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Fu J, Wen L. Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review. Mol Ecol 2023; 32:4497-4514. [PMID: 37332105 DOI: 10.1111/mec.17053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
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Affiliation(s)
- Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Longying Wen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Key Laboratory of Sichuan Institute for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University, Leshan, China
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2
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Zhang L, Chen J, Zhao R, Zhong J, Lin L, Li H, Ji X, Qu Y. Genomic insights into local adaptation in the Asiatic toad Bufo gargarizans, and its genomic offset to climate warming. Evol Appl 2023; 16:1071-1083. [PMID: 37216027 PMCID: PMC10197391 DOI: 10.1111/eva.13555] [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: 11/03/2022] [Revised: 03/31/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Genomic signatures of local adaptation have been identified in many species but remain sparsely studied in amphibians. Here, we explored genome-wide divergence within the Asiatic toad, Bufo gargarizans, to study local adaptation and genomic offset (i.e., the mismatch between current and future genotype-environment relationships) under climate warming scenarios. We obtained high-quality SNP data for 94 Asiatic toads from 21 populations in China to study spatial patterns of genomic variation, local adaptation, and genomic offset to warming in this wide-ranging species. Population structure and genetic diversity analysis based on high-quality SNPs revealed three clusters of B. gargarizans in the western, central-eastern, and northeastern portions of the species' range in China. Populations generally dispersed along two migration routes, one from the west to the central-east and one from the central-east to the northeast. Both genetic diversity and pairwise F ST were climatically correlated, and pairwise F ST was also correlated with geographic distance. Spatial genomic patterns in B. gargarizans were determined by the local environment and geographic distance. Global warming will increase the extirpation risk of B. gargarizans.
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Affiliation(s)
- Lu‐Wen Zhang
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Jun‐Qiong Chen
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Ru‐Meng Zhao
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Jun Zhong
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Long‐Hui Lin
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhouChina
| | - Hong Li
- College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Xiang Ji
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Yan‐Fu Qu
- College of Life SciencesNanjing Normal UniversityNanjingChina
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Li J, Fu C, Ai Q, Xie S, Huang C, Zhao M, Fu J, Wu H. Whole-genome resequencing reveals complex effects of geographical-palaeoclimatic interactions on diversification of moustache toads in East Asia. Mol Ecol 2023; 32:644-659. [PMID: 36380736 DOI: 10.1111/mec.16781] [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: 01/29/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Geographical features and palaeoclimatic fluctuations are two classical evolutionary forces that shape genetic diversification within species. Fine-grained analysis of the mechanisms involved through population demographic processes, however, remains limited. Taking advantage of two recently published reference genomes, we resequenced the genomes and examined the evolutionary history of the moustache toads, a group endemic to East Asia where complex topography and fluctuating palaeoclimate are known to have had profound impacts on organisms. Moustache toads probably originated in southeast Yunnan, China, and diversified towards the northwestern of Yunnan, as well as central and eastern China. Further exploration based on three widespread species (Leptobrachium ailaonicum, L. boringii and L. liui) using demographic modelling and species distribution models revealed that mountains and river valleys in East Asia not only functioned as geographical barriers, but also provided dispersal corridors and facilitated continuous migration or post-glacial secondary contact among moustache toad populations. Furthermore, periodic oscillation of effective population sizes accompanying fluctuations of historical temperature and population contraction at the Last Glacial Maximum support the widespread impact of climatic changes of the Pleistocene on species diversification in East Asia. This impact was moderate for populations of L. ailaonicum and L. boringii in the southwestern mountains but severe for populations of L. liui in the eastern lowland regions of continental East Asia, which is supported by different degrees of change of their effective population sizes. Our findings reveal mechanisms underlying genetic diversification among moustache toads, and highlight the power of genomic data and demographic modelling for examining complex historical population-level processes and for understanding how geographical and palaeoclimatic factors interactively shape current intraspecific diversity.
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Affiliation(s)
- Jun Li
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Chao Fu
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qingbo Ai
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Siyu Xie
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Chunhua Huang
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Mian Zhao
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Hua Wu
- Institute of Evolution and Ecology, International Research Centre of Ecology and Environment, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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Kerry RG, Montalbo FJP, Das R, Patra S, Mahapatra GP, Maurya GK, Nayak V, Jena AB, Ukhurebor KE, Jena RC, Gouda S, Majhi S, Rout JR. An overview of remote monitoring methods in biodiversity conservation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80179-80221. [PMID: 36197618 PMCID: PMC9534007 DOI: 10.1007/s11356-022-23242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.
