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Cunningham-Eurich I, Kontou D, Yordanova M, Maeda-Obregon A, Favreau E, Wang J, Hart AG, Sumner S. Using citizen science data to assess the population genetic structure of the common yellowjacket wasp, Vespula vulgaris. INSECT MOLECULAR BIOLOGY 2023; 32:634-647. [PMID: 37599385 DOI: 10.1111/imb.12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/22/2023] [Indexed: 08/22/2023]
Abstract
Monitoring insect genetic diversity and population structure has never been more important to manage the biodiversity crisis. Citizen science has become an increasingly popular tool to gather ecological data affordably across a wide range of spatial and temporal scales. To date, most insect-related citizen science initiatives have focused on occurrence and abundance data. Here, we show that poorly preserved insect samples collected by citizen scientists can yield population genetic information, providing new insights into population connectivity, genetic diversity and dispersal behaviour of little-studied insects. We analysed social wasps collected by participants of the Big Wasp Survey, a citizen science project that aims to map the diversity and distributions of vespine wasps in the UK. Although Vespula vulgaris is a notorious invasive species around the world, it remains poorly studied in its native range. We used these data to assess the population genetic structure of the common yellowjacket V. vulgaris at different spatial scales. We found a single, panmictic population across the UK with little evidence of population genetic structuring; the only possible limit to gene flow is the Irish sea, resulting in significant differentiation between the Northern Ireland and mainland UK populations. Our results suggest that queens disperse considerable distances from their natal nests to found new nests, resulting in high rates of gene flow and thus little differentiation across the landscape. Citizen science data has made it feasible to perform this study, and we hope that it will encourage future projects to adopt similar practices in insect population monitoring.
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Affiliation(s)
- Iona Cunningham-Eurich
- Centre for Biodiversity and Environment Research, University College London, London, UK
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Danai Kontou
- Centre for Biodiversity and Environment Research, University College London, London, UK
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Monika Yordanova
- Centre for Biodiversity and Environment Research, University College London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Emeline Favreau
- Centre for Biodiversity and Environment Research, University College London, London, UK
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, London, UK
| | - Adam G Hart
- Department of Natural and Social Science, University of Gloucestershire, UK
| | - Seirian Sumner
- Centre for Biodiversity and Environment Research, University College London, London, UK
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Wang G, Gao J, Ma Z, Liu Y, Wang M, Xing D, Li C, Guo X, Zhao T, Jiang Y, Dong Y, Zhang H, Zhao T. Population genetic characteristics of Aedes aegypti in 2019 and 2020 under the distinct circumstances of dengue outbreak and the COVID-19 pandemic in Yunnan Province, China. Front Genet 2023; 14:1107893. [PMID: 36968606 PMCID: PMC10033842 DOI: 10.3389/fgene.2023.1107893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Introduction: Since Aedes aegypti invaded Yunnan Province in 2002, its total population has continued to expand. Shi et al. used microsatellite and mitochondrial molecular markers to study the Ae. aegypti populations in Yunnan Province in 2015 and 2016, found that it showed high genetic diversity and genetic structure. However, there are few studies on the population genetic characteristics of Ae. aegypti in Yunnan Province under different levels of human intervention. This study mainly used two common types of molecular markers to analyze the genetic characteristics of Ae. aegypti, revealing the influence of different input, prevention and control pressures on the genetic diversity and structure of this species. Understanding the genetic characteristics of Ae. aegypti populations and clarifying the diversity, spread status, and source of invasion are