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Phylogeographic Diversity Analysis of Bipolaris sorokiniana (Sacc.) Shoemaker Causing Spot Blotch Disease in Wheat and Barley. Genes (Basel) 2022; 13:genes13122206. [PMID: 36553473 PMCID: PMC9778185 DOI: 10.3390/genes13122206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022] Open
Abstract
Bipolaris sorokiniana is a fungal pathogen that infects wheat, barley, and other crops, causing spot blotch disease. The disease is most common in humid, warm, wheat-growing regions, with South Asia's Eastern Gangetic Plains serving as a hotspot. There is very little information known about its genetic variability, demography, and divergence period. The current work is the first to study the phylogeographic patterns of B. sorokiniana isolates obtained from various wheat and barley-growing regions throughout the world, with the goal of elucidating the demographic history and estimating divergence times. In this study, 162 ITS sequences, 18 GAPDH sequences, and 74 TEF-1α sequences from B. sorokiniana obtained from the GenBank, including 21 ITS sequences produced in this study, were used to analyse the phylogeographic pattern of distribution and evolution of B. sorokiniana infecting wheat and barley. The degrees of differentiation among B. sorokiniana sequences from eighteen countries imply the presence of a broad and geographically undifferentiated global population. The study provided forty haplotypes. The H_1 haplotype was identified to be the ancestral haplotype, followed by H_29 and H_27, with H_1 occupying a central position in the median-joining network and being shared by several populations from different continents. The phylogeographic patterns of species based on multi-gene analysis, as well as the predominance of a single haplotype, suggested that human-mediated dispersal may have played a significant role in shaping this pathogen's population. According to divergence time analysis, haplogroups began at the Plio/Pleistocene boundary.
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Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01461-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Zhang Y, Zhang C, Wu L, Luo C, Guo X, Yang R, Zhang Y. Population genetic structure and evolutionary genetics of Anopheles sinensis based on knockdown resistance (kdr) mutations and mtDNA-COII gene in China-Laos, Thailand-Laos, and Cambodia-Laos borders. Parasit Vectors 2022; 15:229. [PMID: 35754022 PMCID: PMC9233850 DOI: 10.1186/s13071-022-05366-9] [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: 03/22/2022] [Accepted: 06/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vector control is still a pivotal method for preventing malaria, and its potency is weakened by the increasing resistance of vectors to chemical insecticides. As the most abundant and vital malaria vector in Southeast Asia, the chemical insecticide resistance status in Anopheles sinensis remains elusive in Laos, which makes it imperative to evaluate the true nature of chemical insecticide resistance-associated genetic mutations in An. sinensis in Laos. METHODS Adult An. sinensis were collected from three border regions in Laos. DNA was extracted from individual mosquitoes. PCR amplification and DNA sequencing of a fragment containing codon 1014 of the voltage-gated sodium channel (vgsc) gene were completed to study the kdr allele frequency distribution, kdr intron polymorphism, population genetic diversity, and the evolutionary status of the kdr codon. The mitochondrial cytochrome c oxidase subunit II gene (COII) was amplified and sequenced to examine population variations, genetic differentiation, spatial population structure, population expansion, and gene flow patterns. RESULTS Nine wild kdr haplotypes of the vgsc gene were detected in this study, and eight of them, namely 1014L1, 1014L2, 1014L4, 1014L7, 1014L9, 1014L10, 1014L11, and 1014L21, were discovered in the China-Laos border (northern Laos), while 1014L3 was only detected in the Thailand-Laos border (northwestern Laos) and Cambodia-Laos border (southern Laos). The newly identified haplotype, 1014L21, was uniquely distributed in the China-Laos border and was not identified in other countries. Based on sequence analysis of the mitochondrial COII genes, significant genetic differentiation and limited gene flow were detected between the China-Laos and Cambodia-Laos An. sinensis populations, which suggested that those two regions were genetically isolated. The distinct distribution of the kdr haplotype frequencies is probably the result of geographical isolation in mosquito populations. CONCLUSIONS Lack of kdr mutations in the vgsc gene was probably due to genetic isolation and the absence of intense selection pressure in the three border regions of Laos. This study reveals that pyrethroid-based chemical insecticides are still appropriate for battling An. sinensis in parts of Laos, and routine monitoring of chemical insecticide resistance should be continuously implemented and focused on more restricted areas as part of chemical insecticide resistance management.
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Affiliation(s)
- Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China
| | - Canglin Zhang
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Linbo Wu
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Chunhai Luo
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Rui Yang
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China.
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
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Trewick SA, Henderson IM, Pohe SR, Morgan-Richards M. Spatial Variation of Acanthophlebia cruentata (Ephemeroptera), a Mayfly Endemic to Te Ika-a-Māui—North Island of Aotearoa, New Zealand. INSECTS 2022; 13:insects13070567. [PMID: 35886743 PMCID: PMC9316242 DOI: 10.3390/insects13070567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/09/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Patterns of variation within a widespread species can provide evidence of population history. Adjacent stable populations with gene flow show clinal genetic divergence forming a pattern of isolation by distance. Populations that have grown due to an increase in potential habitat such as forest cover since the last glacial maximum will have low genetic variation showing patterns of range expansion. The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in streams of North Island but absent from the cooler South Island. Mayfly nymphs are restricted to streams but adults fly, facilitating gene flow among catchments. We detected higher genetic diversity at lower latitudes of this mayfly’s range compared to most of its distribution, concordant with predictions of limited forest cover in New Zealand during Pleistocene glacial periods. A signature of recent range expansion was observed in the higher latitudes. Despite initial observation suggesting mayfly size correlated with latitude, we found sex, elevation and sampling date were significant predictors of size, and some size variation is also explained by three regional groups based on haplotype distribution. Abstract The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in Te Ika-a-Māui North Island streams, but has never been collected from South Island despite land connection during the last glacial maximum. Population structure of this mayfly might reflect re-colonisation after volcanic eruptions in North Island c1800 years ago, climate cycling or conceal older, cryptic diversity. We collected population samples from 33 locations to estimate levels of population genetic diversity and to document phenotypic variation. Relatively low intraspecific haplotype divergence was recorded among mitochondrial cytb sequences from 492 individuals, but these resolved three geographic-haplotype regions (north, west, east). We detected a signature of isolation by distance at low latitudes (north) but evidence of recent population growth in the west and east. We did not detect an effect of volcanic eruptions but infer range expansion into higher latitudes from a common ancestor during the last glacial period. As judged from wing length, both sexes of adult mayflies were larger at higher elevation and we found that haplotype region was also a significant predictor of Acanthophlebia cruentata size. This suggests that our mitochondrial marker is concordant with nuclear genetic differences that might be explained by founder effect during range expansion.
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Affiliation(s)
- Steven A. Trewick
- Wildlife & Ecology Group, School of Natural Science, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; (I.M.H.); (M.M.-R.)
- Correspondence:
| | - Ian M. Henderson
- Wildlife & Ecology Group, School of Natural Science, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; (I.M.H.); (M.M.-R.)
| | | | - Mary Morgan-Richards
- Wildlife & Ecology Group, School of Natural Science, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand; (I.M.H.); (M.M.-R.)
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Mitochondrial genetic diversity, phylogeography and historical demography of Moroccan native freshwater fishes: a case study of the genus Luciobarbus Heckel, 1843. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01107-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Panicz R, Eljasik P, Wrzecionkowski K, Śmietana N, Biernaczyk M. First report and molecular analysis of population stability of the invasive Gulf wedge clam, Rangia cuneata (G.B. Sowerby I, 1832) in the Pomerian Bay (Southern Baltic Sea). THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2061612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- R. Panicz
- Department of Meat Science, Faculty of Food Science and Fisheries, West Pomeranian University of Technology, Szczecin, Poland
| | - P. Eljasik
- Department of Meat Science, Faculty of Food Science and Fisheries, West Pomeranian University of Technology, Szczecin, Poland
| | | | - N. Śmietana
- Department of Meat Science, Faculty of Food Science and Fisheries, West Pomeranian University of Technology, Szczecin, Poland
| | - M. Biernaczyk
- Department of Aquatic Bioengineering and Aquaculture, Faculty of Food Science and Fisheries, West Pomeranian University of Technology, Szczecin, Poland
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Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boars. PLoS One 2022; 17:e0254299. [PMID: 35344556 PMCID: PMC8959178 DOI: 10.1371/journal.pone.0254299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
The Philippine archipelago was believed to have never been connected to the Asian continent even during the severe Quaternary sea-level drops. As a result, the history of domestic pig (Sus scrofa) dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine domestic pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boar corresponding to their geographic origin. The results revealed considerable genetic diversity (0.900±0.016) and widespread Asian pig-ancestry (94.60%) in the phylogenetic analysis, with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine domestic pigs corroborates our hypothesis of a genetic signal that may be associated with the recently reported multiple waves of human migrations to the Philippines. The Haplogroup D7, reported to occur only in Indo-Burma Biodiversity Hotspots, included a high frequency of Philippine domestic pig haplotypes (54.08%), which poses an interesting challenge because its distribution is not consistent with the hypothesized migration route of Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes (Asian major) on several Philippine islands. The analyses of mismatch distribution and neutrality test were consistent with the Bayesian skyline plot which showed a long stationary period of effective population size. The population decline was consistent with the pronounced population bottleneck in Asian and European pigs during the interglacial periods of the Pleistocene. The results of this study will support the conservation strategies and improvements of economically important genetic resources in the Philippines.