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Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | | | - Rajeswari Das
- Department of Soil Science and Agricultural Chemistry, School of Agriculture, GIET University, Gunupur, Rayagada, Odisha 765022 India
| | - Sushmita Patra
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | | | - Ganesh Kumar Maurya
- Zoology Section, Mahila MahaVidyalya, Banaras Hindu University, Varanasi, 221005 India
| | - Vinayak Nayak
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | - Atala Bihari Jena
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Ram Chandra Jena
- Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Sushanto Gouda
- Department of Zoology, Mizoram University, Aizawl, 796009 India
| | - Sanatan Majhi
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Jyoti Ranjan Rout
- School of Biological Sciences, AIPH University, Bhubaneswar, Odisha 752101 India
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Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar. BIOLOGY 2022; 11:biology11020203. [PMID: 35205070 PMCID: PMC8869248 DOI: 10.3390/biology11020203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023]
Abstract
The wild boar is the wild ancestor of the domestic pig and one of the most common species of ungulates. At the beginning of the 20th century, the wild boar was practically exterminated in the European part of Russia. In the period 1935-1988, 7705 boars were caught in various regions of the European part of Russia, the Far East, Ukraine, Belarus, Kyrgyzstan, Kazakhstan, Latvia, Lithuania, Estonia, Tajikistan and resettled in the territory of Russia. Asian and European wild boars dwell the territory of Russia. The aim of our research was to study the genetic diversity and structure of wild boar populations in different regions of Russia using genome-wide genotyping. We have determined the genetic distances, population structure, parameters of genetic diversity and significantly expanded our understanding of the genetic state of the Russian wild boar. For the first time, we calculated autozygosity of the wild boar of the European and Asian subspecies using Homozygous-by-Descent (HBD) Segments analysis, which is important in terms of population recovery. We also found evidence of hybridization between Russian wild boar and domestic pigs. A group of European wild boars showed introgression of the Asian boar into population. The mean level of the inbreeding coefficient in European wild boar was higher than in Asian wild boar, and combined groups of the European boar had higher inbreeding coefficient than Russian wild boars. These results obtained can be used in population management.
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Anderson D, Negishi Y, Ishiniwa H, Okuda K, Hinton TG, Toma R, Nagata J, Tamate HB, Kaneko S. Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima. Proc Biol Sci 2021; 288:20210874. [PMID: 34187197 PMCID: PMC8242833 DOI: 10.1098/rspb.2021.0874] [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] [Indexed: 12/12/2022] Open
Abstract
Natural and anthropogenic disasters have the capability to cause sudden extrinsic environmental changes and long-lasting perturbations including invasive species, species expansion and influence evolution as selective pressures force adaption. Such disasters occurred on 11 March 2011, in Fukushima, Japan, when an earthquake, tsunami and meltdown of a nuclear power plant all drastically reformed anthropogenic land use. Using genetic data, we demonstrate how wild boar (Sus scrofa leucomystax) have persevered against these environmental changes, including an invasion of escaped domestic pigs (Sus scrofa domesticus). Concurrently, we show evidence of successful hybridization between pigs and native wild boar in this area; however in future offspring, the pig legacy has been diluted through time. We speculate that the range expansion dynamics inhibit long-term introgression and introgressed alleles will continue to decrease at each generation while only maternally inherited organelles will persist. Using the gene flow data among wild boar, we assume that offspring from hybrid lineages will continue dispersal north at low frequencies as climates warm. We conclude that future risks for wild boar in this area include intraspecies competition, revitalization of human-related disruptions and disease outbreaks.
