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Gai Z, Zhai J, Chen X, Jiao P, Zhang S, Sun J, Qin R, Liu H, Wu Z, Li Z. Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of Populus sect. Turanga in Northwest China. FRONTIERS IN PLANT SCIENCE 2021; 12:705083. [PMID: 34456946 PMCID: PMC8385373 DOI: 10.3389/fpls.2021.705083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/14/2021] [Indexed: 05/28/2023]
Abstract
Populus sect. Turanga (hereafter referred to as "Populus"), including Populus euphratica and Populus pruinosa, are the predominant tree species in desert riparian forests in northwestern China. These trees play key roles in maintaining ecosystem balance, curbing desertification, and protecting biodiversity. However, the distribution area of Populus forests has been severely diminished and degraded in recent years due to increased habitat destruction and human activity. Understanding the genetic diversity among Populus individuals and populations is essential for designing conservation strategies, but comprehensive studies of their genetic diversity in northwest China are lacking. Here, we assessed the population structures and genetic diversity of 1,620 samples from 85 natural populations of Populus (59 P. euphratica and 26 P. pruinosa populations) covering all of northwestern China using 120 single nucleotide polymorphism (SNP) markers. Analysis of population structure revealed significant differentiation between these two sister species and indicated that strong geographical distribution patterns, a geographical barrier, and environmental heterogeneity shaped the extant genetic patterns of Populus. Both P. euphratica and P. pruinosa populations in southern Xinjiang had higher genetic diversity than populations in other clades, perhaps contributing to local geographic structure and strong gene flow. Analysis of molecular variance (AMOVA) identified 15% variance among and 85% variance within subpopulations. Mantel tests suggested that the genetic variation among P. euphratica and P. pruinosa populations could be explained by both geographical and environmental distance. The genetic diversity of P. euphratica showed a significant negative correlation with latitude and longitude and a positive correlation with various environmental factors, such as precipitation of warmest quarter and driest month, temperature seasonality, and annual mean temperature. These findings provide insights into how the genetic differentiation of endangered Populus species was driven by geographical and environmental factors, which should be helpful for designing strategies to protect these genetic resources in the future.
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Affiliation(s)
- Zhongshuai Gai
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Juntuan Zhai
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Xiangxiang Chen
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Peipei Jiao
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Shanhe Zhang
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Jianhao Sun
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Zhijun Li
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
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Capblancq T, Munson H, Butnor JR, Keller SR. Genomic drivers of early-life fitness in Picea rubens. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01378-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Luo Z, Wang X, Yang S, Cheng X, Liu Y, Hu J. Combining the responses of habitat suitability and connectivity to climate change for an East Asian endemic frog. Front Zool 2021; 18:14. [PMID: 33771163 PMCID: PMC7995727 DOI: 10.1186/s12983-021-00398-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/14/2021] [Indexed: 11/25/2022] Open
Abstract
Background Understanding the impacts of past and contemporary climate change on biodiversity is critical for effective conservation. Amphibians have weak dispersal abilities, putting them at risk of habitat fragmentation and loss. Both climate change and anthropogenic disturbances exacerbate these risks, increasing the likelihood of additional amphibian extinctions in the near future. The giant spiny frog (Quasipaa spinosa), an endemic species to East Asia, has faced a dramatic population decline over the last few decades. Using the giant spiny frog as an indicator to explore how past and future climate changes affect landscape connectivity, we characterized the shifts in the suitable habitat and habitat connectivity of the frog. Results We found a clear northward shift and a reduction in the extent of suitable habitat during the Last Glacial Maximum for giant spiny frogs; since that time, there has been an expansion of the available habitat. Our modelling showed that “overwarm” climatic conditions would most likely cause a decrease in the available habitat and an increase in the magnitude of population fragmentation in the future. We found that the habitat connectivity of the studied frogs will decrease by 50–75% under future climate change. Our results strengthen the notion that the mountains in southern China and the Sino-Vietnamese transboundary regions can act as critical refugia and priority areas of conservation planning going forward. Conclusions Given that amphibians are highly sensitive to environmental changes, our findings highlight that the responses of habitat suitability and connectivity to climate change can be critical considerations in future conservation measures for species with weak dispersal abilities and should not be neglected, as they all too often are. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-021-00398-w.
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Affiliation(s)
- Zhenhua Luo
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xiaoyi Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, China
| | - Shaofa Yang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xinlan Cheng
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junhua Hu
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin Nan Road, Chengdu, 610041, China.
