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- Volume 9, 2021
Annual Review of Animal Biosciences - Volume 9, 2021
Volume 9, 2021
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Vertebrate Chromosome Evolution
Vol. 9 (2021), pp. 1–27More LessThe study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation
Vol. 9 (2021), pp. 29–53More LessThe genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.
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Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes
Vol. 9 (2021), pp. 55–79More LessEvolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution. We survey genome-wide data and the available literature covering 438 cichlid populations (412 species) across multiple radiations to synthesize information about patterns and sharing of genetic variation. Nucleotide diversity within species is low in cichlids, with 92% of surveyed populations having less diversity than the median value found in other vertebrates. Divergence within radiations is also low, and a large proportion of variation is shared among species due to incomplete lineage sorting and widespread hybridization. Population genetics therefore provides a suitable conceptual framework for evolutionary genomic studies of cichlid radiations. We focus in detail on the roles of hybridization in shaping the patterns of genetic variation and in promoting cichlid diversification.
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Genomics and the Evolutionary History of Equids
Vol. 9 (2021), pp. 81–101More LessThe equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.
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The Diversity of Primates: From Biomedicine to Conservation Genomics
Vol. 9 (2021), pp. 103–124More LessUntil now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.
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Genetics and Evolution of Mammalian Coat Pigmentation
Vol. 9 (2021), pp. 125–148More LessThe diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.
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Physiological Genomics of Adaptation to High-Altitude Hypoxia
Vol. 9 (2021), pp. 149–171More LessPopulation genomic studies of humans and other animals at high altitude have generated many hypotheses about the genes and pathways that may have contributed to hypoxia adaptation. Future advances require experimental tests of such hypotheses to identify causal mechanisms. Studies to date illustrate the challenge of moving from lists of candidate genes to the identification of phenotypic targets of selection, as it can be difficult to determine whether observed genotype–phenotype associations reflect causal effects or secondary consequences of changes in other traits that are linked via homeostatic regulation. Recent work on high-altitude models such as deer mice has revealed both plastic and evolved changes in respiratory, cardiovascular, and metabolic traits that contribute to aerobic performance capacity in hypoxia, and analyses of tissue-specific transcriptomes have identified changes in regulatory networks that mediate adaptive changes in physiological phenotype. Here we synthesize recent results and discuss lessons learned from studies of high-altitude adaptation that lie at the intersection of genomics and physiology.
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Programmed DNA Elimination in Vertebrates
Vol. 9 (2021), pp. 173–201More LessOver the last few decades, an increasing number of vertebrate taxa have been identified that undergo programmed genome rearrangement, or programmed DNA loss, during development. In these organisms, the genome of germ cells is often reproducibly different from the genome of all other cells within the body. Although we clearly have not identified all vertebrate taxa that undergo programmed genome loss, the list of species known to undergo loss now represents ∼10% of vertebrate species, including several basally diverging lineages. Recent studies have shed new light on the targets and mechanisms of DNA loss and their association with canonical modes of DNA silencing. Ultimately, expansion of these studies into a larger collection of taxa will aid in reconstructing patterns of shared/independent ancestry of programmed DNA loss in the vertebrate lineage, as well as more recent evolutionary events that have shaped the structure and content of eliminated DNA.
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Epigenetic Regulation of the Nuclear and Mitochondrial Genomes: Involvement in Metabolism, Development, and Disease
Vol. 9 (2021), pp. 203–224More LessOur understanding of the interactions between the nuclear and mitochondrial genomes is becoming increasingly important as they are extensively involved in establishing early development and developmental progression. Evidence from various biological systems indicates the interdependency between the genomes, which requires a high degree of compatibility and synchrony to ensure effective cellular function throughout development and in the resultant offspring. During development, waves of DNA demethylation, de novo methylation, and maintenance methylation act on the nuclear genome and typify oogenesis and pre- and postimplantation development. At the same time, significant changes in mitochondrial DNA copy number influence the metabolic status of the developing organism in a typically cell-type-specific manner. Collectively, at any given stage in development, these actions establish genomic balance that ensures each developmental milestone is met and that the organism's program for life is established.
