Two Separate Brain Networks for Predicting Trainability and Tracking Training-Related Plasticity in Working Dogs

Functional brain connectivity based on resting-state functional magnetic resonance imaging (fMRI) has been shown to be correlated with human personality and behavior. In this study, we sought to know whether capabilities and traits in dogs can be predicted from their resting-state connectivity, as in humans. We trained awake dogs to keep their head still inside a 3T MRI scanner while resting-state fMRI data was acquired. Canine behavior was characterized by an integrated behavioral score capturing their hunting, retrieving, and environmental soundness. Functional scans and behavioral measures were acquired at three different time points across detector dog training. The first time point (TP1) was prior to the dogs entering formal working detector dog training. The second time point (TP2) was soon after formal detector dog training. The third time point (TP3) was three months' post detector dog training while the dogs were engaged in a program of maintenance training for detection work. We hypothesized that the correlation between resting-state FC in the dog brain and behavior measures would significantly change during their detection training process (from TP1 to TP2) and would maintain for the subsequent several months of detection work (from TP2 to TP3). To further study the resting-state FC features that can predict the success of training, dogs at TP1 were divided into a successful group and a non-successful group. We observed a core brain network which showed relatively stable (with respect to time) patterns of interaction that were significantly stronger in successful detector dogs compared to failures and whose connectivity strength at the first time point predicted whether a given dog was eventually successful in becoming a detector dog. A second ontologically based flexible peripheral network was observed whose changes in connectivity strength with detection training tracked corresponding changes in behavior over the training program. Comparing dog and human brains, the functional connectivity between the brain stem and the frontal cortex in dogs corresponded to that between the locus coeruleus and left middle frontal gyrus in humans, suggestive of a shared mechanism for learning and retrieval of odors. Overall, the findings point toward the influence of phylogeny and ontogeny in dogs producing two dissociable functional neural networks.

The evolution of glandularity as a defense against herbivores in the tarweed clade

PREMISE

Glandular trichomes are implicated in direct and indirect defense of plants. However, the degree to which glandular and non-glandular trichomes have evolved as a consequence of herbivory remains unclear, because their heritability, their association with herbivore resistance, their trade-offs with one another, and their association with other functions are rarely quantified.

METHODS

We conducted a phylogenetic comparison of trichomes and herbivore resistance against the generalist caterpillar, Heliothis virescens, among tarweed species (Asteraceae: Madiinae) and a genetic correlation study comparing those same traits among maternal half-sibs of three tarweed species.

RESULTS

Within a tarweed species, we found no evidence that herbivore growth rate decreased on tarweed individuals or maternal sib groups with more glandularity or denser trichomes. However, tarweed species with more glandularity and fewer non-glandular trichomes resulted in slower-growing herbivores. Likewise, a trade-off between glandular and non-glandular trichomes was apparent among tarweed species, but not among individuals or sib groups within a species.

CONCLUSIONS

Our results suggest that this key herbivore does not select for trichomes as a direct defense in tarweed species. However, trichomes differed substantially among species and likely affect herbivore pressure on those species. Our results demonstrate that trade-offs among plant traits, as well as inference on the function of those traits, can depend on scale.

Artificial intelligence for neurodegenerative experimental models

INTRODUCTION

Experimental models are essential tools in neurodegenerative disease research. However, the translation of insights and drugs discovered in model systems has proven immensely challenging, marred by high failure rates in human clinical trials.

METHODS

Here we review the application of artificial intelligence (AI) and machine learning (ML) in experimental medicine for dementia research.

RESULTS

Considering the specific challenges of reproducibility and translation between other species or model systems and human biology in preclinical dementia research, we highlight best practices and resources that can be leveraged to quantify and evaluate translatability. We then evaluate how AI and ML approaches could be applied to enhance both cross-model reproducibility and translation to human biology, while sustaining biological interpretability.

DISCUSSION

AI and ML approaches in experimental medicine remain in their infancy. However, they have great potential to strengthen preclinical research and translation if based upon adequate, robust, and reproducible experimental data.

HIGHLIGHTS

There are increasing applications of AI in experimental medicine. We identified issues in reproducibility, cross-species translation, and data curation in the field. Our review highlights data resources and AI approaches as solutions. Multi-omics analysis with AI offers exciting future possibilities in drug discovery.

Why did glutamate, GABA, and melatonin become intercellular signalling molecules in plants?

Intercellular signalling is an indispensable part of multicellular life. Understanding the commonalities and differences in how signalling molecules function in two remote branches of the tree of life may shed light on the reasons these molecules were originally recruited for intercellular signalling. Here we review the plant function of three highly studied animal intercellular signalling molecules, namely glutamate, γ-aminobutyric acid (GABA), and melatonin. By considering both their signalling function in plants and their broader physiological function, we suggest that molecules with an original function as key metabolites or active participants in reactive ion species scavenging have a high chance of becoming intercellular signalling molecules. Naturally, the evolution of machinery to transduce a message across the plasma membrane is necessary. This fact is demonstrated by three other well-studied animal intercellular signalling molecules, namely serotonin, dopamine, and acetylcholine, for which there is currently no evidence that they act as intercellular signalling molecules in plants.

Sulcal morphology of posteromedial cortex substantially differs between humans and chimpanzees

Recent studies identify a surprising coupling between evolutionarily new sulci and the functional organization of human posteromedial cortex (PMC). Yet, no study has compared this modern PMC sulcal patterning between humans and non-human hominoids. To fill this gap in knowledge, we first manually defined 918 sulci in 120 chimpanzee ( Pan Troglodytes ) hemispheres and 1619 sulci in 144 human hemispheres. We uncovered four new PMC sulci, and quantitatively identified species differences in incidence, depth, and surface area. Interestingly, some PMC sulci are more common in humans and others, in chimpanzees. Further, we found that the prominent marginal ramus of the cingulate sulcus differs significantly between species. Contrary to classic observations, the present results reveal that the surface anatomy of PMC substantially differs between humans and chimpanzees â€" findings which lay a foundation for better understanding the evolution of neuroanatomical-functional and neuroanatomical-behavioral relationships in this highly expanded region of the human cerebral cortex.