essential for the prevention, control and elimination of this disease vector.Methods: We analyzed the genetic diversity and genetic structure of 22 populations sampled in Yunnan Province in 2019 and 17 populations sampled in 2020 through nine microsatellite loci and COI and ND4 fragments of mitochondrial DNA. In 2019, a total of 22 natural populations were obtained, each containing 30 samples, a total of 660 samples. In 2020, a total of 17 natural populations were obtained. Similarly, each population had 30 samples, and a total of 510 samples were obtained.Results: Analysis of Ae. aegypti populations in 2019 and 2020 based on microsatellite markers revealed 67 and 72 alleles, respectively. The average allelic richness of the populations in 2019 was 3.659, while that in 2020 was 3.965. The HWE analysis of the 22 populations sampled in 2019 revealed significant departure only in the QSH-2 population. The 17 populations sampled in 2020 were all in HWE. The average polymorphic information content (PIC) values were 0.546 and 0.545, respectively, showing high polymorphism. The average observed heterozygosity of the 2019 and 2020 populations was 0.538 and 0.514, respectively, and the expected average heterozygosity was 0.517 and 0.519, showing high genetic diversity in all mosquito populations. By analyzing the COI and ND4 fragments in the mitochondrial DNA of Ae. aegypti, the populations sampled in 2019 had a total of 10 COI haplotypes and 17 ND4 haplotypes. A total of 20 COI haplotypes were found in the populations sampled in 2020, and a total of 24 ND4 haplotypes were obtained. STRUCTURE, UPGMA and DAPC cluster analyses and a network diagram constructed based on COI and ND4 fragments showed that the populations of Ae. aegypti in Yunnan Province sampled in 2019 and 2020 could be divided into two clusters. At the beginning of 2020, due to the impact of COVID-19, the flow of goods between the port areas of Yunnan Province and neighboring countries was reduced, and the sterilization was more effective when goods enter the customs, leading to different immigration pressures on Ae. aegypti population in Yunnan Province between 2019 and 2020, the source populations of the 2019 and 2020 populations changed. Mantel test is generally used to detect the correlation between genetic distance and geographical distance, the analysis indicated that population geographic distance and genetic distance had a moderately significant correlation in 2019 and 2020 (2019: p < 0.05 R2 = 0.4807, 2020: p < 0.05 R2 = 0.4233).Conclusion:Ae. aegypti in Yunnan Province maintains a high degree of genetic diversity. Human interference is one reason for the changes in the genetic characteristics of this disease vector.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Tongyan Zhao
- *Correspondence: Hengduan Zhang, ; Tongyan Zhao,
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Griciuvienė L, Janeliūnas Ž, Pilevičienė S, Jurgelevičius V, Paulauskas A. Changes in the Genetic Structure of Lithuania's Wild Boar ( Sus scrofa) Population Following the Outbreak of African Swine Fever. Genes (Basel) 2022; 13:1561. [PMID: 36140730 PMCID: PMC9498859 DOI: 10.3390/genes13091561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence of African swine fever (ASF) in Lithuania and its subsequent persistence has led to a decline in the population of wild boar (Sus scrofa). ASF has been spreading in Lithuania since its introduction, therefore it is important to understand any genetic impact of ASF outbreaks on wild boar populations. The aim of this study was to assess how the propensity for an outbreak has shaped genetic variation in the wild boar population. A total of 491 wild boar samples were collected and genotyped using 16 STR markers. Allele richness varied between 15 and 51, and all SSR loci revealed a significant deviation from the Hardy-Weinberg equilibrium. Fixation indices indicated a significant reduction in heterozygosity within and between subpopulations. PCoA and STRUCTURE analysis demonstrated genetic differences between the western region which had had no outbreaks (restricted zone I) and the region with ASF infection (restricted zones II and III). It is concluded that environmental factors may play a particular role in shaping the regional gene flow and influence the genetic structure of the wild boar population in the region with ASF outbreaks.