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Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs
Vol. 9 (2021), pp. 225–248More LessEndogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include (a) recombination to result in ERV–XRV chimeras, (b) ERV induction of immune self-tolerance to XRV antigens, (c) ERV antigen interference with XRV receptor binding, and (d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts.
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Toxoplasmosis: Recent Advances in Understanding the Link Between Infection and Host Behavior
Vol. 9 (2021), pp. 249–264More LessHumans, wildlife, and domestic animals are intimately linked through shared infections. Many parasites and pathogens use multiple host species, either opportunistically or sequentially, such that managing disease risk frequently requires a broader understanding of the ecological community. The coccidian protozoan Toxoplasma gondii infects more than one hundred species of vertebrates, ranging from bats to beluga whales. In humans, acute toxoplasmosis can have serious health consequences for immunocompromised individuals. Even amongst asymptomatic patients, however, toxoplasmosis has been linked to a range of behavioral alterations and conditions, such as changes in risk tolerance, neuroticism, mental illness, suicide, and accident proneness. Whether such links are causal or simply correlational has been the subject of intense study and debate; from an evolutionary standpoint, selection may favor parasite-induced alterations in host behavior that increase the likelihood a host is consumed by the definitive host—in this case a domestic or wild felid. Here, we examine current evidence for parasite-induced manipulations of host behavior, in both humans and other animals. We critically evaluate proposed mechanisms through which infection might influence host behavior, which range from inflammation in the brain to changes in hormones or neurotransmitters. Considering estimates that T. gondii may infect up to one-third of the global human population, we conclude by examining the implications of these changes for human behavior, individual fitness, and emergent cultural properties.
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Coral Probiotics: Premise, Promise, Prospects
Vol. 9 (2021), pp. 265–288More LessThe use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.
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Advances in Microbiome Research for Animal Health
Vol. 9 (2021), pp. 289–311More LessHost-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host–microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic.
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Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions
Vol. 9 (2021), pp. 313–332More LessAntimicrobial resistance (AMR) is a threat to animal and human health. Antimicrobial use has been identified as a major driver of AMR, and reductions in use are a focal point of interventions to reduce resistance. Accordingly, stakeholders in human health and livestock production have implemented antimicrobial stewardship programs aimed at reducing use. Thus far, these efforts have yielded variable impacts on AMR. Furthermore, scientific advances are prompting an expansion and more nuanced appreciation of the many nonantibiotic factors that drive AMR, as well as how these factors vary across systems, geographies, and contexts. Given these trends, we propose a framework to prioritize AMR interventions. We use this framework to evaluate the impact of interventions that focus on antimicrobial use. We conclude by suggesting that priorities be expanded to include greater consideration of host–microbial interactions that dictate AMR, as well as anthropogenic and environmental systems that promote dissemination of AMR.
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Insects: A Potential Source of Protein and Other Nutrients for Feed and Food
Vol. 9 (2021), pp. 333–354More LessSustainable production of healthy food for a growing global population, in the face of the uncertainties of climate change, represents a major challenge for the coming decade. Livestock provide food with high nutritional value but are frequently fed on human-edible crops and are associated with significant production of greenhouse gases. Recent years have seen increasing interest in the farming of insects as a sustainable source of human food, or as a replacement of ingredients such as soya or fishmeal in the feeds of terrestrial livestock or fish. This review provides an overview of insect physiology and growth regulation, considers the requirements for insect farming and mass production, and summarizes the nutritional value of the 10 most commonly studied insect species, before reviewing the literature on the use of insects as feed and food. We highlight the challenges required to develop a sustainable, safe, and affordable insect farming industry.