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Zhang Y, Zhang C, Yang R, Luo C, Deng Y, Liu Y, Zhang Y, Zhou H, Zhang D. Molecular phylogeny of Anopheles nivipes based on mtDNA-COII and mosquito diversity in Cambodia-Laos border. Malar J 2022; 21:91. [PMID: 35300704 PMCID: PMC8932176 DOI: 10.1186/s12936-022-04121-w] [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: 08/24/2021] [Accepted: 03/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Few studies have been conducted to investigate the distribution of mosquito vectors and the population structure of secondary vectors in the border region of Cambodia-Laos. The aim of this work was to study the mosquito diversity and molecular phylogeny of secondary vectors, i.e., Anopheles nivipes in this area. METHODS 1440 adult mosquitoes were trapped in the Cambodia-Laos border. mtDNA-COII were amplified and sequenced from 53 An. nivipes DNA samples. Together with COII sequences deposited in GenBank, a total of 86 COII sequences were used for examining population variations, genetic differentiation, spatial population structure, population expansion, and gene flow patterns. RESULTS The adult mosquitoes were classified into 5 genera and 27 species in this border region. The predominant genera were Culex (60.07%, 865/1440) and Anopheles (31.25%, 450/1440), and the major Anopheles species were An. nivipes (73.56%, 331/450) and Anopheles maculatus (14.22%, 64/450). Based on sequences analysis of COII, a high level of genetic differentiation was reported in two Northwest India (Cheema and Bathinda, Punjab) and Cambodia-Laos (Siem Pang, Stung treng) populations (FST = 0.97824, 0.97343, P < 0.05), as well as lower gene flow (Nm = 0.01112, 0.01365) in the An. nivipes populations. Phylogenetic analysis and SAMOVA revealed a gene barrier restricting gene flow among three An. nivipes populations. Mantel test suggested a significant correlation between geography and gene distance in all An. nivipes populations (Z = 44,983.1865, r = 0.5575, P = 0.0070). Neutrality test and Mismatch distribution revealed a recent population expansion of An. nivipes in the Cambodia-Laos population. CONCLUSIONS Anopheles nivipes was one of the major Anopheles species in the Cambodia-Laos border. Based on sequences analysis of COII, a genetic barrier between Cambodia-Laos and two Indian populations was found, and a recent population expanding or selecting of An. nivipes occurred in the Cambodia-Laos population, suggesting that COII might be an effective marker for describing the molecular phylogeny of An. nivipes. Further investigation and continuous surveillance of An. nivipes are warranted in this region.
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Affiliation(s)
- Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China
| | - Canglin Zhang
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Rui Yang
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Chunhai Luo
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Yan Deng
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Yan Liu
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China.
| | - Dongmei Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
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Guo R, Zhang YH, Zhang HJ, Landis JB, Zhang X, Wang HC, Yao XH. Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot. BMC PLANT BIOLOGY 2022; 22:89. [PMID: 35227218 PMCID: PMC8883688 DOI: 10.1186/s12870-022-03464-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic-continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic-continental gradient and 'oceanic' adaptation. RESULTS The phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic-continental gradient of the species and fit the 'refugia in refugia' pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to 'oceanic' adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods. CONCLUSIONS Overall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic-continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to 'oceanic' adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.
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Affiliation(s)
- Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Yong-Hua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Hua-Jie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiao-Hong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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You J, Lougheed SC, Zhao Y, Zhang G, Liu W, Lu F, Wang Y, Zhang W, Yang J, Qiong L, Song Z. Comparative phylogeography study reveals introgression and incomplete lineage sorting during rapid diversification of Rhodiola. ANNALS OF BOTANY 2022; 129:185-200. [PMID: 34718397 PMCID: PMC8796671 DOI: 10.1093/aob/mcab133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Many plant taxa in the Qinghai-Tibetan Plateau (QTP) and the Hengduan Mountains (HM) radiated rapidly during the Quaternary but with frequent secondary contact between diverging populations. Incomplete lineage sorting and introgressive hybridization might be involved during the rapid radiation, but their effects on phylogeography have not been fully determined. METHODS We investigated the chloroplast DNA (cpDNA)/internal transcribed spacer (ITS) sequence variations of 611 samples of Rhodiola bupleuroides, R. discolor, R. fastigiata and R. chrysanthemifolia from the QTP and HM to compare the phylogeographic patterns between the four species with different evolutionary histories, geographic ranges and reproductive modes. KEY RESULTS The divergence times of these species were consistent with the last peak of in situ speciation in the HM. While closely related species exhibited different phylogeographic patterns, they shared several ribotypes and haplotypes in sympatric populations, suggesting introgressive hybridization. A significant phylogenetic discordance between ribotypes and haplotypes was detected in three species, implying incomplete lineage sorting. Rhodiola discolor houses an extraordinary richness of cpDNA haplotypes, and this finding may be attributed to adaptive radiation. CONCLUSION In addition to geographic isolation and climate oscillations during the Quaternary, both introgressive hybridization and incomplete lineage sorting play important roles in species that experienced rapid diversification in the QTP and HM.
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Affiliation(s)
- Jianling You
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
- BGI-Yunnan, BGI-Shenzhen, Kunming, China
| | | | - Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Wensheng Liu
- College of Life Science and Technology, Central South University of Forestry and Techonology, Changsha, China
| | - Fan Lu
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Yuguo Wang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Wenju Zhang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Ji Yang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - La Qiong
- Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Tibet University, Thasa, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
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Wooding SP, Ramirez VA. Worldwide diversity, association potential, and natural selection in the superimposed taste genes, CD36 and GNAT3. Chem Senses 2022; 47:6491270. [PMID: 34972209 DOI: 10.1093/chemse/bjab052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CD36 and GNAT3 mediate taste responses, with CD36 acting as a lipid detector and GNAT3 acting as the α subunit of gustducin, a G protein governing sweet, savory, and bitter transduction. Strikingly, the genes encoding CD36 and GNAT3 are genomically superimposed, with CD36 completely encompassing GNAT3. To characterize genetic variation across the CD36-GNAT3 region, its implications for phenotypic diversity, and its recent evolution, we analyzed from ~2,500 worldwide subjects sequenced by the 1000 Genomes Project (1000GP). CD36-GNAT3 harbored extensive diversity including 8,688 single-nucleotide polymorphisms (SNPs), 414 indels, and other complex variants. Sliding window analyses revealed that nucleotide diversity and population differentiation across CD36-GNAT3 were consistent with genome-wide trends in the 1000GP (π = 0.10%, P = 0.64; FST = 9.0%, P = 0.57). In addition, functional predictions using SIFT and PolyPhen-2 identified 60 variants likely to alter protein function, and they were in weak linkage disequilibrium (r2 < 0.17), suggesting their effects are largely independent. However, the frequencies of predicted functional variants were low (P¯ = 0.0013), indicating their contributions to phenotypic variance on population scales are limited. Tests using Tajima's D statistic revealed that pressures from natural selection have been relaxed across most of CD36-GNAT3 during its recent history (0.39 < P < 0.67). However, CD36 exons showed signs of local adaptation consistent with prior reports (P < 0.035). Thus, CD36 and GNAT3 harbor numerous variants predicted to affect taste sensitivity, but most are rare and phenotypic variance on a population level is likely mediated by a small number of sites.
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Affiliation(s)
- Stephen P Wooding
- Department of Anthropology, University of California, Merced, Merced, CA, USA
| | - Vicente A Ramirez
- Department of Public Health, University of California, Merced, Merced, CA, USA
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Wang RH, Yang ZP, Zhang ZC, Comes HP, Qi ZC, Li P, Fu CX. Plio-Pleistocene climatic change drives allopatric speciation and population divergence within the Scrophularia incisa complex (Scrophulariaceae) of desert and steppe subshrubs in Northwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:985372. [PMID: 36212368 PMCID: PMC9532938 DOI: 10.3389/fpls.2022.985372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/19/2022] [Indexed: 05/07/2023]
Abstract
Numerous temperate plants and animals on the Qinghai-Tibet Plateau (QTP) are hypothesized to have differentiated due to vicariant allopatric speciation associated with the geologic uplifts. However, this hypothesis has rarely been tested through a phylogeographic study of relative species in a broader geographic context, including the QTP, Tianshan Mountains, Mongolian Plateau, and surrounding regions. To understand the speciation and diversification process of plants across this wide area, phylogeographic analysis were examined from Scrophularia incisa and two other closely relative species comprising S. kiriloviana and S. dentata. Thirty-two populations of the three close relatives were genotyped using chloroplast DNA fragments and nuclear microsatellite loci to assess population structure and diversity, supplemented by phylogenetic dating, ancestral area reconstructions and species distribution modelings, as well as niche identity tests. Our chloroplast DNA (cpDNA) phylogeny showed that this monophyletic group of desert and steppe semi-shrub is derived from a Middle Pliocene ancestor of the Central Asia. Lineages in Central Asia vs. China diverged through climate/tectonic-induced vicariance during Middle Pliocene. Genetic and ENM data in conjunction with niche differentiation analyses support that the divergence of S. incisa, S. dentata and S. kiriloviana in China lineage proceeded through allopatric speciation, might triggered by early Pleistocene climate change of increase of aridification and enlargement of deserts, while subsequent climate-induced cycles of range contractions/expansions enhanced the geographical isolation and habit fragmentation of these taxa. These findings highlight the importance of the Plio-Pleistocene climate change in shaping genetic diversity and driving speciation in temperate steppes and deserts of Northwestern China.
