Age determination and validation studies of marine fishes: do deep-dwellers live longer?

Life in the fastlane? A comparative analysis of gene expression profiles across annual, semi-annual, and non-annual killifishes (Cyprinodontiformes: Nothobranchiidae)

The Turquoise Killifish is an important vertebrate for the study of aging and age-related diseases due to its short lifespan. Within Nothobranchiidae, species possess annual, semi-annual, or non-annual life-histories. We took a comparative approach and examined gene expression profiles (QuantSeq) from 62 individuals from eleven nothobranchid species that span three life-histories. Our results show significant differences in differentially expressed genes (DEGs) across life-histories with non-annuals and semi-annuals being most similar, and annuals being the most distinct. At finer scales, we recovered significant differences in DEGs for DNA repair genes and show that non-annual and semi-annuals share similar gene expression profiles, while annuals are distinct. Most of the GO terms enriched in annuals are related to metabolic processes. However, GO terms, including translation, protein transport, and DNA replication initiation also are enriched in annuals. Non-annuals are enriched in Notch signaling pathway genes and downregulated in the canonical Wnt signaling pathway compared to annual species, which suggests that non-annuals have stronger regulation in cellular processes. This study provides support for congruency in DEGs involved in these life-histories and provides strong evidence that a particular set of candidate genes may be worthy of study to investigate their role in the aging process.

Genetic and Epigenetic Interactions Involved in Senescence of Stem Cells

Cellular senescence is a permanent condition of cell cycle arrest caused by a progressive shortening of telomeres defined as replicative senescence. Stem cells may also undergo an accelerated senescence response known as premature senescence, distinct from telomere shortening, as a response to different stress agents. Various treatment protocols have been developed based on epigenetic changes in cells throughout senescence, using different drugs and antioxidants, senolytic vaccines, or the reprogramming of somatic senescent cells using Yamanaka factors. Even with all the recent advancements, it is still unknown how different epigenetic modifications interact with genetic profiles and how other factors such as microbiota physiological conditions, psychological states, and diet influence the interaction between genetic and epigenetic pathways. The aim of this review is to highlight the new epigenetic modifications that are involved in stem cell senescence. Here, we review recent senescence-related epigenetic alterations such as DNA methylation, chromatin remodeling, histone modification, RNA modification, and non-coding RNA regulation outlining new possible targets for the therapy of aging-related diseases. The advantages and disadvantages of the animal models used in the study of cellular senescence are also briefly presented.

Microplastics in different tissues of historical and live samples of endangered mega-fish (Acipenser sinensis) and their potential relevance to exposure pathways

The Chinese sturgeon (Acipenser sinensis) is an endangered freshwater mega-fish (IUCN-red listed) that survives in the Yangtze River Basin, but the population of which has declined significantly in response to environmental pressures generated by human activities. In order to evaluate the interaction between Chinese sturgeon and microplastics (MPs) for the first time, we examined the gut and gills of historical samples (n = 27), in conjunction with the blood and mucus of live samples (n = 10), to explore the potential pathways involved in MP uptake. We detected MPs in 62.9 % of the field fish, with no significant difference between guts (mean=0.9 items/individual) and gills (mean=0.8 items/individual). The abundance of MPs in fish from 2017 was significantly higher than that from 2015 to 2016 with regards to both gills and gut samples. The size of MPs in gills was significantly smaller than those in guts, yet both contained mostly fibers (90.2 %). No MPs were confirmed in blood, however 62.5 % of mucus samples contained MPs. The MPs in mucus indicated the possibility of MPs entering Chinese sturgeons if their skins were damaged. The body size of Chinese sturgeons affected their MPs uptake by ingestion and inhalation, as less MPs were detected in the gut and gills of smaller individuals. Combining the evidence from historical and live samples, we revealed the presence of MPs in different tissues of Chinese sturgeon and their potential relevance to exposure pathways. Our work expands the understanding of multiple exposure pathways between MPs and long-lived mega-fish, while emphasizing the potential risks of long-term exposure in the field.

Eye lens-derived Δ14C signatures validate extreme longevity in the deepwater scorpaenid blackbelly rosefish (Helicolenus dactylopterus)

Many members of the scorpaenid subfamily: Sebastinae (rockfishes and their relatives) exhibit slow growth and extreme longevity (> 100 y), thus are estimated to be vulnerable to overfishing. Blackbelly rosefish (Helicolenus dactylopterus) is a deepwater sebastine whose longevity estimates range widely, possibly owing to different regional levels of fisheries exploitation across its Atlantic Ocean range. However, age estimation has not been validated for this species and ageing for sebastines in general is uncertain. We performed age validation of northern Gulf of Mexico blackbelly rosefish via an application of the bomb radiocarbon chronometer which utilized eye lens cores instead of more traditional otolith cores as the source of birth year Δ¹⁴C signatures. The correspondence of eye lens core Δ¹⁴C with a regional reference series was tested with a novel Bayesian spline analysis, which revealed otolith opaque zone counts provide accurate age estimates. Maximum observed longevity was 90 y, with 17.5% of individuals aged to be > 50 y. Bayesian growth analysis, with estimated length-at-birth included as a prior, revealed blackbelly rosefish exhibit extremely slow growth (k = 0.08 y^-1). Study results have important implications for the management of blackbelly rosefish stocks, as extreme longevity and slow growth imply low resilience to fishing pressure.

Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor

Long-term biological time series that monitor ecosystems across the ocean's full water column are extremely rare. As a result, classic paradigms are yet to be tested. One such paradigm is that variations in coastal upwelling drive changes in marine ecosystems throughout the water column. We examine this hypothesis by using data from three multidecadal time series spanning surface (0 m), midwater (200 to 1,000 m), and benthic (~4,000 m) habitats in the central California Current Upwelling System. Data include microscopic counts of surface plankton, video quantification of midwater animals, and imaging of benthic seafloor invertebrates. Taxon-specific plankton biomass and midwater and benthic animal densities were separately analyzed with principal component analysis. Within each community, the first mode of variability corresponds to most taxa increasing and decreasing over time, capturing seasonal surface blooms and lower-frequency midwater and benthic variability. When compared to local wind-driven upwelling variability, each community correlates to changes in upwelling damped over distinct timescales. This suggests that periods of high upwelling favor increase in organism biomass or density from the surface ocean through the midwater down to the abyssal seafloor. These connections most likely occur directly via changes in primary production and vertical carbon flux, and to a lesser extent indirectly via other oceanic changes. The timescales over which species respond to upwelling are taxon-specific and are likely linked to the longevity of phytoplankton blooms (surface) and of animal life (midwater and benthos), which dictate how long upwelling-driven changes persist within each community.

Convergent genomics of longevity in rockfishes highlights the genetics of human life span variation

Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years. Multiple shifts in rockfish longevity have occurred independently and in a short evolutionary time frame, thus empowering convergence analyses. Our analyses reveal a common network of genes under convergent evolution, encompassing established aging regulators such as insulin signaling, yet also identify flavonoid (aryl-hydrocarbon) metabolism as a pathway modulating longevity. The selective pressures on these pathways indicate the ancestral state of rockfishes was long lived and that the changes in short-lived lineages are adaptive. These pathways were also used to explore genome-wide association studies of human longevity, identifying the aryl-hydrocarbon metabolism pathway to be significantly associated with human survival to the 99th percentile. This evolutionary intersection defines and cross-validates a previously unappreciated genetic architecture that associates with the evolution of longevity across vertebrates.

Is Aging an Inevitable Characteristic of Organic Life or an Evolutionary Adaptation?

Aging is an evolutionary paradox. Several hypotheses have been proposed to explain it, but none fully explains all the biochemical and ecologic data accumulated over decades of research. We suggest that senescence is a primitive immune strategy which acts to protect an individual's kin from chronic infections. Older organisms are exposed to pathogens for a longer period of time and have a higher likelihood of acquiring infectious diseases. Accordingly, the parasitic load in aged individuals is higher than in younger ones. Given that the probability of pathogen transmission is higher within the kin, the inclusive fitness cost of infection might exceed the benefit of living longer. In this case, programmed lifespan termination might be an evolutionarily stable strategy. Here, we discuss the classical evolutionary hypotheses of aging and compare them with the pathogen control hypothesis, discuss the consistency of these hypotheses with existing empirical data, and present a revised conceptual framework to understand the evolution of aging.

So Close Yet So Far: Age and Growth of Blue Antimora Antimora rostrata (Moridae, Gadiformes, Teleostei) off New Zealand and Macquarie Island (Southwestern Pacific Ocean)

Age and growth of blue antimora Antimora rostrata were examined in the waters off New Zealand and Macquarie Island (southwestern Pacific). Samples off Macquarie Island were collected from bycatch in the Patagonian toothfish longline fishery. Individuals between 20 and 44 years in age measured between 37.6–71.1 cm in total length. Bottom trawl catches from New Zealand waters consisted of smaller and younger fish (11 to 38 years), measuring 22.5–52.5 cm long. The age classes with the greatest numbers in the former area were represented by fish aged 33–34 years (25.7%). In the latter area, the most numerous age classes were 21–23 years (12.1%), 28–29 years (17.6%), and 32 years (6.6%). The blue antimora from off the Macquarie Island show similar growth rates to those of individual fish from the Ross, Lazarev and Weddell Seas, waters off the Kerguelen and Crozet Islands, and southeastern Greenland. Individuals from New Zealand waters demonstrate the slowest growth rates compared to other parts of the species’ range but are quite similar to individuals from the Flemish Cap area. Further research to identify the stock structure of this broadly distributed species is warranted to provide context to differences in growth rates observed between populations.

Large and expensive brain comes with a short lifespan: The relationship between brain size and longevity among fish taxa

Vertebrates show substantial interspecific variation in brain size in relation to body mass. It has long been recognized that the evolution of large brains is associated with both costs and benefits, and it is their net benefit which should be favoured by natural selection. On one hand, the substantial energetic cost imposed by the maintenance of neural tissue is expected to compromise the energetic budget of organisms with large brains and their investment in other critical organs (expensive brain framework, EBF) or important physiological process, such as somatic maintenance and repair, thus accelerating ageing that shortens lifespan, as predicted by the disposable soma theory (DST). However, selection towards larger brain size can provide cognitive benefits (e.g., high behavioural flexibility) that may mitigate extrinsic mortality pressures, and thus may indirectly select for slower ageing that prolongs lifespan, as predicted by the cognitive buffer hypothesis (CBH). The relationship between longevity and brain size has been investigated to date only among terrestrial vertebrates, although the same selective forces acting on those species may also affect vertebrates living in aquatic habitats, such as fish. Thus, whether this evolutionary trade-off for brain size and longevity exists on a large scale among fish clades remains to be addressed. In this study, using a global dataset of 407 fish species, I undertook the first phylogenetic test of the brain size/longevity relationship in aquatic vertebrate species. The study revealed a negative relationship between brain size and longevity among cartilaginous fish confirming EBF and DST. However, no pattern emerged among bony fish species. Among sharks and rays, the high metabolic cost of producing neural tissue transcends the cognitive benefits of evolving a larger brain. Consequently, my findings suggest that the cost of maintaining brain tissue is relatively higher in ectothermic species than in endothermic ones.

