{"title":"Vertebrate Chromosome Evolution.","authors":"Joana Damas, Marco Corbo, Harris A Lewin","doi":"10.1146/annurev-animal-020518-114924","DOIUrl":"https://doi.org/10.1146/annurev-animal-020518-114924","url":null,"abstract":"<p><p>The 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"1-27"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-020518-114924","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38597817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Strategies to Improve Poultry Food Safety, a Landscape Review.","authors":"Steven C Ricke","doi":"10.1146/annurev-animal-061220-023200","DOIUrl":"https://doi.org/10.1146/annurev-animal-061220-023200","url":null,"abstract":"<p><p>Food 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. <i>Salmonella</i> and <i>Campylobacter</i> 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"379-400"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-061220-023200","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38574407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nuno Borges, Tina Keller-Costa, Gracinda M M Sanches-Fernandes, António Louvado, Newton C M Gomes, Rodrigo Costa
{"title":"Bacteriome Structure, Function, and Probiotics in Fish Larviculture: The Good, the Bad, and the Gaps.","authors":"Nuno Borges, Tina Keller-Costa, Gracinda M M Sanches-Fernandes, António Louvado, Newton C M Gomes, Rodrigo Costa","doi":"10.1146/annurev-animal-062920-113114","DOIUrl":"https://doi.org/10.1146/annurev-animal-062920-113114","url":null,"abstract":"<p><p>Aquaculture 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"423-452"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-062920-113114","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38658786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Epigenetic Regulation of the Nuclear and Mitochondrial Genomes: Involvement in Metabolism, Development, and Disease.","authors":"Justin C St John","doi":"10.1146/annurev-animal-080520-083353","DOIUrl":"https://doi.org/10.1146/annurev-animal-080520-083353","url":null,"abstract":"<p><p>Our 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"203-224"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25372798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Toxoplasmosis: Recent Advances in Understanding the Link Between Infection and Host Behavior.","authors":"Stefanie K Johnson, Pieter T J Johnson","doi":"10.1146/annurev-animal-081720-111125","DOIUrl":"https://doi.org/10.1146/annurev-animal-081720-111125","url":null,"abstract":"<p><p>Humans, 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 <i>Toxoplasma gondii</i> 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 <i>T. gondii</i> 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"249-264"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-081720-111125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38561507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes.","authors":"Hannes Svardal, Walter Salzburger, Milan Malinsky","doi":"10.1146/annurev-animal-061220-023129","DOIUrl":"https://doi.org/10.1146/annurev-animal-061220-023129","url":null,"abstract":"<p><p>Evolutionary 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"55-79"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-061220-023129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38616979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sulaiman K Matarneh, Saulo L Silva, David E Gerrard
{"title":"New Insights in Muscle Biology that Alter Meat Quality.","authors":"Sulaiman K Matarneh, Saulo L Silva, David E Gerrard","doi":"10.1146/annurev-animal-021419-083902","DOIUrl":"https://doi.org/10.1146/annurev-animal-021419-083902","url":null,"abstract":"<p><p>Fresh 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"355-377"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-021419-083902","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38737064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Raquel S Peixoto, Michael Sweet, Helena D M Villela, Pedro Cardoso, Torsten Thomas, Christian R Voolstra, Lone Høj, David G Bourne
{"title":"Coral Probiotics: Premise, Promise, Prospects.","authors":"Raquel S Peixoto, Michael Sweet, Helena D M Villela, Pedro Cardoso, Torsten Thomas, Christian R Voolstra, Lone Høj, David G Bourne","doi":"10.1146/annurev-animal-090120-115444","DOIUrl":"https://doi.org/10.1146/annurev-animal-090120-115444","url":null,"abstract":"<p><p>The 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 (<i>a</i>) promoting coral nutrition and growth, (<i>b</i>) mitigating stress and impacts of toxic compounds, (<i>c</i>) deterring pathogens, and (<i>d</i>) 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"265-288"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-090120-115444","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38715677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jeramiah J Smith, Vladimir A Timoshevskiy, Cody Saraceno
{"title":"Programmed DNA Elimination in Vertebrates.","authors":"Jeramiah J Smith, Vladimir A Timoshevskiy, Cody Saraceno","doi":"10.1146/annurev-animal-061220-023220","DOIUrl":"https://doi.org/10.1146/annurev-animal-061220-023220","url":null,"abstract":"<p><p>Over 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.</p>","PeriodicalId":48953,"journal":{"name":"Annual Review of Animal Biosciences","volume":"9 ","pages":"173-201"},"PeriodicalIF":12.0,"publicationDate":"2021-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-animal-061220-023220","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38428320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}