Exploring Patterns of Human Mortality and Aging: A Reliability Theory Viewpoint.

The most important manifestation of aging is an increased risk of death with advancing age, a mortality pattern characterized by empirical regularities known as mortality laws. We highlight three significant ones: the Gompertz law, compensation effect of mortality (CEM), and late-life mortality deceleration and describe new developments in this area. It is predicted that CEM should result in declining relative variability of mortality at older ages. The quiescent phase hypothesis of negligible actuarial aging at younger adult ages is tested and refuted by analyzing mortality of the most recent birth cohorts. To comprehend the aging mechanisms, it is crucial to explain the observed empirical mortality patterns. As an illustrative example of data-directed modeling and the insights it provides, we briefly describe two different reliability models applied to human mortality patterns. The explanation of aging using a reliability theory approach aligns with evolutionary theories of aging, including idea of chronic phenoptosis. This alignment stems from their focus on elucidating the process of organismal deterioration itself, rather than addressing the reasons why organisms are not designed for perpetual existence. This article is a part of a special issue of the journal that commemorates the legacy of the eminent Russian scientist Vladimir Petrovich Skulachev (1935-2023) and his bold ideas about evolution of biological aging and phenoptosis.

The hierarchical radiation of phyllostomid bats as revealed by adaptive molar morphology.

Adaptive radiations are bursts in biodiversity that generate new evolutionary lineages and phenotypes. However, because they typically occur over millions of years, it is unclear how their macroevolutionary dynamics vary through time and among groups of organisms. Phyllostomid bats radiated extensively for diverse diets-from insects to vertebrates, fruit, nectar, and blood-and we use their molars as a model system to examine the dynamics of adaptive radiations. Three-dimensional shape analyses of lower molars of Noctilionoidea (Phyllostomidae and close relatives) indicate that different diet groups exhibit distinct morphotypes. Comparative analyses further reveal that phyllostomids are a striking example of a hierarchical radiation; phyllostomids' initial, higher-level diversification involved an "early burst" in molar morphological disparity as lineages invaded new diet-affiliated adaptive zones, followed by subsequent lower-level diversifications within adaptive zones involving less dramatic morphological changes. We posit that strong selective pressures related to initial shifts to derived diets may have freed molars from morpho-functional constraints associated with the ancestral molar morphotype. Then, lineages with derived diets (frugivores and nectarivores) diversified within broad adaptive zones, likely reflecting finer-scale niche partitioning. Importantly, the observed early burst pattern is only evident when examining molar traits that are strongly linked to diet, highlighting the value of ecomorphological traits in comparative studies. Our results support the hypothesis that adaptive radiations are commonly hierarchical and involve different tempos and modes at different phylogenetic levels, with early bursts being more common at higher levels.

Testing the Tropical Niche Conservatism Hypothesis: Climatic Niche Evolution of Escallonia Mutis ex L. F. (Escalloniaceae).

We assess the Tropical Niche Conservatism Hypothesis in the genus Escallonia in South America using phylogeny, paleoclimate estimation and current niche modelling. We tested four predictions: (1) the climatic condition where the ancestor of Escallonia grew is megathermal; (2) the temperate niche is a derived condition from tropical clades; (3) the most closely related species have a similar current climate niche (conservation of the phylogenetic niche); and (4) there is a range expansion from the northern Andes to high latitudes during warm times. Our phylogenetic hypothesis shows that Escallonia originated 52.17 ± 0.85 My, in the early Eocene, with an annual mean temperature of 13.8 °C and annual precipitation of 1081 mm, corresponding to a microthermal to mesothermal climate; the species of the northern and central tropical Andes would be the ancestral ones, and the temperate species evolved between 32 and 20 My in a microthermal climate. The predominant evolutionary models were Brownian and Ornstein-Uhlenbeck. There was phylogenetic signal in 7 of the 9 variables, indicating conservation of the climatic niche. Escallonia would have originated in the central and southern Andes and reached the other environments by dispersion.

Turtle body size evolution is determined by lineage-specific specializations rather than global trends.