Cellular Senescence: Mechanisms and Therapeutic Potential

Cellular senescence is a complex and multistep biological process which cells can undergo in response to different stresses. Referring to a highly stable cell cycle arrest, cellular senescence can influence a multitude of biological processes-both physiologically and pathologically. While phenotypically diverse, characteristics of senescence include the expression of the senescence-associated secretory phenotype, cell cycle arrest factors, senescence-associated β-galactosidase, morphogenesis, and chromatin remodelling. Persistent senescence is associated with pathologies such as aging, while transient senescence is associated with beneficial programmes, such as limb patterning. With these implications, senescence-based translational studies, namely senotherapy and pro-senescence therapy, are well underway to find the cure to complicated diseases such as cancer and atherosclerosis. Being a subject of major interest only in the recent decades, much remains to be studied, such as regarding the identification of unique biomarkers of senescent cells. This review attempts to provide a comprehensive understanding of the diverse literature on senescence, and discuss the knowledge we have on senescence thus far.

Understanding the Impacts of Blue Economy Growth on Deep-Sea Ecosystem Services

The deep sea is the vastest environment on Earth and provides many services and goods. Understanding the services and goods of deep-sea ecosystems would enable better resource governance and decision-making. In the present study, we reviewed and assessed deep-sea ecosystems services using the Ma conceptual framework, which incorporates ecosystems services and goods with human welfare. We also analyzed and measured the scientific production between 2012 and 2021 using the Dimension dataset. The bibliometric analysis showed a lack of studies related to deep-sea ecosystem services, which suggest the urgent need to overcome the existing knowledge gap regarding deep-sea components. However, the current knowledge revealed the crucial role that these ecosystems provide to the planet. Furthermore, we highlighted that there are common services and goods, and every ecosystem service feeds into another one. Developing actions and policies based on approaches that combine all deep-sea ecosystems services and goods are needed for the sustainable growth of the deep-sea economy in accordance with the United Nations Development Goal 14: Life Below Water.

Notes on age determination, size and age structure, longevity and growth of co-occurring macrourid fishes

Nineteen species of the deep-water fish family Macrouridae inhabit the Mid-Atlantic Ridge (MAR) of the North Atlantic. Size and age structure, longevity and length at age were explored for seven of the more abundant species: Coryphaenoides armatus, Coryphaenoides brevibarbis, Coryphaenoides carapinus, Coryphaenoides guentheri, Coryphaenoides mediterraneus, Coryphaenoides rupestris and Macrourus berglax. The otoliths from these species had growth increments resembling those accepted as annuli in other deep-water species for which validation experiments have been conducted. Based on the counts of these growth increments, age estimates were derived as the basis for studies of age structure, growth and longevity. All the species appeared to have relatively low growth rates, but the interspecific variation in longevity illustrates that there is a considerable variation within the family and among species inhabiting the same deep-sea environment. Most of the species likely complete full life cycles on the MAR, but it is probable that both the youngest and the largest-oldest individuals of some of the species were not sampled adequately.

New scale analyses reveal centenarian African coelacanths

The extant coelacanth was discovered in 1938;¹ its biology and ecology remain poorly known due to the low number of specimens collected. Only two previous studies^1,2 have attempted to determine its age and growth. They suggested a maximum lifespan of 20 years, placing the coelacanth among the fastest growing marine fish. These findings are at odds with the coelacanth's other known biological features including low oxygen-extraction capacity, slow metabolism, ovoviviparity, and low fecundity, typical of fish with slow life histories and slow growth. In this study, we use polarized light microscopy to study growth on scales based on a large sample of 27 specimens. Our results demonstrate for the first time nearly imperceptible annual calcified structures (circuli) on the scales and show that maximal age of the coelacanth was underestimated by a factor of 5. Our validation method suggests that circuli are indeed annual, thus supporting that the coelacanth is among the longest-living fish species, its lifespan being probably around 100 years. Like deep-sea sharks with a reduced metabolism, the coelacanth has among the slowest growth for its size. Further reappraisals of age at first sexual maturity (in the range 40 to 69 years old) and gestation duration (of around 5 years) show that the living coelacanth has one of the slowest life histories of all marine fish and possibly the longest gestation. As long-lived species with slow life histories are extremely vulnerable to natural and anthropogenic perturbations, our results suggest that coelacanths may be more threatened than previously considered.

Optimal sample size for calibrating DNA methylation age estimators

Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validation of these epigenetic clocks. However, wild animals with known ages are frequently difficult to obtain. Here, we perform Monte‐Carlo simulations to determine the optimal sample size required to create an accurate calibration model for age estimation by elastic net regression modelling of cytosine‐phosphate‐guanine methylation data. Our results suggest a minimum calibration population size of 70, but ideally 134 individuals or more for accurate and precise models. We also provide estimates to the extent a model can be extrapolated beyond a distribution of ages that was used during calibration. The findings can assist researchers to better design age estimation models and decide if their model is adequate for determining key population attributes.

Alternative Animal Models of Aging Research

Most research on mechanisms of aging is being conducted in a very limited number of classical model species, i.e., laboratory mouse (Mus musculus), rat (Rattus norvegicus domestica), the common fruit fly (Drosophila melanogaster) and roundworm (Caenorhabditis elegans). The obvious advantages of using these models are access to resources such as strains with known genetic properties, high-quality genomic and transcriptomic sequencing data, versatile experimental manipulation capabilities including well-established genome editing tools, as well as extensive experience in husbandry. However, this approach may introduce interpretation biases due to the specific characteristics of the investigated species, which may lead to inappropriate, or even false, generalization. For example, it is still unclear to what extent knowledge of aging mechanisms gained in short-lived model organisms is transferable to long-lived species such as humans. In addition, other specific adaptations favoring a long and healthy life from the immense evolutionary toolbox may be entirely missed. In this review, we summarize the specific characteristics of emerging animal models that have attracted the attention of gerontologists, we provide an overview of the available data and resources related to these models, and we summarize important insights gained from them in recent years. The models presented include short-lived ones such as killifish (Nothobranchius furzeri), long-lived ones such as primates (Callithrix jacchus, Cebus imitator, Macaca mulatta), bathyergid mole-rats (Heterocephalus glaber, Fukomys spp.), bats (Myotis spp.), birds, olms (Proteus anguinus), turtles, greenland sharks, bivalves (Arctica islandica), and potentially non-aging ones such as Hydra and Planaria.

