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Hasselgren M, Dussex N, von Seth J, Angerbjörn A, Dalén L, Norén K. Strongly deleterious mutations influence reproductive output and longevity in an endangered population. Nat Commun 2024; 15:8378. [PMID: 39333094 PMCID: PMC11436772 DOI: 10.1038/s41467-024-52741-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/19/2024] [Indexed: 09/29/2024] Open
Abstract
Inbreeding depression has been documented in various fitness traits in a wide range of species and taxa, however, the mutational basis is not yet well understood. We investigate how putatively deleterious variation influences fitness and is shaped by individual ancestry by re-sequencing complete genomes of 37 individuals in a natural arctic fox (Vulpes lagopus) population subjected to both inbreeding depression and genetic rescue. We find that individuals with high proportion of homozygous loss of function genotypes (LoFs), which are predicted to exert a strong effect on fitness, generally have lower lifetime reproductive success and live shorter lives compared with individuals with lower proportion of LoFs. We also find that juvenile survival is negatively associated with the proportion of homozygous missense genotypes and positively associated with genome wide heterozygosity. Our results demonstrate that homozygosity of strongly and moderately deleterious mutations can be an important cause of trait specific inbreeding depression in wild populations, and mark an important step towards making more informed decisions using applied conservation genetics.
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Affiliation(s)
| | - Nicolas Dussex
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Johanna von Seth
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Love Dalén
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
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2
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Rando HM, Alexander EP, Preckler-Quisquater S, Quinn CB, Stutchman JT, Johnson JL, Bastounes ER, Horecka B, Black KL, Robson MP, Shepeleva DV, Herbeck YE, Kharlamova AV, Trut LN, Pauli JN, Sacks BN, Kukekova AV. Missing history of a modern domesticate: Historical demographics and genetic diversity in farm-bred red fox populations. J Hered 2024; 115:411-423. [PMID: 38624218 PMCID: PMC11235124 DOI: 10.1093/jhered/esae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The first record of captive-bred red foxes (Vulpes vulpes) dates to 1896 when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n = 161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- vs. intra-farm genetic diversity alongside the historical record is critical to understanding the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations.
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Affiliation(s)
- Halie M Rando
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Computer Science, Smith College, Northampton, MA 01063, United States
| | - Emmarie P Alexander
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
- National Genomics Center for Wildlife and Fish Conservation, USDA Forest Service, Rocky Mountain Research Station, Missoula, MT, United States
| | - Jeremy T Stutchman
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jennifer L Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Estelle R Bastounes
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Beata Horecka
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Kristina L Black
- Department of Forestry and Wildlife Ecology, University of Wisconsin, Madison, WI 53706, United States
| | - Michael P Robson
- Department of Computer Science, Smith College, Northampton, MA 01063, United States
| | - Darya V Shepeleva
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yury E Herbeck
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Anastasiya V Kharlamova
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Jonathan N Pauli
- Department of Forestry and Wildlife Ecology, University of Wisconsin, Madison, WI 53706, United States
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, United States
| | - Anna V Kukekova
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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3
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Driscoll RMH, Beaudry FEG, Cosgrove EJ, Bowman R, Fitzpatrick JW, Schoech SJ, Chen N. Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population. Genetics 2024; 227:iyae075. [PMID: 38722645 PMCID: PMC11228872 DOI: 10.1093/genetics/iyae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 06/12/2024] Open
Abstract
Sex-biased demography, including sex-biased survival or migration, can alter allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females make similar contributions to autosomal allele frequency change, but males make higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in characterizing genome-wide allele frequency change in wild populations.
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Affiliation(s)
- Rose M H Driscoll
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Felix E G Beaudry
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Elissa J Cosgrove
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Reed Bowman
- Avian Ecology Program, Archbold Biological Station, Venus, FL 33960, USA
| | | | - Stephan J Schoech
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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4
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Nguyen AK, Blacksmith MS, Kidd JM. Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies. Genome Biol Evol 2024; 16:evae142. [PMID: 38946312 PMCID: PMC11259980 DOI: 10.1093/gbe/evae142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 05/08/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024] Open
Abstract
Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that ∼8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with metrics supporting a greater quality of the PacBio HiFi mCanLor1.2 assembly. Comparison between the wolf and other canine assemblies found that 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies.
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Affiliation(s)
- Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Matthew S Blacksmith
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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5
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Ortiz-Leal I, Torres MV, López-Beceiro A, Fidalgo L, Shin T, Sanchez-Quinteiro P. First Immunohistochemical Demonstration of the Expression of a Type-2 Vomeronasal Receptor, V2R2, in Wild Canids. Int J Mol Sci 2024; 25:7291. [PMID: 39000398 PMCID: PMC11241633 DOI: 10.3390/ijms25137291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/29/2024] [Indexed: 07/16/2024] Open
Abstract
The mammalian vomeronasal system enables the perception of chemical signals crucial for social communication via the receptor families V1R and V2R. These receptors are linked with the G-protein subunits, Gαi2 and Gαo, respectively. Exploring the evolutionary pathways of V1Rs and V2Rs across mammalian species remains a significant challenge, particularly when comparing genomic data with emerging immunohistochemical evidence. Recent studies have revealed the expression of Gαo in the vomeronasal neuroepithelium of wild canids, including wolves and foxes, contradicting predictions based on current genomic annotations. Our study provides detailed immunohistochemical evidence, mapping the expression of V2R receptors in the vomeronasal sensory epithelium, focusing particularly on wild canids, specifically wolves and foxes. An additional objective involves contrasting these findings with those from domestic species like dogs to highlight the evolutionary impacts of domestication on sensory systems. The employment of a specific antibody raised against the mouse V2R2, a member of the C-family of vomeronasal receptors, V2Rs, has confirmed the presence of V2R2-immunoreactivity (V2R2-ir) in the fox and wolf, but it has revealed the lack of expression in the dog. This may reflect the impact of domestication on the regression of the VNS in this species, in contrast to their wild counterparts, and it underscores the effects of artificial selection on sensory functions. Thus, these findings suggest a more refined chemical detection capability in wild species.
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Affiliation(s)
- Irene Ortiz-Leal
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Av. Carballo Calero s/n, 27002 Lugo, Spain
| | - Mateo V Torres
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Av. Carballo Calero s/n, 27002 Lugo, Spain
| | - Ana López-Beceiro
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Av. Carballo Calero s/n, 27002 Lugo, Spain
| | - Luis Fidalgo
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Av. Carballo Calero s/n, 27002 Lugo, Spain
| | - Taekyun Shin
- College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Republic of Korea
| | - Pablo Sanchez-Quinteiro
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Av. Carballo Calero s/n, 27002 Lugo, Spain
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6
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Preckler-Quisquater S, Quinn CB, Sacks BN. Maintenance of a narrow hybrid zone between native and introduced red foxes (Vulpes vulpes) despite conspecificity and high dispersal capabilities. Mol Ecol 2024; 33:e17418. [PMID: 38847182 DOI: 10.1111/mec.17418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 06/27/2024]
Abstract
Human-facilitated introductions of nonnative populations can lead to secondary contact between allopatric lineages, resulting in lineage homogenisation or the formation of stable hybrid zones maintained by reproductive barriers. We investigated patterns of gene flow between the native Sacramento Valley red fox (Vulpes vulpes patwin) and introduced conspecifics of captive-bred origin in California's Central Valley. Considering their recent divergence (20-70 kya), we hypothesised that any observed barriers to gene flow were primarily driven by pre-zygotic (e.g. behavioural differences) rather than post-zygotic (e.g. reduced hybrid fitness) barriers. We also explored whether nonnative genes could confer higher fitness in the human-dominated landscape resulting in selective introgression into the native population. Genetic analysis of red foxes (n = 682) at both mitochondrial (cytochrome b + D-loop) and nuclear (19,051 SNPs) loci revealed narrower cline widths than expected under a simulated model of unrestricted gene flow, consistent with the existence of reproductive barriers. We identified several loci with reduced introgression that were previously linked to behavioural divergence in captive-bred and domestic canids, supporting pre-zygotic, yet possibly hereditary, barriers as a mechanism driving the narrowness and stability of the hybrid zone. Several loci with elevated gene flow from the nonnative into the native population were linked to genes associated with domestication and adaptation to human-dominated landscapes. This study contributes to our understanding of hybridisation dynamics in vertebrates, particularly in the context of species introductions and landscape changes, underscoring the importance of considering how multiple mechanisms may be maintaining lineages at the species and subspecies level.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Missoula, Montana, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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7
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Zhu Y, Yuan Y, Si H, Li S, Zhao F, Mu R, Lin Z, Wang X, Qiu Q, Xu C, Ji L, Li Z. Lipidomic and transcriptomic profiles provide new insights into the triacylglycerol and glucose handling capacities of the Arctic fox. Front Vet Sci 2024; 11:1388532. [PMID: 38988981 PMCID: PMC11233799 DOI: 10.3389/fvets.2024.1388532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
The Arctic fox (Vulpes lagopus) is a species indigenous to the Arctic and has developed unique lipid metabolism, but the mechanisms remain unclear. Here, the significantly increased body weight of Arctic foxes was consistent with the significantly increased serum very-low-density lipoprotein (VLDL), and the 40% crude fat diet further increased the Arctic fox body weight. The enhanced body weight gain stems primarily from increased subcutaneous adipose tissue accumulation. The adipose triacylglycerol and phosphatidylethanolamine were significantly greater in Arctic foxes. The adipose fatty-acid synthase content was significantly lower in Arctic foxes, highlighting the main role of exogenous fatty-acids in fat accumulation. Considering the same diet, liver-derived fat dominates adipose expansion in Arctic foxes. Liver transcriptome analysis revealed greater fat and VLDL synthesis in Arctic foxes, consistent with the greater VLDL. Glucose homeostasis wasn't impacted in Arctic foxes. And the free fatty-acids in adipose, which promote insulin resistance, also did not differ between groups. However, the hepatic glycogen was greater in Arctic foxes and transcriptome analysis revealed upregulated glycogen synthesis, improving glucose homeostasis. These results suggest that the superior fat accumulation capacity and distinct characteristics of hepatic and adipose lipid and glucose metabolism facilitate glucose homeostasis and massive fat accumulation in Arctic foxes.