Organisms display a considerable variety of body sizes and shapes, and macroevolutionary investigations help to understand the evolutionary dynamics behind such variations. Turtles (Testudinata) show great body size disparity, especially when their rich fossil record is accounted for. We explored body size evolution in turtles, testing which factors might influence the observed patterns and evaluating the existence of long-term directional trends. We constructed the most comprehensive body size dataset for the group to date, tested for correlation with paleotemperature, estimated ancestral body sizes, and performed macroevolutionary model-fitting analyses. We found no evidence for directional body size evolution, even when using very flexible models, thereby rejecting the occurrence of Cope's rule. We also found no significant effect of paleotemperature on overall through-time body size patterns. In contrast, we found a significant influence of habitat preference on turtle body size. Freshwater turtles display a rather homogeneous body size distribution through time. In contrast, terrestrial and marine turtles show more pronounced variation, with terrestrial forms being restricted to larger body sizes, up to the origin of testudinids in the Cenozoic, and marine turtles undergoing a reduction in body size disparity after the extinctions of many groups in the mid-Cenozoic. Our results, therefore, suggest that long-term, generalized patterns are probably explained by factors specific to certain groups and related at least partly to habitat use.

A non-homogeneous model of chromosome-number evolution to reveal shifts in the transition patterns across the phylogeny.

Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades.

Ancestral State Reconstruction Using BayesTraits.

The fossil record is the best evidence of the characteristics of extinct species, but only a narrow range of traits fossilize or survive the fossilization process. Lacking fossil or other evidence about the past, ancestral states can be reconstructed. Three pieces of information are combined when reconstructing ancestral states: extant or known trait values (data); the evolutionary history, linking the species of interest (phylogeny); and the evolutionary model of trait change. These reconstructed ancestral states can be interpreted as our best guess as to the route evolution took, given the distribution of the trait across species, the relationships among them, and our model of evolution. Because the information we use to reconstruct the past is often not known without error, uncertainty about their true values should be accounted for when reconstructing ancestral states. In this chapter we describe how ancestral states can be reconstructed using a Bayesian framework implemented in the software BayesTraits to account for uncertainty in the phylogenetic tree and the model of evolution.

Variation in eye abundance among scallops reveals ontogenetic and evolutionary convergence associated with life habits.

Eyes are remarkable systems to investigate the complex interaction between ecological drivers and phenotypic outcomes. Some animals, such as scallops, have many eyes for visual perception, but to date, the evolution of multiple-eye systems remains obscure. For instance, it is unclear whether eye number changes over a lifetime or varies among species. Scallops are a suitable model group to investigate these questions considering the interspecific variation of adult size and ecological diversity. We tested whether eye abundance scales with body size among individuals and species and whether it varies with life habits. We performed comparative analyses, including a phylogenetic ANCOVA and evolutionary model comparisons, based on eye count and shell height (as a proxy of body size) across 31 scallop species. Our analyses reveal that patterns of increasing relationship with body size are not concordant among taxa and suggest ontogenetic convergence caused by similar ecologies. Accordingly, selective optima in eye numbers are associated with shifts in life habits. For instance, species with increased mobility have significantly more eyes than less mobile species. The convergent evolution of greater eye abundance in more mobile scallops likely indicates a visual improvement based on increased levels of oversampling of the surrounding environment.

Bernoulli and binomial proliferation on evolutionary graphs.

In this paper we introduce random proliferation models on graphs. We consider two types of particles: type-1/mutant/invader/red particles proliferates on a population of type-2/wild-type/resident/blue particles. Unlike the well-known Moran model on graphs -as introduced in Lieberman et al. (2005)-, type-1 particles can occupy in a single iteration several neighbouring sites previously occupied by type-2 particles. Two variants are considered, depending on the random distribution involving the proliferation mechanism: Bernoulli and binomial proliferation. By comparison with fixation probability of type-1 particles in the Moran process, critical parameters are introduced. Properties of proliferation are studied and some particular cases are analytically solved. Finally, by updating the parameters that drive the processes through a density-dependent mechanism, it is possible to capture additional relevant features as fluctuating waves of type-1 particles over long periods of time. In fact, the models can be adapted to tackle more general, complex and realistic situations.

The model-specific Markov embedding problem for symmetric group-based models.

