biochemistry: mechanisms, adaptations, and evolution.

Historically, the discipline of comparative physiology and biochemistry has had two major goals: (1) elucidation of mechanisms and their adaptative significance, and (2) understanding of the evolution of mechanisms and adaptations. In general, the first goal has dominated the field. In a mechanistic/adaptational approach, the diversity of organisms is an experimental parameter in the investigation. Lineage-specific characteristics reveal both how physiological systems work and how different kinds of animals are adapted to different kinds of environments. We believe that this approach is far from outdated, in part because many animal groups have been investigated superficially if at all, and in part because the incorporation of fundamentally new technologies into our discipline permits us to address previously intractable questions about even intensively studied animal groups. In evolutionary physiology and biochemistry, the diversity of lineage-specific physiological systems and how they came to be is the subject of investigation. Early attempts to employ the evolutionary approach were not only few in number, they were unsatisfying in outcome because neither phylogenetic nor mechanistic/adaptational knowledge was adequate to serve as a firm foundation. We agree with earlier authors that new and more sophisticated applications of this approach, together with progress in understanding both animal phylogeny and mechanisms/adaptations, all promise to allow us at last to fulfill our second historic goal. In our view, an integration of the two approaches seems to present the most productive trajectory into the next century.

Adaptation, Physiological↗

Incremental training of first order recurrent neural networks to predict a context-sensitive language.

In recent years it has been shown that first order recurrent neural networks trained by gradient-descent can learn not only regular but also simple context-free and context-sensitive languages. However, the success rate was generally low and severe instability issues were encountered. The present study examines the hypothesis that a combination of evolutionary hill climbing with incremental learning and a well-balanced training set enables first order recurrent networks to reliably learn context-free and mildly context-sensitive languages. In particular, we trained the networks to predict symbols in string sequences of the context-sensitive language [a(n)b(n)c(n); n > or = 1. Comparative experiments with and without incremental learning indicated that incremental learning can accelerate and facilitate training. Furthermore, incrementally trained networks generally resulted in monotonic trajectories in hidden unit activation space, while the trajectories of non-incrementally trained networks were oscillating. The non-incrementally trained networks were more likely to generalise.

Language↗

Female post-reproductive lifespan: a general mammalian trait.

Traditional explanations for the evolution of menopause and post-reproductive lifespan in human females have been based on the benefits of maternal or grand-maternal care outweighing the cost of lost reproduction. These explanations assume an evolutionary origin of menopause since human divergence with the most recent common ancestor. In this study, I conduct a literature survey of studies of 42 mammal species from eight orders, showing that post-reproductive lifespan appears to be widespread among mammals. I then propose an alternative to traditional hypotheses: following accepted theories of trade-offs and senescence, I suggest that the cost of extending reproductive lifespan might be relatively high in female mammals. Somatic and reproductive senescence appear to follow separate trajectories, so it is not surprising that the two processes should occur on different schedules. The timing of each process is probably determined by maximization of reproductive performance and survival early in adulthood, with consequent trajectories resulting in a post-reproductive lifespan. The early end of reproduction relative to lifespan may be due to the cost of production and/or maintenance of oocytes, which decline exponentially over time. Oocyte number below a threshold may trigger an end to normal hormonal cycling.

Aging↗

Insights to metabolic network evolution by fusion proteins.

Human fusion proteins consisting of two or more fusion partners of prokaryotic origin exhibit accreted function. Recent studies have elucidated the importance of fusion proteins in complex regulatory networks. The significance of fusion proteins in cellular networks and their evolutionary mechanism is largely unknown. Here, we discuss the association of six fusion proteins with the citric acid cycle. We define possible gene fusion scenarios and show that they produce metabolites with high connectivity for complex networking. Complex networking of metabolites requires proteins with incremental structural architectures and functional capabilities. Such higher order functionality is frequently provided by fusion proteins. Therefore, evolution of fusion proteins capable of producing metabolites with greater connectivity for enhanced cross-talk between pathways is critical for the selection of multiple trajectories in maintaining a stoichiometric balance during regulation. The association of six fusion proteins with the citric acid cycle and their capability to produce metabolites with high connectivity index is intriguing. This suggests that fusion gene products and their evolution have had a key role in the selection of complex multifaceted networks. In addition, we propose that fusion proteins have gained additive biochemical function for a balanced regulation of metabolic networks.