Using axenic and gnotobiotic insects to examine the role of different microbes on the development and reproduction of the kissing bug Rhodnius prolixus (Hemiptera: Reduviidae)

Kissing bugs (Hempitera: Reduviidae) are obligately and exclusively blood feeding insects. Vertebrate blood is thought to provide insufficient B vitamins to insects, which rely on symbiotic relationships with bacteria that provision these nutrients. Kissing bugs harbour environmentally acquired bacteria in their gut lumen, without which they are unable to develop to adulthood. Rhodococcus rhodnii was initially identified as the sole symbiont of Rhodnius prolixus, but modern studies of the kissing bug microbiome suggest that R. rhodnii is not always present or abundant in wild-caught individuals. We asked whether R. rhodnii or other bacteria alone could function as symbionts of R. prolixus. We produced insects with no bacteria (axenic) or with known microbiomes (gnotobiotic). Gnotobiotic insects harbouring R. rhodnii alone developed faster, had higher survival, and laid more eggs than those harbouring other bacterial monocultures, including other described symbionts of kissing bugs. R. rhodnii grew to high titre in the guts of R. prolixus while other tested species were found at much lower abundance. Rhodococcus species tested had nearly identical B vitamin biosynthesis genes, and dietary supplementation of B vitamins had a relatively minor effect on development and survival of gnotobiotic R. prolixus. Our results indicate that R. prolixus have a higher fitness when harbouring R. rhodnii than other bacteria tested, that this may be due to R. rhodnii existing at higher titres and providing more B vitamins to the host, and that symbiont B vitamin synthesis is probably a necessary but not sufficient function of gut bacteria in kissing bugs.

It is time to move on from homology in comparative biology

The continued use of the idea of homology is questionable on philosophical and scientific grounds. It is based on the widespread idea that a "homologue" in extant taxa can be "traced back" to a feature in common ancestor. In contrast, Richard Owen, who first used the term in 1846, saw homology (homologue) differently, as "sameness": "the same organ in different animals under every variety of form and function." At that point in time, he was not influenced by evolutionary thinking, and more focused on the details and approaches to biological comparison and description. His was a perceptive approach to comparison. This paper argues that the concept of homology no longer plays a useful role in comparative biology. It is a conceptual idea with little or no empirical implications for modern comparisons among phenotypes. Comparative biology now uses formal phylogenetic analysis in which similar features in individuals of two or more taxa are treated as characters on a tree and tested for historical "sameness" in terms of the concept of synapomorphy. If we are to understand the complexities of phenotypic evolution, applying this method to detailed comparative data will be essential. At the same time, a deep understanding of the phenotype and its history will emerge only through the use of multidisciplinary approaches that address historical changes at different hierarchical levels.

A refreshed approach to homology-Prioritizing epistemology over metaphysics

Unease with the inclusion of "sameness" in Owen's definition of homology characterizes a substantial part of the literature on this subject, where this term has acquired an increasingly strict metaphysical flavor. Taken for granted the existence of body features that are "the same," their existence has been explained by appealing to universal laws of form, as the product of common ancestry, or in terms of proximal causes responsible for the emergence of conserved developmental modules. However, a fundamentally different approach is possible, if we shift attention from metaphysics to epistemology. We may reword Owen's statement as follows: organs of different animals, in so far as they can be described as the same despite any difference in form and function, are called homologues. The proposed framework provides an umbrella for both the traditional, all-or-nothing concept of homology, and the less fashionable alternatives of factorial or partial homology, as well as for an extension of homology from form to function. No less attractive is the prospect to handle also ghost homologues, the body parts or organs of which there is non-objective evidence in a given clade, but can nevertheless be represented, in a description that encapsulates some of the traits observable in their extant homologue in the sister clade. Stripped of its different and constraining metaphysical explanations, homology survives as an anchor concept to which different nomadic disciplines and research agendas can be associated.

Lifespan and telomere length variation across populations of wild-derived African killifish

Telomeres and telomerase prevent the continuous erosion of chromosome-ends caused by lifelong cell division. Shortened telomeres are associated with age-related pathologies. While short telomere length is positively correlated with increased lethality at the individual level, in comparisons across species short telomeres are associated with long (and not short) lifespans. Here, we tested this contradiction between individual and evolutionary patterns in telomere length using African annual killifish. We analysed lifespan and telomere length in a set of captive strains derived from well-defined wild populations of Nothobranchius furzeri and its sister species, N. kadleci, from sites along a strong gradient of aridity which ultimately determines maximum natural lifespan. Overall, males were shorter-lived than females, and also had shorter telomeres. Male lifespan (measured in controlled laboratory conditions) was positively associated with the amount of annual rainfall in the site of strain origin. However, fish from wetter climates had shorter telomeres. In addition, individual fish which grew largest over the juvenile period possessed shorter telomeres at the onset of adulthood. This demonstrates that individual condition and environmentally-driven selection indeed modulate the relationship between telomere length and lifespan in opposite directions, validating the existence of inverse trends within a single taxon. Intraindividual heterogeneity of telomere length (capable to detect very short telomeres) was not associated with mean telomere length, suggesting that the shortest telomeres are controlled by regulatory pathways other than those that determine mean telomere length. The substantial variation in telomere length between strains from different environments identifies killifish as a powerful system in understanding the adaptive value of telomere length.

Life history mediates the trade-offs among different components of demographic resilience

Accelerating rates of biodiversity loss underscore the need to understand how species achieve resilience—the ability to resist and recover from a/biotic disturbances. Yet, the factors determining the resilience of species remain poorly understood, due to disagreements on its definition and the lack of large‐scale analyses. Here, we investigate how the life history of 910 natural populations of animals and plants predicts their intrinsic ability to be resilient. We show that demographic resilience can be achieved through different combinations of compensation, resistance and recovery after a disturbance. We demonstrate that these resilience components are highly correlated with life history traits related to the species’ pace of life and reproductive strategy. Species with longer generation times require longer recovery times post‐disturbance, whilst those with greater reproductive capacity have greater resistance and compensation. Our findings highlight the key role of life history traits to understand species resilience, improving our ability to predict how natural populations cope with disturbance regimes.