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Affiliation(s)
- Yuhang Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Yuan Yuan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Huazhe Si
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Songze Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Fei Zhao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Ruina Mu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zihan Lin
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Xiaoxu Wang
- Department of Special Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Chao Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Lele Ji
- National Demonstration Center for Experimental Preclinical Medicine Education, The Fourth Military Medical University, Xi'an, China
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Lab of Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, China
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8
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Alexandrovich YV, Antonov EV, Shikhevich SG, Kharlamova AV, Meister LV, Makovka YV, Shepeleva DV, Gulevich RG, Herbeck YE. The expression profile of genes associated with behavior, stress, and adult neurogenesis along the hippocampal dorsoventral axis in tame and aggressive foxes. Vavilovskii Zhurnal Genet Selektsii 2023; 27:651-661. [PMID: 38213464 PMCID: PMC10782033 DOI: 10.18699/vjgb-23-76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/18/2022] [Accepted: 06/30/2023] [Indexed: 01/13/2024] Open
Abstract
The hippocampus plays the key role in stress response regulation, and stress response appears to be weakened in domesticated animals compared to their wild relatives. The hippocampus is functionally heterogeneous along its dorsoventral axis, with its ventral compartment being more closely involved in stress regulation. An earlier series of experiments was conducted with a unique breeding model of animal domestication, the farm silver fox (Vulpes vulpes), which included tame, aggressive, and unselected animals. A decrease in many indices of the hypothalamic-pituitary-adrenal activity was observed in tame animals. Also, adult hippocampal neurogenesis was more intense in tame foxes, and this fact may relate to reduced stress levels in this experimental population of foxes. Nevertheless, the molecular mechanisms responsible for the reduced stress response in tame animals remain obscure. In this study, serum cortisol levels and the mRNA levels of 13 genes in the dorsal and ventral hippocampus have been measured and compared in tame, aggressive, and unselected foxes. At the current stage of domestication, stress-induced cortisol levels in tame, aggressive, and unselected animals differ significantly from each other: tame foxes show the lowest levels, and aggressive ones, the highest. Twelve genes tested demonstrate significant gene expression differences between the dorsal and ventral hippocampi. These differences are mainly consistent with those found in rodents and humans. In tame foxes, significantly elevated mRNA levels were recorded for several genes: CYP26B1 for cytochrome P450 26B1 and ADRA1A for α1A adrenergic receptor in the dorsal hippocampus, whereas the level of NR3C2 mRNA for mineralocorticoid receptor was higher in the ventral. It is presumed that these genes constitute an important part of the mechanism reducing stress induced by contacts with humans and contribute to linking stress regulation with adult neurogenesis in tame foxes and domesticated animals in general.
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Affiliation(s)
- Yu V Alexandrovich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V Antonov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Sirius University of Science and Technology, Scientific Center for Translational Medicine, Sochi, Russia
| | - S G Shikhevich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Kharlamova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - L V Meister
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y V Makovka
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D V Shepeleva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - R G Gulevich
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Yu E Herbeck
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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9
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Liu X, Liu W, Lenstra JA, Zheng Z, Wu X, Yang J, Li B, Yang Y, Qiu Q, Liu H, Li K, Liang C, Guo X, Ma X, Abbott RJ, Kang M, Yan P, Liu J. Evolutionary origin of genomic structural variations in domestic yaks. Nat Commun 2023; 14:5617. [PMID: 37726270 PMCID: PMC10509194 DOI: 10.1038/s41467-023-41220-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Yak has been subject to natural selection, human domestication and interspecific introgression during its evolution. However, genetic variants favored by each of these processes have not been distinguished previously. We constructed a graph-genome for 47 genomes of 7 cross-fertile bovine species. This allowed detection of 57,432 high-resolution structural variants (SVs) within and across the species, which were genotyped in 386 individuals. We distinguished the evolutionary origins of diverse SVs in domestic yaks by phylogenetic analyses. We further identified 334 genes overlapping with SVs in domestic yaks that bore potential signals of selection from wild yaks, plus an additional 686 genes introgressed from cattle. Nearly 90% of the domestic yaks were introgressed by cattle. Introgression of an SV spanning the KIT gene triggered the breeding of white domestic yaks. We validated a significant association of the selected stratified SVs with gene expression, which contributes to phenotypic variations. Our results highlight that SVs of different origins contribute to the phenotypic diversity of domestic yaks.
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Affiliation(s)
- Xinfeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China
| | - Wenyu Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3508 TD, The Netherlands
| | - Zeyu Zheng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Qiang Qiu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hongyu Liu
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xian Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Xiaoming Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, KY16 9AJ, UK
| | - Minghui Kang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China.
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10
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Torres MV, Ortiz-Leal I, Ferreiro A, Rois JL, Sanchez-Quinteiro P. Immunohistological study of the unexplored vomeronasal organ of an endangered mammal, the dama gazelle (Nanger dama). Microsc Res Tech 2023; 86:1206-1233. [PMID: 37494657 DOI: 10.1002/jemt.24392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/11/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023]
Abstract
Dama gazelle is a threatened and rarely studied species found primarily in northern Africa. Human pressure has depleted the dama gazelle population from tens of thousands to a few hundred individuals. Since 1970, a founder population consisting of the last 17 surviving individuals in Western Sahara has been maintained in captivity, reproducing naturally. In preparation for the future implementation of assisted reproductive technology, certain aspects of dama gazelle reproductive biology have been established. However, the role played by semiochemical-mediated communications in the sexual behavior of dama gazelle remains unknown due partially to a lack of a neuroanatomical or morphofunctional characterization of the dama gazelle vomeronasal organ (VNO), which is the sensory organ responsible for pheromone processing. The present study characterized the dama gazelle VNO, which appears fully equipped to perform neurosensory functions, contributing to current understanding of interspecies VNO variability among ruminants. By employing histological, lectin-histochemical, and immunohistochemical techniques, we conducted a detailed morphofunctional evaluation of the dama gazelle VNO along its entire longitudinal axis. Our findings of significant structural and neurochemical transformation along the entire VNO suggest that future studies of the VNO should take a similar approach. The present study contributes to current understanding of dama gazelle VNO, providing a basis for future studies of semiochemical-mediated communications and reproductive management in this species. RESEARCH HIGHLIGHTS: This exhaustive immunohistological study of the vomeronasal organ (VNO) of the dama gazelle provides the first evidence of notable differences in the expression of neuronal markers along the rostrocaudal axis of the VNO. This provides a morphological basis for the implementation of pheromones in captive populations of dama gazelle.
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Affiliation(s)
- Mateo V Torres
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Irene Ortiz-Leal
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | | | | | - Pablo Sanchez-Quinteiro
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
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11
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Bionda A, Cortellari M, Liotta L, Crepaldi P. The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds. Animals (Basel) 2023; 13:2438. [PMID: 37570247 PMCID: PMC10417656 DOI: 10.3390/ani13152438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: FST, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.
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Affiliation(s)
- Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy;
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
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12
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Dou M, Li M, Zheng Z, Chen Q, Wu Y, Wang J, Shan H, Wang F, Dai X, Li Y, Yang Z, Tan G, Luo F, Chen L, Shi YS, Wu JW, Luo XJ, Asadollahpour Nanaei H, Niyazbekova Z, Zhang G, Wang W, Zhao S, Zheng W, Wang X, Jiang Y. A missense mutation in RRM1 contributes to animal tameness. SCIENCE ADVANCES 2023; 9:eadf4068. [PMID: 37352351 PMCID: PMC10289655 DOI: 10.1126/sciadv.adf4068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/18/2023] [Indexed: 06/25/2023]
Abstract
The increased tameness to reduce avoidance of human in wild animals has been long proposed as the key step of animal domestication. The tameness is a complex behavior trait and largely determined by genetic factors. However, the underlying genetic mutations remain vague and how they influence the animal behaviors is yet to be explored. Behavior tests of a wild-domestic hybrid goat population indicate the locus under strongest artificial selection during domestication may exert a huge effect on the flight distance. Within this locus, only one missense mutation RRM1I241V which was present in the early domestic goat ~6500 years ago. Genome editing of RRM1I241V in mice showed increased tameness and sociability and reduced anxiety. These behavioral changes induced by RRM1I241V were modulated by the alternation of activity of glutamatergic synapse and some other synapse-related pathways. This study established a link between RRM1I241V and tameness, demonstrating that the complex behavioral change can be achieved by mutations under strong selection during animal domestication.