Biological Evolution↗

Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.

The analysis of the dynamic behavior of enzymes is fundamental to structural biology. A direct relationship between protein flexibility and biological function has been shown for bovine pancreatic ribonuclease (RNase A) (Rasmussen et al., Nature 1992;357:423-424). More recently, crystallographic studies have shown that functional motions in RNase A involve the enzyme beta-sheet regions that move concertedly on substrate binding and release (Vitagliano et al., Proteins 2002;46:97-104). These motions have been shown to correspond to intrinsic dynamic properties of the native enzyme by molecular dynamics (MD) simulations. To unveil the occurrence of these collective motions in other members of pancreatic-like superfamily, we carried out MD simulations on human angiogenin (Ang). Essential dynamics (ED) analyses performed on the trajectories reveal that Ang exhibits collective motions similar to RNase A, despite the limited sequence identity (33%) of the two proteins. Furthermore, we show that these collective motions are also present in ensembles of experimentally determined structures of both Ang and RNase A. Finally, these subtle concerted beta-sheet motions were also observed for other two members of the pancreatic-like superfamily by comparing the ligand-bound and ligand-free structures of these enzymes. Taken together, these findings suggest that pancreatic-like ribonucleases share an evolutionary conserved dynamic behavior consisting of subtle beta-sheet motions, which are essential for substrate binding and release.

Animals↗

Hepatic metabolic adaptation to endurance exercise: temporal and sex differences by multiomics integration and validation.

BACKGROUND: Although endurance exercise benefits liver health, sex-specific adaptive trajectories remain unclear. This study mapped dynamic liver adaptation in males and females during prolonged training and identified underlying molecular programs. METHODS: Using publicly available time-resolved liver multi-omics data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we established a computational pipeline for differential analysis of transcriptomic, proteomic, phosphoproteomic, and metabolomic data with FDR correction, followed by FGSEA pathway enrichment. Kinase activities were inferred through ortholog mapping and PhosphoSitePlus. Cross-omics co-expression networks were constructed using WGCNA and topological overlap to link omics features with physiological phenotypes. For experimental validation, liver tissues were collected from endurance-trained Sprague-Dawley rats, and key nodes were confirmed by Western blotting, qRT-PCR, and immunofluorescence/immunohistochemical staining. Public scRNA-seq data were further integrated to map multi-omics signals to single-cell resolution and assess functional changes in specific cell types. RESULTS: The hepatic response to exercise stress was stage-specific, shifting from early transcriptional activation to later proteomic and metabolic remodeling. Multi-omics integration revealed distinct sex-associated adaptive trajectories: males were more strongly associated with energy metabolism, redox-related programs, and amino acid/organic acid catabolism, whereas females showed prominent membrane lipid remodeling, proteostasis -related programs, and mitochondrial/ribosomal translational features. Single-cell analysis showed that tissue remodeling occurred without major lineage turnover, instead involving altered communication among pre-existing cell communities. Validation of PPP1R3G identified a protein-dominant exercise-responsive marker, supporting the contribution of post-transcriptional or protein-level regulation. CONCLUSIONS: Hepatic adaptation to endurance stress follows a cross-omics evolutionary pattern with sex-specific reprogramming of energy supply and homeostatic maintenance. This time-resolved framework clarifies how exercise improves liver function and supports sex-oriented metabolic interventions and therapeutic target discovery.

Animals↗

Relative growth of the limbs and trunk in sifakas: heterochronic, ecological, and functional considerations.