DomArchive: a century of published dominance data

Dominance behaviours have been collected for many groups of animals since 1922 and serve as a foundation for research on social behaviour and social structure. Despite a wealth of data from the last century of research on dominance hierarchies, these data are only rarely used for comparative insight. Here, we aim to facilitate comparative studies of the structure and function of dominance hierarchies by compiling published dominance interaction datasets from the last 100 years of work. This compiled archive includes 436 datasets from 190 studies of 367 unique groups (mean group size 13.8, s.d. = 13.4) of 135 different species, totalling over 243 000 interactions. These data are presented in an R package alongside relevant metadata and a tool for subsetting the archive based on biological or methodological criteria. In this paper, we explain how to use the archive, discuss potential limitations of the data, and reflect on best practices in publishing dominance data based on our experience in assembling this dataset. This archive will serve as an important resource for future comparative studies and will promote the development of general unifying theories of dominance in behavioural ecology that can be grounded in testing with empirical data. This article is part of the theme issue 'The centennial of the pecking order: current state and future prospects for the study of dominance hierarchies'.

Sex-specific aging in animals: Perspective and future directions

Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age-associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer-lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well-characterized processes. In particular, understanding the role of sex-determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs.

ZOOMICS: Comparative Metabolomics of Red Blood Cells From Guinea Pigs, Humans, and Non-human Primates During Refrigerated Storage for Up to 42 Days

Unlike other rodents, guinea pigs (Cavia porcellus) have evolutionarily lost their capacity to synthesize vitamin C (ascorbate) de novo and, like several non-human primates and humans, rely on dietary intake and glutathione-dependent recycling to cope with oxidant stress. This is particularly relevant in red blood cell physiology, and especially when modeling blood storage, which exacerbates erythrocyte oxidant stress. Herein we provide a comprehensive metabolomics analysis of fresh and stored guinea pig red blood cell concentrates (n = 20), with weekly sampling from storage day 0 through 42. Results were compared to previously published ZOOMICS studies on red blood cells from three additional species with genetic loss of L-gulonolactone oxidase function, including humans (n = 21), olive baboons (n = 20), and rhesus macaques (n = 20). While metabolic trends were comparable across all species, guinea pig red blood cells demonstrated accelerated alterations of the metabolic markers of the storage lesion that are consistent with oxidative stress. Compared to the other species, guinea pig red blood cells showed aberrant glycolysis, pentose phosphate pathway end product metabolites, purine breakdown products, methylation, glutaminolysis, and markers of membrane lipid remodeling. Consistently, guinea pig red blood cells demonstrated higher end storage hemolysis, and scanning electron microscopy confirmed a higher degree of morphological alterations of their red blood cells, as compared to the other species. Despite a genetic inability to produce ascorbate that is common to the species evaluated, guinea pig red blood cells demonstrate accelerated oxidant stress under standard storage conditions. These data may offer relevant insights into the basal and cold storage metabolism of red blood cells from species that cannot synthesize endogenous ascorbate.

MapToCleave: High-throughput profiling of microRNA biogenesis in living cells

Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they have been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously profile processing of thousands of distinct RNA structures in living cells. We find that miRNA precursors with a stable lower basal stem are more efficiently processed and also have higher expression in vivo in tissues from 20 animal species. We systematically compare the importance of known and novel sequence and structural features and test biogenesis of miRNA precursors from 10 animal and plant species in human cells. Lastly, we provide evidence that the GHG motif better predicts processing when defined as a structure rather than sequence motif, consistent with recent cryogenic electron microscopy (cryo-EM) studies. In summary, we apply a screening assay in living cells to reveal the importance of lower basal stem stability for miRNA processing and in vivo expression.

A comparative biology approach to DNN modeling of vision: A focus on differences, not similarities

Deep neural networks (DNNs) have revolutionized computer science and are now widely used for neuroscientific research. A hot debate has ensued about the usefulness of DNNs as neuroscientific models of the human visual system; the debate centers on to what extent certain shortcomings of DNNs are real failures and to what extent they are redeemable. Here, we argue that the main problem is that we often do not understand which human functions need to be modeled and, thus, what counts as a falsification. Hence, not only is there a problem on the DNN side, but there is also one on the brain side (i.e., with the explanandum-the thing to be explained). For example, should DNNs reproduce illusions? We posit that we can make better use of DNNs by adopting an approach of comparative biology by focusing on the differences, rather than the similarities, between DNNs and humans to improve our understanding of visual information processing in general.

Motilin Comparative Study: Structure, Distribution, Receptors, and Gastrointestinal Motility

Motilin, produced in endocrine cells in the mucosa of the upper intestine, is an important regulator of gastrointestinal (GI) motility and mediates the phase III of interdigestive migrating motor complex (MMC) in the stomach of humans, dogs and house musk shrews through the specific motilin receptor (MLN-R). Motilin-induced MMC contributes to the maintenance of normal GI functions and transmits a hunger signal from the stomach to the brain. Motilin has been identified in various mammals, but the physiological roles of motilin in regulating GI motility in these mammals are well not understood due to inconsistencies between studies conducted on different species using a range of experimental conditions. Motilin orthologs have been identified in non-mammalian vertebrates, and the sequence of avian motilin is relatively close to that of mammals, but reptile, amphibian and fish motilins show distinctive different sequences. The MLN-R has also been identified in mammals and non-mammalian vertebrates, and can be divided into two main groups: mammal/bird/reptile/amphibian clade and fish clade. Almost 50 years have passed since discovery of motilin, here we reviewed the structure, distribution, receptor and the GI motility regulatory function of motilin in vertebrates from fish to mammals.

