Evolutionary analysis of life span, competition, and adaptive radiation, motivated by the Pacific rockfishes (Sebastes)

Ecological constraint, rather than opportunity, promotes adaptive radiation in three-spined stickleback (Gasterosteus aculeatus) on North Uist

The context and cause of adaptive radiations have been widely described and explored but why rapid evolutionary diversification does not occur in related evolutionary lineages has yet to be understood. The standard answer is that evolutionary diversification is provoked by ecological opportunity and that some lineages do not encounter the opportunity. Three-spined sticklebacks on the Scottish island of North Uist show enormous diversification, which seems to be associated with the diversity of aquatic habitats. Sticklebacks on the neighboring island of South Uist have not been reported to show the same level of evolutionary diversity, despite levels of environmental variation that we might expect to be similar to North Uist. In this study, we compared patterns of morphological and environmental diversity on North and South Uist. Ancestral anadromous sticklebacks from both islands exhibited similar morphology including size and bony "armor." Resident sticklebacks showed significant variation in armor traits in relation to pH of water. However, North Uist sticklebacks exhibited greater diversity of morphological traits than South Uist and this was associated with greater diversity in pH of the waters of lochs on North Uist. Highly acidic and highly alkaline freshwater habitats are missing, or uncommon, on South Uist. Thus, pH appears to act as a causal factor driving the evolutionary diversification of stickleback in local adaptation in North and South Uist. This is consistent with diversification being more associated with ecological constraint than ecological opportunity.

Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality

Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.

Origins and evolution of extreme life span in Pacific Ocean rockfishes

Pacific Ocean rockfishes (genus Sebastes) exhibit extreme variation in life span, with some species being among the most long-lived extant vertebrates. We de novo assembled the genomes of 88 rockfish species and from these identified repeated signatures of positive selection in DNA repair pathways in long-lived taxa and 137 longevity-associated genes with direct effects on life span through insulin signaling and with pleiotropic effects through size and environmental adaptations. A genome-wide screen of structural variation reveals copy number expansions in the immune modulatory butyrophilin gene family in long-lived species. The evolution of different rockfish life histories is coupled to genetic diversity and reshapes the mutational spectrum driving segregating CpG→TpG variants in long-lived species. These analyses highlight the genetic innovations that underlie life history trait adaptations and, in turn, how they shape genomic diversity.

Footprints in the Sand: Deep Taxonomic Comparisons in Vertebrate Genomics to Unveil the Genetic Programs of Human Longevity

With the modern quality, quantity, and availability of genomic sequencing across species, as well as across the expanse of human populations, we can screen for shared signatures underlying longevity and lifespan. Knowledge of these mechanisms would be medically invaluable in combating aging and age-related diseases. The diversity of longevities across vertebrates is an opportunity to look for patterns of genetic variation that may signal how this life history property is regulated, and ultimately how it can be modulated. Variation in human longevity provides a unique window to look for cases of extreme lifespan within a population, as well as associations across populations for factors that influence capacity to live longer. Current large cohort studies support the use of population level analyses to identify key factors associating with human lifespan. These studies are powerful in concept, but have demonstrated limited ability to resolve signals from background variation. In parallel, the expanding catalog of sequencing and annotation from diverse species, some of which have evolved longevities well past a human lifespan, provides independent cases to look at the genomic signatures of longevity. Recent comparative genomic work has shown promise in finding shared mechanisms associating with longevity among distantly related vertebrate groups. Given the genetic constraints between vertebrates, we posit that a combination of approaches, of parallel meta-analysis of human longevity along with refined analysis of other vertebrate clades having exceptional longevity, will aid in resolving key regulators of enhanced lifespan that have proven to be elusive when analyzed in isolation.