Limb, trunk, and body weight measurements were obtained for growth series of Milne-Edwards's diademed sifaka, Propithecus diadema edwardsi, and the golden-crowned sifaka, Propithecus tattersalli. Similar measures were obtained also for primarily adults of two subspecies of the western sifaka: Propithecus verreauxi coquereli, Coquerel's sifaka, and Propithecus verreauxi verreauxi, Verreaux's sifaka. Ontogenetic series for the larger-bodied P. d. edwardsi and the smaller-bodied P. tattersalli were compared to evaluate whether species-level differences in body proportions result from the differential extension of common patterns of relative growth. In bivariate plots, both subspecies of P. verreauxi were included to examine whether these taxa also lie along a growth trajectory common to all sifakas. Analyses of the data indicate that postcranial proportions for sifakas are ontogenetically scaled, much as demonstrated previously with cranial dimensions for all three species (Ravosa, 1992). As such, P. d. edwardsi apparently develops larger overall size primarily by growing at a faster rate, but not for a longer duration of time, than P. tattersalli and P. verreauxi; this is similar to results based on cranial data. A consideration of Malagasy lemur ecology suggests that regional differences in forage quality and resource availability have strongly influenced the evolutionary development of body-size variation in sifakas. On one hand, the rainforest environment of P. d. edwardsi imposes greater selective pressures for larger body size than the dry-forest environment of P. tattersalli and P. v. coquereli, or the semi-arid climate of P. v. verreauxi. On the other hand, as progressively smaller-bodied adult sifakas are located in the east, west, and northwest, this apparently supports suggestions that adult body size is set by dry-season constraints on food quality and distribution (i.e., smaller taxa are located in more seasonal habitats such as the west and northeast). Moreover, the fact that body-size differentiation occurs primarily via differences in growth rate is also due apparently to differences in resource seasonality (and juvenile mortality risk in turn) between the eastern rainforest and the more temperate northeast and west. Most scaling coefficients for both arm and leg growth range from slight negative allometry to slight positive allometry. Given the low intermembral index for sifakas, which is also an adaptation for propulsive hindlimb-dominated jumping, this suggests that differences in adult limb proportions are largely set prenatally rather than being achieved via higher rates of postnatal hindlimb growth.(ABSTRACT TRUNCATED AT 400 WORDS)

Adaptation, Biological↗

Are We Witnessing a Speciation Continuum? Evidence From Current and Past Gene Flow in the Genus Oritrophium s.s. (Asteraceae) From the Tropical High Andes.

Determining species boundaries is key for appropriately assessing biodiversity. However, the continuity of the speciation process makes delimiting species a difficult task, especially for recently diverged taxa. Furthermore, past introgression may leave traces that result in reticulate evolutionary patterns, challenging the estimation of species relationships. The fastest-evolving biodiversity hotspot on Earth is the Páramo. Its flora in the tropical high Andes is known for extraordinarily high species richness and endemism. However, the recent origin, fast diversification and complex taxonomy of many genera challenge species delimitation and phylogenetic reconstruction. In this study, we reconstructed phylogenetic relationships and addressed the role of introgression in the diversification of Oritrophium s.s. (Asteraceae) based on phylogenomic data. We combined genomic, phenotypic and ecological data to test species boundaries and compared trajectories across the speciation continuum within the taxonomically complex 'O. peruvianum group'. We found that historical introgression played an important role in the evolution of Oritrophium s.s., and many of the taxa within the 'O. peruvianum group' are at various stages of speciation. These results highlight the importance of testing for introgression to understand the diversification of recently evolved groups. Likewise, they suggest that heterogeneous speciation trajectories associated with geographic isolation and secondary contact, possibly during the Pleistocene, contributed to plant diversity in the tropical high Andes.

Genetic Speciation↗

Mutations arising in the wave front of an expanding population.

The ability to infer the time and place of origin of a mutation can be very useful when reconstructing the evolutionary histories of populations and species. We use forward computer simulations of population growth, migration, and mutation in an analysis of an expanding population with a wave front that advances at a constant slow rate. A pronounced founder effect can be observed among mutations arising in this wave front where extreme population bottlenecks arise and are followed by major population growth. A fraction of mutations travel with the wave front and generate mutant populations that are on average much larger than those that remain stationary. Analysis of the diffusion of these mutants makes it possible to reconstruct migratory trajectories during population expansions, thus helping us better understand observed patterns in the evolution of species such as modern humans. Examination of some historical data supports our model.