Comparative Computational Modeling of the Bat and Human Immune Response to Viral Infection with the Comparative Biology Immune Agent Based Model

Given the impact of pandemics due to viruses of bat origin, there is increasing interest in comparative investigation into the differences between bat and human immune responses. The practice of comparative biology can be enhanced by computational methods used for dynamic knowledge representation to visualize and interrogate the putative differences between the two systems. We present an agent based model that encompasses and bridges differences between bat and human responses to viral infection: the comparative biology immune agent based model, or CBIABM. The CBIABM examines differences in innate immune mechanisms between bats and humans, specifically regarding inflammasome activity and type 1 interferon dynamics, in terms of tolerance to viral infection. Simulation experiments with the CBIABM demonstrate the efficacy of bat-related features in conferring viral tolerance and also suggest a crucial role for endothelial inflammasome activity as a mechanism for bat systemic viral tolerance and affecting the severity of disease in human viral infections. We hope that this initial study will inspire additional comparative modeling projects to link, compare, and contrast immunological functions shared across different species, and in so doing, provide insight and aid in preparation for future viral pandemics of zoonotic origin.

Homology of process: developmental dynamics in comparative biology

Comparative biology builds up systematic knowledge of the diversity of life, across evolutionary lineages and levels of organization, starting with evidence from a sparse sample of model organisms. In developmental biology, a key obstacle to the growth of comparative approaches is that the concept of homology is not very well defined for levels of organization that are intermediate between individual genes and morphological characters. In this paper, we investigate what it means for ontogenetic processes to be homologous, focusing specifically on the examples of insect segmentation and vertebrate somitogenesis. These processes can be homologous without homology of the underlying genes or gene networks, since the latter can diverge over evolutionary time, while the dynamics of the process remain the same. Ontogenetic processes like these therefore constitute a dissociable level and distinctive unit of comparison requiring their own specific criteria of homology. In addition, such processes are typically complex and nonlinear, such that their rigorous description and comparison requires not only observation and experimentation, but also dynamical modelling. We propose six criteria of process homology, combining recognized indicators (sameness of parts, morphological outcome and topological position) with novel ones derived from dynamical systems modelling (sameness of dynamical properties, dynamical complexity and evidence for transitional forms). We show how these criteria apply to animal segmentation and other ontogenetic processes. We conclude by situating our proposed dynamical framework for homology of process in relation to similar research programmes, such as process structuralism and developmental approaches to morphological homology.

Brachionus rotifers as a model for investigating dietary and metabolic regulators of aging

Because every species has unique attributes relevant to understanding specific aspects of aging, using a diversity of study systems and a comparative biology approach for aging research has the potential to lead to novel discoveries applicable to human health. Monogonont rotifers, a standard model for studies of aquatic ecology, evolutionary biology, and ecotoxicology, have also been used to study lifespan and healthspan for nearly a century. However, because much of this work has been published in the ecology and evolutionary biology literature, it may not be known to the biomedical research community. In this review, we provide an overview of Brachionus rotifers as a model to investigate nutritional and metabolic regulators of aging, with a focus on recent studies of dietary and metabolic pathway manipulation. Rotifers are microscopic, aquatic invertebrates with many advantages as a system for studying aging, including a two-week lifespan, easy laboratory culture, direct development without a larval stage, sexual and asexual reproduction, easy delivery of pharmaceuticals in liquid culture, and transparency allowing imaging of cellular morphology and processes. Rotifers have greater gene homology with humans than do established invertebrate models for aging, and thus rotifers may be used to investigate novel genetic mechanisms relevant to human lifespan and healthspan. The research on caloric restriction; dietary, pharmaceutical, and genetic interventions; and transcriptomics of aging using rotifers provide insights into the metabolic regulators of lifespan and health and suggest future directions for aging research. Capitalizing on the unique biology of Brachionus rotifers, referencing the vast existing literature about the influence of diet and drugs on rotifer lifespan and health, continuing the development of genetic tools for rotifers, and growing the rotifer research community will lead to new discoveries a better understanding of the biology of aging.

ZOOMICS: Comparative Metabolomics of Red Blood Cells From Old World Monkeys and Humans

As part of the ZOOMICS project, we set out to investigate common and diverging metabolic traits in the blood metabolome across various species by taking advantage of recent developments in high-throughput metabolomics. Here we provide the first comparative metabolomics analysis of fresh and stored human (n = 21, 10 males, 11 females), olive baboon (n = 20), and rhesus macaque (n = 20) red blood cells at baseline and upon 42 days of storage under blood bank conditions. The results indicated similarities and differences across species, which ultimately resulted in a differential propensity to undergo morphological alterations and lyse as a function of the duration of refrigerated storage. Focusing on purine oxidation, carboxylic acid, fatty acid, and arginine metabolism further highlighted species-specific metabolic wiring. For example, through a combination of steady state measurements and ¹³C₆¹⁵N₄-arginine tracing experiments, we report an increase in arginine catabolism into ornithine in humans, suggestive of species-specific arginase 1 activity and nitric oxide synthesis—an observation that may impact the translatability of cardiovascular disease studies carried out in non-human primates (NHPs). Finally, we correlated metabolic measurements to storage-induced morphological alterations via scanning electron microscopy and hemolysis, which were significantly lower in human red cells compared to both NHPs.

Proteomics in Non-model Organisms: A New Analytical Frontier

For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly, and annotation, non-model organisms may be studied with the same advanced bioanalytical toolkit as model organisms. Proteomics is one such technique, which classically relies on predicted protein sequences to catalog and measure complex proteomes across tissues and biofluids. Applying proteomics to non-model organisms can advance and accelerate biomimicry studies, biomedical advancements, veterinary medicine, agricultural research, behavioral ecology, and food safety. In this postmodel organism era, we can study almost any species, meaning that many non-model organisms are, in fact, important emerging model organisms. Herein we specifically focus on eukaryotic organisms and discuss the steps to generate sequence databases, analyze proteomic data with or without a database, and interpret results as well as future research opportunities. Proteomics is more accessible than ever before and will continue to rapidly advance in the coming years, enabling critical research and discoveries in non-model organisms that were hitherto impossible.