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Affiliation(s)
- Loreta Griciuvienė
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
| | - Žygimantas Janeliūnas
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
- National Food and Veterinary Risk Assessment Institute, J. Kairiūkščio 10, 08409 Vilnius, Lithuania
| | - Simona Pilevičienė
- National Food and Veterinary Risk Assessment Institute, J. Kairiūkščio 10, 08409 Vilnius, Lithuania
| | - Vaclovas Jurgelevičius
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
| | - Algimantas Paulauskas
- Faculty of Natural Sciences, Vytautas Magnus University, K. Donelaičio 58, 44248 Kaunas, Lithuania
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Li Y, Li M, Xing T, Liu J. Resolving the origins of invertebrate colonists in the Yangtze River Estuary with molecular markers: Implications for ecological connectivity. Ecol Evol 2021; 11:13898-13911. [PMID: 34707826 PMCID: PMC8525129 DOI: 10.1002/ece3.8095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding connectivity over different spatial and temporal scales is fundamental for managing of ecological systems. However, controversy exists for wintertime ecological connectivity between the Yangtze River Estuary (YRE) and inner southwestern Yellow Sea. Here, we investigated ecological connectivity between the YRE and inner southwestern Yellow Sea in wintertime by precisely pinpointing the source of the newly colonized populations of a winter-spawning rocky intertidal invertebrate, Littorina brevicula (Philippi, 1844), on artificial structures along the coast of the Yangtze River Delta (YRD) using mitochondrial ND6 sequences and microsatellite data. Clear phylogeographic and genetic differentiation were detected between natural rocky populations south and north of the YRE, which resulted from the lack of hard substrate for rocky invertebrates in the large YRD coast. For the newly colonized populations on the coast of YRD, most individuals (98%) to the south of ~33.5°N were from natural rocky populations to the south of the YRE and most of those (94%) to the north of ~33.5°N were from the northern natural rocky populations, which demonstrated strong ecological connectivity between the inner southwestern Yellow Sea and the YRE in winter time. We presented the first genetic evidence that demonstrated a northward wintertime coastal current in the inner southwestern Yellow Sea, and precisely illustrated the boundary of the coastal current recently proposed by numerical experiment. These results indicated that the YRE serves as an important source of materials and energy for the inner southwestern Yellow Sea in winter, which can be crucial for the function of the Yellow Sea ecosystem.
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Affiliation(s)
- Yu‐Qiang Li
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Meng‐Yu Li
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Teng‐Fei Xing
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jin‐Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of OceanologyChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Ecology and Environmental ScienceQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
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Chew PC, Christianus A, Zudaidy JM, Ina-Salwany MY, Chong CM, Tan SG. Microsatellite Characterization of Malaysian Mahseer ( Tor spp.) for Improvement of Broodstock Management and Utilization. Animals (Basel) 2021; 11:ani11092633. [PMID: 34573599 PMCID: PMC8471032 DOI: 10.3390/ani11092633] [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: 04/28/2021] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei's genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.
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Affiliation(s)
- Poh Chiang Chew
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Annie Christianus
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: ; Tel.: +60-3-8947-4884
| | - Jaapar M. Zudaidy
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Md Yasin Ina-Salwany
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Chou Min Chong
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
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Thintip J, Singchat W, Ahmad SF, Ariyaraphong N, Muangmai N, Chamchumroon W, Pitiwong K, Suksavate W, Duangjai S, Duengkae P, Srikulnath K. Reduced genetic variability in a captive-bred population of the endangered Hume's pheasant (Syrmaticus humiae, Hume 1881) revealed by microsatellite genotyping and D-loop sequencing. PLoS One 2021; 16:e0256573. [PMID: 34449789 PMCID: PMC8396778 DOI: 10.1371/journal.pone.0256573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Captive breeding programs are crucial to ensure the survival of endangered species and ultimately to reintroduce individuals into the wild. However, captive-bred populations can also deteriorate due to inbreeding depression and reduction of genetic variability. We genotyped a captive population of 82 individuals of the endangered Hume's pheasant (Syrmaticus humiae, Hume 1881) at the Doi Tung Wildlife Breeding Center to assess the genetic consequences associated with captive breeding. Analysis of microsatellite loci and mitochondrial D-loop sequences reveal significantly reduced genetic differentiation and a shallow population structure. Despite the low genetic variability, no bottleneck was observed but 12 microsatellite loci were informative in reflecting probable inbreeding. These findings provide a valuable source of knowledge to maximize genetic variability and enhance the success of future conservation plans for captive and wild populations of Hume's pheasant.