Biological Evolution↗

Complexity, pattern, and evolutionary trade-offs in animal aggregation.

One of the most striking patterns in biology is the formation of animal aggregations. Classically, aggregation has been viewed as an evolutionarily advantageous state, in which members derive the benefits of protection, mate choice, and centralized information, balanced by the costs of limiting resources. Consisting of individual members, aggregations nevertheless function as an integrated whole, displaying a complex set of behaviors not possible at the level of the individual organism. Complexity theory indicates that large populations of units can self-organize into aggregations that generate pattern, store information, and engage in collective decision-making. This begs the question, are all emergent properties of animal aggregations functional or are some simply pattern? Solutions to this dilemma will necessitate a closer marriage of theoretical and modeling studies linked to empirical work addressing the choices, and trajectories, of individuals constrained by membership in the group.

Animals↗

Compensation for a bad start: grow now, pay later?

Nutritional conditions during key periods of development, when the architecture and modus operandi of the body become established, are of profound importance in determining the subsequent life-history trajectory of an organism. If developing individuals experience a period of nutritional deficit, they can subsequently show accelerated growth should conditions improve, apparently compensating for the initial setback. However, recent research suggests that, although compensatory growth can bring quick benefits, it is also associated with a surprising variety of costs that are often not evident until much later in adult life. Clearly, the nature of these costs, the timescale over which they are incurred and the mechanisms underlying them will play a crucial role in determining compensatory strategies. Nonetheless, such effects remain poorly understood and largely neglected by ecologists and evolutionary biologists.

Journal Article↗

If bone is the answer, then what is the question?

In the 19th century, several scientists attempted to relate bone trabecular morphology to its mechanical, load-bearing function. It was suggested that bone architecture was an answer to requirements of optimal stress transfer, pairing maximal strength to minimal weight, according to particular mathematical design rules. Using contemporary methods of analysis, stress transfer in bones was studied and compared with anatomical specimens, from which it was hypothesised that trabecular architecture is associated with stress trajectories. Others focused on the biological processes by which trabecular architectures are formed and on the question of how bone could maintain the relationship between external load and architecture in a variable functional environment. Wilhelm Roux introduced the principle of functional adaptation as a self-organising process based in the tissues. Julius Wolff, anatomist and orthopaedic surgeon, entwined these 3 issues in his book The Law of Bone Remodeling (translation), which set the stage for biomechanical research goals in our day. 'Wolff's Law' is a question rather than a law, asking for the requirements of structural optimisation. In this article, based on finite element analysis (FEA) results of stress transfer in bones, it is argued that it was the wrong question, putting us on the wrong foot. The maximal strength/minimal weight principle does not provide a rationale for architectural formation or adaptation; the similarity between trabecular orientation and stress trajectories is circumstantial, not causal. Based on computer simulations of bone remodelling as a regulatory process, governed by mechanical usage and orchestrated by osteocyte mechanosensitivity, it is shown that Roux's paradigm, conversely, is a realistic proposition. Put in a quantitative regulatory context, it can predict both trabecular formation and adaptation. Hence, trabecular architecture is not an answer to Wolff's question, in the sense of this article's title. There are no mathematical optimisation rules for bone architecture; there is just a biological regulatory process, producing a structure adapted to mechanical demands by the nature of its characteristics, adequate for evolutionary endurance. It is predicted that computer simulation of this process can help us to unravel its secrets.

Animals↗

A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters.