Assisted reproductive technologies for endangered species conservation: developing sophisticated protocols with limited access to animals with unique reproductive mechanisms

Assisted reproductive technologies (ARTs) have been proposed as a means of overcoming the significant challenges of managing small, isolated populations of endangered species in zoos. However, efficient protocols for ARTs do not exist for most endangered species. This review will focus on research efforts to characterize unique reproductive mechanisms and develop species-specific ARTs. Central to these studies are assays to measure steroid metabolites in urine or feces and/or training programs to allow unrestrained blood collections and ultrasound evaluations. The resulting information about estrous cycle dynamics, combined with studies of semen collection and processing, provides the foundation for the development of artificial insemination (AI). In vitro fertilization and embryo transfer are also discussed in relation to the advantages these techniques could provide relative to AI, as well as the significant challenges involved with technologies that require oocytes and embryos. Finally, an argument is made for additional research of nontraditional model species (e.g., domestic cats and dogs) and the development of novel models representing unique taxa. Whether these species are studied by zoo-based researchers with the expressed intent of developing ARTs for conservation or academic scientists interested in basic biology, the resulting information will provide a unique, evolutionary perspective on reproduction that could have wide-reaching benefits. The more information we have available, the better our chances will be of developing effective ARTs and making a difference in conservation efforts for endangered species.

The role of herbivory in the macroevolution of vertebrate hormone dynamics

Vertebrates have high species-level variation in circulating hormone concentrations, and the functional significance of this variation is largely unknown. We tested the hypothesis that interspecific differences in hormone concentrations are partially driven by plant consumption, based on the prediction that herbivores should have higher basal hormone levels to 'outcompete' plant endocrine disruptors. We compared levels of glucocorticoids (GCs), the hormones with the most available data, across 166 species. Using phylogenetically informed comparisons, we found that herbivores had higher GC levels than carnivores. Furthermore, we found that the previously described negative relationship between GC levels and body mass only held in herbivores, not carnivores, and that the effect of diet was greatest at extreme body sizes. These findings demonstrate the far-reaching effects of diet on animal physiology, and provide evidence that herbivory influences circulating hormone concentrations. We urge future direct testing of the relationship between phytochemical load and GC levels.

Multisensory modulation of body ownership in mice

Body ownership is a fundamental aspect of self-consciousness that reflects more than the presence of physical body parts. As demonstrated by the rubber hand illusion (RHI), human brains construct body ownership experiences using available multisensory information. Experimental conditions similar to those that induce the RHI in humans have been recently adapted to induce the rubber tail illusion (RTI) in mice. Here, we show that the RTI is enhanced in both sexes of mice by repetitive synchronous stroking comprised of correlated visual and tactile stimulation of real and rubber tails compared to visual-only mimicked stroking conducted without tactile stimulation. The RTI also appears to be enhanced in female but not male mice by slow compared to fast stroking that reflects an interoceptive manipulation associated with affective touch in humans. Sex differences in slow stroking effects are exploratory and require replication in mice. Sex differences have not been reported for the RHI in healthy humans, but women rate slow stroking as more affectively pleasant compared to the ratings of men. Results suggest that the RHI in humans resembles aspects of the RTI in mice. Studies of mice may therefore provide neurobiological insights on evolutionarily conserved mechanisms of bodily self-consciousness in humans.

Faraway, so close. The comparative method and the potential of non-model animals in mitochondrial research

Inference from model organisms has been the engine for many discoveries in life science, but indiscriminate generalization leads to oversimplifications and misconceptions. Model organisms and inductive reasoning are irreplaceable: there is no other way to tackle the complexity of living systems. At the same time, it is not advisable to infer general patterns from a restricted number of species, which are very far from being representative of the diversity of life. Not all models are equal. Some organisms are suitable to find similarities across species, other highly specialized organisms can be used to focus on differences. In this opinion piece, we discuss the dominance of the mechanistic/reductionist approach in life sciences and make a case for an enhanced application of the comparative approach to study processes in all their various forms across different organisms. We also enlist some rising animal models in mitochondrial research, to exemplify how non-model organisms can be chosen in a comparative framework. These taxa often do not possess implemented tools and dedicated methods/resources. However, because of specific features, they have the potential to address still unanswered biological questions. Finally, we discuss future perspectives and caveats of the comparative method in the age of 'big data'. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.

Evolutionary Ecology of Senescence and a Reassessment of Williams' 'Extrinsic Mortality' Hypothesis

The evolutionary theory of senescence underpins research in life history evolution and the biology of aging. In 1957 G.C. Williams predicted that higher adult death rates select for earlier senescence and shorter length of life, but preadult mortality does not matter to the evolution of senescence. This was subsequently interpreted as predicting that senescence should be caused by 'extrinsic' sources of mortality. This idea still motivates empirical studies, although formal, mathematical theory shows it is wrong. It has nonetheless prospered because it offers an intuitive explanation for patterns observed in nature. We review the flaws in Williams' model, explore alternative explanations for comparative patterns that are consistent with the evolutionary theory of senescence, and discuss how hypotheses based on it can be tested. We argue that focusing on how sources of mortality affect ages differently offers greater insight into evolutionary processes.

Longevity and life history coevolve with oxidative stress in birds

1. The mechanisms that underpin the evolution of ageing and life histories remain elusive. Oxidative stress, which results in accumulated cellular damages, is one of the mechanisms suggested to play a role. 2. In this paper, we set out to test the "oxidative stress theory of ageing" and the "oxidative stress hypothesis of life histories" using a comprehensive phylogenetic comparison based on an unprecedented dataset of oxidative physiology in 88 free-living bird species. 3. We show for the first time that bird species with longer lifespan have higher non-enzymatic antioxidant capacity and suffer less oxidative damage to their lipids. We also found that bird species featuring a faster pace-of-life either have lower non-enzymatic antioxidant capacity or are exposed to higher levels of oxidative damage, while adult annual mortality does not relate to oxidative state. 4. These results reinforce the role of oxidative stress in the evolution of lifespan and also corroborate the role of oxidative state in the evolution of life histories among free-living birds.