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Affiliation(s)
- Jitmat Thintip
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Nattakan Ariyaraphong
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
- Faculty of Fisheries, Department of Fishery Biology, Kasetsart University, Bangkok, Thailand
| | - Wiyada Chamchumroon
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Klinsak Pitiwong
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Warong Suksavate
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
| | - Sutee Duangjai
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
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Porto-Hannes I, Burlakova LE, Zanatta DT, Lasker HR. Boundaries and hybridization in a secondary contact zone between freshwater mussel species (Family:Unionidae). Heredity (Edinb) 2021; 126:955-973. [PMID: 33883699 PMCID: PMC8178349 DOI: 10.1038/s41437-021-00424-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Correct species identification and delineation are crucial for effective conservation and management. However, species delineation can be problematic in the presence of morphological ambiguities due to phenotypic plasticity, convergence, and/or interspecific hybridization. Here, we investigated the degree of hybridization between two closely related freshwater mussel species [Bivalvia: Unionidae; Lampsilis siliquoidea (Barnes) and L. radiata (Gmelin)] that present intermediate forms in areas of sympatry. Unionids have a distinct form of mitochondrial DNA (mtDNA) inheritance, termed doubly uniparental inheritance (DUI) where female mtDNA (F-type) is transmitted to all progeny but male mtDNA (M-type) is mostly inherited by the males resulting in mostly homoplasmic females and heteroplasmic males. An individual was identified as hybrid when F-type and M-type mtDNA of the two different species were found in the same individual. Twelve out of 116 sequenced males were identified as hybrids indicating that these species hybridize where their geographic range overlaps in the lower Great Lakes and St. Lawrence basins. Microsatellite analyses further support the occurrence of hybridization but at a larger spatial scale than indicated by the mitochondrial analyses. We also found that strong within-species population genetic structure affects the detection of purebred individuals overestimating the number of hybrids. Given the large geographic scale and proportion of hybrids found in this study, natural hybridization and introgression need to be considered when implementing local biodiversity inventories, identifying waterbodies as source of organisms for relocation and restoration projects and when setting appropriate conservation policies.
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Affiliation(s)
- Isabel Porto-Hannes
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA.
| | | | - David T Zanatta
- Institute for Great Lakes Research, Biology Department, Central Michigan University, Mount Pleasant, MI, USA
| | - Howard R Lasker
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA
- Department of Environment and Sustainability, University at Buffalo, Buffalo, NY, USA
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Gao J, Zhang HD, Guo XX, Xing D, Dong YD, Lan CJ, Wang G, Li CJ, Li CX, Zhao TY. Dispersal patterns and population genetic structure of Aedes albopictus (Diptera: Culicidae) in three different climatic regions of China. Parasit Vectors 2021; 14:12. [PMID: 33407824 PMCID: PMC7789686 DOI: 10.1186/s13071-020-04521-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022] Open
Abstract
Background Aedes albopictus is an indigenous primary vector for dengue and Zika viruses in China. Compared with its insecticide resistance, biology and vector competence, little is known about its genetic variation, which corresponds to environmental variations. Thus, the present study examines how Ae. albopictus varies among different climatic regions in China and deciphers its potential dispersal patterns. Methods The genetic variation and population structure of 17 Ae. albopictus populations collected from three climatic regions of China were investigated with 11 microsatellite loci and the mitochondrial coxI gene. Results Of 44 isolated microsatellite markers, 11 pairs were chosen for genotyping analysis and had an average PIC value of 0.713, representing high polymorphism. The number of alleles was high in each population, with the ne value increasing from the temperate region (3.876) to the tropical region (4.144). Twenty-five coxI haplotypes were detected, and the highest diversity was observed in the tropical region. The mean Ho value (ca. 0.557) of all the regions was significantly lower than the mean He value (ca. 0.684), with nearly all populations significantly departing from HWE and displaying significant population expansion (p value < 0.05). Two genetically isolated groups and three haplotype clades were evaluated via STRUCTURE and haplotype phylogenetic analyses, and the tropical populations were significantly isolated from those in the other regions. Most genetic variation in Ae. albopictus was detected within populations and individuals at 31.40 and 63.04%, respectively, via the AMOVA test, and a relatively significant positive correlation was observed among only the temperate populations via IBD analysis (R2 = 0.6614, p = 0.048). Recent dispersions were observed among different Ae. albopictus populations, and four major migration trends with high gene flow (Nm > 0.4) were reconstructed between the tropical region and the other two regions. Environmental factors, especially temperature and rainfall, may be the leading causes of genetic diversity in different climatic regions. Conclusions Continuous dispersion contributes to the genetic communication of Ae. albopictus populations across different climatic regions, and environmental factors, especially temperature and rainfall, may be the leading causes of genetic variation. Graphical abstract ![]()
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Affiliation(s)