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.

Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer

Cetaceans are the longest-living species of mammals and the largest in the history of the planet. They have developed mechanisms against diseases such cancer, although the underlying molecular bases of these remain unknown. The goal of this study was to investigate the role of natural selection in the evolution of 1077 tumour suppressor genes (TSGs) in cetaceans. We used a comparative genomic approach to analyse two sources of molecular variation in the form of d_N/d_S rates and gene copy number variation. We found a signal of positive selection in the ancestor of cetaceans within the CXCR2 gene, an important regulator of DNA damage, tumour dissemination and immune system. Further, in the ancestor of baleen whales, we found six genes exhibiting positive selection relating to diseases such as breast carcinoma, lung neoplasm (ADAMTS8) and leukaemia (ANXA1). The TSGs turnover rate (gene gain and loss) was almost 2.4-fold higher in cetaceans when compared with other mammals, and notably even faster in baleen whales. The molecular variants in TSGs found in baleen whales, combined with the faster gene turnover rate, could have favoured the evolution of their particular traits of anti-cancer resistance, gigantism and longevity. Additionally, we report 71 genes with duplications, of which 11 genes are linked to longevity (e.g. NOTCH3 and SIK1) and are important regulators of senescence, cell proliferation and metabolism. Overall, these results provide evolutionary evidence that natural selection in TSGs could act on species with large body sizes and extended lifespan, providing novel insights into the genetic basis of disease resistance.

Scientific Methods to Understand Fish Population Dynamics and Support Sustainable Fisheries Management

Fisheries play a significant role in the livelihoods of the world population, while the dependence on fisheries is acute in developing countries. Fisheries are consequently a critical element for meeting the sustainable development (SDG) and FAO goals to reduce poverty, hunger and improve health and well-being. However, 90% of global marine fish stocks are fully or over-exploited. The amount of biologically unsustainable stocks increased from 10% in 1975 to 33% in 2015. Freshwater ecosystems are the most endangered ecosystems and freshwater fish stocks are worldwide in a state of crisis. The continuous fish stock decline indicates that the world is still far from achieving SDG 14 (Life Below Water), FAO’s Blue Growth Initiative goal and SDG 15 (Life on Land, including freshwater systems). Failure to effectively manage world fish stocks can have disastrous effects on biodiversity and the livelihoods and socio-economic conditions of millions of people. Therefore, management strategies that successfully conserve the stocks and provide optimal sustainable yields are urgently needed. However, successful management is only possible when the necessary data are obtained and decision-makers are well informed. The main problem for the management of fisheries, particularly in developing countries, is the lack of information on the past and current status of the fish stocks. Sound data collection and validation methods are, therefore, important. Stock assessment models, which support sustainable fisheries, require life history traits as input parameters. In order to provide accurate estimates of these life history traits, standardized methods for otolith preparation and validation of the rate of growth zone deposition are essential. This review aims to assist researchers and fisheries managers, working on marine and freshwater fish species, in understanding concepts and processes related to stock assessment and population dynamics. Although most examples and case studies originate from developing countries in the African continent, the review remains of great value to many other countries.

The life history characteristics of Neosebastes pandus and the relationship between sexually dimorphic growth and reproductive strategy among Scorpaeniformes

Scorpaeniformes are an important component of commercial and recreational fisheries world-wide. The Neosebastes species, found in the western Pacific and south-east Indian Ocean, have received little attention from a research perspective. Samples of the bighead gurnard perch, Neosebastes pandus, collected from the lower west and south coasts of Western Australia, were used to undertake the first comprehensive investigation of the biological characteristics of a Neosebastes species. Opaque zones in sectioned sagittal otoliths were validated as forming annually. Female N. pandus grow to a significantly larger size, on average, than males and dominate the largest size classes, while males, growing to a smaller size, accumulate in the intermediate size classes. Although males were far less numerous than females in those age classes in which both sexes were found, males and females attain similar maximum ages >25 years. Neosebastes pandus spawns over a brief period between May (austral late autumn) and July (austral mid-autumn) when water temperature and day length are declining. The mean monthly gonadosomatic indices (GSI, I_GS ) values of females during the spawning period are 37-50 times higher than those of males, which mature at an earlier age and smaller length compared to females. Histological examination of the ovaries of females indicate that their structure is consistent with "general" teleost ovarian anatomy and thus differs from Scorpaena, Helicolenus and Sebastes species whose ovaries are adapted for specialized reproductive modes. The reproductive strategy of N. pandus of maximizing the reproductive output of females, by this sex attaining a larger size than males and pair spawning (i.e., large disparity in I_GS values) demonstrates the close lineage between the Neosebastes and other Scorpaeniformes, such as the Scorpaena, Helicolenus and Sebastes.

Comparative Transcriptomics Reveals Patterns of Adaptive Evolution Associated with Depth and Age Within Marine Rockfishes (Sebastes)

The genetic underpinnings that contribute to ecological adaptation and speciation are not completely understood, especially within marine ecosystems. These evolutionary processes can be elucidated by studying adaptive radiations, because they provide replicates of divergence within a given environment or time-frame. Marine rockfishes (genus Sebastes) are an adaptive radiation and unique model system for studying adaptive evolution in the marine realm. We investigated molecular evolution associated with ecological (depth) and life history (lifespan) divergence in 2 closely related clades of Sebastes. Brain transcriptomes were sequenced via RNA-Seq from 3 species within the subgenus Pteropodus and a pair of related congeners from the subgenus Sebastosomus in order to identify patterns of adaptive evolution. De novo assemblies from these transcriptomes were used to identify 3867 orthologous clusters, and genes subject to positive selection were identified based on all 5 species, depth, and lifespan. Within all our analyses, we identified hemoglobin subunit α to be under strong positive selection and is associated with the depth of occurrence. In our lifespan analysis we identified immune function genes under positive selection in association with maximum lifespan. This study provides insight on the molecular evolution of rockfishes and these candidate genes may provide a better understanding of how these subgenera radiated within the Northeast Pacific.