Phylogenetic Comparative Methods can Provide Important Insights into the Evolution of Toxic Weaponry

The literature on chemical weaponry of organisms is vast and provides a rich understanding of the composition and mechanisms of the toxins and other components involved. However, an ecological or evolutionary perspective has often been lacking and is largely limited to (1) molecular evolutionary studies of particular toxins (lacking an ecological view); (2) comparisons across different species that ignore phylogenetic relatedness (lacking an evolutionary view); or (3) descriptive studies of venom composition and toxicology that contain post hoc and untested ecological or evolutionary interpretations (a common event but essentially uninformative speculation). Conveniently, comparative biologists have prolifically been developing and using a wide range of phylogenetic comparative methods that allow us to explicitly address many ecological and evolutionary questions relating to venoms and poisons. Nevertheless, these analytical tools and approaches are rarely used and poorly known by biological toxinologists and toxicologists. In this review I aim to (1) introduce phylogenetic comparative methods to the latter audience; (2) highlight the range of questions that can be addressed using them; and (3) encourage biological toxinologists and toxicologists to either seek out adequate training in comparative biology or seek collaboration with comparative biologists to reap the fruits of a powerful interdisciplinary approach to the field.

Insulin-Like Growth Factor-Binding Proteins of Teleost Fishes

The insulin-like growth factor (Igf) binding protein (Igfbp) family has a broad range of physiological functions and a fascinating evolutionary history. This review focuses on the Igfbps of teleost fishes, where genome duplication events have diversified gene repertoire, function, and physiological regulation-with six core Igfbps expanded into a family of over twenty genes in some lineages. In addition to briefly summarizing the current state of knowledge on teleost Igfbp evolution, function, and expression-level regulation, we highlight gaps in our understanding and promising areas for future work.

Do Chimeras Have Minds?

Suppose that a colleague proposed a fantastic experiment: to introduce human stem cells into a neonatal mouse so that its entire brain developed into "human-like" neuronal structures. The colleague claimed it would still be a mouse, and that its chimeric brain would be nothing like a "human" one. It would not, as a result, have a moral status beyond its nonhuman animal origins. Thus, the "human neuron mouse" would allow scientists to tinker with human-like neurology in ways that would be precluded if it were a human being, and that would promise to lead to substantial understanding of the destructive and incurable brain diseases that befall humanity. The colleague does admit, however, that for reasons of comparative fidelity, experiments in human patients would be scientifically preferable, although in this case, neither ethically justified nor legally permitted. For that reason, it might be desirable to create a human brain in a nonhuman primate, where it would be more likely that significant human-like neuronal development would occur, but still could not become a person. This article explores the significance of a "human neuron chimpanzee," and suggests that contradictions in the design of the experiment make it unethical to proceed in either murine or primate models.

Translation fidelity coevolves with longevity

Whether errors in protein synthesis play a role in aging has been a subject of intense debate. It has been suggested that rare mistakes in protein synthesis in young organisms may result in errors in the protein synthesis machinery, eventually leading to an increasing cascade of errors as organisms age. Studies that followed generally failed to identify a dramatic increase in translation errors with aging. However, whether translation fidelity plays a role in aging remained an open question. To address this issue, we examined the relationship between translation fidelity and maximum lifespan across 17 rodent species with diverse lifespans. To measure translation fidelity, we utilized sensitive luciferase‐based reporter constructs with mutations in an amino acid residue critical to luciferase activity, wherein misincorporation of amino acids at this mutated codon re‐activated the luciferase. The frequency of amino acid misincorporation at the first and second codon positions showed strong negative correlation with maximum lifespan. This correlation remained significant after phylogenetic correction, indicating that translation fidelity coevolves with longevity. These results give new life to the role of protein synthesis errors in aging: Although the error rate may not significantly change with age, the basal rate of translation errors is important in defining lifespan across mammals.

Molecular Mechanisms Determining Lifespan in Short- and Long-Lived Species

Aging is a global decline of physiological functions, leading to an increased susceptibility to diseases and ultimately death. Maximum lifespans differ up to 200-fold between mammalian species. Although considerable progress has been achieved in identifying conserved pathways that regulate individual lifespan within model organisms, whether the same pathways are responsible for the interspecies differences in longevity remains to be determined. Recent cross-species studies have begun to identify pathways responsible for interspecies differences in lifespan. Here, we review the evidence supporting the role of anticancer mechanisms, DNA repair machinery, insulin/insulin-like growth factor 1 signaling, and proteostasis in defining species lifespans. Understanding the mechanisms responsible for the dramatic differences in lifespan between species will have a transformative effect on developing interventions to improve human health and longevity.

Toward a Predictive Framework for Convergent Evolution: Integrating Natural History, Genetic Mechanisms, and Consequences for the Diversity of Life

A charm of biology as a scientific discipline is the diversity of life. Although this diversity can make laws of biology challenging to discover, several repeated patterns and general principles govern evolutionary diversification. Convergent evolution, the independent evolution of similar phenotypes, has been at the heart of one approach to understand generality in the evolutionary process. Yet understanding when and why organismal traits and strategies repeatedly evolve has been a central challenge. These issues were the focus of the American Society of Naturalists Vice Presidential Symposium in 2016 and are the subject of this collection of articles. Although naturalists have long made inferences about convergent evolution and its importance, there has been confusion in the interpretation of the pattern of convergence. Does convergence primarily indicate adaptation or constraint? How often should convergence be expected? Are there general principles that would allow us to predict where and when and by what mechanisms convergent evolution should occur? What role does natural history play in advancing our understanding of general evolutionary principles? In this introductory article, I address these questions, review several generalizations about convergent evolution that have emerged over the past 15 years, and present a framework for advancing the study and interpretation of convergence. Perhaps the most important emerging conclusion is that the genetic mechanisms of convergent evolution are phylogenetically conserved; that is, more closely related species tend to share the same genetic basis of traits, even when independently evolved. Finally, I highlight how the articles in this special issue further develop concepts, methodologies, and case studies at the frontier of our understanding of the causes and consequences of convergent evolution.