We study model embeddability, which is a variation of the famous embedding problem in probability theory, when apart from the requirement that the Markov matrix is the matrix exponential of a rate matrix, we additionally ask that the rate matrix follows the model structure. We provide a characterisation of model embeddable Markov matrices corresponding to symmetric group-based phylogenetic models. In particular, we provide necessary and sufficient conditions in terms of the eigenvalues of symmetric group-based matrices. To showcase our main result on model embeddability, we provide an application to hachimoji models, which are eight-state models for synthetic DNA. Moreover, our main result on model embeddability enables us to compute the volume of the set of model embeddable Markov matrices relative to the volume of other relevant sets of Markov matrices within the model.

A Probabilistic Model for Indel Evolution: Differentiating Insertions from Deletions.

Insertions and deletions (indels) are common molecular evolutionary events. However, probabilistic models for indel evolution are under-developed due to their computational complexity. Here, we introduce several improvements to indel modeling: 1) While previous models for indel evolution assumed that the rates and length distributions of insertions and deletions are equal, here we propose a richer model that explicitly distinguishes between the two; 2) we introduce numerous summary statistics that allow approximate Bayesian computation-based parameter estimation; 3) we develop a method to correct for biases introduced by alignment programs, when inferring indel parameters from empirical data sets; and 4) using a model-selection scheme, we test whether the richer model better fits biological data compared with the simpler model. Our analyses suggest that both our inference scheme and the model-selection procedure achieve high accuracy on simulated data. We further demonstrate that our proposed richer model better fits a large number of empirical data sets and that, for the majority of these data sets, the deletion rate is higher than the insertion rate.

Non-vertical cultural transmission, assortment and the evolution of cooperation.

Cultural evolution of cooperation under vertical and non-vertical cultural transmission is studied, and conditions are found for fixation and coexistence of cooperation and defection. The evolution of cooperation is facilitated by its horizontal transmission and by an association between social interactions and horizontal transmission. The effect of oblique transmission depends on the horizontal transmission bias. Stable polymorphism of cooperation and defection can occur, and when it does, reduced association between social interactions and horizontal transmission evolves, which leads to a decreased frequency of cooperation and lower population mean fitness. The deterministic conditions are compared to outcomes of stochastic simulations of structured populations. Parallels are drawn with Hamilton's rule incorporating relatedness and assortment.

Quest for the Best Evolutionary Model.

In the early 1980s, DNA sequencing became a routine and the increasing computing power opened the door to reconstruct molecular phylogenies using probabilistic approaches. DNA sequence alignments provided a large number of positions containing phylogenetic information, which could be extracted using explicit statistical models that described the mutation process using appropriate parameters. Consequently, an active quest started for building increasingly improved (more realistic) statistical models of nucleotide substitution. The simplest model assumed that nucleotide frequencies were in equilibrium and one single category of substitutions. Subsequent models allowed either unequal nucleotide frequencies or separate rates for transitions and transversions. The HKY85 model (Hasegawa et al. in J Mol Evol 22:160, 1985) combined elegantly both options into a single model, which became one of the most useful ones and has been the choice in many molecular phylogenetic studies ever since. The use of improved substitution models such as HKY85 allows reconstructing more accurate and reliable phylogenies, which in turn provide robust frameworks for understanding how biological diversity evolved and for performing a wealth of comparative studies in different disciplines such as ecology, biogeography, developmental biology, biochemistry, genomics, epidemiology, and biomedicine.

Modeling a cancerous tumor development in a virtual patient suffering from a depressed state of mind: Simulation of somatic evolution with a customized genetic algorithm.

Cancer is a disease of evolutionary origin in which a group of cells in the body initiate evolutionary changes under certain circumstances that can lead to the formation of a tumor. It is currently believed that a hostile cell environment can lead to the cells of an organ or tissue initiating a whole series of physiological changes that will lead to the transformation of healthy cells into cancerous ones. During the process of transformation, cells evolve under a paradigm known as somatic evolution. In this work the first stages of the formation of a cancerous tumor have been simulated assuming that the cause of the formation is the genetic instability of the cells, being the cause of this instability the presence of chronic inflammation, phenomenon responsible for the appearance of a hostile cellular environment. The model simulates a virtual patient where an altered state of mind, whether depressive, stressed or similar, will lead to disturbed hormone levels that will eventually lead to a condition of chronic inflammation. A novelty of the work is the design of a genetic algorithm oriented to the simulation of somatic evolution, representing the cells by means of a vector that encodes the nodes of a stochastic network. These nodes represent the states of the genes, hallmarks of the cancer and genetic stability of a cell, simulating the formation of a tumor in the caverns of the colon. Another novelty of the model is the design of a virtual patient in which a chatbot for the simulation of the state of mind is hybridized with differential equations simulating both the hormones of the so-called hypothalamic-pituitary-adrenal axis and the cytokines involved in the mechanism of cellular inflammation. The work is a first step in the design of models that under a holistic vision allow the simulation and therefore a greater understanding of the different facets of a disease as complex as cancer.