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Affiliation(s)
- Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, 830011, China
| | - Yongji Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Jinxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Huiquan Shan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Yunjia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Zhirui Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Guanghui Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Funong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Medical School, Nanjing University, Nanjing, Jiangsu, 210032, China
| | - Jiang Wei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Xiong-Jian Luo
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1983969412, Iran
| | - Zhannur Niyazbekova
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Guojie Zhang
- Centre for Evolutionary and Organismal Biology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310000, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shanting Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Wenxin Zheng
- Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, 830011, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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13
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Dudek SM, Phoenix AN, Scappini E, Shepeleva DV, Herbeck YE, Trut LN, Farris S, Kukekova AV. Defining hippocampal area CA2 in the fox (Vulpes vulpes) brain. Hippocampus 2023; 33:700-711. [PMID: 37159095 PMCID: PMC10274530 DOI: 10.1002/hipo.23546] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
Since 1959, the Russian Farm-Fox study has bred foxes to be either tame or, more recently, aggressive, and scientists have used them to gain insight into the brain structures associated with these behavioral features. In mice, hippocampal area CA2 has emerged as one of the essential regulators of social aggression, and so to eventually determine whether we could identify differences in CA2 between tame and aggressive foxes, we first sought to identify CA2 in foxes (Vulpes vulpes). As no clearly defined area of CA2 has been described in species such as cats, dogs, or pigs, it was not at all clear whether CA2 could be identified in foxes. In this study, we cut sections of temporal lobes from male and female red foxes, perpendicular to the long axis of the hippocampus, and stained them with markers of CA2 pyramidal cells commonly used in tissue from rats and mice. We observed that antibodies against Purkinje cell protein 4 best stained the pyramidal cells in the area spanning the end of the mossy fibers and the beginning of the pyramidal cells lacking mossy fibers, resembling the pattern seen in rats and mice. Our findings indicate that foxes do have a "molecularly defined" CA2, and further, they suggest that other carnivores like dogs and cats might as well. With this being the case, these foxes could be useful in future studies looking at CA2 as it relates to aggression.
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Affiliation(s)
- Serena M Dudek
- National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Ashley N Phoenix
- National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Erica Scappini
- National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Darya V Shepeleva
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Yury E Herbeck
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Lyudmila N Trut
- Siberian Branch of the Russian Academy of Sciences, Institute of Cytology and Genetics, Novosibirsk, Russian Federation
| | - Shannon Farris
- Fralin Biomedical Research Institute, Virginia Tech, Roanoke, Virginia, USA
| | - Anna V Kukekova
- Department of Animal Science, The University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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14
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Rogers Flattery CN, Abdulla M, Barton SA, Michlich JM, Trut LN, Kukekova AV, Hecht EE. The brain of the silver fox (Vulpes vulpes): a neuroanatomical reference of cell-stained histological and MRI images. Brain Struct Funct 2023; 228:1177-1189. [PMID: 37160458 PMCID: PMC11192273 DOI: 10.1007/s00429-023-02648-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023]
Abstract
Although the silver fox (Vulpes vulpes) has been largely overlooked by neuroscientists, it has the potential to serve as a powerful model for the investigation of brain-behavior relationships. The silver fox is a melanistic variant of the red fox. Within this species, the long-running Russian farm-fox experiment has resulted in different strains bred to show divergent behavior. Strains bred for tameness, aggression, or without selection on behavior present an excellent opportunity to investigate neuroanatomical changes underlying behavioral characteristics. Here, we present a histological and MRI neuroanatomical reference of a fox from the conventional strain, which is bred without behavioral selection. This can provide an anatomical basis for future studies of the brains of foxes from this particular experiment, as well as contribute to an understanding of fox brains in general. In addition, this can serve as a resource for comparative neuroscience and investigations into neuroanatomical variation among the family Canidae, the order Carnivora, and mammals more broadly.
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Affiliation(s)
| | - Munawwar Abdulla
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Sophie A Barton
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Jenny M Michlich
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA
| | - Lyudmila N Trut
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anna V Kukekova
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Ave, Cambridge, MA, 02138, USA.
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15
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Zhang Z, Xia T, Zhou S, Yang X, Lyu T, Wang L, Fang J, Wang Q, Dou H, Zhang H. High-Quality Chromosome-Level Genome Assembly of the Corsac Fox ( Vulpes corsac) Reveals Adaptation to Semiarid and Harsh Environments. Int J Mol Sci 2023; 24:ijms24119599. [PMID: 37298549 DOI: 10.3390/ijms24119599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
The Corsac fox (Vulpes corsac) is a species of fox distributed in the arid prairie regions of Central and Northern Asia, with distinct adaptations to dry environments. Here, we applied Oxford-Nanopore sequencing and a chromosome structure capture technique to assemble the first Corsac fox genome, which was then assembled into chromosome fragments. The genome assembly has a total length of 2.2 Gb with a contig N50 of 41.62 Mb and a scaffold N50 of 132.2 Mb over 18 pseudo-chromosomal scaffolds. The genome contained approximately 32.67% of repeat sequences. A total of 20,511 protein-coding genes were predicted, of which 88.9% were functionally annotated. Phylogenetic analyses indicated a close relation to the Red fox (Vulpes vulpes) with an estimated divergence time of ~3.7 million years ago (MYA). We performed separate enrichment analyses of species-unique genes, the expanded and contracted gene families, and positively selected genes. The results suggest an enrichment of pathways related to protein synthesis and response and an evolutionary mechanism by which cells respond to protein denaturation in response to heat stress. The enrichment of pathways related to lipid and glucose metabolism, potentially preventing stress from dehydration, and positive selection of genes related to vision, as well as stress responses in harsh environments, may reveal adaptive evolutionary mechanisms in the Corsac fox under harsh drought conditions. Additional detection of positive selection for genes associated with gustatory receptors may reveal a unique desert diet strategy for the species. This high-quality genome provides a valuable resource for studying mammalian drought adaptation and evolution in the genus Vulpes.
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Affiliation(s)
- Zhihao Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tian Xia
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Xiufeng Yang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Tianshu Lyu
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- School of Life Science, Qufu Normal University, Qufu 273165, China
| | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir 021000, China
| | - Honghai Zhang
- School of Life Science, Qufu Normal University, Qufu 273165, China
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16
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Holtby AR, Hall TJ, McGivney BA, Han H, Murphy KJ, MacHugh DE, Katz LM, Hill EW. Integrative genomics analysis highlights functionally relevant genes for equine behaviour. Anim Genet 2023. [DOI: 10.1111/age.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/29/2023]
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17
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Ortiz-Leal I, Torres MV, Vargas-Barroso V, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. The olfactory limbus of the red fox ( Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Front Neuroanat 2023; 16:1097467. [PMID: 36704406 PMCID: PMC9871471 DOI: 10.3389/fnana.2022.1097467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents. Methods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques. Results: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity. Discussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.
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Affiliation(s)
- Irene Ortiz-Leal
- Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Mateo V. Torres
- Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Víctor Vargas-Barroso
- Cellular Neuroscience, IST Austria (Institute of Science and Technology Austria), Klosterneuburg, Austria
| | | | | | - Jorge A. Larriva-Sahd
- Institute of Neurobiology, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Pablo Sánchez-Quinteiro
- Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain,*Correspondence: Pablo Sanchez-Quinteiro
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18
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Bionda A, Cortellari M, Bigi D, Chiofalo V, Liotta L, Crepaldi P. Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs. Vet Sci 2022; 10:3. [PMID: 36669004 PMCID: PMC9862740 DOI: 10.3390/vetsci10010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using FST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.
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Affiliation(s)
- Arianna Bionda
- Department of Agricultural and Environmental Sciences, Milan University, Via Celoria 2, 20133 Milan, Italy
| | - Matteo Cortellari
- Department of Agricultural and Environmental Sciences, Milan University, Via Celoria 2, 20133 Milan, Italy
| | - Daniele Bigi
- Department of Agricultural and Food Science and Technology (DISTAL), University of Bologna, Viale Fanin 46, 40127 Bologna, Italy
| | - Vincenzo Chiofalo
- Department of Veterinary Sciences, Messina University, Viale Palatucci 13, 98168 Messina, Italy
- Consortium of Research for Meat Chain and Agrifood (CoRFilCarni), Viale Palatucci 13, 98168 Messina, Italy
| | - Luigi Liotta
- Department of Veterinary Sciences, Messina University, Viale Palatucci 13, 98168 Messina, Italy
| | - Paola Crepaldi
- Department of Agricultural and Environmental Sciences, Milan University, Via Celoria 2, 20133 Milan, Italy
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19
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Cockerill CA, Hasselgren M, Dussex N, Dalén L, von Seth J, Angerbjörn A, Wallén JF, Landa A, Eide NE, Flagstad Ø, Ehrich D, Sokolov A, Sokolova N, Norén K. Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox ( Vulpes lagopus). Genes (Basel) 2022; 13:2124. [PMID: 36421799 PMCID: PMC9690288 DOI: 10.3390/genes13112124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck in the late 19th century. The future persistence of the entire Scandinavian population is highly dependent on the northernmost Fennoscandian subpopulations (Scandinavia and the Kola Peninsula), to provide a link to the viable Siberian population. By analyzing 43 arctic fox genomes, we quantified genomic variation and inbreeding in these populations. Signatures of genome erosion increased from Siberia to northern Sweden indicating a stepping-stone model of connectivity. In northern Fennoscandia, runs of homozygosity (ROH) were on average ~1.47-fold longer than ROH found in Siberia, stretching almost entire scaffolds. Moreover, consistent with recent inbreeding, northern Fennoscandia harbored more homozygous deleterious mutations, whereas Siberia had more in heterozygous state. This study underlines the value of documenting genome erosion following population fragmentation to identify areas requiring conservation priority. With the increasing fragmentation and isolation of Arctic habitats due to global warming, understanding the genomic and demographic consequences is vital for maintaining evolutionary potential and preventing local extinctions.