The chinchilla as a novel animal model of pregnancy

Several parameters are important when choosing the most appropriate animal to model human obstetrics, including gestation period, number of fetuses per gestation and placental structure. The domesticated long-tailed chinchilla (Chinchilla lanigera) is a well-suited and appropriate animal model of pregnancy that often will carry only one offspring and has a long gestation period of 105-115 days. Furthermore, the chinchilla placenta is of the haemomonochorial labyrinthine type and is therefore comparable to the human villous haemomonochorial placenta. This proof-of-concept study demonstrated the feasibility in laboratory settings, and demonstrated the potential of the pregnant chinchilla as an animal model for obstetric research and its potential usefulness for non-invasive measurements in the placenta. We demonstrate measurements of the placental and fetal metabolism (demonstrated in vivo by hyperpolarized MRI and in vitro by qPCR analyses), placental vessels (demonstrated ex vivo by contrast-enhanced CT angiography) and overall anatomy (demonstrated in vivo by whole-body CT).

Abscisic Acid as Pathogen Effector and Immune Regulator

Abscisic acid (ABA) is a sesquiterpene signaling molecule produced in all kingdoms of life. To date, the best known functions of ABA are derived from its role as a major phytohormone in plant abiotic stress resistance. Different organisms have developed different biosynthesis and signal transduction pathways related to ABA. Despite this, there are also intriguing common themes where ABA often suppresses host immune responses and is utilized by pathogens as an effector molecule. ABA also seems to play an important role in compatible mutualistic interactions such as mycorrhiza and rhizosphere bacteria with plants, and possibly also the animal gut microbiome. The frequent use of ABA in inter-species communication could be a possible reason for the wide distribution and re-invention of ABA as a signaling molecule in different organisms. In humans and animal models, it has been shown that ABA treatment or nutrient-derived ABA is beneficial in inflammatory diseases like colitis and type 2 diabetes, which confer potential to ABA as an interesting nutraceutical or pharmacognostic drug. The anti-inflammatory activity, cellular metabolic reprogramming, and other beneficial physiological and psychological effects of ABA treatment in humans and animal models has sparked an interest in this molecule and its signaling pathway as a novel pharmacological target. In contrast to plants, however, very little is known about the ABA biosynthesis and signaling in other organisms. Genes, tools and knowledge about ABA from plant sciences and studies of phytopathogenic fungi might benefit biomedical studies on the physiological role of endogenously generated ABA in humans.

Extended Postnatal Brain Development in the Longest-Lived Rodent: Prolonged Maintenance of Neotenous Traits in the Naked Mole-Rat Brain

The naked mole-rat (NMR) is the longest-lived rodent with a maximum lifespan >31 years. Intriguingly, fully-grown naked mole-rats (NMRs) exhibit many traits typical of neonatal rodents. However, little is known about NMR growth and maturation, and we question whether sustained neotenous features when compared to mice, reflect an extended developmental period, commensurate with their exceptionally long life. We tracked development from birth to 3 years of age in the slowest maturing organ, the brain, by measuring mass, neural stem cell proliferation, axonal, and dendritic maturation, synaptogenesis and myelination. NMR brain maturation was compared to data from similar sized rodents, mice, and to that of long-lived mammals, humans, and non-human primates. We found that at birth, NMR brains are significantly more developed than mice, and rather are more similar to those of newborn primates, with clearly laminated hippocampi and myelinated white matter tracts. Despite this more mature brain at birth than mice, postnatal NMR brain maturation occurs at a far slower rate than mice, taking four-times longer than required for mice to fully complete brain development. At 4 months of age, NMR brains reach 90% of adult size with stable neuronal cytostructural protein expression whereas myelin protein expression does not plateau until 9 months of age in NMRs, and synaptic protein expression continues to change throughout the first 3 years of life. Intriguingly, NMR axonal composition is more similar to humans than mice whereby NMRs maintain expression of three-repeat (3R) tau even after brain growth is complete; mice experience an abrupt downregulation of 3R tau by postnatal day 8 which continues to diminish through 6 weeks of age. We have identified key ages in NMR cerebral development and suggest that the long-lived NMR may provide neurobiologists an exceptional model to study brain developmental processes that are compressed in common short-lived laboratory animal models.

Anther and pollen development: A conserved developmental pathway

Pollen development is a critical step in plant development that is needed for successful breeding and seed formation. Manipulation of male fertility has proved a useful trait for hybrid breeding and increased crop yield. However, although there is a good understanding developing of the molecular mechanisms of anther and pollen anther development in model species, such as Arabidopsis and rice, little is known about the equivalent processes in important crops. Nevertheless the onset of increased genomic information and genetic tools is facilitating translation of information from the models to crops, such as barley and wheat; this will enable increased understanding and manipulation of these pathways for agricultural improvement.

What haplodiploids can teach us about hybridization and speciation

Most evolutionary theory focuses on species that reproduce through sexual reproduction where both sexes have a diploid chromosome count. Yet a substantial proportion of multicellular species display complex life cycles, with both haploid and diploid life stages. A classic example is haplodiploidy, where females develop from fertilized eggs and are diploid, while males develop from unfertilized eggs and are haploid. Although haplodiploids make up about 15% of all animals (de la Filia et al. ), this type of reproduction is rarely considered in evolutionary theory. In this issue of Molecular Ecology, Patten et al. () develop a theoretical model to compare the rate of nuclear and mitochondrial introgression in haplodiploid and diploid species. They show that when two haplodiploid species hybridize, nuclear genes are much less likely to cross the species barrier than if both species were to be diploids. The reason for this is that only half of the offspring resulting from matings between haplodiploid species are true hybrids: sons from such mating only inherit their mother genes and therefore only contain genes of the maternal species. Truly, hybrid males can only occur through backcrossing of a hybrid female to a male of one of the parental species. While this twist of haplodiploid transmission genetics limits nuclear introgression, mitochondrial genes, which are maternally inherited, are unaffected by the scarcity of hybrid males. In other words, the rate of mitochondrial introgression is the same for haplodiploid and diploid species. As a result, haplodiploid species on average show a bias of mitochondrial compared to nuclear introgression.