Analysis of longevity in Chordata identifies species with exceptional longevity among taxa and points to the evolution of longer lifespans

Animals have a considerable variation in their longevity. This fundamental life-history trait is shaped by both intrinsic and extrinsic mortality pressures, influenced by multiple parameters including ecological variables and mode-of-life traits. Here, we examined the distribution of maximum age at multiple taxonomic ranks (class, order and family) in Chordata, and identified species with exceptional longevity within various taxa. We used a curated dataset of maximum longevity of animals from AnAge database, containing a total of 2542 chordates following our filtering criteria. We determined shapes of maximum age distributions at class, order and family taxonomic ranks, and calculated skewness values for each distribution, in R programming environment. We identified species with exceptional longevity compared to other species belonging to the same taxa, based on our definition of outliers. We collected data on ecological variables and mode-of-life traits which might possibly contribute, at least in part, to the exceptional lifespans of certain chordates. We found that 23, 12 and 4 species have exceptional longevity when we grouped chordates by their class, order and family, respectively. Almost all distributions of maximum age among taxa were positively skewed (towards increased longevity), possibly showing the emergence of longer lifespans in contrast to shorter lifespans, through the course of evolution. However, potential biases in the collection of data should be taken into account. Most of the identified species in the current study have not been previously studied in the context of animal longevity. Our analyses point that certain chordates may have evolved to have longer lifespans compared to other species belonging to the same taxa, and that among taxa, outliers in terms of maximum age have always longer lifespans, not shorter. Future research is required to understand how and why increased longevity have arose in certain species.

The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.

The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.

The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local adaptations like fur or feathers, which characterize species in particular environments, and universal adaptations like microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms driving the universal adaptations of multicellulars should themselves be universal, and propose a mechanism based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. Metabolic networks channel some of this energy to form cooperating, interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it long enough to replicate, and dismantles those that do not. Interactions, energy-charged and dynamic, restrain entropy and enable survival and propagation of integrated living systems. This fosters survival-of-the-fitted - those entities that resist entropic destruction - and not only of the fittest - the entities with the greatest reproductive success. The "unit" of evolution is not a discrete entity, such as a gene, individual, or species; what evolves are collections of related interactions at multiple scales. Survival-of-the-fitted explains universal adaptations, including resident microbiomes, sexual reproduction, continuous diversification, programmed turnover, seemingly wasteful phenotypes, altruism, co-evolving environmental niches, and advancing complexity. Indeed survival-of-the-fittest may be a particular case of the survival-of-the-fitted mechanism, promoting local adaptations that express reproductive advantages in addition to resisting entropy. Survival-of-the-fitted accounts for phenomena that have been attributed to neutral evolution: in the face of entropy, there is no neutrality; all variations are challenged by ubiquitous energy and entropy, retaining those that are "fit enough". We propose experiments to test predictions of the survival-of-the-fitted theory, and discuss implications for the wellbeing of humans and the biosphere.

The Power of Fish Models to Elucidate Skin Cancer Pathogenesis and Impact the Discovery of New Therapeutic Opportunities

Animal models play important roles in investigating the pathobiology of cancer, identifying relevant pathways, and developing novel therapeutic tools. Despite rapid progress in the understanding of disease mechanisms and technological advancement in drug discovery, negative trial outcomes are the most frequent incidences during a Phase III trial. Skin cancer is a potential life-threatening disease in humans and might be medically futile when tumors metastasize. This explains the low success rate of melanoma therapy amongst other malignancies. In the past decades, a number of skin cancer models in fish that showed a parallel development to the disease in humans have provided important insights into the fundamental biology of skin cancer and future treatment methods. With the diversity and breadth of advanced molecular genetic tools available in fish biology, fish skin cancer models will continue to be refined and expanded to keep pace with the rapid development of skin cancer research. This review begins with a brief introduction of molecular characteristics of skin cancers, followed by an overview of teleost models that have been used in the last decades in melanoma research. Next, we will detail the importance of the zebrafish (Danio rerio) animal model and other emerging fish models including platyfish (Xiphophorus sp.), and medaka (Oryzias latipes) in future cutaneous malignancy studies. The last part of this review provides the recent development and genome editing applications of skin cancer models in zebrafish and the progress in small molecule screening.

Current versus future reproduction and longevity: a re-evaluation of predictions and mechanisms