- Jian Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Heng-Duan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xiao-Xia Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yan-De Dong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ce-Jie Lan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ge Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Chao-Jie Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Chun-Xiao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Tong-Yan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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Cruz A, da Costa F, Fernández-Pérez J, Nantón A, Fernández-Boo S, Insua A, Méndez J. Genetic variability in Ruditapes decussatus clam combined with Perkinsus infection level to support founder population selection for a breeding program. PeerJ 2020; 8:e9728. [PMID: 33194343 PMCID: PMC7602687 DOI: 10.7717/peerj.9728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/24/2020] [Indexed: 11/20/2022] Open
Abstract
Clam farmers worldwide face several challenges, including irregular seed supply and high mortalities due to pathogenic organisms such as Perkinsus olseni. In Europe, there is a high unmet consumer demand for native clam species such as Ruditapes decussatus. The high market value of R. decussatus makes the culture of this species potentially more attractive than that culture of the alien species Ruditapes philippinarum. Thus, there is a market opportunity in breeding and producing R. decussatus at an industrial scale. A selective breeding program to improve R. decussatus performance will be carried out in Portugal; and the first critical step to develop such a breeding program is the establishment of a founder population. In this study, intra- and interpopulation genetic diversity was assessed using 13 microsatellite markers in eight natural beds located in Portugal, Spain and Italy. Also, allele and genotypic frequencies of each microsatellite locus were assessed discriminating between clams infected and non-infected by P. olseni. All locations showed similar values for several genetic diversity parameters. Analyses of population differentiation (FST, Bayesian clustering and AMOVAs) revealed five genetically differentiated regions: Rías Altas and Rías Baixas (NW Spain), North/Central Coast of Portugal, Gulf of Cadiz and Adriatic Sea. Significant differences in the allelic and genotypic frequency distribution between infected clams and non-infected ones at four microsatellite loci are reported suggesting that resistance to the disease could have a genetic basis. Moreover, a positive or negative relationship between the frequency of certain alleles and the parasite infection was inferred. Further studies should confirm the potential use of those alleles as genetic markers for P. olseni infection. Integrating results of genetic diversity within and between populations and Perkinsus infection levels, a founder population for a R. decussatus breeding program is proposed, composed by individuals from Barallobre (Rías Altas), Pontevedra or Cangas (Rías Baixas), Óbidos (North/Central Coast of Portugal), Algarve (Gulf of Cadiz) and Venice (Adriatic Sea).
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Affiliation(s)
| | | | - Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
| | - Ana Nantón
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
| | - Sergio Fernández-Boo
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Matosinhos, Portugal
| | - Ana Insua
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Biología, Facultade de Ciencias and Centro de Investigación Científicas Avanzadas (CICA), Universidad de La Coruña, A Coruña, Spain
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10
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Rudd JL, Clifford DL, Cypher BL, Hull JM, Jane Riner A, Foley JE. Molecular epidemiology of a fatal sarcoptic mange epidemic in endangered San Joaquin kit foxes (Vulpes macrotis mutica). Parasit Vectors 2020; 13:456. [PMID: 32894172 PMCID: PMC7487715 DOI: 10.1186/s13071-020-04328-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/30/2020] [Indexed: 11/22/2022] Open
Abstract
Background In 2013, sarcoptic mange, caused by Sarcoptes scabiei mites, precipitated a catastrophic decline of the formerly stable urban population of endangered San Joaquin kit foxes (Vulpes macrotis mutica) in Bakersfield, California, USA. In 2019, a smaller sarcoptic mange outbreak affected kit foxes 58 km southwest of Bakersfield in the town of Taft, California. To determine whether the Taft outbreak could have occurred as spillover from the Bakersfield outbreak and whether epidemic control efforts must involve not only kit foxes but also sympatric dogs (Canis lupus familiaris), coyotes (Canis latrans), and red foxes (Vulpes vulpes), we evaluated genotypes and gene flow among mites collected from each host species. Methods We used 10 Sarcoptes microsatellite markers (SARM) to perform molecular typing of 445 S. scabiei mites collected from skin scrapings from twenty-two infested kit foxes, two dogs, five coyotes, and five red foxes from Bakersfield, Taft, and other nearby cities. Results We identified 60 alleles across all SARM loci; kit fox- and red fox-derived mites were relatively monomorphic, while genetic variability was greatest in Bakersfield coyote- and dog-derived mites. AMOVA analysis documented distinct mite populations unique to hosts, with an overall FST of 0.467. The lowest FST (i.e. closest genetic relationship, FST = 0.038) was between Bakersfield and Taft kit fox-derived mites while the largest genetic difference was between Ventura coyote- and Taft kit fox-derived mites (FST = 0.843). Conclusions These results confirm the close relationship between the Taft and Bakersfield outbreaks. Although a spillover event likely initiated the kit fox mange outbreak, mite transmission is now primarily kit fox-to-kit fox. Therefore, any large-scale population level intervention should focus on treating kit foxes within the city.![]()
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Affiliation(s)
- Jaime L Rudd
- Department of Medicine and Epidemiology, University of California, Davis, CA, 95616, USA. .,Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA, 95670, USA.