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Affiliation(s)
- Donovan Anderson
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Yuki Negishi
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Hiroko Ishiniwa
- Institute of Environmental Radioactivity, Fukushima University, Fukushima City, Fukushima, Japan
| | - Kei Okuda
- Faculty of Human Environmental Studies, Hiroshima Shudo University, Hiroshima, Hiroshima, Japan
| | - Thomas G Hinton
- Centre for Environmental Radioactivity, Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Rio Toma
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Junco Nagata
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | | | - Shingo Kaneko
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan.,Institute of Environmental Radioactivity, Fukushima University, Fukushima City, Fukushima, Japan
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Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China. Animals (Basel) 2021; 11:ani11020346. [PMID: 33572967 PMCID: PMC7912324 DOI: 10.3390/ani11020346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The wild boar is native to the temperate region of Eurasia, which is now one of the most widely distributed mammals worldwide. The recent expansion in the wild boar population has attracted a lot of attention, which may cause great damage to ecosystems. Elucidating the patterns of the population structure, genetic diversity, population origin, and colonization route of wild boar is very helpful in the conservation and management of wild populations. Phylogeographic analysis has proven to be a powerful tool. Here, 82 samples of wild boars in 16 sampling locations were collected in Qinling Mountains (QM). Genetic analysis was conducted based on the mitochondrial control region and nuclear genes. The level of genetic diversity of wild boars in QM was lower than the total population in East Asia, but higher than European population. No obvious phylogeographic pattern were found. The effective population size was under demographic equilibrium in the past. Abstract Species dispersal patterns and population genetic structure can be influenced by geographical features. Qinling Mountains (QM) provide an excellent area for phylogeographic study. The phylogeography of Asian-wide wild boars revealed the colonization route. However, the impact of the QM on genetic diversity, genetic structure and population origin is still poorly understood. In this study, genetic analysis of wild boar in the QM was conducted based on the mitochondrial control region (943 bp) and twelve microsatellite loci of 82 individuals in 16 sampling locations. Overall genetic haplotype diversity was 0.86, and the nucleotide diversity was 0.0079. A total of 17 new haplotypes were detected. The level of genetic diversity of wild boars in QM was lower than in East Asia, but higher than in Europe. Phylogenetic analysis showed the weak genetic divergence in QM. Mismatch analysis, neutrality tests, and Bayesian Skyline Plot (BSP) results revealed that the estimates of effective population size were under demographic equilibrium in the past. Spatial analysis of molecular variance indicated no obvious phylogeographic structure.
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Choi SK, Kim KS, Ranyuk M, Babaev E, Voloshina I, Bayarlkhagva D, Chong JR, Ishiguro N, Yu L, Min MS, Lee H, Markov N. Asia-wide phylogeography of wild boar (Sus scrofa) based on mitochondrial DNA and Y-chromosome: Revising the migration routes of wild boar in Asia. PLoS One 2020; 15:e0238049. [PMID: 32834019 PMCID: PMC7444817 DOI: 10.1371/journal.pone.0238049] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/07/2020] [Indexed: 01/04/2023] Open
Abstract
Genetics of pigs has been well studied in Europe and Asia, but most of previous studies of molecular phylogeny of Sus scrofa have been based on sequences of both wild and domestic forms. In this study we analysed genetic traits of Sus scrofa from 13 regions in Asia (including previously undisclosed Eastern Caucasus and Trans-Baikal regions) using purely wild boar samples. Mitochondrial control region and Y-chromosome genes (AMELY & USP9Y) were employed to resolve phylogeographic relationships. We discussed spatio-temporal dynamics of wild boar distribution and compared molecular data to morphological and cytogenetic data on wild boar variability and taxonomy. A total of 51 haplotypes were detected in mtDNA control region and five haplotypes were found in combined sequences of Y-chromosome genes. The phylogeography of Asia-wide wild boars supported a hypothesis of migration from South-East Asia to South Asia, followed by migration to East and West Asia. We present a hypothesis about independent dispersal of wild boars into West Asia from South and North-East Asia. Mitochondrial DNA phylogeny generally fits the morphologically based intraspecies taxonomy. Distribution of chromosomal variants of wild boar presently does not show clear correlation with mtDNA clades.
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Affiliation(s)
- Sung Kyoung Choi
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- National Forensic Service Seoul Institute, Seoul, Republic of Korea
| | - Kyung Seok Kim
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, United States of America
| | - Maryana Ranyuk
- Institute of Plant and Animal Ecology Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
| | - Elmar Babaev
- Caspian Institute of biological Resources of Dagestan Scientific Center of Russian Academy of Sciences, Makhachkala, Russian Federation
| | - Inna Voloshina
- Lazovsky State Nature Reserve, Lazo, Primorsky Krai, Russian Federation
| | | | | | - Naotaka Ishiguro
- Laboratory of Food and Environmental Hygiene, Veterinary Medicine, Gifu University, Gifu, Japan
| | - Li Yu
- Laboratory for Conservation and Utilization of Bio-resource and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- * E-mail: (HL); (NM)
| | - Nickolay Markov
- Institute of Plant and Animal Ecology Ural Branch of Russian Academy of Sciences, Yekaterinburg, Russian Federation
- * E-mail: (HL); (NM)
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