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Havlíček J, Riegert J, Bandhauerová J, Fuchs R, Šálek M. Species-specific breeding habitat association of declining farmland birds within urban environments: conservation implications. Urban Ecosyst 2021. [DOI: 10.1007/s11252-021-01111-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Zarepourfard H, Riasi A, Frouzanfar M, Hajian M, Nasr Esfahani MH. Pomegranate seed in diet, affects sperm parameters of cloned goats following freezing-thawing. Theriogenology 2019; 125:203-209. [DOI: 10.1016/j.theriogenology.2018.10.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 01/07/2023]
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Zhang M, Evans TA. Determining urban exploiter status of a termite using genetic analysis. Urban Ecosyst 2016. [DOI: 10.1007/s11252-016-0628-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Population genomics applications for conservation: the case of the tropical dry forest dweller Peromyscus melanophrys. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0907-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Geue JC, Vágási CI, Schweizer M, Pap PL, Thomassen HA. Environmental selection is a main driver of divergence in house sparrows ( Passer domesticus) in Romania and Bulgaria. Ecol Evol 2016; 6:7954-7964. [PMID: 27891219 PMCID: PMC5108248 DOI: 10.1002/ece3.2509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/24/2016] [Accepted: 09/06/2016] [Indexed: 01/25/2023] Open
Abstract
Both neutral and adaptive evolutionary processes can cause population divergence, but their relative contributions remain unclear. We investigated the roles of these processes in population divergence in house sparrows (Passer domesticus) from Romania and Bulgaria, regions characterized by high landscape heterogeneity compared to Western Europe. We asked whether morphological divergence, complemented with genetic data in this human commensal species, was best explained by environmental variation, geographic distance, or landscape resistance—the effort it takes for an individual to disperse from one location to the other—caused by either natural or anthropogenic barriers. Using generalized dissimilarity modeling, a matrix regression technique that fits biotic beta diversity to both environmental predictors and geographic distance, we found that a small set of climate and vegetation variables explained up to ~30% of the observed divergence, whereas geographic and resistance distances played much lesser roles. Our results are consistent with signals of selection on morphological traits and of isolation by adaptation in genetic markers, suggesting that selection by natural environmental conditions shapes population divergence in house sparrows. Our study thus contributes to a growing body of evidence that adaptive evolution may be a major driver of diversification.
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Affiliation(s)
- Julia C Geue
- Comparative Zoology Institute for Evolution and Ecology University of Tübingen Tübingen Germany
| | - Csongor I Vágási
- MTA-DE 'Lendület' Behavioural Ecology Research Group Department of Evolutionary Zoology and Human Biology University of Debrecen Debrecen Hungary; Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş-Bolyai University Cluj- Napoca Romania
| | - Mona Schweizer
- Animal Physiological Ecology Institute for Evolution and Ecology University of Tübingen Tübingen Germany
| | - Péter L Pap
- MTA-DE 'Lendület' Behavioural Ecology Research Group Department of Evolutionary Zoology and Human Biology University of Debrecen Debrecen Hungary; Evolutionary Ecology Group Hungarian Department of Biology and Ecology Babeş-Bolyai University Cluj- Napoca Romania
| | - Henri A Thomassen
- Comparative Zoology Institute for Evolution and Ecology University of Tübingen Tübingen Germany
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Doboro FA, Njiro S, Sibeko-Matjila K, Van Vuuren M. Molecular Analysis of South African Ovine Herpesvirus 2 Strains Based on Selected Glycoprotein and Tegument Genes. PLoS One 2016; 11:e0147019. [PMID: 27002629 PMCID: PMC4803344 DOI: 10.1371/journal.pone.0147019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/28/2015] [Indexed: 11/18/2022] Open
Abstract
Ovine herpesvirus 2 (OvHV-2), is the causative agent of sheep-associated malignant catarrhal fever (SA-MCF), a generally fatal disease of cattle and other captive wild ruminants. Information on the OvHV-2 strains circulating in South Africa (SA) and other African countries with regard to genetic structure and diversity, and pattern of distribution is not available. This study aimed to characterize the OvHV-2 strains circulating in SA using selected genes encoding glycoproteins and tegument proteins. To establish the genetic diversity of OvHV-2 strains, four genes, Ov 7, Ov 8 ex2, ORF 27 and ORF 73 were selected for analysis by PCR and DNA sequencing. Nucleotide and amino acid multiple sequence analyses revealed two genotypes for ORF 27 and ORF 73, and three genotypes for Ov 7 and Ov 8 ex2, randomly distributed throughout the regions. Ov 7 and ORF 27 nucleotide sequence analysis revealed variations that distinguished SA genotypes from those of reference OvHV-2 strains. Epitope mapping analysis showed that mutations identified from the investigated genes are not likely to affect the functions of the gene products, particularly those responsible for antibody binding activities associated with B-cell epitopes. Knowledge of the extent of genetic diversity existing among OvHV-2 strains has provided an understanding on the distribution patterns of OvHV-2 strains or genotypes across the regions of South Africa. This can facilitate the management of SA-MCF in SA, in terms of introduction of control measures or safe practices to monitor and control OvHV-2 infection. The products encoded by the Ov 7, Ov 8 ex2 and ORF 27 genes are recommended for evaluation of their coded proteins as possible antigens in the development of an OvHV-2 specific serodiagnostic assay.
