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Li Y, Xu W, Wang J, Liu H, Liu J, Zhang L, Hou R, Shen F, Liu Y, Cai K. Giant pandas in captivity undergo short-term adaptation in nerve-related pathways. BMC ZOOL 2024; 9:4. [PMID: 38383502 PMCID: PMC10880213 DOI: 10.1186/s40850-024-00195-y] [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: 08/12/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Behaviors in captive animals, including changes in appetite, activity level, and social interaction, are often seen as adaptive responses. However, these behaviors may become progressively maladaptive, leading to stress, anxiety, depression, and other negative reactions in animals. RESULTS In this study, we investigated the whole-genome sequencing data of 39 giant panda individuals, including 11 in captivity and 28 in the wild. To eliminate the mountain range effect and focus on the factor of captivity only, we first performed a principal component analysis. We then enumerated the 21,474,180 combinations of wild giant pandas (11 chosen from 28) and calculated their distances from the 11 captive individuals. The 11 wild individuals with the closest distances were used for the subsequent analysis. The linkage disequilibrium (LD) patterns demonstrated that the population was almost eliminated. We identified 505 robust selected genomic regions harboring at least one SNP, and the absolute frequency difference was greater than 0.6 between the two populations. GO analysis revealed that genes in these regions were mainly involved in nerve-related pathways. Furthermore, we identified 22 GO terms for which the selection strength significantly differed between the two populations, and there were 10 nerve-related pathways among them. Genes in the differentially abundant regions were involved in nerve-related pathways, indicating that giant pandas in captivity underwent minor genomic selection. Additionally, we investigated the relationship between genetic variation and chromatin conformation structures. We found that nucleotide diversity (θπ) in the captive population was correlated with chromatin conformation structures, which included A/B compartments, topologically associated domains (TADs) and TAD-cliques. For each GO term, we then compared the expression level of genes regulated by the above four factors (AB index, TAD intactness, TAD clique and PEI) with the corresponding genomic background. The retained 10 GO terms were all coordinately regulated by the four factors, and three of them were associated with nerve-related pathways. CONCLUSIONS This study revealed that giant pandas in captivity undergo short-term adaptation in nerve-related pathways. Furthermore, it provides new insights into the molecular mechanism of gene expression regulation under short-term adaptation to environmental change.
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Affiliation(s)
- Yan Li
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Wei Xu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Juan Wang
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Hong Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Jiawen Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Yuliang Liu
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China
| | - Kailai Cai
- Chengdu Research Base of Giant Panda Breeding, Panda Avenue, Northern Suburb, Chengdu, China.
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, Panda Avenue, Northern Suburb, Chengdu, China.
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Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-Pereira TT, Camargo NCS, de Souza Filho AF, Ikuta CY, Neto JSF, Setubal JC, Heinemann MB, Guimaraes AMS. Global Distribution and Evolution of Mycobacterium bovis Lineages. Front Microbiol 2020; 11:843. [PMID: 32477295 PMCID: PMC7232559 DOI: 10.3389/fmicb.2020.00843] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3, and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis (South Siberian infected skeletons at ∼2,000 years before present) and indicates that extant M. bovis originated between 715 and 3,556 years BP, with later emergence in the New World and Oceania, likely influenced by trades among countries.
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Affiliation(s)
- Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Salvatore L Patané
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Cellular Cycle, Butantan Institute, São Paulo, Brazil
| | - Aureliano Coelho Proença Guedes
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Robson F de Souza
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana T Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila C Soler Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Antônio F de Souza Filho
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Soares Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sa Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Robins A. The Alpha Hypothesis: Did Lateralized Cattle-Human Interactions Change the Script for Western Culture? Animals (Basel) 2019; 9:E638. [PMID: 31480488 PMCID: PMC6769460 DOI: 10.3390/ani9090638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/16/2019] [Accepted: 08/27/2019] [Indexed: 11/16/2022] Open
Abstract
Domestic cattle possess lateralized cognitive processing of human handlers. This has been recently demonstrated in the preference for large groups of cattle to view a human closely within the predominantly left visual field. By contrast, the same stimulus viewed predominantly within the right visual field promotes a significantly greater frequency of dispersal from a standing position, including flight responses. The respective sets of behaviours correspond with the traditional terms of "near side" for the left side of cattle and horses, and the "off" or "far side" for the right side. These traditional terms of over 300 years usage in the literature communicate functional practicalities for handling livestock and the recognition of lateralized cognitive processing. In this review, the possibility of even earlier recognition and the significance of laterality in cattle-human interaction was argued, from the earliest representations of the letter "A", originally illustrated from nearly 4000 years before the present time as the head of an ox as viewed not from the front or from the right, but from the left (near) side. By extension, this knowledge of lateralization in cattle may represent the earliest written example of applied ethology-the study of the behaviour of animals under human management.
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Affiliation(s)
- Andrew Robins
- Centre for Animal Welfare and Ethics, School of Veterinary Science, University of Queensland, Gatton Campus, Gatton, Queensland 4343, Australia.
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Browett S, McHugo G, Richardson IW, Magee DA, Park SDE, Fahey AG, Kearney JF, Correia CN, Randhawa IAS, MacHugh DE. Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed. Front Genet 2018. [PMID: 29520297 PMCID: PMC5827531 DOI: 10.3389/fgene.2018.00051] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Kerry cattle are an endangered landrace heritage breed of cultural importance to Ireland. In the present study we have used genome-wide SNP array data to evaluate genomic diversity within the Kerry population and between Kerry cattle and other European breeds. Patterns of genetic differentiation and gene flow among breeds using phylogenetic trees with ancestry graphs highlighted historical gene flow from the British Shorthorn breed into the ancestral population of modern Kerry cattle. Principal component analysis (PCA) and genetic clustering emphasised the genetic distinctiveness of Kerry cattle relative to comparator British and European cattle breeds. Modelling of genetic effective population size (Ne) revealed a demographic trend of diminishing Ne over time and that recent estimated Ne values for the Kerry breed may be less than the threshold for sustainable genetic conservation. In addition, analysis of genome-wide autozygosity (FROH) showed that genomic inbreeding has increased significantly during the 20 years between 1992 and 2012. Finally, signatures of selection revealed genomic regions subject to natural and artificial selection as Kerry cattle adapted to the climate, physical geography and agro-ecology of southwest Ireland.
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Affiliation(s)
- Sam Browett
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Gillian McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Alan G Fahey
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Imtiaz A S Randhawa
- Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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5
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The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2017; 204:423-434. [PMID: 27729493 DOI: 10.1534/genetics.116.194860] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
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McCauley DJ, Hardesty‐Moore M, Halpern BS, Young HS. A mammoth undertaking: harnessing insight from functional ecology to shape de‐extinction priority setting. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12728] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Douglas J. McCauley
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara CA93106 USA
| | - Molly Hardesty‐Moore
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara CA93106 USA
| | - Benjamin S. Halpern
- Bren School of Environmental Science & Management University of California Santa Barbara CA93106 USA
- National Center for Ecological Analysis and Synthesis University of California 735 State St. Suite 300 Santa Barbara CA93101 USA
- Imperial College London Silwood Park Campus Buckhurst Rd AscotSL57PY UK
| | - Hillary S. Young
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara CA93106 USA
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