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Affiliation(s)
- Rui-Hong Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhao-Ping Yang
- Key Laboratory of Biological Resources and Conservation and Application, College of Life Sciences, Tarim University, Alaer, China
| | - Zhi-Cheng Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Hans Peter Comes
- Department of Biosciences, Salzburg University, Salzburg, Austria
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- *Correspondence: Zhe-Chen Qi,
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
- Pan Li,
| | - Cheng-Xin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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Miyake T, Nakajima J, Umemura K, Onikura N, Ueda T, Smith C, Kawamura K. Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA, with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus. JOURNAL OF FISH BIOLOGY 2021; 99:1677-1695. [PMID: 34498257 DOI: 10.1111/jfb.14876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/23/2021] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
Abstract
The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause. Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55-0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10 Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.
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Affiliation(s)
| | - Jun Nakajima
- Fukuoka Institute of Health and Environmental Sciences, Fukuoka, Japan
| | - Keitaro Umemura
- Fishery Research Laboratory, Kyushu University, Fukuoka, Japan
| | - Norio Onikura
- Fishery Research Laboratory, Kyushu University, Fukuoka, Japan
| | | | - Carl Smith
- Department of Ecology & Vertebrate Zoology, University of Łódź, Łódź, Poland
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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14
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Byrne MS, Ruiz-García M, Túnez JI. Phylogeography of the capybara, Hydrochoerus hydrochaeris, in a large portion of its distribution area in South America. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09569-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Fuentes G, González F, Saavedra J, López-Sepúlveda P, Victoriano PF, Stuessy TF, Ruiz-Ponce E. Assessing signals of selection and historical demography to develop conservation strategies in the Chilean emblematic Araucaria araucana. Sci Rep 2021; 11:20504. [PMID: 34654850 PMCID: PMC8521589 DOI: 10.1038/s41598-021-98662-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/27/2021] [Indexed: 11/25/2022] Open
Abstract
Loss of genetic diversity reduces the ability of species to evolve and respond to environmental change. Araucaria araucana is an emblematic conifer species from southern South America, with important ethnic value for the Mapuche people (Pehuenche); the Chilean Government has catalogued its conservation status as vulnerable. Climatic fluctuations were potentially a major impact in the genetic variation within many tree species. In this context, the restricted geographic distribution of A. araucana in Chile appears to be a consequence of the Last Glacial Maximum (LGM). During the past two centuries, strong human intervention has also affected the geographical distribution and population sizes of A. araucana. Reduction of population size may cause loss of genetic diversity, which could affect frequency of adaptive loci. The aims of this study were to know the existence of potential loci under selection and populations with genetic, demographic disequilibrium in the Chilean distribution of A. araucana. Based on 268 polymorphic AFLP loci, we have investigated potential loci under selection and genetic, demographic disequilibrium within seven Chilean populations of Araucaria araucana. Correlation of 41 outlier loci with the environmental variables of precipitation and temperature reveals signatures of selection, whereas 227 neutral loci provide estimates of demographic equilibrium and genetic population structure. Three populations are recommended as priorities for conservation.
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Affiliation(s)
- Glenda Fuentes
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Fidelina González
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - Javier Saavedra
- Departamento de Agronomia, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, PR, Brasil
| | - Patricio López-Sepúlveda
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Pedro F Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Tod F Stuessy
- Herbarium and Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA.,Department of Botany and Biodiversity Research, University of Vienna, 1030, Vienna, Austria
| | - Eduardo Ruiz-Ponce
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
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Zhang C, Yang R, Wu L, Luo C, Guo X, Deng Y, Zhou H, Zhang Y. Molecular phylogeny of the Anopheles hyrcanus group (Diptera: Culicidae) based on rDNA-ITS2 and mtDNA-COII. Parasit Vectors 2021; 14:454. [PMID: 34488860 PMCID: PMC8420049 DOI: 10.1186/s13071-021-04971-4] [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: 07/01/2021] [Accepted: 08/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Anopheles hyrcanus group, which includes 25 species, is widely distributed in the Oriental and Palaearctic regions. Given the difficulty in identifying cryptic or sibling species based on their morphological characteristics, molecular identification is regarded as an important complementary approach to traditional morphological taxonomy. The aim of this study was to reconstruct the phylogeny of the Hyrcanus group using DNA barcoding markers in order to determine the phylogenetic correlations of closely related taxa and to compare these markers in terms of identification efficiency and genetic divergence among species. METHODS Based on data extracted from the GenBank database and data from the present study, we used 399 rDNA-ITS2 sequences of 19 species and 392 mtDNA-COII sequences of 14 species to reconstruct the molecular phylogeny of the Hyrcanus group across its worldwide range. We also compared the performance of rDNA-ITS2 against that of mtDNA-COII to assess the genetic divergence of closely related species within the Hyrcanus group. RESULTS Average interspecific divergence for the rDNA-ITS2 sequence (0.376) was 125-fold higher than the average intraspecies divergence (0.003), and average interspecific divergence for the mtDNA-COII sequence (0.055) was eightfold higher than the average intraspecies divergence (0.007). The barcoding gap ranged from 0.015 to 0.073 for rDNA-ITS2, and from 0.017 to 0.025 for mtDNA-COII. Two sets of closely related species, namely, Anophels lesteri and An. paraliae, and An. sinensis, An. belenrae and An. kleini, were resolved by rDNA-ITS2. In contrast, the relationship of An. sinensis/An. belenrae/An. kleini was poorly defined in the COII tree. The neutrality test and mismatch distribution revealed that An. peditaeniatus, An. hyrcanus, An. sinensis and An. lesteri were likely to undergo hitchhiking or population expansion in accordance with both markers. In addition, the population of an important vivax malaria vector, An. sinensis, has experienced an expansion after a bottleneck in northern and southern Laos. CONCLUSIONS The topology of the Hyrcanus group rDNA-ITS2 and mtDNA-COII trees conformed to the morphology-based taxonomy for species classification rather than for that for subgroup division. rDNA-ITS2 is considered to be a more reliable diagnostic tool than mtDNA-COII in terms of investigating the phylogenetic correlation between closely related mosquito species in the Hyrcanus group. Moreover, the population expansion of an important vivax malaria vector, An. sinensis, has underlined a potential risk of malaria transmission in northern and southern Laos. This study contributes to the molecular identification of the Anopheles hyrcanus group in vector surveillance.
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Affiliation(s)
- Canglin Zhang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Rui Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Linbo Wu
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Chunhai Luo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Yan Deng
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Hongning Zhou
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433 People’s Republic of China
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Cortez T, Amaral RV, Sobral-Souza T, Andrade SCS. Genome-wide assessment elucidates connectivity and the evolutionary history of the highly dispersive marine invertebrate Littoraria flava (Littorinidae: Gastropoda). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
An important goal of marine population genetics is to understand how spatial connectivity patterns are influenced by historical and evolutionary factors. In this study, we evaluate the demographic history and population structure of Littoraria flava, a highly dispersive marine gastropod in the Brazilian intertidal zone. To test the hypotheses that the species has (1) historically high levels of gene flow on a macrogeographical spatial scale and (2) a distribution in rocky shores that consists of subpopulations, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, ITS-2 and single nucleotide polymorphisms) with niche-based modelling to predict its palaeodistribution. Low genetic structure was observed, as well as high gene flow over long distances. The demographic analyses suggest that L. flava has had periods of population bottlenecks followed by expansion. According to both palaeodistribution and coalescent simulations, these expansion events occurred during the Pleistocene interglacial cycles (21 kya) and the associated climatic changes were the probable drivers of the distribution of the species. This is the first phylogeographical study of a marine gastropod on the South American coast based on genomic markers associated with niche modelling.