Discrete evolutionary population models: a new approach.

In this paper, we apply a new approach to a special class of discrete time evolution models and establish a solid mathematical foundation to analyse them. We propose new single and multi-species evolutionary competition models using the evolutionary game theory that require a more advanced mathematical theory to handle effectively. A key feature of this new approach is to consider the discrete models as non-autonomous difference equations. Using the powerful tools and results developed in our recent work [E. D'Aniello and S. Elaydi, The structure of ω-limit sets of asymptotically non-autonomous discrete dynamical systems, Discr. Contin. Dyn. Series B. 2019 (to appear).], we embed the non-autonomous difference equations in an autonomous discrete dynamical systems in a higher dimension space, which is the product space of the phase space and the space of the functions defining the non-autonomous system. Our current approach applies to two scenarios. In the first scenario, we assume that the trait equations are decoupled from the equations of the populations. This requires specialized biological and ecological assumptions which we clearly state. In the second scenario, we do not assume decoupling, but rather we assume that the dynamics of the trait is known, such as approaching a positive stable equilibrium point which may apply to a much broader evolutionary dynamics.

The effect of spatiotemporal antibiotic inhomogeneities on the evolution of resistance.

Combating the evolution of widespread antibiotic resistance is one of the most pressing challenges facing modern medicine. Recent research has demonstrated that the evolution of pathogens with high levels of resistance can be accelerated by spatial and temporal inhomogeneities in antibiotic concentration, which frequently arise in patients and the environment. Strategies to predict and counteract the effects of such inhomogeneities will be critical in the fight against resistance. In this paper we develop a mechanistic framework for modelling the adaptive evolution of resistance in the presence of spatiotemporal antibiotic concentrations, which treats the adaptive process as an interaction between two mutually orthogonal forces; the first returns cells to their wild-type state in the absence of antibiotic selection, and the second selects for increased coping ability in the presence of an antibiotic. We apply our model to investigate laboratory adaptation experiments, and then extend it to consider the case in which multiple strategies for resistance undergo competitive evolution.

Elevation does not strongly influence interspecific variation in body size of small Tropical endotherms

Introduction: Body size is an essential trait for endotherms to face the physiological requirements of cold, so there is a tendency to large body size at high altitudes and latitudes, known as Bergmann's rule. However, the validity of this ecomorphological rule to small-bodied endotherms across altitudinal gradients is poorly known. Objective: To understand the effects of environmental variation on body size, we assessed whether interspecific variation in body size of small tropical endotherms follows Bergmann's rule along tropical altitudinal gradients. Methods: We compiled data on elevational ranges and body masses for 133 species of hummingbirds of Colombia. We then assessed the association between body mass and mid-point of the altitudinal distribution using phylogenetic generalized least squares (PGLS) analyses under different evolutionary models. Results: We found a decelerating rate of evolution for body size since the Early Burst model of evolution provided a better fit to body mass data. For elevational range, we found a slow and constant rate since Pagel's lambda model provided a better fit to the mid-point of the altitudinal distribution data. Besides, phylogenetic regression analysis indicated that body mass and the altitudinal range of hummingbirds are associated through the phylogeny, with a positive but slight association (R2= 0.036). Conclusions: We found that body mass and altitude of hummingbirds are positively related, which is in agreement with expectations under Bergmann's rule. However, this association was weaker than expected for small and non-passerine birds like hummingbirds. Thus, our results suggest that environmental changes across altitudinal gradients do not strongly influence body mass in small tropical endotherms as hummingbirds.