Effects of hypoxia on the behavior and physiology of kelp forest fishes

Forecasts from climate models and oceanographic observations indicate increasing deoxygenation in the global oceans and an elevated frequency and intensity of hypoxic events in the coastal zone, which have the potential to affect marine biodiversity and fisheries. Exposure to low dissolved oxygen (DO) conditions may have deleterious effects on early life stages in fishes. This study aims to identify thresholds to hypoxia while testing behavioral and physiological responses of two congeneric species of kelp forest fish to four DO levels, ranging from normoxic to hypoxic (8.7, 6.0, 4.1, and 2.2 mg O2 /L). Behavioral tests identified changes in exploratory behavior and turning bias (lateralization), whereas physiological tests focused on determining changes in hypoxia tolerance (pCrit), ventilation rates, and metabolic rates, with impacts on the resulting capacity for aerobic activity. Our findings indicated that copper rockfish (Sebastes caurinus) and blue rockfish (Sebastes mystinus) express sensitivity to hypoxia; however, the strength of the response differed between species. Copper rockfish exhibited reduced absolute lateralization and increased escape time at the lowest DO levels, whereas behavioral metrics for blue rockfish did not vary with oxygen level. Both species exhibited decreases in aerobic scope (as a function of reduced maximum metabolic rate) and increases in ventilation rates to compensate for decreasing oxygen levels. Blue rockfish had a lower pCrit and stronger acclimation response compared to copper rockfish. The differences expressed by each species suggest that acclimatization to changing ocean conditions may vary, even among related species that recruit to the same kelp forest habitat, leading to winners and losers under future ocean conditions. Exposure to hypoxia can decrease individual physiological fitness through metabolic and aerobic depression and changes to anti-predator behavior, with implications for the outcome of ecological interactions and the management of fish stocks in the face of climate change.

Revamping the evolutionary theories of aging

Radical lifespan disparities exist in the animal kingdom. While the ocean quahog can survive for half a millennium, the mayfly survives for less than 48 h. The evolutionary theories of aging seek to explain why such stark longevity differences exist and why a deleterious process like aging evolved. The classical mutation accumulation, antagonistic pleiotropy, and disposable soma theories predict that increased extrinsic mortality should select for the evolution of shorter lifespans and vice versa. Most experimental and comparative field studies conform to this prediction. Indeed, animals with extreme longevity (e.g., Greenland shark, bowhead whale, giant tortoise, vestimentiferan tubeworms) typically experience minimal predation. However, data from guppies, nematodes, and computational models show that increased extrinsic mortality can sometimes lead to longer evolved lifespans. The existence of theoretically immortal animals that experience extrinsic mortality - like planarian flatworms, panther worms, and hydra - further challenges classical assumptions. Octopuses pose another puzzle by exhibiting short lifespans and an uncanny intelligence, the latter of which is often associated with longevity and reduced extrinsic mortality. The evolutionary response to extrinsic mortality is likely dependent on multiple interacting factors in the organism, population, and ecology, including food availability, population density, reproductive cost, age-mortality interactions, and the mortality source.

Bigmouth Buffalo Ictiobus cyprinellus sets freshwater teleost record as improved age analysis reveals centenarian longevity

Understanding the age structure and population dynamics of harvested species is crucial for sustainability, especially in fisheries. The Bigmouth Buffalo (Ictiobus cyprinellus) is a fish endemic to the Mississippi and Hudson Bay drainages. A valued food-fish for centuries, they are now a prized sportfish as night bowfishing has become a million-dollar industry in the past decade. All harvest is virtually unregulated and unstudied, and Bigmouth Buffalo are declining while little is known about their biology. Using thin-sectioned otoliths and bomb-radiocarbon dating, we find Bigmouth Buffalo can reach 112 years of age, more than quadrupling previous longevity estimates, making this the oldest known freshwater teleost (~12,000 species). We document numerous populations that are comprised largely (85-90%) of individuals over 80 years old, suggesting long-term recruitment failure since dam construction in the 1930s. Our findings indicate Bigmouth Buffalo require urgent attention, while other understudied fishes may be threatened by similar ecological neglect.

On the Success of the Hadal Snailfishes

Deep-sea trenches, depths 6000-11,000 m, are characterized by high pressures, low temperatures, and absence of sunlight. These features make up the majority of the deepest marine habitat-the hadal zone-home to distinct communities from those in the surrounding abyssal plains. The snailfishes, family Liparidae (Scorpaeniformes), have found notable success in the hadal zone from ∼6000 to 8200 m, comprising the dominant ichthyofauna in at least six trenches worldwide. The hadal fish community is distinct from the abyssal community where elongate, scavenging fishes such as rattails (Macrouridae), cutthroat eels (Synaphobranchidae), tripodfishes (Ipnopidae), eelpouts (Zoarcidae), and cusk eels (Ophidiidae) are most common. Until recently, little was known about the biology of these deepest-living fishes, or the factors that drive their success at hadal depths. Here, I review recent investigations spanning the abyssal-hadal boundary and discuss the factors structuring these communities, including the roles of pressure adaptation, feeding ecology, and life history. Hadal fishes show specialized adaptation to hydrostatic pressure both in accumulation of the pressure-counteractant trimethylamine n-oxide and in intrinsic changes to enzymes. Stomach content and amino acid isotope analyses, and jaw morphology suggest that suction-feeding predatory fishes like hadal liparids may find an advantage to descending into the trench where amphipods are increasingly abundant. Analysis of otolith growth zones suggest that snailfishes may be adapted to a seismically active, high-disturbance hadal environment by having relatively short life-spans. This review synthesizes the known literature on the planet's deepest-living fishes and informs new understanding of adaptations to life in the trenches.