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New Insights in Muscle Biology that Alter Meat Quality
Vol. 9 (2021), pp. 355–377More LessFresh meat quality is greatly determined through biochemical changes occurring in the muscle during its conversion to meat. These changes are key to imparting a unique set of characteristics on fresh meat, including its appearance, ability to retain moisture, and texture. Skeletal muscle is an extremely heterogeneous tissue composed of different types of fibers that have distinct contractile and metabolic properties. Fiber type composition determines the overall biochemical and functional properties of the muscle tissue and, subsequently, its quality as fresh meat. Therefore, changing muscle fiber profile in living animals through genetic selection or environmental factors has the potential to modulate fresh meat quality. We provide an overview of the biochemical processes responsible for the development of meat quality attributes and an overall understanding of the strong relationship between muscle fiber profile and meat quality in different meat species.
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Strategies to Improve Poultry Food Safety, a Landscape Review
Vol. 9 (2021), pp. 379–400More LessFood safety remains a significant public health issue for the poultry industry. Foodborne pathogens can be in contact at all phases of poultry production, from initial hatch to processing and ultimately to retail and meal preparation. Salmonella and Campylobacter have been considered the primary foodborne pathogens associated with poultry. Both organisms are major causative agents of human foodborne illness. Limiting these pathogens in poultry production requires identifying their sources and routes of transmission. This involves the ability to isolate and precisely identify them using methodologies capable of discernment at the genome level. Interventions to reduce their occurrence in poultry production employ two basic strategies: prevention of establishment and elimination of already-established pathogens. This review provides an overview of current findings and prospects for further research on poultry food safety issues.
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Applications of Nanobodies
Vol. 9 (2021), pp. 401–421More LessUnique, functional, homodimeric heavy chain–only antibodies, devoid of light chains, are circulating in the blood of Camelidae. These antibodies recognize their cognate antigen via one single domain, known as VHH or Nanobody. This serendipitous discovery made three decades ago has stimulated a growing number of researchers to generate highly specific Nanobodies against a myriad of targets. The small size, strict monomeric state, robustness, and easy tailoring of these Nanobodies have inspired many groups to design innovative Nanobody-based multi-domain constructs to explore novel applications. As such, Nanobodies have been employed as an exquisite research tool in structural, cell, and developmental biology. Furthermore, Nanobodies have demonstrated their benefit for more sensitive diagnostic tests. Finally, several Nanobody-based constructs have been designed to develop new therapeutic products.
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Bacteriome Structure, Function, and Probiotics in Fish Larviculture: The Good, the Bad, and the Gaps
Vol. 9 (2021), pp. 423–452More LessAquaculture is the fastest-growing sector in food production worldwide. For decades, research on animal physiology, nutrition, and behavior established the foundations of best practices in land-based fish rearing and disease control. Current DNA sequencing, bioinformatics, and data science technologies now allow deep investigations of host-associated microbiomes in a tractable fashion. Adequate use of these technologies can illuminate microbiome dynamics and aid the engineering of microbiome-based solutions to disease prevention in an unprecedented manner. This review examines molecular studies of bacterial diversity, function, and host immunitymodulation at early stages of fish development, where microbial infections cause important economic losses. We uncover host colonization and virulence factors within a synthetic assemblage of fish pathogens using high-end comparative genomics and address the use of probiotics and paraprobiotics as applicable disease-prevention strategies in fish larval and juvenile rearing. We finally propose guidelines for future microbiome research of presumed relevance to fish larviculture.
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Genetic Engineering of Livestock: The Opportunity Cost of Regulatory Delay
Vol. 9 (2021), pp. 453–478More LessGenetically engineered (GE) livestock were first reported in 1985, and yet only a single GE food animal, the fast-growing AquAdvantage salmon, has been commercialized. There are myriad interconnected reasons for the slow progress in this once-promising field, including technical issues, the structure of livestock industries, lack of public research funding and investment, regulatory obstacles, and concern about public opinion. This review focuses on GE livestock that have been produced and documents the difficulties that researchers and developers have encountered en route. Additionally, the costs associated with delayed commercialization of GE livestock were modeled using three case studies: GE mastitis-resistant dairy cattle, genome-edited porcine reproductive and respiratory syndrome virus–resistant pigs, and the AquAdvantage salmon. Delays of 5 or 10 years in the commercialization of GE livestock beyond the normative 10-year GE product evaluation period were associated with billions of dollars in opportunity costs and reduced global food security.
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