Oxidative damage is predicted to be a mediator of trade-offs between current reproduction and future reproduction or survival, but most studies fail to support such predictions. We suggest that two factors underlie the equivocal nature of these findings: (1) investigators typically assume a negative linear relationship between current reproduction and future reproduction or survival, even though this is not consistently shown by empirical studies; and (2) studies often fail to target mechanisms that could link interactions between sequential life-history events. Here, we review common patterns of reproduction, focusing on the relationships between reproductive performance, survival and parity in females. Observations in a range of species show that performance between sequential reproductive events can decline, remain consistent or increase. We describe likely bioenergetic consequences of reproduction that could underlie these changes in fitness, including mechanisms that could be responsible for negative effects being ephemeral, persistent or delayed. Finally, we make recommendations for designing future studies. We encourage investigators to carefully consider additional or alternative measures of bioenergetic function in studies of life-history trade-offs. Such measures include reactive oxygen species production, oxidative repair, mitochondrial biogenesis, cell proliferation, mitochondrial DNA mutation and replication error and, importantly, a measure of the respiratory function to determine whether measured differences in bioenergetic state are associated with a change in the energetic capacity of tissues that could feasibly affect future reproduction or lifespan. More careful consideration of the life-history context and bioenergetic variables will improve our understanding of the mechanisms that underlie the life-history patterns of animals.

Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes)

Background

The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates.

Results

We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3’ and 5’ UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions.

Conclusions

We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1870-0) contains supplementary material, which is available to authorized users.

Evolution of lifespan

Present-day evolutionary theory, modern synthesis and evo-devo, appear to explain evolution. There remain however several points of contention. These include: biological time, direction, macroevolution verses microevolution, ageing and the extent of internal as opposed to external mediation. A new theoretical model for the control of biological time in vertebrates/bilaterians is introduced. Rather than biological time being controlled solely by a molecular cascade domino effect, it is suggested there is also an intracellular oscillatory clock. This clock (life's timekeeper) is synchronised across all cells in an organism and runs at a constant frequency throughout life. Slower frequencies extend lifespan, increase body/brain size and advance behaviour. They also create a time void which could aid additional evolutionary change. Faster frequencies shorten lifespan, reduce body/brain size and diminish behaviour. They are therefore less likely to mediate evolution in vertebrates/mammals. It is concluded that in vertebrates, especially mammals, there is a direction in evolution towards longer lifespan/advanced behaviour. Lifespan extension could equate with macroevolution and subsequent modifications with microevolution. As life's timekeeper controls the rate of ageing it constitutes a new genetic theory of ageing. Finally, as lifespan extension is internally mediated, this suggests a major role for internal mediation in evolution.

Life's timekeeper

Life's timekeeper is a 'free-running' intracellular oscillator synchronised across all cells. It runs throughout life splitting lifespan into equal length phases. During the maturational period it controls the overall rate of progression whereas in the post-maturational period it controls the overall rate of ageing. This includes the rate of senescence and hence time to death. As such life's timekeeper equates maturational and post-maturational time, hence explains the tight correlation between these time periods that has existed throughout mammalian evolution. Life's timekeeper is proposed to have played an important role in vertebrate evolution. A slower oscillatory frequency results in proportional life phase prolongation. This leads to increased body and brain size, together with extended lifespan. Higher brain centres, neocortex in mammals, are disproportionately enlarged. Hence behavioural capacity is increased. The extended post-maturational period ensures that there is enough time in order that the behavioural advantages can be fully manifest in the environment. A faster oscillatory frequency would result in proportional life phase reduction. This process however would lead to reduced behavioural capacity, and is hence unlikely to be positively selected. Therefore throughout evolution life's timekeeper has operated to extend lifespan. It has hence functioned to promote longevity as opposed to ageing.

Comparative endocrinology of aging and longevity regulation

Hormones regulate growth, development, metabolism, and other complex processes in multicellular animals. For many years it has been suggested that hormones may also influence the rate of the aging process. Aging is a multifactorial process that causes biological systems to break down and cease to function in adult organisms as time passes, eventually leading to death. The exact underlying causes of the aging process remain a topic for debate, and clues that may shed light on these causes are eagerly sought after. In the last two decades, gene mutations that result in delayed aging and extended longevity have been discovered, and many of the affected genes have been components of endocrine signaling pathways. In this review we summarize the current knowledge on the roles of endocrine signaling in the regulation of aging and longevity in various animals. We begin by discussing the notion that conserved systems, including endocrine signaling pathways, "regulate" the aging process. Findings from the major model organisms: worms, flies, and rodents, are then outlined. Unique lessons from studies of non-traditional models: bees, salmon, and naked mole rats, are also discussed. Finally, we summarize the endocrinology of aging in humans, including changes in hormone levels with age, and the involvement of hormones in aging-related diseases. The most well studied and widely conserved endocrine pathway that affects aging is the insulin/insulin-like growth factor system. Mutations in genes of this pathway increase the lifespan of worms, flies, and mice. Population genetic evidence also suggests this pathway's involvement in human aging. Other hormones including steroids have been linked to aging only in a subset of the models studied. Because of the value of comparative studies, it is suggested that the aging field could benefit from adoption of additional model organisms.