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Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Rafael V Amaral
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, MTBrazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
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Godinez CJP, Dadios PJD, Espina DM, Matsunaga M, Nishibori M. Population Genetic Structure and Contribution of Philippine Chickens to the Pacific Chicken Diversity Inferred From Mitochondrial DNA. Front Genet 2021; 12:698401. [PMID: 34367257 PMCID: PMC8340678 DOI: 10.3389/fgene.2021.698401] [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: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
The Philippines is considered one of the biodiversity hotspots for animal genetic resources. In spite of this, population genetic structure, genetic diversity, and past population history of Philippine chickens are not well studied. In this study, phylogeny reconstruction and estimation of population genetic structure were based on 107 newly generated mitochondrial DNA (mtDNA) complete D-loop sequences and 37 previously published sequences of Philippine chickens, consisting of 34 haplotypes. Philippine chickens showed high haplotypic diversity (Hd = 0.915 ± 0.011) across Southeast Asia and Oceania. The phylogenetic analysis and median-joining (MJ) network revealed predominant maternal lineage haplogroup D classified throughout the population, while support for Philippine-Pacific subclade was evident, suggesting a Philippine origin of Pacific chickens. Here, we observed Philippine red junglefowls (RJFs) at the basal position of the tree within haplogroup D indicating an earlier introduction into the Philippines potentially via mainland Southeast Asia (MSEA). Another observation was the significantly low genetic differentiation and high rate of gene flow of Philippine chickens into Pacific chicken population. The negative Tajima's D and Fu's Fs neutrality tests revealed that Philippine chickens exhibited an expansion signal. The analyses of mismatch distribution and neutrality tests were consistent with the presence of weak phylogeographic structuring and evident population growth of Philippine chickens (haplogroup D) in the islands of Southeast Asia (ISEA). Furthermore, the Bayesian skyline plot (BSP) analysis showed an increase in the effective population size of Philippine chickens, relating with human settlement, and expansion events. The high level of genetic variability of Philippine chickens demonstrates conservation significance, thus, must be explored in the future.
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Affiliation(s)
- Cyrill John P. Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Peter June D. Dadios
- College of Aquatic and Applied Life Sciences, Southern Leyte State University, Southern Leyte, Philippines
| | - Dinah M. Espina
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
| | - Megumi Matsunaga
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan
- Department of Animal Science, College of Agriculture and Food Science, Visayas State University, Baybay City, Philippines
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Liu HL, Chen ZT, Liu C, Wu XL, Xiao KJ, Pu DQ. Population Genetics of the Black Citrus Aphid Aphis aurantii (Hemiptera, Aphididae) in China. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.702178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The black citrus aphid, Aphis aurantiiBoyer de Fonscolombe, 1841, is one of the most destructive pests in commercial tea plantations and gardens in China. In this study, we investigated the population genetic structure of A. aurantii based on the concatenated sequences of two mitochondrial genes, cytochrome c oxidase I (cox1) and cytochrome b (cytb). A total of 166 haplotypes were identified from 177 individuals collected at 11 locations in China. The whole Chinese A. aurantii population showed a low nucleotide diversity (0.00968) and a high population diversity (haplotype diversity; 0.9991). The haplotypes of the 11 local populations were widely distributed in the neighbor-joining phylogenetic tree and haplotype network diagram, whereas no apparent lineages were detected. Gene flow analysis showed gene exchanges among local populations. The pairwise Fst values revealed a certain amount of genetic difference among local populations. Analysis of molecular variance (AMOVA) reflected genetic differences both within and among populations. The isolation by distance (IBD) analysis revealed a high positive correlation between the geographic distance and genetic distance of the different populations. Neutral test and mismatch distribution suggested that A. aurantii may have experienced recent population expansion events.
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Wang Z, Zhong C, Li D, Yan C, Yao X, Li Z. Cytotype distribution and chloroplast phylogeography of the Actinidia chinensis complex. BMC PLANT BIOLOGY 2021; 21:325. [PMID: 34229602 PMCID: PMC8259359 DOI: 10.1186/s12870-021-03099-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant phylogeographic studies of species in subtropical China have mainly focused on rare and endangered species, whereas few studies have been conducted on taxa with relatively wide distribution, especially polyploid species. We investigated the cytotype and haplotype distribution pattern of the Actinidia chinensis complex, a widespread geographically woody liana with variable ploidy in subtropical China comprising two varieties, with three chloroplast fragments DNA (ndhF-rpl132, rps16-trnQ and trnE-trnT). Macroevolutionary, microevolutionary and niche modeling tools were also combined to disentangle the origin and the demographic history of the species or cytotypes. RESULTS The ploidy levels of 3338 individuals from 128 populations sampled throughout the species distribution range were estimated with flow cytometry. The widespread cytotypes were diploids followed by tetraploids and hexaploids, whereas triploids and octoploids occurred in a few populations. Thirty-one chloroplast haplotypes were detected. The genetic diversity and genetic structure were found to be high between varieties (or ploidy races) chinensis and deliciosa. Our results revealed that these two varieties inhabit significantly different climatic niche spaces. Ecological niche models (ENMs) indicate that all varieties' ranges contracted during the Last Inter Glacial (LIG), and expanded eastward or northward during the Last Glacial Maximum (LGM). CONCLUSIONS Pliocene and Plio-Pleistocene climatic fluctuations and vicariance appear to have played key roles in shaping current population structure and historical demography in the A. chinensis complex. The polyploidization process also appears to have played an important role in the historical demography of the complex through improving their adaptability to environmental changes.
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Affiliation(s)
- Zhi Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caihong Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Dawei Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Chunlin Yan
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
| | - Zuozhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Ariyaraphong N, Laopichienpong N, Singchat W, Panthum T, Farhan Ahmad S, Jattawa D, Duengkae P, Muangmai N, Suwanasopee T, Koonawootrittriron S, Srikulnath K. High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing. Animals (Basel) 2021; 11:ani11061680. [PMID: 34199963 PMCID: PMC8227385 DOI: 10.3390/ani11061680] [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: 04/08/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup "I", were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.
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Affiliation(s)
- Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Danai Jattawa
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Special Research Unit, Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok 10900, Thailand
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Studying genetic population structure to shed light on the demographic explosion of the rare species Barbitistes vicetinus (Orthoptera, Tettigoniidae). PLoS One 2021; 16:e0250507. [PMID: 33956844 PMCID: PMC8101909 DOI: 10.1371/journal.pone.0250507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/07/2021] [Indexed: 11/19/2022] Open
Abstract
Insect outbreaks usually involve important ecological and economic consequences for agriculture and forestry. The short-winged bush-cricket Barbitistes vicetinus Galvagni & Fontana, 1993 is a recently described species that was considered rare until ten years ago, when unexpected population outbreaks causing severe defoliations across forests and crops were observed in north-eastern Italy. A genetic approach was used to analyse the origin of outbreak populations. The analysis of two mitochondrial regions (Cytochrome Oxidase I and II and 12S rRNA-Control Region) of 130 samples from the two disjunct ranges (Euganean and Berici Hills) showed high values of haplotype diversity and revealed a high geographical structure among populations of the two ranges. The high genetic variability observed supports the native origin of this species. In addition, results suggest that unexpected outbreaks are not a consequence of a single or few pestiferous haplotypes but rather the source of outbreaks are local populations which have experienced an increase in each area. The recent outbreaks have probably appeared independently of the genetic haplotypes whereas environmental conditions could have affected the outbreak populations. These findings contribute to a growing understanding of the status and evolutionary history of the pest that would be useful for developing and implementing biological control strategies for example by maximizing efforts to locate native natural enemies.
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Drahun I, Wiebe KF, Koloski CW, van Herk WG, Cassone BJ. Genetic structure and population demographics of Hypnoidus bicolor (Coleoptera: Elateridae) in the Canadian Prairies. PEST MANAGEMENT SCIENCE 2021; 77:2282-2291. [PMID: 33421259 DOI: 10.1002/ps.6255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/17/2020] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Following banning of the pesticide lindane in most counties, wireworms (i.e., the soil-living larval stages of click beetles) have become major pests of a variety of economically important field crops. Hypnoidus bicolor is a common pest species in the Canadian Prairies. However, little is known about its life history, which impedes the development of effective integrated pest management (IPM) strategies. Population genetic approaches have the potential to assist in the development of IPM. RESULTS We sequenced a 622-bp fragment of the COX1 gene from 326 H. bicolor wireworm and click beetles collected from 13 localities on the Canadian Prairies. Two genetically distinct (>4.66% sequence divergence) clades were identified, suggesting that they may be part of a species complex. Clade A predominated and increased in prevalence the further east samples were collected, whereas the opposite was true for clade B. Clade B appears to be comprised of two mitochondrial DNA groups, however, one group was represented by only one haplotype. Both clades were characterized by uneven gene flow among populations with low levels of regional genetic structuring. Clade A appeared to have undergone population and range expansions, which may coincide with the advent of intensive agriculture practices in the prairies. CONCLUSION Knowledge of species composition and population structure is important for the development of effective IPM strategies but is often lacking for wireworms. Our study fills these knowledge gaps for a predominant pest species in the prairies, H. bicolor, by providing robust evidence for cryptic forms and characterizing its dispersal patterns and population dynamics. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Ivan Drahun
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
| | - Kiana F Wiebe
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
| | - Cody W Koloski
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
| | - Willem G van Herk
- Agassiz Research and Development Centre, Agriculture and Agri-Food Canada, Agassiz, British Columbia, Canada
| | - Bryan J Cassone
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
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24
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Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes. Genes (Basel) 2021; 12:genes12050642. [PMID: 33925980 PMCID: PMC8145813 DOI: 10.3390/genes12050642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene.