Comparative Analysis of the Blood Plasma Metabolome of Negligible, Gradual and Rapidly Ageing Fishes

There are a number of different animals that belong to long- and short-lived species and show a various rate of ageing, providing an ideal model to investigate mechanisms of longevity. In this work, a metabolome profiling of blood plasma from fishes with various ageing rates—negligible (Pike Esox Lucius and Sterlet Acipenser ruthenus), gradual (Zander Sander lucioperca and Perch Perca fluviatilis) and rapid (Chum Salmon Oncorhynchus keta and Pink Salmon Oncorhynchus gorbuscha)—was assessed by means of direct infusion to quadrupole time-of-flight mass spectrometry. Of the 2056 distinct m/z features detected by a mass spectrometry metabolic profiling of blood plasma samples, fifteen metabolites in the classes of dipeptides, fatty acids, glycerolipids, phosphoethanolamines and phosphatidylcholines were significantly associated with ageing rate, independent of species differences. This is the first study of the metabolome of fishes with various ageing rate, and this untargeted approach highlighted the metabolic conditions that may serve to assess the ageing process.

Complete Mitochondrial Genome Sequences of Five Rockfishes (Perciformes: Sebastes)

Rockfishes of the genus Sebastes rank among the longest-lived vertebrate animals. In order to facilitate comparative genomic research in animal longevity, the complete mitochondrial genome sequences are presented for Sebastes aleutianus, Sebastes minor, Sebastes nigrocinctus, Sebastes rubrivinctus, and Sebastes steindachneri.

Strong linkages between depth, longevity and demographic stability across marine sessile species

Understanding the role of the environment in shaping the evolution of life histories remains a major challenge in ecology and evolution. We synthesize longevity patterns of marine sessile species and find strong positive relationships between depth and maximum lifespan across multiple sessile marine taxa, including corals, bivalves, sponges and macroalgae. Using long-term demographic data on marine sessile and terrestrial plant species, we show that extreme longevity leads to strongly dampened population dynamics. We also used detailed analyses of Mediterranean red coral, with a maximum lifespan of 532 years, to explore the life-history patterns of long-lived taxa and the vulnerability to external mortality sources that these characteristics can create. Depth-related environmental gradients-including light, food availability, temperature and disturbance intensity-drive highly predictable distributions of life histories that, in turn, have predictable ecological consequences for the dynamics of natural populations.

Predicting life history parameters for all fishes worldwide

Scientists and resource managers need to know life history parameters (e.g., average mortality rate, individual growth rate, maximum length or mass, and timing of maturity) to understand and respond to risks to natural populations and ecosystems. For over 100 years, scientists have identified "life history invariants" (LHI) representing pairs of parameters whose ratio is theorized to be constant across species. LHI then promise to allow prediction of many parameters from field measurements of a few important traits. Using LHI in this way, however, neglects any residual patterns in parameters when making predictions. We therefore apply a multivariate model for eight variables (seven parameters and temperature) in over 32,000 fishes, and include taxonomic structure for residuals (with levels for class, order, family, genus, and species). We illustrate that this approach predicts variables probabilistically for taxa with many or few data. We then use this model to resolve three questions regarding life history parameters in fishes. Specifically we show that (1) on average there is a 1.24% decrease in the Brody growth coefficient for every 1% increase in maximum size; (2) the ratio of natural mortality rate and growth coefficient is not an LHI but instead varies systematically based on the timing of maturation, where movement along this life history axis is predictably correlated with species taxonomy; and (3) three variables must be known per species to precisely predict remaining life history variables. We distribute our predictive model as an R package, FishLife, to allow future life history predictions for fishes to be conditioned on taxonomy and life history data for fishes worldwide. This package also contains predictions (and predictive intervals) for mortality, maturity, size, and growth parameters for all described fishes.

Using comparative biology to understand how aging affects mitochondrial metabolism

Lifespan varies considerably among even closely related species, as exemplified by rodents and primates. Despite these disparities in lifespan, most studies have focused on intra-specific aging pathologies, primarily within a select few systems. While mice have provided much insight into aging biology, it is unclear if such a short-lived species lack defences against senescence that may have evolved in related longevous species. Many age-related diseases have been linked to mitochondrial dysfunction that are measured by decreased energy generation, structural damage to cellular components, and even cell death. Post translational modifications (PTMs) orchestrate many of the pathways associated with cellular metabolism, and are thought to be a key regulator in biological senescence. We propose hyperacylation as one such modification that may be implicated in numerous mitochondrial impairments affecting energy metabolism.

Nature's Electric Potential: A Systematic Review of the Role of Bioelectricity in Wound Healing and Regenerative Processes in Animals, Humans, and Plants

Natural endogenous voltage gradients not only predict and correlate with growth and development but also drive wound healing and regeneration processes. This review summarizes the existing literature for the nature, sources, and transmission of information-bearing bioelectric signals involved in controlling wound healing and regeneration in animals, humans, and plants. It emerges that some bioelectric characteristics occur ubiquitously in a range of animal and plant species. However, the limits of similarities are probed to give a realistic assessment of future areas to be explored. Major gaps remain in our knowledge of the mechanistic basis for these processes, on which regenerative therapies ultimately depend. In relation to this, it is concluded that the mapping of voltage patterns and the processes generating them is a promising future research focus, to probe three aspects: the role of wound/regeneration currents in relation to morphology; the role of endogenous flux changes in driving wound healing and regeneration; and the mapping of patterns in organisms of extreme longevity, in contrast with the aberrant voltage patterns underlying impaired healing, to inform interventions aimed at restoring them.