Speciation along a depth gradient in a marine adaptive radiation

Oceans are home to much of the world's biodiversity, but we know little about the processes driving speciation in marine ecosystems with few geographical barriers to gene flow. Ecological speciation resulting from divergent natural selection between ecological niches can occur in the face of gene flow. Sister species in the young and ecologically diverse rockfish genus Sebastes coexist in the northeast Pacific, implying that speciation may not require geographical isolation. Here, I use a novel phylogenetic comparative analysis to show that rockfish speciation is instead associated with divergence in habitat depth and depth-associated morphology, consistent with models of parapatric speciation. Using the same analysis, I find no support for alternative hypotheses that speciation involves divergence in diet or life history, or that speciation involves geographic isolation by latitude. These findings support the hypothesis that rockfishes undergo ecological speciation on an environmental gradient.

Density dependence, lifespan and the evolutionary dynamics of longevity

Longevity is a life-history trait that is shaped by natural selection. Evolution will shape mortality trajectories and lifespans, but until now the evolutionary analysis of longevity is based principally on a density-independent (Euler-Lotka) framework. The effects of density dependence on the evolution of lifespan and mortality remain largely unexplored. We investigate the influence of different population demographies on the evolution of longevity, and show how these can be linked to adaptive radiations. We present a range of models to explore the intraspecific and interspecific density effects on longevity and, consequently, diversification. We show how the magnitude, type, and timing of mutation can also affect fitness, invasion and diversification. We argue that fitness of alternative strategies under a range of different demographic structures leads to flat, as opposed to rugged, landscapes and that these flat fitness surfaces are important in the evolution of lifespan and senescence.

Phenotypic evolutionary models in stem cell biology: replacement, quiescence, and variability

Phenotypic evolutionary models have been used with great success in many areas of biology, but thus far have not been applied to the study of stem cells except for investigations of cancer. We develop a framework that allows such modeling techniques to be applied to stem cells more generally. The fundamental modeling structure is the stochastic kinetics of stem cells in their niche and of transit amplifying and fully differentiated cells elsewhere in the organism, with positive and negative feedback. This formulation allows graded signals to be turned into all or nothing responses, and shows the importance of looking beyond the niche for understanding how stem cells behave. Using the deterministic version of this framework, we show how competition between different stem cell lines can be analyzed, and under what circumstances stem cells in a niche will be replaced by other stem cells with different phenotypic characteristics. Using the stochastic version of our framework and state dependent life history theory, we show that the optimal behavior of a focal stem cell will involve long periods of quiescence and that a population of identical stem cells will show great variability in the times at which activity occurs; we compare our results with classic ones on quiescence and variability in the hematopoietic system.

The interactive effects of parasites, disturbance, and productivity on experimental adaptive radiations

Disturbance, productivity, and natural enemies are significant determinants of the evolution of diversity, but their interactive effect remains unresolved. We develop a simple, qualitative model assuming trade-offs between growth rate, competitive ability and parasite resistance, to address the interactive effects of these variables on the evolution of host diversity. Consistent with previous studies our model predicts maximum diversity at intermediate levels of disturbance and productivity in the absence of parasitism. However, parasites break down these unimodal diversity relationships with productivity and disturbance, as selection for parasite resistance reduces the importance of growth rate-competitive ability trade-offs. We tested these predictions using the bacterium Pseudomonas fluorescens, which undergoes an adaptive radiation into spatial niche specialists under laboratory conditions. This is the first study of adaptive radiation in response to experimental manipulation of the three-way interaction between productivity, disturbance, and natural enemies. As hypothesized, unimodal diversity relationships with disturbance and productivity were weakened or disappeared in the presence of parasitic phages. This was the result of phages increasing diversity at environmental extremes, by imposing selection for phage-resistant variants, but decreasing diversity in less stressful environments, probably through reductions in resource competition. Phages had a net effect of increasing host diversity. Parasites and other natural enemies are therefore likely to have a large effect in mitigating the influence of other environmental variables on the evolution and maintenance of diversity.