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Affiliation(s)
| | - Malin Hasselgren
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Nicolas Dussex
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
| | - Love Dalén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
| | - Johanna von Seth
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Johan F. Wallén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Arild Landa
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Nina E. Eide
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | | | - Dorothee Ehrich
- Department of Arctic and Marine Biology, UiT Arctic University of Tromsø, 9037 Tromsø, Norway
| | - Aleksandr Sokolov
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str. 21, 629400 Labytnangi, Russia
| | - Natalya Sokolova
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str. 21, 629400 Labytnangi, Russia
| | - Karin Norén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
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20
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Lan T, Li H, Yang S, Shi M, Han L, Sahu SK, Lu Y, Wang J, Zhou M, Liu H, Huang J, Wang Q, Zhu Y, Wang L, Xu Y, Lin C, Liu H, Hou Z. The chromosome-scale genome of the raccoon dog: Insights into its evolutionary characteristics. iScience 2022; 25:105117. [PMID: 36185367 PMCID: PMC9523411 DOI: 10.1016/j.isci.2022.105117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/07/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangchen Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaxian Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Jiangang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mengchao Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Hui Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Junxuan Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanchun Xu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518120, China
- Corresponding author
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Corresponding author
| | - Zhijun Hou
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
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21
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Lobo D, Linheiro R, Godinho R, Archer JP. On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves. PLoS One 2022; 17:e0274591. [PMID: 36136981 PMCID: PMC9498955 DOI: 10.1371/journal.pone.0274591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
The evolution of RNA-seq technologies has yielded datasets of scientific value that are often generated as condition associated biological replicates within expression studies. With expanding data archives opportunity arises to augment replicate numbers when conditions of interest overlap. Despite correction procedures for estimating transcript abundance, a source of ambiguity is transcript level intra-condition count variation; as indicated by disjointed results between analysis tools. We present TVscript, a tool that removes reference-based transcripts associated with intra-condition count variation above specified thresholds and we explore the effects of such variation on differential expression analysis. Initially iterative differential expression analysis involving simulated counts, where levels of intra-condition variation and sets of over represented transcripts are explicitly specified, was performed. Then counts derived from inter- and intra-study data representing brain samples of dogs, wolves and foxes (wolves vs. dogs and aggressive vs. tame foxes) were used. For simulations, the sensitivity in detecting differentially expressed transcripts increased after removing hyper-variable transcripts, although at levels of intra-condition variation above 5% detection became unreliable. For real data, prior to applying TVscript, ≈20% of the transcripts identified as being differentially expressed were associated with high levels of intra-condition variation, an over representation relative to the reference set. As transcripts harbouring such variation were removed pre-analysis, a discordance from 26 to 40% in the lists of differentially expressed transcripts is observed when compared to those obtained using the non-filtered reference. The removal of transcripts possessing intra-condition variation values within (and above) the 97th and 95th percentiles, for wolves vs. dogs and aggressive vs. tame foxes, maximized the sensitivity in detecting differentially expressed transcripts as a result of alterations within gene-wise dispersion estimates. Through analysis of our real data the support for seven genes with potential for being involved with selection for tameness is provided. TVscript is available at: https://sourceforge.net/projects/tvscript/.
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Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail: (DL); (JPA)
| | - Raquel Linheiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - John Patrick Archer
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- * E-mail: (DL); (JPA)
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22
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Chavez DE, Gronau I, Hains T, Dikow RB, Frandsen PB, Figueiró HV, Garcez FS, Tchaicka L, de Paula RC, Rodrigues FHG, Jorge RSP, Lima ES, Songsasen N, Johnson WE, Eizirik E, Koepfli KP, Wayne RK. Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids. Proc Natl Acad Sci U S A 2022; 119:e2205986119. [PMID: 35969758 PMCID: PMC9407222 DOI: 10.1073/pnas.2205986119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.
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Affiliation(s)
- Daniel E. Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Reichman University, Herzliya 46150, Israel
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Henrique V. Figueiró
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Fabrício S. Garcez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
| | - Ligia Tchaicka
- Rede de Biodiversidade e Biotecnologia da Amazônia, Curso de Pós-Graduação em Recursos Aquáticos e Pesca, Universidade Estadual do Maranhão, São Luis, 2016-8100, Brazil
| | - Rogério C. de Paula
- Centro Nacional de Pesquisa e Conservação de Mamíferos Carnívoros, Instituto Chico Mendes de Conservação da Biodiversidade, 12952-011, Atibaia, Brazil
| | - Flávio H. G. Rodrigues
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Rodrigo S. P. Jorge
- Centro Nacional de Avaliação da Biodiversidade e de Pesquisa e Conservação do Cerrado, Instituto Chico Mendes de Conservação da Biodiversidade, Brasilia, 70670-350, Brazil
| | - Edson S. Lima
- Private address, Nova Xavantina, MT, 78690-000, Brazil
| | - Nucharin Songsasen
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Warren E. Johnson
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, 90619-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, 12945-010, Brazil
- Instituto Nacional de Ciência e Tecnologia em Ecologia Evolução Conservação da Biodiverside, Universidade Federal de GoiásGoiânia, 74690-900, Brazil
| | - Klaus-Peter Koepfli
- Smithsonian’s National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, VA 22630
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
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23
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Anastasiadi D, Piferrer F, Wellenreuther M, Benítez Burraco A. Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders. Genes (Basel) 2022; 13:genes13060987. [PMID: 35741749 PMCID: PMC9222608 DOI: 10.3390/genes13060987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
Modern humans exhibit phenotypic traits and molecular events shared with other domesticates that are thought to be by-products of selection for reduced aggression. This is the human self-domestication hypothesis. As one of the first types of responses to a novel environment, epigenetic changes may have also facilitated early self-domestication in humans. Here, we argue that fish species, which have been recently domesticated, can provide model systems to study epigenetic drivers in human self-domestication. To test this, we used in silico approaches to compare genes with epigenetic changes in early domesticates of European sea bass with genes exhibiting methylation changes in anatomically modern humans (comparison 1), and neurodevelopmental cognitive disorders considered to exhibit abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome, and autism spectrum disorders (comparison 2). Overlapping genes in comparison 1 were involved in processes like limb morphogenesis and phenotypes like abnormal jaw morphology and hypopigmentation. Overlapping genes in comparison 2 affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. These findings pave the way for future studies using fish species as models to investigate epigenetic changes as drivers of human self-domestication and as triggers of cognitive disorders.
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Affiliation(s)
- Dafni Anastasiadi
- Seafood Technologies, The New Zealand Institute for Plant and Food Research, Nelson 7010, New Zealand;
- Correspondence:
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), 08003 Barcelona, Spain;
| | - Maren Wellenreuther
- Seafood Technologies, The New Zealand Institute for Plant and Food Research, Nelson 7010, New Zealand;
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Antonio Benítez Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, 41004 Seville, Spain;
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24
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Roth-Nebelsick A. How much biology is in the product? Role and relevance of biological evolution and function for bio-inspired design. Theory Biosci 2022; 141:233-247. [PMID: 35344153 PMCID: PMC9474337 DOI: 10.1007/s12064-022-00367-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/11/2022] [Indexed: 11/25/2022]
Abstract
Bio-inspired design (BID) means the concept of transferring functional principles from biology to technology. The core idea driving BID-related work is that evolution has shaped functional attributes, which are termed “adaptations” in biology, to a high functional performance by relentless selective pressure. For current methods and tools, such as data bases, it is implicitly supposed that the considered biological models are adaptations and their functions already clarified. Often, however, the identification of adaptations and their functional features is a difficult task which is not yet accomplished for numerous biological structures, as happens to be the case also for various organismic features from which successful BID developments were derived. This appears to question the relevance of the much stressed importance of evolution for BID. While it is obviously possible to derive an attractive technical principle from an observed biological effect without knowing its original functionality, this kind of BID (“analog BID”) has no further ties to biology. In contrast, a BID based on an adaptation and its function (“homolog BID”) is deeply embedded in biology. It is suggested that a serious and honest clarification of the functional background of a biological structure is an essential first step in devising a BID project, to recognize possible problems and pitfalls as well as to evaluate the need for further biological analysis.
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Affiliation(s)
- Anita Roth-Nebelsick
- Department of Palaeontology, State Museum of Natural History Stuttgart, Stuttgart, Germany.
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25
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Abstract
We found the three-dimensional (3D) structure of chromatin at the chromosome level to be highly conserved for more than 50 million y of carnivore evolution. Intrachromosomal contacts were maintained even after chromosome rearrangements within carnivore lineages, demonstrating that the maintenance of 3D chromatin architecture is essential for conserved genome functions. These discoveries enabled the identification of orthologous chromosomal DNA segments among related species, a method we call 3D comparative scaffotyping. The method has application for putative chromosome assignment of chromosome-scale DNA sequence scaffolds produced by de novo genome sequencing. Broadly applied to biodiversity genome sequencing efforts, the approach can reduce costs associated with karyotyping and the physical mapping of DNA segments to chromosomes. High throughput chromatin conformation capture (Hi-C) of leukocyte DNA was used to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families: Felidae, Canidae, and Ursidae. Chromosome-scale scaffolds (C-scaffolds) of each species were initially used for whole-genome alignment to a reference genome within each family. This approach established putative orthologous relationships between C-scaffolds among the different species. Hi-C contact maps for all C-scaffolds were then visually compared and found to be distinct for a given reference chromosome or C-scaffold within a species and indistinguishable for orthologous C-scaffolds having a 1:1 relationship within a family. The visual patterns within families were strongly supported by eigenvectors from the Hi-C contact maps. Analysis of Hi-C contact maps and eigenvectors across the three carnivore families revealed that most cross-family orthologous subchromosomal fragments have a conserved three-dimensional (3D) chromatin structure and thus have been under strong evolutionary constraint for ∼54 My of carnivore evolution. The most pronounced differences in chromatin conformation were observed for the X chromosome and the red fox genome, whose chromosomes have undergone extensive rearrangements relative to other canids. We also demonstrate that Hi-C contact map pattern analysis can be used to accurately identify orthologous relationships between C-scaffolds and chromosomes, a method we termed “3D comparative scaffotyping.” This method provides a powerful means for estimating karyotypes in de novo sequenced species that have unknown karyotype and no physical mapping information.