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Affiliation(s)
- Fulufhelo Amanda Doboro
- Molecular Epidemiology and Diagnostics programme, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, Pretoria, South Africa
- * E-mail:
| | - Stephen Njiro
- Food, feed & Veterinary Public Health Programme, Agricultural Research Council-Onderstepoort Veterinary Institute, Onderstepoort, Pretoria, South Africa
| | - Kgomotso Sibeko-Matjila
- Faculty of Veterinary Sciences, University of Pretoria, Onderstepoort, Pretoria, South Africa
| | - Moritz Van Vuuren
- Faculty of Veterinary Sciences, University of Pretoria, Onderstepoort, Pretoria, South Africa
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Garrido‐Garduño T, Téllez‐Valdés O, Manel S, Vázquez‐Domínguez E. Role of habitat heterogeneity and landscape connectivity in shaping gene flow and spatial population structure of a dominant rodent species in a tropical dry forest. J Zool (1987) 2015. [DOI: 10.1111/jzo.12307] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- T. Garrido‐Garduño
- Departamento de Ecología de la Biodiversidad Instituto de Ecología Universidad Nacional Autónoma de México Ciudad Universitaria México DF México
- Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México. Av. Universidad 3000 México DF México
| | - O. Téllez‐Valdés
- Laboratorio de Recursos Naturales Unidad de Biología Tecnología y Prototipos (UBIPRO) Facultad de Estudios Superiores Iztacala Universidad Nacional Autónoma de México Tlalnepantla Estado de México México
| | - S. Manel
- CEFE UMR 5175 CNRS‐Université de Montpellier‐Université Paul‐Valéry Montpellier‐EPHE laboratoire Biogéographie et écologie des vertébrés 1919 route de Mende, 34293 Montpellier Cedex 5 France
| | - E. Vázquez‐Domínguez
- Departamento de Ecología de la Biodiversidad Instituto de Ecología Universidad Nacional Autónoma de México Ciudad Universitaria México DF México
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Winter density and habitat preferences of three declining granivorous farmland birds: The importance of the keeping of poultry and dairy farms. J Nat Conserv 2015. [DOI: 10.1016/j.jnc.2015.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Xue HL, Xu JH, Chen L, Xu LX. Genetic variation of the striped hamster (Cricetulus barabensis) and the impact of population density and environmental factors. Zool Stud 2014. [DOI: 10.1186/s40555-014-0063-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Wetlands explain most in the genetic divergence pattern of Oncomelania hupensis. INFECTION GENETICS AND EVOLUTION 2014; 27:436-44. [PMID: 25183028 DOI: 10.1016/j.meegid.2014.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/10/2014] [Accepted: 08/15/2014] [Indexed: 11/22/2022]
Abstract
Understanding the divergence patterns of hosts could shed lights on the prediction of their parasite transmission. No effort has been devoted to understand the drivers of genetic divergence pattern of Oncomelania hupensis, the only intermediate host of Schistosoma japonicum. Based on a compilation of two O. hupensis gene datasets covering a wide geographic range in China and an array of geographical distance and environmental dissimilarity metrics built from earth observation data and ecological niche modeling, we conducted causal modeling analysis via simple, partial Mantel test and local polynomial fitting to understand the interactions among isolation-by-distance, isolation-by-environment, and genetic divergence. We found that geography contributes more to genetic divergence than environmental isolation, and among all variables involved, wetland showed the strongest correlation with the genetic pairwise distances. These results suggested that in China, O. hupensis dispersal is strongly linked to the distribution of wetlands, and the current divergence pattern of both O. hupensis and schistosomiasis might be altered due to the changed wetland pattern with the accomplishment of the Three Gorges Dam and the South-to-North water transfer project.
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