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25
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Forcina G, Woutersen K, Sánchez-Ramírez S, Angelone S, Crampe JP, Pérez JM, Fandos P, Granados JE, Jowers MJ. Demography reveals populational expansion of a recently extinct Iberian ungulate. ZOOSYST EVOL 2021. [DOI: 10.3897/zse.97.61854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.
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26
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Supmee V, Songrak A, Suppapan J, Sangthong P. Population Genetic Structure of Ornate Threadfin Bream ( Nemipterus hexodon) in Thailand. Trop Life Sci Res 2021; 32:63-82. [PMID: 33936551 PMCID: PMC8054670 DOI: 10.21315/tlsr2021.32.1.4] [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] [Indexed: 10/27/2022] Open
Abstract
Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise F ST , and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.
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Affiliation(s)
- Verakiat Supmee
- Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat Campus, Nakhon Si Thammarat 80110, Thailand
| | - Apirak Songrak
- Department of Fishery Technology, Faculty of Science and Fisheries Technology, Rajamangala University of Technology Srivijaya, Trang Campus, Trang 92150, Thailand
| | - Juthamas Suppapan
- Faculty of Education, Nakhon Si Thammarat Rajabhat University, Nakhon Si Thammarat 80280, Thailand
| | - Pradit Sangthong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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Alminas OSV, Heffelfinger JR, Statham MJ, Latch EK. Phylogeography of Cedros and Tiburón Island Mule Deer in North America's Desert Southwest. J Hered 2021; 112:260-275. [PMID: 33755178 DOI: 10.1093/jhered/esab013] [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: 11/02/2020] [Accepted: 03/22/2021] [Indexed: 11/14/2022] Open
Abstract
Though mule deer (Odocoileus hemionus) persist in robust populations throughout most of their North American distribution, habitat loss, unregulated hunting, and other factors have reduced their historical range in México. Two of the 6 putative subspecies inhabiting México's deserts and Baja California peninsula are of conservation concern, occupying islands in the Pacific Ocean (Odocoileus hemionus cerrosensis on Cedros Island: endangered) and Sea of Cortés (Odocoileus hemionus sheldoni on Tiburón Island: threatened). Focusing on the desert southwest (n = 448), we sampled Tiburón (n = 22) and Cedros (n = 15) Island mule deer using contemporary samples and natural history museum specimens to complete a phylogeographic evaluation of the species complex, and assess the phylogeography of these insular subspecies. Both insular subspecies formed endemic haplotype lineages, consistent with island biogeographic theory. Bayesian skyline plots were consistent with Holocene demographic expansion. Cedros Island deer were genetically most similar to adjacent mainland Baja California deer, but exhibited a suite of unique haplotypes and reduced genetic variation. Tiburón Island deer haplotypes unexpectedly nested within a mainland lineage found in distant New Mexico, rather than the adjacent mainland Sonoran lineage. Such findings suggest the importance of postglacial climate fluctuations and biotic community turnover in the phylogeographic history of mule deer in the desert southwest. Our genetic data corroborates cultural, archaeological, and phenotypic evidence supporting Cedros and Tiburón deer endemicity and subspecies status. Reduced genetic variation, divergence from mainland populations, and demographic trends on both islands indicate that conservation, monitoring, and management are critical to ensure persistence of these endemic insular subspecies.
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Affiliation(s)
- Ona S V Alminas
- California Department of Fish and Wildlife, 715 P Street, Sacramento, CA.,the Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | | | - Mark J Statham
- the Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, One Shields Avenue/Old Davis Road, Davis, CA 95616-8744
| | - Emily K Latch
- the Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
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Nakamoto A, Harada M, Mitsuhashi R, Tsuchiya K, Kryukov AP, Shinohara A, Suzuki H. Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation. ZOOLOGICAL LETTERS 2021; 7:2. [PMID: 33588942 PMCID: PMC7885446 DOI: 10.1186/s40851-021-00169-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Quaternary environmental changes fundamentally influenced the genetic diversity of temperate-zone terrestrial animals, including those in the Japanese Archipelago. The genetic diversity of present-day populations is taxon- and region-specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1140 bp) of mitochondrial DNA (mtDNA) to elucidate the factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura, which occur in central and southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta, which occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (τ values) were grouped into five classes in terms of the level, implying the occurrence of five stages for rapid expansion. It is conceivable that severe cold periods and subsequent warm periods during the late Quaternary were responsible for the population expansion events. The first and third oldest events included island-derived haplotypes, indicative of the involvement of land bridge formation between remote islands, hence suggesting an association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third event was followed by the fourth, it is plausible that the termination of the Younger Dryas and subsequent abrupt warming ca. 11,500 years ago facilitated the fourth expansion event. The second event most likely corresponded to early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period were predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500 years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing a time-dependent manner whose pattern was similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5800 years ago with a rate of 0.10 substitutions/site/million years ago during the mid-Holocene, suggestive of the influence of humans or other unspecified reasons, such as the Jomon marine transgression.
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Affiliation(s)
- Azusa Nakamoto
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo, 060-0810 Japan
| | - Masashi Harada
- Laboratory Animal Center, Osaka City University Graduate School of Medical School, Osaka, 545-8585 Japan
| | - Reiko Mitsuhashi
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo, 060-0810 Japan
| | - Kimiyuki Tsuchiya
- Oyo-seibutsu Co. Ltd., 4-12-3, Minami-Aoyama, Minato-ku, Tokyo, 107-0062 Japan
| | - Alexey P. Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022 Russia
| | - Akio Shinohara
- Frontier Science Research Center, University of Miyazaki, Kihara 5200, Miyazaki, 889-1692 Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo, 060-0810 Japan
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29
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De AK, Sawhney S, Bhattacharya D, Sujatha T, Sunder J, Ponraj P, Ravi SK, Mondal S, Malakar D, Kundu A. Origin, genetic diversity and evolution of Andaman local duck, a native duck germplasm of an insular region of India. PLoS One 2021; 16:e0245138. [PMID: 33561119 PMCID: PMC7872295 DOI: 10.1371/journal.pone.0245138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/23/2020] [Indexed: 11/29/2022] Open
Abstract
Domestic ducks are of paramount importance as a cheap source of protein in rural India. Andaman local duck (ALD) is an indigenous avian genetic resource of Andaman and Nicobar islands (ANI) and is mainly distributed in Middle and Northern parts of these islands. Negligence has brought this breed on the edge of extinction necessitating immediate conservation efforts. Here, we report the genetic diversity, population structure and matrilineal genetic root of ALD. Partial mtDNA D-loop sequences were analyzed in 71 ALD samples and analysis revealed 19 polymorphic sites and 13 haplotypes. Estimated haplotype (Hd ± SD) and nucleotide diversity (π ± SD) were 0.881 ± 0.017 and 0.00897 ± 0.00078 respectively. The high genetic diversity of ALD indicates introgression of genetic material from other local duck breeds. In addition, it can be postulated that ALD bearing high genetic diversity has strong ability to adapt to environmental changes and can withstand impending climate change. Phylogenetic and network analysis indicate that ALD falls under Eurasian clade of mallard and ALD forms three clusters; one cluster is phylogenetically close to Southeast Asian countries, one close to Southern part of mainland India and the third one forms an independent cluster. Therefore, ALD might have migrated either from Southeast Asian countries which enjoy a close cultural bondage with ANI from time immemorial or from Southern part of India. The independent cluster may have evolved locally in these islands and natural selection pressure imposed by environmental conditions might be the driving force for evaluation of these duck haplotypes; which mimics Darwin’s theory of natural selection. The results of the study will be beneficial for formulating future breeding programme and conservation strategy towards sustainable development of the duck breed.
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Affiliation(s)
- Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
- * E-mail:
| | - Sneha Sawhney
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Debasis Bhattacharya
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - T. Sujatha
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Perumal Ponraj
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - S. K. Ravi
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Samiran Mondal
- Department of Veterinary Pathology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Dhruba Malakar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - A. Kundu
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
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30
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Genetic diversity and phylogenetic analysis of blackbuck (Antilope cervicapra) in southern India. Mol Biol Rep 2021; 48:1255-1268. [PMID: 33555530 DOI: 10.1007/s11033-021-06180-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
Blackbuck (Antilope cervicapra) is a threatened species endemic to the Indian subcontinent. Many populations of blackbuck are found in southern India. Populations of blackbuck are negatively affected in many places for various reasons, such as habitat destruction and poaching. Their range decreased sharply during the 20th century. There is very limited information available on the population dynamics of blackbuck in southern India. For the phylogenetic and genetic diversity analyses of blackbuck populations among different distribution ranges in southern India, we sequenced mt DNA of cytochrome b (Cyt b) for 120, cytochrome c oxidase subunit-1 (COI) for 137 and the control region (CR) for 137 fecal pellets from eleven different locations in southern India. We analyzed the genetic structure of three mitochondrial markers, the CR, Cyt b and the COI region, separately and in a combined dataset. The haplotype diversity and nucleotide diversity of CR were 0.969 and 0.047, respectively, and were higher than those of Cyt b and COI. A Bayesian phylogeny and an MJ network based on the CR and combined dataset (105 sequences) signified several distinct haplotype clusters within blackbuck, whereas no clusters were identified with the Cyt b and COI phylogenetic analyses. The analysis of molecular variance of the combined data set revealed 52.46% genetic variation within the population. Mismatch distribution analysis revealed that blackbuck populations underwent complex changes with analysis of the combined dataset in each population and analysis of each marker separately in the overall population. The results provide evidence that blackbuck in different geographic locations has a distinct population structure due to habitat fragmentation after the formation of the Western and Eastern Ghats.