Infinite-dimensional characters are those in which the phenotype of an individual is described by a function, rather than by a finite set of measurements. Examples include growth trajectories, morphological shapes, and norms of reaction. Methods are presented here that allow individual phenotypes, population means, and patterns of variance and covariance to be quantified for infinite-dimensional characters. A quantitative-genetic model is developed, and the recursion equation for the evolution of the population mean phenotype of an infinite-dimensional character is derived. The infinite-dimensional method offers three advantages over conventional finite-dimensional methods when applied to this kind of trait: (1) it describes the trait at all points rather than at a finite number of landmarks, (2) it eliminates errors in predicting the evolutionary response to selection made by conventional methods because they neglect the effects of selection on some parts of the trait, and (3) it estimates parameters of interest more efficiently.

Analysis of Variance↗

Antagonistic coevolution between a bacterium and a bacteriophage.

Antagonistic coevolution between hosts and parasites is believed to play a pivotal role in host and parasite population dynamics, the evolutionary maintenance of sex and the evolution of parasite virulence. Furthermore, antagonistic coevolution is believed to be responsible for rapid differentiation of both hosts and parasites between geographically structured populations. Yet empirical evidence for host-parasite antagonistic coevolution, and its impact on between-population genetic divergence, is limited. Here we demonstrate a long-term arms race between the infectivity of a viral parasite (bacteriophage; phage) and the resistance of its bacterial host. Coevolution was largely driven by directional selection, with hosts becoming resistant to a wider range of parasite genotypes and parasites infective to a wider range of host genotypes. Coevolution followed divergent trajectories between replicate communities despite establishment with isogenic bacteria and phage, and resulted in bacteria adapted to their own, compared with other, phage populations.

Biological Evolution↗

Why Specialized Metabolism Recurrently Emerges in Plants: Chemical and Genomic Biases in Metabolic Diversification.

Specialized metabolism plays a central role in mediating ecological interactions and adaptive responses in plants, while leaving enduring signatures in genome structure and evolution. Here, we synthesize advances in genomics, biochemistry, and evolutionary biology into a metabolite-driven genetic diversification (MGD) framework, in which metabolite chemistry biases the generation, retention, and reuse of genetic variation. When metabolic flux produces reactive, inhibitory, or otherwise costly intermediates, pathways handling these liabilities recurrently recruit gene dosage changes, duplication, and divergence at catalytic and regulatory choke points. These biases do not impose deterministic outcomes; instead, they shape which genomic variants are preferentially sampled and retained under selection, giving rise to predictable patterns of genomic change. Genome multiplication-through whole-genome duplication, allopolyploidy, and cell type-specific endoreduplication-amplifies these effects by altering dosage balance, regulatory context, and retention trajectories. Integrating MGD with genome-scale dosage dynamics explains why specialized metabolism repeatedly converges on similar solutions across plant lineages, even amid extensive genomic turnover and chemical diversity.

Journal Article↗

Limits to human locomotor performance: phylogenetic origins and comparative perspectives.

Studies of human exercise physiology have been conducted from a largely ahistorical perspective. This approach usefully elucidates proximate limits to locomotor performance, but ignores potential sources of biomechanical and physiological variation that derive from adaptation to ancestral environments. Phylogenetic reconstruction suggests that multiple hominoid lineages, including that leading to Homo sapiens, evolved in African highlands at altitudes of 1000-2000 m. The evolution of human locomotor physiology therefore occurred under conditions of hypobaric hypoxia. In contrast to present-day humans running on treadmills or exercising in otherwise rectilinear trajectories, ancestral patterns of hominid locomotion probably involved intermittent knuckle-walking over variable terrain, occasional bouts of arboreality and an evolving capacity for bipedalism. All such factors represent potential axes of locomotor variation at present unstudied in extant hominoid taxa. As with humans, hummingbirds evolved in mid-montane contexts but pose an extreme contrast with respect to body size, locomotor mode and metabolic capacity. Substantial biomechanical and physiological challenges are associated with flight in hypobaria. Nonetheless, hummingbird lineages demonstrate a progressive invasion of higher elevations and a remarkable tolerance to hypoxia during hovering. Upregulation of aerobic capacity and parallel resistance to hypoxia may represent coupled evolutionary adaptations to flight under high-altitude conditions.

Altitude↗