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26
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Palma-Vera SE, Reyer H, Langhammer M, Reinsch N, Derezanin L, Fickel J, Qanbari S, Weitzel JM, Franzenburg S, Hemmrich-Stanisak G, Schoen J. Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. BMC Biol 2022; 20:52. [PMID: 35189878 PMCID: PMC8862358 DOI: 10.1186/s12915-022-01248-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. RESULTS Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. CONCLUSIONS The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
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Affiliation(s)
- Sergio E Palma-Vera
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
| | - Henry Reyer
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Martina Langhammer
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Norbert Reinsch
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Lorena Derezanin
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Joerns Fickel
- Department of Evolutionary Genetics, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- University of Potsdam, Institute for Biochemistry and Biology, Potsdam, Germany
| | - Saber Qanbari
- Institute of Genetics and Biometry, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Joachim M Weitzel
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | | | - Jennifer Schoen
- Institute of Reproductive Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Reproduction Biology, Research Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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27
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Eusebi PG, Sevane N, O'Rourke T, Pizarro M, Boeckx C, Dunner S. Age Effects Aggressive Behavior: RNA-Seq Analysis in Cattle with Implications for Studying Neoteny Under Domestication. Behav Genet 2022; 52:141-153. [PMID: 35032285 PMCID: PMC8860811 DOI: 10.1007/s10519-021-10097-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 12/18/2021] [Indexed: 11/30/2022]
Abstract
The reactive type of aggression is regulated mostly by the brain's prefrontal cortex; however, the molecular changes underlying aggressiveness in adults have not been fully characterized. We used an RNA-seq approach to investigate differential gene expression in the prefrontal cortex of bovines from the aggressive Lidia breed at different ages: young three-year old and adult four-year-old bulls. A total of 50 up and 193 down-regulated genes in the adult group were identified. Furthermore, a cross-species comparative analysis retrieved 29 genes in common with previous studies on aggressive behaviors, representing an above-chance overlap with the differentially expressed genes in adult bulls. We detected changes in the regulation of networks such as synaptogenesis, involved in maintenance and refinement of synapses, and the glutamate receptor pathway, which acts as excitatory driver in aggressive responses. The reduced reactive aggression typical of domestication has been proposed to form part of a retention of juvenile traits as adults (neoteny).
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Affiliation(s)
- Paulina G Eusebi
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain.
| | - Natalia Sevane
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Thomas O'Rourke
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain
| | - Manuel Pizarro
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Cedric Boeckx
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Susana Dunner
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
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28
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Ortiz-Leal I, Torres MV, Villamayor PR, Fidalgo LE, López-Beceiro A, Sanchez-Quinteiro P. Can domestication shape Canidae brain morphology? The accessory olfactory bulb of the red fox as a case in point. Ann Anat 2021; 240:151881. [PMID: 34896556 DOI: 10.1016/j.aanat.2021.151881] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND The accessory olfactory bulb (AOB) is the first integrative center of the vomeronasal system (VNS), and the general macroscopic, microscopic, and neurochemical organizational patterns of the AOB differ fundamentally among species. Therefore, the low degree of differentiation observed for the dog AOB is surprising. As the artificial selection pressure exerted on domestic dogs has been suggested to play a key role in the involution of the dog VNS, a wild canid, such as the fox, represents a useful model for studying the hypothetical effects of domestication on the AOB morphology. METHODS A comprehensive histological, lectin-histochemical, and immunohistochemical study of the fox AOB was performed. Anti-Gαo and anti-Gαi2 antibodies were particularly useful, as they label the transduction cascade of the vomeronasal receptor types 1 (V1R) and 2 (V2R), respectively. Other employed antibodies included those against proteins such as microtubule-associated protein 2 (MAP-2), tubulin, glial fibrillary acidic protein, growth-associated protein 43 (GAP-43), olfactory marker protein (OMP), calbindin, and calretinin. RESULTS The cytoarchitecture of the fox AOB showed a clear lamination, with neatly differentiated layers; a highly developed glomerular layer, rich in periglomerular cells; and large inner cell and granular layers. The immunolabeling of Gαi2, OMP, and GAP-43 delineated the outer layers, whereas Gαo and MAP-2 immunolabeling defined the inner layers. MAP-2 characterized the somas of AOB principal cells and their dendritic trees. Anti-calbindin and anti-calretinin antibodies discriminated neural subpopulations in both the mitral-plexiform layer and the granular cell layer, and the lectin Ulex europeus agglutinin I (UEA-I) showed selectivity for the AOB and the vomeronasal nerves. CONCLUSION The fox AOB presents unique characteristics and a higher degree of morphological development compared with the dog AOB. The comparatively complex neural basis for semiochemical information processing in the fox compared with that observed in dogs suggests loss of AOB anatomical complexity during the evolutionary history of dogs and opens a new avenue of research for studying the effects of domestication on brain structures.
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Affiliation(s)
- Irene Ortiz-Leal
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Mateo V Torres
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Paula R Villamayor
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Luis Eusebio Fidalgo
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Ana López-Beceiro
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain
| | - Pablo Sanchez-Quinteiro
- Department of Anatomy, Animal Production and Clinical Veterinary Sciences, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain.
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McDevitt AD, Coscia I, Browett SS, Ruiz-González A, Statham MJ, Ruczyńska I, Roberts L, Stojak J, Frantz AC, Norén K, Ågren EO, Learmount J, Basto M, Fernandes C, Stuart P, Tosh DG, Sindicic M, Andreanszky T, Isomursu M, Panek M, Korolev A, Okhlopkov IM, Saveljev AP, Pokorny B, Flajšman K, Harrison SWR, Lobkov V, Ćirović D, Mullins J, Pertoldi C, Randi E, Sacks BN, Kowalczyk R, Wójcik JM. Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe. Mol Ecol 2021; 31:993-1006. [PMID: 34775636 DOI: 10.1111/mec.16276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022]
Abstract
Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.
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Affiliation(s)
- Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Mark J Statham
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, California, USA
| | - Iwona Ruczyńska
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Liam Roberts
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, Luxembourg, Luxembourg
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Erik O Ågren
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Jane Learmount
- National Wildlife Management Centre, Animal and Plant Health Agency, Sand Hutton, UK
| | - Mafalda Basto
- Department of Animal Biology, Faculty of Sciences, CE3C - Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Carlos Fernandes
- Department of Animal Biology, Faculty of Sciences, CE3C - Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Peter Stuart
- Biological and Pharmaceutical Sciences Department, Institute of Technology Tralee, Kerry, Ireland
| | - David G Tosh
- National Museums of Northern Ireland, Hollywood, UK
| | - Magda Sindicic
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Marja Isomursu
- Finnish Food Authority, Veterinary Bacteriology and Pathology Research Unit, Oulu, Finland
| | | | - Andrey Korolev
- Institute of Biology of Komi Science, Remote Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | | | | | - Stephen W R Harrison
- School of Animal Rural & Environmental Sciences, Nottingham Trent University, Southwell, UK
| | - Vladimir Lobkov
- Faculty of Biology, Odessa I.I. Mechnykov National University, Odessa, Ukraine
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Jacinta Mullins
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Benjamin N Sacks
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, California, USA
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Jan M Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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30
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Baecklund TM, Donaldson ME, Hueffer K, Kyle CJ. Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations. PLoS One 2021; 16:e0258975. [PMID: 34714859 PMCID: PMC8555846 DOI: 10.1371/journal.pone.0258975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/10/2021] [Indexed: 11/24/2022] Open
Abstract
Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. FST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.
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Affiliation(s)
- Tristan M. Baecklund
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- * E-mail:
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, Fairbanks, AK, United States of America
| | - Christopher J. Kyle
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- Forensic Science Department, Trent University, Peterborough, ON, Canada
- Natural Resources DNA Profiling & Forensic Centre, Trent University, Peterborough, ON, Canada
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31
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Baesjou JP, Wellenreuther M. Genomic Signatures of Domestication Selection in the Australasian Snapper ( Chrysophrys auratus). Genes (Basel) 2021; 12:1737. [PMID: 34828341 PMCID: PMC8623400 DOI: 10.3390/genes12111737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 10/26/2021] [Indexed: 01/10/2023] Open
Abstract
Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.