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31
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Osman MM, Hassan HY, Elnour MA, Makkan H, Gebremeskel EI, Gais T, Koko ME, Soodyall H, Ibrahim ME. Mitochondrial HVRI and whole mitogenome sequence variations portray similar scenarios on the genetic structure and ancestry of northeast Africans. Meta Gene 2021. [DOI: 10.1016/j.mgene.2020.100837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Li Y, Fujiwara K, Osada N, Kawai Y, Takada T, Kryukov AP, Abe K, Yonekawa H, Shiroishi T, Moriwaki K, Saitou N, Suzuki H. House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences. Heredity (Edinb) 2021; 126:132-147. [PMID: 32934361 PMCID: PMC7852662 DOI: 10.1038/s41437-020-00364-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 11/09/2022] Open
Abstract
The Eurasian house mouse Mus musculus is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, M. m. musculus (MUS) and M. m. castaneus (CAS). We revealed directional dispersals reaching as far as the Japanese Archipelago from their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: (1) broad spatial expansion into eastern Europe and the western part of western China, (2) dispersal to the eastern part of western China, (3) dispersal to northern China, (4) dispersal to the Korean Peninsula and (5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2000-18,000 years. The dispersal of CAS was characterised by three events: initial divergences (ca. 7000-9000 years ago) of haplogroups in northernmost China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basin to broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4000-6000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2000-3500). This study provides a solid framework for the spatiotemporal movement of the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.
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Affiliation(s)
- Yue Li
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, 1-21-1, Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Alexey P Kryukov
- Far Eastern Branch of the Russian Academy of Sciences, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok, 690022, Russia
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Hiromichi Yonekawa
- Laboratory for Transgenic Technology, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kami-kitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | | | - Kazuo Moriwaki
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
- National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
- School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, 903-0215, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan.
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Anguiano-Constante MA, Zamora-Tavares P, Ruiz-Sanchez E, Dean E, Rodríguez A, Munguía-Lino G. Population differentiation and phylogeography in Lycianthes moziniana (Solanaceae: Capsiceae), a perennial herb endemic to the Mexican Transition Zone. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Abstract
Lycianthes moziniana (Solanaceae: Capsiceae) is a perennial herb with edible fruits that is endemic to Mexico. Three varieties are recognized, all known in the Mexican Transition Zone. Lycianthes moziniana var. margaretiana grows in the Sierra Madre Oriental, whereas L. moziniana var. moziniana is common along the Trans-Mexican Volcanic Belt and in the Sierra Madre Occidental. Lycianthes moziniana var. oaxacana is found exclusively in the Sierra Madre del Sur. The Mexican Transition Zone is a complex geological, climatic and biogeographical area, the result of tectonic and volcanic activity that has promoted genetic divergence and speciation. We determined the genetic variation and structure of L. moziniana. Using phylogeographical approaches, we described the demographic history and evolutionary processes leading its divergence. The intergenic spacers rpl32-trnL and ycf1 were sequenced for 133 individuals pertaining to 15 populations. The genealogical relationships were analysed using haplotype networks. Finally, based on ecological niche models, we inferred the palaeodistribution of L. moziniana during the Pleistocene. The genetic differences and the haplogroups matched the three described varieties. Geological and climatic events of the Mexican Transition Zone facilitated these results. The Trans-Mexican Volcanic Belt isolated the populations of the Sierra Madre Oriental and the Sierra Madre del Sur, while allowing the migration to the Sierra Madre Occidental, during the middle Holocene.
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Affiliation(s)
- Marco Antonio Anguiano-Constante
- Maestría en Ciencias en Biosistemática y Manejo de Recursos Naturales y Agrícolas (BIMARENA), Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
| | - Pilar Zamora-Tavares
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg), Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
| | - Eduardo Ruiz-Sanchez
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg), Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
| | - Ellen Dean
- UC Davis Center for Plant Diversity, Plant Sciences M.S. 7, Davis, CA, USA
| | - Aarón Rodríguez
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg), Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
| | - Guadalupe Munguía-Lino
- Laboratorio Nacional de Identificación y Caracterización Vegetal (LaniVeg), Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
- Cátedras CONACYT-Universidad de Guadalajara, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Nextipac, Zapopan, Jalisco, Mexico
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Hou H, Ye H, Wang Z, Wu J, Gao Y, Han W, Na D, Sun G, Wang Y. Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus). BMC PLANT BIOLOGY 2020; 20:526. [PMID: 33203402 PMCID: PMC7672979 DOI: 10.1186/s12870-020-02723-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.
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Affiliation(s)
- Huimin Hou
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Hang Ye
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Zhi Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Jiahui Wu
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Yue Gao
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Wei Han
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Dongchen Na
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Genlou Sun
- Saint Mary’s University, Halifax, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
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Ghaedi Z, Badri S, Saberi-Pirooz R, Vaissi S, Javidkar M, Ahmadzadeh F. The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We investigated the phylogeographic structure of the genus Saara and studied whether the Zagros Mountain ranges influence the gene flow and dispersal at the landscape scale between the Iranian Saara species, including S. asmussi in the central Iranian plateau and S. loricata in the Mesopotamian lowlands. Phylogenetic analyses clearly show three well-supported species, including S. loricata, S. asmussi and S. hardwickii, that are distinct from Uromastyx species. The S-DIVA and BBM analyses demonstrate that species of Saara originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Our results indicate that the separation of S. loricata from S. asmussi coincides with the orogenic events of the Zagros Mountains during the Pliocene, and thus it may show a vicariance event. Diversification within populations of S. loricata and S. assmussi are estimated to have occurred during the Pleistocene. The haplotype network indicates one haplogroup for each of the Iranian Saara species. Population genetic analyses shows signals of demographic expansions at the beginning of the Holocene for S. loricata. Our results support the hypothesis that the Zagros Mountains act as a barrier for gene flow and Quaternary climatic oscillations affected intraspecific genetic divergences of S. loricata and S. asmussi.
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Affiliation(s)
- Zeinab Ghaedi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Sahar Badri
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Reihaneh Saberi-Pirooz
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Somaye Vaissi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
- Department of Biology, Faculty of Science, Baghabrisham, Razi University, Kermanshah, Iran
| | - Mohammad Javidkar
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
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Late Quaternary Environmental and Human Impacts on the Mitochondrial DNA Diversity of Four Commensal Rodents in Myanmar. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09519-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractWe addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome b gene (Cytb) in the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytb sequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends.
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Buranelli RC, Mantelatto FL. Comparative genetic differentiation study of three coexisting mangrove crabs in western Atlantic. J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1751889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- R. C. Buranelli
- Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto (SP), Brazil
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Chanthran SSD, Lim PE, Li Y, Liao TY, Poong SW, Du J, Hussein MAS, Sade A, Rumpet R, Loh KH. Genetic diversity and population structure of Terapon jarbua (Forskål, 1775) (Teleostei, Terapontidae) in Malaysian waters. Zookeys 2020; 911:139-160. [PMID: 32104142 PMCID: PMC7031388 DOI: 10.3897/zookeys.911.39222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 11/22/2022] Open
Abstract
A background study is important for the conservation and stock management of a species. Terapon jarbua is a coastal Indo-Pacific species, sourced for human consumption. This study examined 134 samples from the central west and east coasts of Peninsular (West) Malaysia and East Malaysia. A 1446-bp concatenated dataset of mtDNA COI and Cyt b sequences was used in this study and 83 haplotypes were identified, of which 79 are unique haplotypes and four are shared haplotypes. Populations of T. jarbua in Malaysia are genetically heterogenous as shown by the high level of haplotype diversity ranging from 0.9167-0.9952, low nucleotide diversity ranging from 0.0288-0.3434, and high FST values (within population genetic variation). Population genetic structuring is not distinct as shown by the shared haplotypes between geographic populations and mixtures of haplotypes from different populations within the same genetic cluster. The gene flow patterns and population structuring observed among these regions are likely attributed to geographical distance, past historical events, allopatric speciation, dispersal ability and water currents. For instance, the mixture of haplotypes revealed an extraordinary migration ability of T. jarbua (>1200 km) via ancient river connectivity. The negative overall value of the neutrality test and a non-significant mismatch distribution are consistent with demographic expansion(s) in the past. The median-joining network concurred with the maximum likelihood haplotype tree with three major clades resolved. The scarcity of information on this species is an obstacle for future management and conservation purposes. Hence, this study aims to contribute information on the population structure, genetic diversity, and historical demography of T. jarbua in Malaysia.