Introducción: El tamaño corporal es un rasgo importante para determinar la respuesta de los endotermos a los requerimientos que exigen las zonas frías, por lo cual se espera una tendencia hacia el incremento del tamaño corporal al aumentar la altitud y la latitud. Sin embargo, se conoce poco acerca de la validez de esta regla ecomorfológica, conocida como la regla de Bergmann, para endotermos pequeños en gradientes altitudinales tropicales. Objetivo: Con el fin de entender los efectos de la variación ambiental sobre el tamaño corporal, se evaluó sí la variación interespecífica en la masa corporal de endotermos tropicales pequeños se ajusta a la regla de Bergmann a lo largo de gradientes de elevación. Métodos: Se compilaron datos sobre los rangos de distribución altitudinal y los tamaños corporales de 133 especies de colibríes en Colombia. Posteriormente, se evaluó la asociación entre la masa corporal y el punto medio de distribución altitudinal de los colibríes mediante análisis de mínimos cuadrados generalizados filogenéticos (PGLS) bajo diferentes modelos evolutivos. Resultados: La evolución de la masa corporal se ajustó mejor a un modelo de evolución Early Burst, mientras que el rango de elevación al modelo evolutivo lambda de Pagel; lo que indica que la tasa de evolución es desacelerada para el tamaño del cuerpo, mientras es lenta y constante para el rango de elevación. Además, el análisis de regresión filogenética indica que la masa corporal y el rango de elevación están positiva y ligeramente asociados (R2 = 0.036). Conclusiones: De acuerdo con lo esperado por la regla de Bergmann, los resultados indican que los colibríes tienden a ser más grandes a mayores altitudes. Sin embargo, esta asociación es más débil de lo esperado para aves no paseriformes de tamaño pequeño como los colibríes.Por lo tanto, los resultados sugieren que las variaciones ambientales a lo largo de gradientes de elevación no tienen una influencia fuerte sobre el tamaño corporal de endotermos pequeños como los colibríes.

Selection in two-sex stage-structured populations: Genetics, demography, and polymorphism.

The outcome of natural selection depends on the demographic processes of birth, death, and development. Here, we derive conditions for protected polymorphism in a population characterized by age- or stage-dependent demography with two sexes. We do so using a novel two-sex matrix population model including basic Mendelian genetics (one locus, two alleles, random mating). Selection may operate on survival, growth, or fertility, any or all of which may differ between the sexes. The model can therefore incorporate genes with arbitrary pleiotropic and sex-specific effects. Conditions for protected polymorphism are expressed in terms of the eigenvalues of the linearization of the model at the homozygote boundary equilibria. We show that in the absence of sexual dimorphism, polymorphism requires heterozygote superiority in the genotypic population growth rate. In the presence of sexual dimorphism, however, heterozygote superiority is not required; an inferior heterozygote may invade, reducing the population growth rate and even leading to extinction (so-called evolutionary suicide). Our model makes no assumptions about separation of time scales between ecological and evolutionary processes, and can thus be used to project sex×stage×genotype dynamics of eco-evolutionary processes. Empirical evidence that sexual dimorphism affects extinction risk is growing, yet sex differences are often ignored in evolutionary demography and in eco-evolutionary models. Our analysis highlights the importance of sexual dimorphism and suggests mechanisms by which an allele can be favored by selection, yet drive a population to extinction, as a result of the structure and interdependence of sex- and stage-specific processes.

Neutral and niche forces as drivers of species selection.

The evolutionary and ecological processes behind the origin of species are among the most fundamental problems in biology. In fact, many theoretical hypothesis on different type of speciation have been proposed. In particular, models of sympatric speciation leading to the formation of new species without geographical isolation, are based on the niche hypothesis: the diversification of the population is induced by the competition for a limited set of available resources. Interestingly, neutral models of evolution have shown that stochastic forces are sufficient to generate coexistence of different species. In this work, we put forward this dichotomy within the context of species formation, studying how neutral and niche forces contribute to sympatric speciation in a model ecosystem. In particular, we study the evolution of a population of individuals with asexual reproduction whose inherited characters or phenotypes are specified by both niche-based and neutral traits. We analyze the stationary state of the dynamics, and study the distribution of individuals in the whole phenotypic space. We show, both numerically and analytically, that there is a non-trivial coupling between neutral and niche forces induced by stochastic effects in the evolution of the population allowing the formation of clusters, that is, species in the phenotypic space. Remarkably, our framework can be generalized also to sexual reproduction or other type of population dynamics.