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Affiliation(s)
- Jean-Paul Baesjou
- The New Zealand Institute for Plant and Food Research Ltd., 1025 Auckland, New Zealand;
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd., 7010 Nelson, New Zealand
- School of Biological Sciences, University of Auckland, 1010 Auckland, New Zealand
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32
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Yang X, Liu G, Wang Q, Gao X, Xia T, Zhao C, Dou H, Zhang H. Comparative transcriptome provides insights into the selection adaptation between wild and farmed foxes. Ecol Evol 2021; 11:13475-13486. [PMID: 34646484 PMCID: PMC8495804 DOI: 10.1002/ece3.8071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/30/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022] Open
Abstract
The silver fox and blue fox are economically important fur species and were domesticated by humans from their wild counterparts, the arctic fox and red fox, respectively. Farmed foxes show obvious differences from their wild counterparts, including differences in physiology, body size, energy metabolism, and immunity. However, the molecular mechanisms underlying these differences are presently unclear. In this study, we built transcriptome libraries from multiple pooled tissues for each species of farmed fox, used RNA-seq to obtain a comprehensive dataset, and performed selection analysis and sequence-level analyses of orthologous genes to identify the genes that may be influenced by human domestication. More than 153.3, 248.0, 81.6, and 65.8 million clean reads were obtained and assembled into a total of 118,577, 401,520, 79,900, and 186,988 unigenes with an average length range from 521 to 667 bp for AF, BF, RF, and SF, respectively. Selective pressure analysis showed that 11 and 14 positively selected genes were identified, respectively, in the two groups (AF vs. BF and RF vs. SF). Several of these genes were associated with natural immunity (CFI and LRRFIP1), protein synthesis (GOLGA4, CEP19 and SLC35A2), and DNA damage repair (MDC1). Further functional enrichment analyses demonstrated that two positively selected genes (ACO1 and ACAD10) were involved in metabolic process (GO:0008152, p-value = .032), representing a significant enrichment. Sequence analysis of 117 orthologous genes shared by the two groups showed that the LEMD2, RRBP1, and IGBP1 genes might be affected by artificial selection in farmed foxes, with mutation sites located within sequences that are otherwise highly conserved across most mammals. Our results provide a valuable transcriptomic resource for future genetic studies and improvement in the assisted breeding of foxes and other farmed animals.
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Affiliation(s)
- Xiufeng Yang
- College of Life ScienceQufu Normal UniversityQufuChina
| | | | - Qi Wang
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid AreasHulunbuirChina
| | - Xiaodong Gao
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Tian Xia
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Chao Zhao
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid AreasHulunbuirChina
| | - Honghai Zhang
- College of Life ScienceQufu Normal UniversityQufuChina
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33
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Wilkins AS, Wrangham R, Fitch WT. The neural crest/domestication syndrome hypothesis, explained: reply to Johnsson, Henriksen, and Wright. Genetics 2021; 219:iyab098. [PMID: 34849912 PMCID: PMC8633094 DOI: 10.1093/genetics/iyab098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/29/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Adam S Wilkins
- Institute of Theoretical Biology, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Richard Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - W Tecumseh Fitch
- Department of Behavioral and Cognitive Biology, University of Vienna, 1090 Vienna, Austria
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34
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Hecht EE, Kukekova AV, Gutman DA, Acland GM, Preuss TM, Trut LN. Neuromorphological Changes following Selection for Tameness and Aggression in the Russian Farm-Fox experiment. J Neurosci 2021; 41:6144-6156. [PMID: 34127519 PMCID: PMC8276742 DOI: 10.1523/jneurosci.3114-20.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/13/2023] Open
Abstract
The Russian farm-fox experiment is an unusually long-running and well-controlled study designed to replicate wolf-to-dog domestication. As such, it offers an unprecedented window onto the neural mechanisms governing the evolution of behavior. Here we report evolved changes to gray matter morphology resulting from selection for tameness versus aggressive responses toward humans in a sample of 30 male fox brains. Contrasting with standing ideas on the effects of domestication on brain size, tame foxes did not show reduced brain volume. Rather, gray matter volume in both the tame and aggressive strains was increased relative to conventional farm foxes bred without deliberate selection on behavior. Furthermore, tame- and aggressive-enlarged regions overlapped substantially, including portions of motor, somatosensory, and prefrontal cortex, amygdala, hippocampus, and cerebellum. We also observed differential morphologic covariation across distributed gray matter networks. In one prefrontal-cerebellum network, this covariation differentiated the three populations along the tame-aggressive behavioral axis. Surprisingly, a prefrontal-hypothalamic network differentiated the tame and aggressive foxes together from the conventional strain. These findings indicate that selection for opposite behaviors can influence brain morphology in a similar way.SIGNIFICANCE STATEMENT Domestication represents one of the largest and most rapid evolutionary shifts of life on earth. However, its neural correlates are largely unknown. Here we report the neuroanatomical consequences of selective breeding for tameness or aggression in the seminal Russian farm-fox experiment. Compared with a population of conventional farm-bred control foxes, tame foxes show neuroanatomical changes in the PFC and hypothalamus, paralleling wolf-to-dog shifts. Surprisingly, though, aggressive foxes also show similar changes. Moreover, both strains show increased gray matter volume relative to controls. These results indicate that similar brain adaptations can result from selection for opposite behavior, that existing ideas of brain changes in domestication may need revision, and that significant neuroanatomical change can evolve very quickly, within the span of <100 generations.
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Affiliation(s)
- Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agriculture, Consumer, and Environmental Sciences, University of IL Urbana-Champaign, Urbana, IL 61801
| | | | - Gregory M Acland
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, 14853
| | - Todd M Preuss
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322
| | - Lyudmila N Trut
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, 630090
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35
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Piferrer F. Epigenetic mechanisms in sex determination and in the evolutionary transitions between sexual systems. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200110. [PMID: 34247505 PMCID: PMC8273503 DOI: 10.1098/rstb.2020.0110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The hypothesis that epigenetic mechanisms of gene expression regulation have two main roles in vertebrate sex is presented. First, and within a given generation, by contributing to the acquisition and maintenance of (i) the male or female function once during the lifetime in individuals of gonochoristic species; and (ii) the male and female function in the same individual, either at the same time in simultaneous hermaphrodites, or first as one sex and then as the other in sequential hermaphrodites. Second, if environmental conditions change, epigenetic mechanisms may have also a role across generations, by providing the necessary phenotypic plasticity to facilitate the transition: (i) from one sexual system to another, or (ii) from one sex-determining mechanism to another. Furthermore, if the environmental change lasts enough time, epimutations could facilitate assimilation into genetic changes that stabilize the new sexual system or sex-determining mechanism. Examples supporting these assertions are presented, caveats or difficulties and knowledge gaps identified, and possible ways to test this hypothesis suggested. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
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Affiliation(s)
- Francesc Piferrer
- Institut de Ciències del Mar (ICM), Spanish National Research Council (CSIC), Passeig Marítim, 37-49, 08003 Barcelona, Spain
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36
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Sato R. Identity, obedience and individual efforts against infectious diseases. J R Soc Med 2021; 114:341-343. [PMID: 33618578 PMCID: PMC8415808 DOI: 10.1177/0141076821994273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Ryosuke Sato
- Department of Internal Medicine, Sato Clinic, Hamamatsu 433-8127, Japan
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
- Seirei Center for Health Promotion and Preventive Medicine, Hamamatsu 430-0906, Japan
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37
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Trut LN, Kharlamova AV, Pilipenko AS, Herbeck YE. The Fox Domestication Experiment and Dog Evolution: A View Based on Modern Molecular, Genetic, and Archaeological Data. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421070140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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38
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Hasselgren M, Dussex N, von Seth J, Angerbjörn A, Olsen RA, Dalén L, Norén K. Genomic and fitness consequences of inbreeding in an endangered carnivore. Mol Ecol 2021; 30:2790-2799. [PMID: 33955096 DOI: 10.1111/mec.15943] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 12/28/2022]
Abstract
Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower FROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.
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Affiliation(s)
| | - Nicolas Dussex
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Johanna von Seth
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
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39
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Watson KMA, Mikac KM, Schwab SG. Population Genetics of the Invasive Red Fox, Vulpes vulpes, in South-Eastern Australia. Genes (Basel) 2021; 12:genes12050786. [PMID: 34065589 PMCID: PMC8161170 DOI: 10.3390/genes12050786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
The use of genetic information in conservation biology has become more widespread with genetic information more readily available for non-model organisms. It has also been recognized that genetic information from invasive species can inform their management and control. The red fox poses a significant threat to Australian native fauna and the agricultural industry. Despite this, there are few recently published studies investigating the population genetics of foxes in Australia. This study investigated the population genetics of 94 foxes across the Illawarra and Shoalhaven regions of New South Wales, Australia. Diversity Array sequencing technology was used to genotype a large number of single nucleotide polymorphisms (N = 33,375). Moderate genetic diversity and relatedness were observed across the foxes sampled. Low to moderate levels of inbreeding, high-levels of identity-by-state values, as well as high identity-by-descent values were also found. There was limited evidence for population genetic structure among the foxes across the landscape sampled, supporting the presence of a single population across the study area. This indicates that there may be no barriers hindering fox dispersal across the landscape.