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Affiliation(s)
- Shyama Sundari Devi Chanthran
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
- Institute for Advanced Studies, University of Malaya, Kuala Lumpur 50603, MalaysiaThird Institute of Oceanography, Ministry of Natural ResourcesXiamenChina
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
| | - Yuan Li
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaNational Sun Yat-sen UniversityKaohsiungTaiwan
| | - Te-Yu Liao
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung 80424, TaiwanMinistry of Natural ResourcesXiamenChina
| | - Sze-Wan Poong
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
| | - Jianguo Du
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, ChinaNational Sun Yat-sen UniversityKaohsiungTaiwan
- Fujian Provincial Station for Field Observation and Research of Island and Coastal Zone in Zhangzhou, Xiamen 361005, ChinaStation for Field Observation and Research of Island and Coastal ZoneXiamenChina
- Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration, Xiamen 361005, ChinaKey Laboratory of Marine Ecological Conservation and RestorationXiamenChina
| | - Muhammad Ali Syed Hussein
- Endangered Marine Species Research Unit, Borneo Marine Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, MalaysiaUniversiti Malaysia SabahKota KinabaluMalaysia
| | - Ahemad Sade
- Department of Fisheries Sabah, Kota Kinabalu 88624, Sabah, MalaysiaDepartment of Fisheries SabahKota KinabaluMalaysia
| | - Richard Rumpet
- Fisheries Research Institute, Sarawak, Department of Fisheries Malaysia, Kuching 93744, Sarawak, MalaysiaDepartment of Fisheries MalaysiaKuchingMalaysia
| | - Kar-Hoe Loh
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, MalaysiaUniversity of MalayaKuala LumpurMalaysia
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Demırtaş S, Silsüpür M, Searle JB, Bilton D, Gündüz İ. What should we call the Levant mole? Unravelling the systematics and demography of Talpa levantis Thomas, 1906 sensu lato (Mammalia: Talpidae). Mamm Biol 2020. [DOI: 10.1007/s42991-020-00010-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Deng JY, Fu RH, Compton SG, Liu M, Wang Q, Yuan C, Zhang LS, Chen Y. Sky islands as foci for divergence of fig trees and their pollinators in southwest China. Mol Ecol 2020; 29:762-782. [PMID: 31943487 DOI: 10.1111/mec.15353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 11/26/2019] [Accepted: 01/03/2020] [Indexed: 12/11/2022]
Abstract
The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the "sky islands" of mountainous southwest (SW) China have resulted in an area of exceptional botanical diversity. Ficus tikoua is a prostrate fig tree subendemic to the area that displays unique intraspecific diversity, producing figs typical of different pollination modes in different parts of its range. By combining climate models, genetic variation in populations of the tree's obligate fig wasp pollinators and distributions of the different plant phenotypes, we examined how this unusual situation may have developed. We identified three genetically distinct groups of a single Ceratosolen pollinator species that have largely parapatric distributions. The complex topography of the region contributed to genetic divergence among the pollinators by facilitating geographical isolation and providing refugia. Migration along elevations in response to climate oscillations further enhanced genetic differentiation of the three pollinator groups. Their distributions loosely correspond to the distributions of the functionally significant morphological differences in the male figs of their host plants, but postglacial expansion of one group has not been matched by spread of its associated plant phenotype, possibly due to a major river barrier. The results highlight how interplay between the complex topography of the "sky island" complex and climate change has shaped intraspecies differentiation and relationships between the plant and its pollinator. Similar processes may explain the exceptional botanical diversity of SW China.
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Affiliation(s)
- Jun-Yin Deng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China.,Division of Genetics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rong-Hua Fu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | | | - Mei Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Qin Wang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Chuan Yuan
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lu-Shui Zhang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
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Bartáková V, Nagy B, Polačik M, Blažek R, Lamtane H, Reichard M. Genetic diversity of a widespread annual killifish from coastal Tanzania. BMC Evol Biol 2020; 20:1. [PMID: 31906845 PMCID: PMC6943906 DOI: 10.1186/s12862-019-1549-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background African annual killifishes (Nothobranchius spp.) are adapted to seasonally desiccating habitats (ephemeral pools), surviving dry periods as dormant eggs. Given their peculiar life history, geographic aspects of their diversity uniquely combine patterns typical for freshwater taxa (river basin structure and elevation gradient) and terrestrial animals (rivers acting as major dispersal barriers). However, our current knowledge on fine-scale inter-specific and intra-specific genetic diversity of African annual fish is limited to a single, particularly dry region of their distribution (subtropical Mozambique). Using a widespread annual killifish from coastal Tanzania and Kenya, we tested whether the same pattern of genetic divergence pertains to a wet equatorial region in the centre of Nothobranchius distribution. Results In populations of Nothobranchius melanospilus species group across its range, we genotyped a part of mitochondrial cytochrome oxidase subunit 1 (COI) gene (83 individuals from 22 populations) and 10 nuclear microsatellite markers (251 individuals from 16 populations). We found five lineages with a clear phylogeographic structure but frequent secondary contact. Mitochondrial lineages were largely congruent with main population genetic clusters identified on microsatellite markers. In the upper Wami basin, populations are isolated as a putative Nothobranchius prognathus, but include also a population from a periphery of the middle Ruvu basin. Other four lineages (including putative Nothobranchius kwalensis) coexisted in secondary contact zones, but possessed clear spatial pattern. Main river channels did not form apparent barriers to dispersal. The most widespread lineage had strong signal of recent population expansion. Conclusions We conclude that dispersal of a Nothobranchius species from a wet part of the genus distribution (tropical lowland) is not constrained by main river channels and closely related lineages frequently coexist in secondary contact zones. We also demonstrate contemporary connection between the Ruvu and Rufiji river basins. Our data do not provide genetic support for existence of recently described cryptic species from N. melanospilus complex, but cannot resolve this issue.
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Affiliation(s)
- Veronika Bartáková
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic
| | | | - Matej Polačik
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic
| | - Radim Blažek
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic
| | - Hieromin Lamtane
- Department of Animal, Aquaculture and Range Sciences, Sokoine University of Agriculture, P.O. Box 3004, Morogoro, Tanzania
| | - Martin Reichard
- Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic.
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Arslan Y, Demi̇rtaş S, Herman JS, Pustilnik JD, Searle JB, Gündüz İ. The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.
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Affiliation(s)
- Yağmur Arslan
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Sadik Demi̇rtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Jeremy D Pustilnik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
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43
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Boo GH, Qiu YX, Kim JY, Ang PO, Bosch S, De Clerck O, He P, Higa A, Huang B, Kogame K, Liu SL, van Nguyen T, Suda S, Terada R, Miller KA, Boo SM. Contrasting patterns of genetic structure and phylogeography in the marine agarophytes Gelidiophycus divaricatus and G. freshwateri (Gelidiales, Rhodophyta) from East Asia. JOURNAL OF PHYCOLOGY 2019; 55:1319-1334. [PMID: 31390066 DOI: 10.1111/jpy.12910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.
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Affiliation(s)
- Ga Hun Boo
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jung Yeon Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Put O Ang
- Marine Science Laboratory, The Chinese University of Hong Kong, Shatin N.T, Hong Kong SAR, China
| | - Samuel Bosch
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000, Gent, Belgium
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 (S8), 9000, Gent, Belgium
| | - Peimin He
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Atsushi Higa
- Okinawa Environmental Analysis Center Co. Ltd, 3-7-24 Maehara, Ginowan, Okinawa, 901-2215, Japan
| | - Bangqin Huang
- Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Fujian, China
| | - Kazuhiro Kogame
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Shao-Lun Liu
- Department of Life Science, Tunghai University, Taichung, 40704, Taiwan
| | - Tu van Nguyen
- Department of Ecology, Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan, District 3, Ho Chi Minh City, Vietnam
| | - Shoichiro Suda
- Department of Chemistry, Biology & Marine Science, Faculty of Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - Ryuta Terada
- United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto 1-21-24, Kagoshima, 890-0065, Japan
| | - Kathy Ann Miller
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
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44
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Motoki MT, Fonseca DM, Miot EF, Demari-Silva B, Thammavong P, Chonephetsarath S, Phommavanh N, Hertz JC, Kittayapong P, Brey PT, Marcombe S. Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People's Democratic Republic. Parasit Vectors 2019; 12:477. [PMID: 31610813 PMCID: PMC6792217 DOI: 10.1186/s13071-019-3740-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/04/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. METHODS We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. RESULTS We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. CONCLUSIONS Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.