Variation in opsin genes correlates with signalling ecology in North American fireflies

Genes underlying signal reception should evolve to maximize signal detection in a particular environment. In animals, opsins, the protein component of visual pigments, are predicted to evolve according to this expectation. Fireflies are known for their bioluminescent mating signals. The eyes of nocturnal species are expected to maximize the detection of conspecific signal colours emitted in the typical low-light environment. This is not expected for species that have transitioned to diurnal activity in bright daytime environments. Here, we test the hypothesis that opsin gene sequence plays a role in modifying firefly eye spectral sensitivity. We use genome and transcriptome sequencing in four firefly species, transcriptome sequencing in six additional species and targeted gene sequencing in 28 other species to identify all opsin genes present in North American fireflies and to elucidate amino acid sites under positive selection. We also determine whether amino acid substitutions in opsins are linked to evolutionary changes in signal mode, signal colour and light environment. We find only two opsins, one long wavelength and one ultraviolet, in all firefly species and identify 25 candidate sites that may be involved in determining spectral sensitivity. In addition, we find elevated rates of evolution at transitions to diurnal activity, and changes in selective constraint on long wavelength opsin associated with changes in light environment. Our results suggest that changes in eye spectral sensitivity are at least partially due to opsin sequence. Fireflies continue to be a promising system in which to investigate the evolution of signals, receptors and signalling environments.

Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics

Mononuclear phagocytes are organized in a complex system of ontogenetically and functionally distinct subsets, that has been best described in mouse and to some extent in human. Identification of homologous mononuclear phagocyte subsets in other vertebrate species of biomedical, economic, and environmental interest is needed to improve our knowledge in physiologic and physio-pathologic processes, and to design intervention strategies against a variety of diseases, including zoonotic infections. We developed a streamlined approach combining refined cell sorting and integrated comparative transcriptomics analyses which revealed conservation of the mononuclear phagocyte organization across human, mouse, sheep, pigs and, in some respect, chicken. This strategy should help democratizing the use of omics analyses for the identification and study of cell types across tissues and species. Moreover, we identified conserved gene signatures that enable robust identification and universal definition of these cell types. We identified new evolutionarily conserved gene candidates and gene interaction networks for the molecular regulation of the development or functions of these cell types, as well as conserved surface candidates for refined subset phenotyping throughout species. A phylogenetic analysis revealed that orthologous genes of the conserved signatures exist in teleost fishes and apparently not in Lamprey.

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development

Milk has been well established as the optimal nutrition source for infants, yet there is still much to be understood about its molecular composition. Therefore, our objective was to develop and compare comprehensive milk proteomes for human and rhesus macaques to highlight differences in neonatal nutrition. We developed a milk proteomics technique that overcomes previous technical barriers including pervasive post-translational modifications and limited sample volume. We identified 1606 and 518 proteins in human and macaque milk, respectively. During analysis of detected protein orthologs, we identified 88 differentially abundant proteins. Of these, 93% exhibited increased abundance in human milk relative to macaque and include lactoferrin, polymeric immunoglobulin receptor, alpha-1 antichymotrypsin, vitamin D-binding protein, and haptocorrin. Furthermore, proteins more abundant in human milk compared with macaque are associated with development of the gastrointestinal tract, the immune system, and the brain. Overall, our novel proteomics method reveals the first comprehensive macaque milk proteome and 524 newly identified human milk proteins. The differentially abundant proteins observed are consistent with the perspective that human infants, compared with nonhuman primates, are born at a slightly earlier stage of somatic development and require additional support through higher quantities of specific proteins to nurture human infant maturation.

Testing the role of genetic background in parallel evolution using the comparative experimental evolution of antibiotic resistance

Parallel evolution is the independent evolution of the same phenotype or genotype in response to the same selection pressure. There are examples of parallel molecular evolution across divergent genetic backgrounds, suggesting that genetic background may not play an important role in determining the outcome of adaptation. Here, we measure the influence of genetic background on phenotypic and molecular adaptation by combining experimental evolution with comparative analysis. We selected for resistance to the antibiotic rifampicin in eight strains of bacteria from the genus Pseudomonas using a short term selection experiment. Adaptation occurred by 47 mutations at conserved sites in rpoB, the target of rifampicin, and due to the high diversity of possible mutations the probability of within-strain parallel evolution was low. The probability of between-strain parallel evolution was only marginally lower, because different strains substituted similar rpoB mutations. In contrast, we found that more than 30% of the phenotypic variation in the growth rate of evolved clones was attributable to among-strain differences. Parallel molecular evolution across strains resulted in divergent phenotypic evolution because rpoB mutations had different effects on growth rate in different strains. This study shows that genetic divergence between strains constrains parallel phenotypic evolution, but had little detectable impact on the molecular basis of adaptation in this system.

Clock gene evolution: seasonal timing, phylogenetic signal, or functional constraint?

Genetic determinants of seasonal reproduction are not fully understood but may be important predictors of organism responses to climate change. We used a comparative approach to study the evolution of seasonal timing within a fish community in a natural common garden setting. We tested the hypothesis that allelic length variation in the PolyQ domain of a circadian rhythm gene, Clock1a, corresponded to interspecific differences in seasonal reproductive timing across 5 native and 1 introduced cyprinid fishes (n = 425 individuals) that co-occur in the Rio Grande, NM, USA. Most common allele lengths were longer in native species that initiated reproduction earlier (Spearman's r = -0.70, P = 0.23). Clock1a allele length exhibited strong phylogenetic signal and earlier spawners were evolutionarily derived. Aside from length variation in Clock1a, all other amino acids were identical across native species, suggesting functional constraint over evolutionary time. Interestingly, the endangered Rio Grande silvery minnow (Hybognathus amarus) exhibited less allelic variation in Clock1a and observed heterozygosity was 2- to 6-fold lower than the 5 other (nonimperiled) species. Reduced genetic variation in this functionally important gene may impede this species' capacity to respond to ongoing environmental change.

Investigating neuronal cell types through comparative cellular physiology

Comprehensive understanding of nervous systems would require the unambiguous identification of all neuronal cell types, which are distinguished by gene-expression differences, particularly in plasma-membrane receptors and ion channels. Toward this ultimate goal, a recent paper initiated an approach to identify and study divergent neuronal cell types through comparative cellular physiology.