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Affiliation(s)
- Kalynda M.-A. Watson
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong 2522, Australia;
| | - Katarina M. Mikac
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong 2522, Australia;
- Correspondence: ; Tel.: +61-242-213-307
| | - Sibylle G. Schwab
- School of Chemistry and Molecular Biosciences, Faculty of Science, Medicine and Health, University of Wollongong, Northfields Ave, Wollongong 2522, Australia;
- Illawarra Health and Medical Research Institute, Northfields Ave, Wollongong 2522, Australia
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Chueca LJ, Kochmann J, Schell T, Greve C, Janke A, Pfenninger M, Klimpel S. De novo Genome Assembly of the Raccoon Dog ( Nyctereutes procyonoides). Front Genet 2021; 12:658256. [PMID: 33995489 PMCID: PMC8117329 DOI: 10.3389/fgene.2021.658256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Luis J Chueca
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV-EHU), Vitoria-Gasteiz, Spain
| | - Judith Kochmann
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Axel Janke
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Markus Pfenninger
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Sven Klimpel
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
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Peng Y, Li H, Liu Z, Zhang C, Li K, Gong Y, Geng L, Su J, Guan X, Liu L, Zhou R, Zhao Z, Guo J, Liang Q, Li X. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:2093-2108. [PMID: 33829635 DOI: 10.1111/1755-0998.13397] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.
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Affiliation(s)
- Yongdong Peng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhengzhu Liu
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Chuansheng Zhang
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Keqiang Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Mathematics and Information Science, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuanfang Gong
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Liying Geng
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jingjing Su
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, China
| | - Xuemin Guan
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lei Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai-an, China
| | - Ruihong Zhou
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Ziya Zhao
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jianxu Guo
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xianglong Li
- Hebei Key Laboratory of Specialty Animal Germplasm Resources Exploration and Innovation (Under Planning), College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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42
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Eusebi PG, Sevane N, O'Rourke T, Pizarro M, Boeckx C, Dunner S. Gene expression profiles underlying aggressive behavior in the prefrontal cortex of cattle. BMC Genomics 2021; 22:245. [PMID: 33827428 PMCID: PMC8028707 DOI: 10.1186/s12864-021-07505-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Aggressive behavior is an ancient and conserved trait, habitual for most animals in order to eat, protect themselves, compete for mating and defend their territories. Genetic factors have been shown to play an important role in the development of aggression both in animals and humans, displaying moderate to high heritability estimates. Although such types of behaviors have been studied in different animal models, the molecular architecture of aggressiveness remains poorly understood. This study compared gene expression profiles of 16 prefrontal cortex (PFC) samples from aggressive and non-aggressive cattle breeds: Lidia, selected for agonistic responses, and Wagyu, selected for tameness. RESULTS A total of 918 up-regulated and 278 down-regulated differentially expressed genes (DEG) were identified, representing above-chance overlap with genes previously identified in studies of aggression across species, as well as those implicated in recent human evolution. The functional interpretation of the up-regulated genes in the aggressive cohort revealed enrichment of pathways such as Alzheimer disease-presenilin, integrins and the ERK/MAPK signaling cascade, all implicated in the development of abnormal aggressive behaviors and neurophysiological disorders. Moreover, gonadotropins, are up-regulated as natural mechanisms enhancing aggression. Concomitantly, heterotrimeric G-protein pathways, associated with low reactivity mental states, and the GAD2 gene, a repressor of agonistic reactions associated with PFC activity, are down-regulated, promoting the development of the aggressive responses selected for in Lidia cattle. We also identified six upstream regulators, whose functional activity fits with the etiology of abnormal behavioral responses associated with aggression. CONCLUSIONS These transcriptional correlates of aggression, resulting, at least in part, from controlled artificial selection, can provide valuable insights into the complex architecture that underlies naturally developed agonistic behaviors. This analysis constitutes a first important step towards the identification of the genes and metabolic pathways that promote aggression in cattle and, providing a novel model species to disentangle the mechanisms underlying variability in aggressive behavior.
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Affiliation(s)
- Paulina G Eusebi
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain.
| | - Natalia Sevane
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Thomas O'Rourke
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain
| | - Manuel Pizarro
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - Cedric Boeckx
- Universitat de Barcelona, Gran Vía de les Corts Catalanes 585, 08007, Barcelona, Spain.,UBICS, Carrer Martí Franqués 1, 08028, Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Susana Dunner
- Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
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Farm Animals Are Long Away from Natural Behavior: Open Questions and Operative Consequences on Animal Welfare. Animals (Basel) 2021; 11:ani11030724. [PMID: 33800925 PMCID: PMC8001272 DOI: 10.3390/ani11030724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Animal welfare is a very important issue. One of the tasks of researchers is to provide explanations and possible solutions to questions arising from non-experts. This work analyzes part of the extensive literature on relationships between selection and domestic, mainly farm, animals’ behavior and deals with some very important themes, such as the role of regulations, domestication, and selection. Abstract The concept of welfare applied to farm animals has undergone a remarkable evolution. The growing awareness of citizens pushes farmers to guarantee the highest possible level of welfare to their animals. New perspectives could be opened for animal welfare reasoning around the concept of domestic, especially farm, animals as partial human artifacts. Therefore, it is important to understand how much a particular behavior of a farm animal is far from the natural one of its ancestors. This paper is a contribution to better understand the role of genetics of the farm animals on their behavior. This means that the naïve approach to animal welfare regarding returning animals to their natural state should be challenged and that welfare assessment should be considered.
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Vasiliev G, Chadaeva I, Rasskazov D, Ponomarenko P, Sharypova E, Drachkova I, Bogomolov A, Savinkova L, Ponomarenko M, Kolchanov N, Osadchuk A, Oshchepkov D, Osadchuk L. A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes. Int J Mol Sci 2021; 22:2346. [PMID: 33652917 PMCID: PMC7956675 DOI: 10.3390/ijms22052346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq data to compare the effect of co-directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common ancestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene-markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson's χ2 test p < 0.001, Fisher's exact test p < 0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial distribution), thus enforcing the norm (wild type).
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Affiliation(s)
- Gennady Vasiliev
- Novosibirsk State University, 630090 Novosibirsk, Russia;
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Irina Drachkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Alexander Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
| | - Ludmila Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (I.C.); (D.R.); (P.P.); (E.S.); (I.D.); (A.B.); (L.S.); (N.K.); (A.O.); (D.O.); (L.O.)
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Šimić G, Vukić V, Kopić J, Krsnik Ž, Hof PR. Molecules, Mechanisms, and Disorders of Self-Domestication: Keys for Understanding Emotional and Social Communication from an Evolutionary Perspective. Biomolecules 2020; 11:E2. [PMID: 33375093 PMCID: PMC7822183 DOI: 10.3390/biom11010002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
The neural crest hypothesis states that the phenotypic features of the domestication syndrome are due to a reduced number or disruption of neural crest cells (NCCs) migration, as these cells differentiate at their final destinations and proliferate into different tissues whose activity is reduced by domestication. Comparing the phenotypic characteristics of modern and prehistoric man, it is clear that during their recent evolutionary past, humans also went through a process of self-domestication with a simultaneous prolongation of the period of socialization. This has led to the development of social abilities and skills, especially language, as well as neoteny. Disorders of neural crest cell development and migration lead to many different conditions such as Waardenburg syndrome, Hirschsprung disease, fetal alcohol syndrome, DiGeorge and Treacher-Collins syndrome, for which the mechanisms are already relatively well-known. However, for others, such as Williams-Beuren syndrome and schizophrenia that have the characteristics of hyperdomestication, and autism spectrum disorders, and 7dupASD syndrome that have the characteristics of hypodomestication, much less is known. Thus, deciphering the biological determinants of disordered self-domestication has great potential for elucidating the normal and disturbed ontogenesis of humans, as well as for the understanding of evolution of mammals in general.
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Affiliation(s)
- Goran Šimić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Vana Vukić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Janja Kopić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Željka Krsnik
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, 10000 Zagreb, Croatia; (V.V.); (J.K.); (Ž.K.)
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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Friedrich J, Talenti A, Arvelius P, Strandberg E, Haskell MJ, Wiener P. Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioral traits. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10024. [PMID: 36619250 PMCID: PMC9744541 DOI: 10.1002/ggn2.10024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 01/11/2023]
Abstract
Strong selection has resulted in substantial morphological and behavioral diversity across modern dog breeds, which makes dogs interesting model animals to study the underlying genetic architecture of these traits. However, results from between-breed analyses may confound selection signatures for behavior and morphological features that were coselected during breed development. In this study, we assess population genetic differences in a unique resource of dogs of the same breed but with systematic behavioral selection in only one population. We exploit these different breeding backgrounds to identify signatures of recent selection. Selection signatures within populations were found on chromosomes 4 and 19, with the strongest signals in behavior-related genes. Regions showing strong signals of divergent selection were located on chromosomes 1, 24, and 32, and include candidate genes for both physical features and behavior. Some of the selection signatures appear to be driven by loci associated with coat color (Chr 24; ASIP) and length (Chr 32; FGF5), while others showed evidence of association with behavior. Our findings suggest that signatures of selection within dog breeds have been driven by selection for morphology and behavior. Furthermore, we demonstrate that combining selection scans with association analyses is effective for dissecting the traits under selection.