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Affiliation(s)
- Maysa Tiemi Motoki
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic. .,Vysnova Partners Inc., Landover, MD, USA. .,Walter Reed Biosystematics Unit, Smithsonian Institution, Museum Support Center, MRC-534, Suitland, MD, 20746, USA.
| | - Dina Madera Fonseca
- Center for Vector Biology and Department of Entomology, Rutgers University, New Brunswick, NJ, USA
| | - Elliott Frederic Miot
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic.,Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France.,Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France
| | - Bruna Demari-Silva
- Department of Epidemiology, Faculty of Public Health, University of Sao Paulo, Sao Paulo, Brazil
| | - Phoutmany Thammavong
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic
| | - Somsanith Chonephetsarath
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic
| | - Nothasine Phommavanh
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic
| | | | | | - Paul Trevor Brey
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic
| | - Sebastien Marcombe
- Medical Entomology and Vector Borne Disease Unit, Institut Pasteur du Laos, Vientiane, Lao People's Democratic Republic
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45
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Williams DA, Rains ND, Hale AM. Population genetic structure of Texas horned lizards: implications for reintroduction and captive breeding. PeerJ 2019; 7:e7746. [PMID: 31592183 PMCID: PMC6777493 DOI: 10.7717/peerj.7746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/25/2019] [Indexed: 11/20/2022] Open
Abstract
The Texas horned lizard (Phrynosoma cornutum) inhabits much of the southern Great Plains of North America. Since the 1950s, this species has been extirpated from much of its eastern range and has suffered declines and local extinctions elsewhere, primarily due to habitat loss. Plans are underway to use captive breeding to produce large numbers of Texas horned lizards for reintroduction into areas that were historically occupied by this species and that currently have suitable habitat. We used mitochondrial markers and nuclear microsatellite markers to determine levels of genetic diversity and population structure in 542 Texas horned lizards sampled from across Texas and some neighboring states to help inform these efforts. Texas horned lizards still retain high genetic diversity in many parts of their current range. We found two highly divergent mitochondrial clades (eastern and western) and three major genetic groupings at nuclear microsatellite loci: a west group corresponding to the western mitochondrial clade and north and south groups within the eastern mitochondrial clade. We also found some evidence for human-mediated movement between these genetic clusters that is probably related to the historical importance of this species in the pet trade and as an iconic symbol of the southwestern United States. We do not know, however, if there are fitness costs associated with admixture (especially for the western and eastern clades) or if there are fitness costs to moving these lizards into habitats that are distinctly different from their ancestral areas. If present, either one or both of these fitness costs would decrease the effectiveness of reintroduction efforts. We therefore recommend that reintroduction efforts should maintain current genetic structure by restricting breeding to be between individuals within their respective genetic clusters, and by reintroducing individuals only into those areas that encompass their respective genetic clusters. This cautionary approach is based on the strong divergence between genetic groupings and their correspondence to different ecoregions.
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Affiliation(s)
- Dean A Williams
- Department of Biology, Texas Christian University, Fort Worth, TX, United States of America
| | - Nathan D Rains
- Texas Parks and Wildlife Department, Cleburne, TX, United States of America
| | - Amanda M Hale
- Department of Biology, Texas Christian University, Fort Worth, TX, United States of America
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46
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Zhang X, Zhang X, Song N, Gao T, Zhao L. Study on population genetics of Sillago aeolus (Perciformes: Sillaginidae) in the Coast of China. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:825-834. [PMID: 31571512 DOI: 10.1080/24701394.2019.1670820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Sillago aeolus is a species from Sillaginidae, which is a widely distributed species with important scientific and economic value in the coast of China. Its population genetics have not been studied. This study investigated the population genetics of S. aeolus in the eastern and southern coast of China based on the mitochondrial control region markers obtained from 248 individuals of 9 locations. The population was characterized by a high population diversity with a low nucleotide diversity. There were no branches corresponding to the sampling sites according to the haplotype network and NJ tree. Recent asymmetric gene flow exchanges and significant genetic differences were detected between the Haikou population and the other populations. AMOVA result indicated slight genetic structures with homogeneity suggested. The neutral test and the mismatch distribution revealed a recent population expansion event. Historical geographic events may be the reason for the homogeneity within the population.
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Affiliation(s)
- Xiaomeng Zhang
- Fisheries College, Ocean University of China, Qingdao, China
| | - Xiumei Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, National Laboratory for Marine Science and Technology, Qingdao, China.,Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Na Song
- Fisheries College, Ocean University of China, Qingdao, China
| | - Tianxiang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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47
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Skurikhina LA, Oleinik AG, Kukhlevsky AD, Novoselov AP, Sendek DS. Molecular Genetic Analysis of the Relationships and Origin of Smelt (Hypomesus, Osmeridae), a New Component of the Fauna of the Barents Sea. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Asgharzadeh A, Kaboli M, Rajabi-Maham H, Naderi M. Phylogeny and genetic structure of the Yellow ground squirrel, Spermophilus fulvus (Lichtenstein, 1823), in Iran. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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49
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Li J, Jin Q, Zhu G, Jiang C, Zhang A. Phylogeography of Dendrolimus punctatus (Lepidoptera: Lasiocampidae): Population differentiation and last glacial maximum survival. Ecol Evol 2019; 9:7480-7496. [PMID: 31346417 PMCID: PMC6635939 DOI: 10.1002/ece3.5278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 11/10/2022] Open
Abstract
Although the Masson pine moth, Dendrolimus punctatus, is one of the most destructive forest pest insects and is an endemic condition in China, we still do not fully understand the patterns of how its distribution range varies in response to Quaternary climatic oscillations. Here, we sequenced one maternally inherited mitochondrial gene (COI) and biparentally inherited nuclear data (ITS1 and ITS2) among 23 natural populations across the entire range of the species in China. A total of 51 mitotypes and 38 ribotypes were separately obtained using mtDNA and ITS1 data. Furthermore, significant phylogeographical structure (N ST > G ST, p < 0.01) were detected. The spatial distribution of mitotypes implied that two distinct groups existed in the species: one in the southwest distribution, including 10 locations, and the other located in the northeast region of China. It is suggested, therefore, that each group was derived from ancestors that occupied different isolated refugia during previous periods, possibly last glacial maximum. Mismatch distribution and Bayesian population dynamics analysis suggested the population size underwent sudden expansion, which is consistent with the results of ecological niche modeling. As a typical phytophagous insect, the history of population expansion was in accordance with the host plants, providing abundant food resources and habitat. Intraspecific success rate of barcoding identification was lower than interspecific ones, indicating a level of difficulty in barcoding individuals from different populations. However, it still provides an early insight into the pattern of genetic diversity within a species. OPEN RESEARCH BADGES This article has been awarded an Open Data and Open Materials. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.2df87g2. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
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Affiliation(s)
- Jing Li
- College of Life SciencesCapital Normal UniversityBeijingChina
| | - Qian Jin
- College of Life SciencesCapital Normal UniversityBeijingChina
- Suqian Institute of Agricultural SciencesJiangsu Academy of Agricultural SciencesSuqianChina
| | - Geng‐ping Zhu
- College of Life SciencesTianjin Normal UniversityTianjinChina
| | - Chong Jiang
- College of Life SciencesCapital Normal UniversityBeijingChina
| | - Ai‐bing Zhang
- College of Life SciencesCapital Normal UniversityBeijingChina
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50
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Van Nieuwenhove AHM, Ratsimbazafy HA, Kochzius M. Cryptic diversity and limited connectivity in octopuses: Recommendations for fisheries management. PLoS One 2019; 14:e0214748. [PMID: 31083669 PMCID: PMC6513052 DOI: 10.1371/journal.pone.0214748] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/19/2019] [Indexed: 11/19/2022] Open
Abstract
The market demand for octopus grows each year, but landings are decreasing, and prices are rising. The present study investigated (1) diversity of Octopodidae in the Western Indian Ocean (WIO) and (2) connectivity and genetic structure of Octopus cyanea and O. vulgaris populations in order to obtain baseline data for management plans. A fragment of the cytochrome C oxidase subunit 1 (COI) gene was sequenced in 275 octopus individuals from Madagascar, Kenya and Tanzania. In addition, 41 sequences of O. vulgaris from South Africa, Brazil, Amsterdam Island, Tristan da Cunha, Senegal and Galicia were retrieved from databases and included in this study. Five different species were identified using DNA barcoding, with first records for O. oliveri and Callistoctopus luteus in the WIO. For O. cyanea (n = 229, 563 bp), 22 haplotypes were found, forming one haplogroup. AMOVA revealed shallow but significant genetic population structure among all sites (ϕST = 0.025, p = 0.02), with significant differentiation among: (1) Kanamai, (2) southern Kenya, Tanzania, North and West Madagascar, (3) Southwest Madagascar and (4) East Madagascar (ϕCT = 0.035, p = 0.017). For O. vulgaris (n = 71, 482 bp), 15 haplotypes were identified, forming three haplogroups. A significant genetic population structure was found among all sites (ϕST = 0.82, p ≤ 0.01). Based on pairwise ϕST-values and hierarchical AMOVAs, populations of O. vulgaris could be grouped as follows: (1) Brazil, (2) Madagascar and (3) all other sites. A significant increase in genetic distance with increasing geographic distance was found (Z = 232443, 81 r = 0.36, p = 0.039). These results indicate that for O. cyanea four regions should be considered as separate management units in the WIO. The very divergent haplogroups in O. vulgaris from Brazil and Madagascar might be evolving towards speciation and therefore should be considered as separate species in FAO statistics.
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Affiliation(s)
| | | | - Marc Kochzius
- Marine Biology, Ecology and Biodiversity, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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