Extreme longevity in a deep-sea vestimentiferan tubeworm and its implications for the evolution of life history strategies

The deep sea is home to many species that have longer life spans than their shallow-water counterparts. This trend is primarily related to the decline in metabolic rates with temperature as depth increases. However, at bathyal depths, the cold-seep vestimentiferan tubeworm species Lamellibrachia luymesi and Seepiophila jonesi reach extremely old ages beyond what is predicted by the simple scaling of life span with body size and temperature. Here, we use individual-based models based on in situ growth rates to show that another species of cold-seep tubeworm found in the Gulf of Mexico, Escarpia laminata, also has an extraordinarily long life span, regularly achieving ages of 100-200 years with some individuals older than 300 years. The distribution of results from individual simulations as well as whole population simulations involving mortality and recruitment rates support these age estimates. The low 0.67% mortality rate measurements from collected populations of E. laminata are similar to mortality rates in L. luymesi and S. jonesi and play a role in evolution of the long life span of cold-seep tubeworms. These results support longevity theory, which states that in the absence of extrinsic mortality threats, natural selection will select for individuals that senesce slower and reproduce continually into their old age.

Theory and associated phenomenology for intrinsic mortality arising from natural selection

Standard evolutionary theories of aging and mortality, implicitly based on assumptions of spatial averaging, hold that natural selection cannot favor shorter lifespan without direct compensating benefit to individual reproductive success. However, a number of empirical observations appear as exceptions to or are difficult to reconcile with this view, suggesting explicit lifespan control or programmed death mechanisms inconsistent with the classic understanding. Moreover, evolutionary models that take into account the spatial distributions of populations have been shown to exhibit a variety of self-limiting behaviors, maintained through environmental feedback. Here we extend recent work on spatial modeling of lifespan evolution, showing that both theory and phenomenology are consistent with programmed death. Spatial models show that self-limited lifespan robustly results in long-term benefit to a lineage; longer-lived variants may have a reproductive advantage for many generations, but shorter lifespan ultimately confers long-term reproductive advantage through environmental feedback acting on much longer time scales. Numerous model variations produce the same qualitative result, demonstrating insensitivity to detailed assumptions; the key conditions under which self-limited lifespan is favored are spatial extent and locally exhaustible resources. Factors including lower resource availability, higher consumption, and lower dispersal range are associated with evolution of shorter lifespan. A variety of empirical observations can parsimoniously be explained in terms of long-term selective advantage for intrinsic mortality. Classically anomalous empirical data on natural lifespans and intrinsic mortality, including observations of longer lifespan associated with increased predation, and evidence of programmed death in both unicellular and multicellular organisms, are consistent with specific model predictions. The generic nature of the spatial model conditions under which intrinsic mortality is favored suggests a firm theoretical basis for the idea that evolution can quite generally select for shorter lifespan directly.

The economic implications of changing regulations for deep sea fishing under the European Common Fisheries Policy: UK case study

Economic impact assessment methodology was applied to UK fisheries data to better understand the implications of European Commission proposal for regulations to fishing for deep-sea stocks in the North-East Atlantic (EC COM 371 Final 2012) under the Common Fisheries Policy (CFP). The aim was to inform the on-going debate to develop the EC proposal, and to assist the UK fishing industry and Government in evaluating the most effective options to manage deep sea fish stocks. Results indicate that enforcing the EC proposal as originally drafted results in a number of implications for the UK fleet. Because of the proposed changes to the list of species defined as being deep sea species, and a new definition of what constitutes a vessel targeting deep sea species, a total of 695 active UK fishing vessels would need a permit to fish for deep sea species. However, due to existing and capped capacity limits many vessels would potentially not be able to obtain such a permit. The economic impact of these changes from the status quo reveals that in the short term, landings would decrease by 6540 tonnes, reducing gross value added by £3.3 million. Alternative options were also assessed that provide mitigation measures to offset the impacts of the proposed regulations whilst at the same time providing more effective protection of deep sea Vulnerable Marine Ecosystems (VMEs). The options include setting a 400m depth rule that identifies a depth beyond which vessels would potentially be classified as fishing for deep sea species and designating 'core areas' for deep sea fishing at depths>400m to minimise the risk of further impacts of bottom fishing gear on deep sea habitats. Applying a 400m depth limit and 'core fishing' area approach deeper than 400m, the impact of the EC proposal would essentially be reduced to zero, that is, on average no vessels (using the status quo capacity baseline) would be impacted by the proposal.

Molecular biomarkers for chronological age in animal ecology

The chronological age of an individual animal predicts many of its biological characteristics, and these in turn influence population-level ecological processes. Animal age information can therefore be valuable in ecological research, but many species have no external features that allow age to be reliably determined. Molecular age biomarkers provide a potential solution to this problem. Research in this area of molecular ecology has so far focused on a limited range of age biomarkers. The most commonly tested molecular age biomarker is change in average telomere length, which predicts age well in a small number of species and tissues, but performs poorly in many other situations. Epigenetic regulation of gene expression has recently been shown to cause age-related modifications to DNA and to cause changes in abundance of several RNA types throughout animal lifespans. Age biomarkers based on these epigenetic changes, and other new DNA-based assays, have already been applied to model organisms, humans and a limited number of wild animals. There is clear potential to apply these marker types more widely in ecological studies. For many species, these new approaches will produce age estimates where this was previously impractical. They will also enable age information to be gathered in cross-sectional studies and expand the range of demographic characteristics that can be quantified with molecular methods. We describe the range of molecular age biomarkers that have been investigated to date and suggest approaches for developing the newer marker types as age assays in nonmodel animal species.