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Affiliation(s)
- Juliane Friedrich
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothianUK
| | - Andrea Talenti
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothianUK
| | - Per Arvelius
- Swedish Armed Forces Dog Training CenterMärstaSweden
| | - Erling Strandberg
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Marie J. Haskell
- Animal & Veterinary SciencesScotland's Rural College (SRUC)EdinburghUK
| | - Pamela Wiener
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothianUK
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Ortiz‐Leal I, Torres MV, Villamayor PR, López‐Beceiro A, Sanchez‐Quinteiro P. The vomeronasal organ of wild canids: the fox (Vulpes vulpes) as a model. J Anat 2020; 237:890-906. [PMID: 32584430 PMCID: PMC7542198 DOI: 10.1111/joa.13254] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 01/30/2023] Open
Abstract
The vomeronasal system (VNS) has been extensively studied within specific animal families, such as Rodentia. However, the study of the VNS in other families, such as Canidae, has long been neglected. Among canids, the vomeronasal organ (VNO) has only been studied in detail in the dog, and no studies have examined the morphofunctional or immunohistochemical characteristics of the VNS in wild canids, which is surprising, given the well-known importance of chemical senses for the dog and fox and the likelihood that the VNS plays roles in the socio-reproductive physiology and behaviours of these species. In addition, characterising the fox VNS could contribute to a better understanding of the domestication process that occurred in the dog, as the fox would represent the first wild canid to be studied in depth. Therefore, the aim of this study was to analyze the morphological and immunohistochemical characteristics of the fox VNO. Tissue dissection and microdissection techniques were employed, followed by general and specific histological staining techniques, including with immunohistochemical and lectin-histochemical labelling strategies, using antibodies against olfactory marker protein (OMP), growth-associated protein 43 (GAP-43), calbindin (CB), calretinin (CR), α-tubulin, Gαo, and Gαi2 proteins, to highlight the specific features of the VNO in the fox. This study found significant differences in the VNS between the fox and the dog, particularly concerning the expression of Gαi2 and Gαo proteins, which were associated with the expression of the type 1 vomeronasal receptors (V1R) and type 2 vomeronasal receptors (V2R), respectively, in the vomeronasal epithelium. Both are immunopositive in foxes, as opposed to the dog, which only expresses Gαi2. This finding suggests that the fox possesses a well-developed VNO and supports the hypothesis that a profound transformation in the VNS is associated with domestication in the canid family. Furthermore, the unique features identified in the fox VNO confirm the necessity of studying the VNS system in different species to better comprehend specific phylogenetic aspects of the VNS.
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Affiliation(s)
- Irene Ortiz‐Leal
- Department of Anatomy, Animal Production and Clinical Veterinary SciencesFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
| | - Mateo V. Torres
- Department of Anatomy, Animal Production and Clinical Veterinary SciencesFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
| | - Paula R. Villamayor
- Department of Anatomy, Animal Production and Clinical Veterinary SciencesFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
| | - Ana López‐Beceiro
- Department of Anatomy, Animal Production and Clinical Veterinary SciencesFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
| | - Pablo Sanchez‐Quinteiro
- Department of Anatomy, Animal Production and Clinical Veterinary SciencesFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
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Chen SY, Oliveira HR, Schenkel FS, Pedrosa VB, Melka MG, Brito LF. Using imputed whole-genome sequence variants to uncover candidate mutations and genes affecting milking speed and temperament in Holstein cattle. J Dairy Sci 2020; 103:10383-10398. [PMID: 32952011 DOI: 10.3168/jds.2020-18897] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022]
Abstract
Milking speed (MS) and temperament (MT) are 2 workability traits of great importance in dairy cattle production and breeding. This is mainly due to an increased intensification of the worldwide production systems and greater adoption of precision technologies with less human-cattle interaction. Both MS and MT are heritable traits and thus, genomic selection is a promising tool to expedite their genetic progress. However, the genetic architecture and biological mechanisms underlying the phenotypic expression of these traits remain underexplored. In this study, we investigated the association of >5.7 million imputed whole-genome sequence variants with MT and MS in 4,381 and 4,219 North American Holstein cattle, respectively. The statistical analyses were performed using a mixed linear model fitting a polygenic effect. We detected 40 and 35 significant SNPs independently associated with MT and MS, respectively, which were distributed across 26 chromosomes. Eight candidate genes (GRIN3A, KCNJ3, BOSTAUV1R417, BOSTAUV1R419, MAP2K5, KCTD3, GAP43, and LSAMP) were suggested to play an important role in MT as they are involved in biologically relevant pathways, such as glutamatergic synapse, vomeronasal receptor and oxytocin signaling. Within their coding and upstream sequences, we used an independent data set to further detect or validate significantly differentiated SNP between cattle breeds with known differences in MT. There were fewer candidate genes potentially implicated in MS, but immunity-related genes (e.g., BOLA-NC1 and LOC512672), also identified in other populations, were validated in this study. The significant SNP and novel candidate genes identified contribute to a better understanding of the biological mechanisms underlying both traits in dairy cattle. This information will also be useful for the optimization of prediction of genomic breeding values by giving greater weights to SNP located in the genomic regions identified.
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Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Victor B Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Melkaye G Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, 54022
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907.
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49
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Costilla R, Kemper KE, Byrne EM, Porto-Neto LR, Carvalheiro R, Purfield DC, Doyle JL, Berry DP, Moore SS, Wray NR, Hayes BJ. Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament. Genet Sel Evol 2020; 52:51. [PMID: 32842956 PMCID: PMC7448488 DOI: 10.1186/s12711-020-00569-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/07/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Temperament traits are of high importance across species. In humans, temperament or personality traits correlate with psychological traits and psychiatric disorders. In cattle, they impact animal welfare, product quality and human safety, and are therefore of direct commercial importance. We hypothesized that genetic factors that contribute to variation in temperament among individuals within a species will be shared between humans and cattle. Using imputed whole-genome sequence data from 9223 beef cattle from three cohorts, a series of genome-wide association studies was undertaken on cattle flight time, a temperament phenotype measured as the time taken for an animal to cover a short-fixed distance after release from an enclosure. We also investigated the association of cattle temperament with polymorphisms in bovine orthologs of risk genes for neuroticism, schizophrenia, autism spectrum disorders (ASD), and developmental delay disorders in humans. RESULTS Variants with the strongest associations were located in the bovine orthologous region that is involved in several behavioural and cognitive disorders in humans. These variants were also partially validated in independent cattle cohorts. Genes in these regions (BARHL2, NDN, SNRPN, MAGEL2, ABCA12, KIFAP3, TOPAZ1, FZD3, UBE3A, and GABRA5) were enriched for the GO term neuron migration and were differentially expressed in brain and pituitary tissues in humans. Moreover, variants within 100 kb of ASD susceptibility genes were associated with cattle temperament and explained 6.5% of the total additive genetic variance in the largest cattle cohort. The ASD genes with the most significant associations were GABRB3 and CUL3. Using the same 100 kb window, a weak association was found with polymorphisms in schizophrenia risk genes and no association with polymorphisms in neuroticism and developmental delay disorders risk genes. CONCLUSIONS Our analysis showed that genes identified in a meta-analysis of cattle temperament contribute to neuron development functions and are differentially expressed in human brain tissues. Furthermore, some ASD susceptibility genes are associated with cattle temperament. These findings provide evidence that genetic control of temperament might be shared between humans and cattle and highlight the potential for future analyses to leverage results between species.
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Affiliation(s)
- Roy Costilla
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Kathryn E. Kemper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Enda M. Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Laercio R. Porto-Neto
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Brisbane, Australia
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, Sao Paulo State University, Sao Paolo, Brazil
| | | | - Jennifer L. Doyle
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Donagh P. Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Stephen S. Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Ben J. Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
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50
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Gnanadesikan GE, Hare B, Snyder-Mackler N, Call J, Kaminski J, Miklósi Á, MacLean EL. Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions. Integr Comp Biol 2020; 60:976-990. [PMID: 32726413 DOI: 10.1093/icb/icaa112] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Given their remarkable phenotypic diversity, dogs present a unique opportunity for investigating the genetic bases of cognitive and behavioral traits. Our previous work demonstrated that genetic relatedness among breeds accounts for a substantial portion of variation in dog cognition. Here, we investigated the genetic architecture of breed differences in cognition, seeking to identify genes that contribute to variation in cognitive phenotypes. To do so, we combined cognitive data from the citizen science project Dognition.com with published breed-average genetic polymorphism data, resulting in a dataset of 1654 individuals with cognitive phenotypes representing 49 breeds. We conducted a breed-average genome-wide association study to identify specific polymorphisms associated with breed differences in inhibitory control, communication, memory, and physical reasoning. We found five single nucleotide polymorphisms (SNPs) that reached genome-wide significance after Bonferroni correction, located in EML1, OR52E2, HS3ST5, a U6 spliceosomal RNA, and a long noncoding RNA. When we combined results across multiple SNPs within the same gene, we identified 188 genes implicated in breed differences in cognition. This gene set included more genes than expected by chance that were (1) differentially expressed in brain tissue and (2) involved in nervous system functions including peripheral nervous system development, Wnt signaling, presynapse assembly, and synaptic vesicle exocytosis. These results advance our understanding of the genetic underpinnings of complex cognitive phenotypes and identify specific genetic variants for further research.
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Affiliation(s)
- Gitanjali E Gnanadesikan
- School of Anthropology, University of Arizona, Tucson, AZ, USA.,Cognitive Science Program, University of Arizona, Tucson, AZ, USA
| | - Brian Hare
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.,Center for Cognitive Neuroscience, Duke University, Durham, NC, USA
| | - Noah Snyder-Mackler
- Department of Psychology, University of Washington, Seattle, WA, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Josep Call
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
| | - Juliane Kaminski
- Department of Psychology, University of Portsmouth, Portsmouth, UK
| | - Ádám Miklósi
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary.,MTA-ELTE Comparative Ethology Research Group, Budapest, Hungary
| | - Evan L MacLean
- School of Anthropology, University of Arizona, Tucson, AZ, USA.,Cognitive Science Program, University of Arizona, Tucson, AZ, USA.,Psychology Department, University of Arizona, Tucson, AZ, USA.,College of Veterinary Medicine, University of Arizona, Tucson, AZ, USA
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