The zebrafish as a gerontology model in nervous system aging, disease, and repair

Considering the increasing number of elderly in the world's population today, developing effective treatments for age-related pathologies is one of the biggest challenges in modern medical research. Age-related neurodegeneration, in particular, significantly impacts important sensory, motor, and cognitive functions, seriously constraining life quality of many patients. Although our understanding of the causal mechanisms of aging has greatly improved in recent years, animal model systems still have much to tell us about this complex process. Zebrafish (Danio rerio) have gained enormous popularity for this research topic over the past decade, since their life span is relatively short but, like humans, they are still subject to gradual aging. In addition, the extensive characterization of its well-conserved molecular and cellular physiology makes the zebrafish an excellent model to unravel the underlying mechanisms of aging, disease, and repair. This review provides a comprehensive overview of the progress made in zebrafish gerontology, with special emphasis on nervous system aging. We review the evidence that classic hallmarks of aging can also be recognized within this small vertebrate, both at the molecular and cellular level. Moreover, we illustrate the high level of similarity with age-associated human pathologies through a survey of the functional deficits that arise as zebrafish age.

Metazoan parasite communities and diet of the velvet belly lantern shark Etmopterus spinax (Squaliformes: Etmopteridae): a comparison of two deep-sea ecosystems

By combining an examination of stomach contents yielding a snapshot of the most recent trophic niche and the structure of parasite communities reflecting a long-term feeding niche, this study aimed at gaining more comprehensive information on the role of the small-sized deep-water velvet belly lantern shark Etmopterus spinax in the local food webs of the Galicia Bank and the canyon and valley system of the Avilés Canyon, which have been both proposed for inclusion in the Natura 2000 network of protected areas. As far as is known, this study provides the first comparative parasite infracommunity data for a deep-sea shark species. Component parasite communities in E. spinax were relatively rich, whereas the infracommunities were rather depauperate, with similar low diversity at both localities. The significant differences in the composition and structure of both parasite communities and prey assemblages indicate differential effects of the two deep-sea ecosystems on both long-term and most recent trophic niches of E. spinax. These results underline the importance of the use of multivariate analyses for the assessment of geographical variation in shark populations based on parasites and diet data.

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.

A conceptual framework for organismal biology: linking theories, models, and data

Implicit or subconscious theory is especially common in the biological sciences. Yet, theory plays a variety of roles in scientific inquiry. First and foremost, it determines what does and does not count as a valid or interesting question or line of inquiry. Second, theory determines the background assumptions within which inquiries are pursued. Third, theory provides linkages among disciplines. For these reasons, it is important and useful to develop explicit theories for biology. A general theory of organisms is developed, which includes 10 fundamental principles that apply to all organisms, and 6 that apply to multicellular organisms only. The value of a general theory comes from its utility to help guide the development of more specific theories and models. That process is demonstrated by examining two domains: ecoimmunology and development. For the former, a constitutive theory of ecoimmunology is presented, and used to develop a specific model that explains energetic trade-offs that may result from an immunological response of a host to a pathogen. For the latter, some of the issues involved in trying to devise a constitutive theory that covers all of development are explored, and a more narrow theory of phenotypic novelty is presented. By its very nature, little of a theory of organisms will be new. Rather, the theory presented here is a formal expression of nearly two centuries of conceptual advances and practice in research. Any theory is dynamic and subject to debate and change. Such debate will occur as part of the present, initial formulation, as the ideas presented here are refined. The very process of debating the form of the theory acts to clarify thinking. The overarching goal is to stimulate debate about the role of theory in the study of organisms, and thereby advance our understanding of them.

Sarcopenia and piscines: the case for indeterminate-growing fish as unique genetic model organisms in aging and longevity research

Sarcopenia and dynapenia pose significant problems for the aged, especially as life expectancy rises in developed countries. Current therapies are marginally efficacious at best, and barriers to breakthroughs in treatment may result from currently employed model organisms. Here, we argue that the use of indeterminate-growing teleost fish in skeletal muscle aging research may lead to therapeutic advancements not possible with current mammalian models. Evidence from a comparative approach utilizing the subfamily Danioninae suggests that the indeterminate growth paradigm of many teleosts arises from adult muscle stem cells with greater proliferative capacity, even in spite of smaller progenitor populations. We hypothesize that paired-box transcription factors, Pax3/7, are involved with this enhanced self-renewal and that prolonged expression of these factors may allow some fish species to escape, or at least forestall, sarcopenia/dynapenia. Future research efforts should focus on the experimental validation of these genes as key factors in indeterminate growth, both in the context of muscle stem cell proliferation and in prevention of skeletal muscle senescence.

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.

Experimental demonstration of the growth rate--lifespan trade-off

The hypothesized negative relationship between growth rate and lifespan has proved very difficult to test robustly because of potentially confounding variables, particularly nutrient availability and final size. Here we provide, to our knowledge, the first rigorous experimental test of this hypothesis, and find dramatic changes in lifespan in the predicted direction in response to both upward and downward manipulations of growth rates. We used brief (less than 4% of median lifespan) exposure to relatively cold or warm temperatures early in life to deflect juvenile three-spined sticklebacks Gasterosteus aculeatus from their normal growth trajectories; this induced catch-up or slowed-down growth when ambient temperatures were restored, and all groups attained the same average adult size. Catch-up growth led to a reduction in median lifespan of 14.5 per cent, while slowed-down growth extended lifespan by 30.6 per cent. These lifespan effects were independent of eventual size attained or reproductive investment in adult life. Photoperiod manipulations showed that the effects of compensatory growth on lifespan were also influenced by time available for growth prior to breeding, being more extreme when less time was available. These results demonstrate the growth-lifespan trade-off. While growing more slowly can increase longevity, the optimal resolution of the growth-lifespan trade-off is influenced by time constraints in a seasonal environment.