| | - Deana L Clifford
- Department of Medicine and Epidemiology, University of California, Davis, CA, 95616, USA.,Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA, 95670, USA
| | - Brian L Cypher
- Endangered Species Recovery Program, California State University, Stanislaus, Turlock, CA, 95382, USA
| | - Joshua M Hull
- United States Fish and Wildlife Service, Sacramento, CA, 95825, USA
| | - A Jane Riner
- Department of Medicine and Epidemiology, University of California, Davis, CA, 95616, USA.,Wildlife Investigations Laboratory, California Department of Fish and Wildlife, Rancho Cordova, CA, 95670, USA
| | - Janet E Foley
- Department of Medicine and Epidemiology, University of California, Davis, CA, 95616, USA
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11
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Mohan AV, Orozco-terWengel P, Shanker K, Vences M. The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure. Sci Rep 2020; 10:11745. [PMID: 32678130 PMCID: PMC7367275 DOI: 10.1038/s41598-020-68402-7] [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: 10/19/2019] [Accepted: 06/15/2020] [Indexed: 11/20/2022] Open
Abstract
The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus Phelsuma, and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name ‘North’ (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and ‘South’ (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.
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Affiliation(s)
- Ashwini V Mohan
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany. .,Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India.
| | | | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany
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12
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Jangtarwan K, Kamsongkram P, Subpayakom N, Sillapaprayoon S, Muangmai N, Kongphoemph A, Wongsodchuen A, Intapan S, Chamchumroon W, Safoowong M, Peyachoknagul S, Duengkae P, Srikulnath K. Predictive genetic plan for a captive population of the Chinese goral (Naemorhedus griseus) and prescriptive action for ex situ and in situ conservation management in Thailand. PLoS One 2020; 15:e0234064. [PMID: 32497115 PMCID: PMC7272075 DOI: 10.1371/journal.pone.0234064] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/17/2020] [Indexed: 12/26/2022] Open
Abstract
Captive breeding programs for endangered species can increase population numbers for eventual reintroduction to the wild. Captive populations are typically small and isolated, which results in inbreeding and reduction of genetic variability, and may lead to an increased risk of extinction. The Omkoi Wildlife Breeding Center maintains the only Thai captive Chinese goral (Naemorhedus griseus) population, and has plans to reintroduce individuals into natural isolated populations. Genetic variability was assessed within the captive population using microsatellite data. Although no bottleneck was observed, genetic variability was low (allelic richness = 7.091 ± 0.756, He = 0.455 ± 0.219; He < Ho) and 11 microsatellite loci were informative that likely reflect inbreeding. Estimates of small effective population size and limited numbers of founders, combined with wild-born individuals within subpopulations, tend to cause reduction of genetic variability over time in captive programs. This leads to low reproductive fitness and limited ability to adapt to environmental change, thereby increasing the risk of extinction. Management of captive populations as evolutionarily significant units with diverse genetic backgrounds offers an effective strategy for population recovery. Relocation of individuals among subpopulations, or introduction of newly captured wild individuals into the captive program will help to ensure the future security of Chinese goral. Implications for future conservation actions for the species are discussed herein.
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Affiliation(s)
- Kornsuang Jangtarwan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Peerapong Kamsongkram
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Navapong Subpayakom
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Adisorn Kongphoemph
- Deparment of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Apinya Wongsodchuen
- Deparment of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Sanya Intapan
- Deparment of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Wiyada Chamchumroon
- Deparment of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Mongkol Safoowong
- Deparment of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand (CASTNAR, NRU-KU, Thailand)
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, Thailand (CASTNAR, NRU-KU, Thailand)
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand
- Amphibian Research Center, Hiroshima University, Kagamiyama, Higashihiroshima, Japan
- * E-mail:
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13
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Austrich A, Mora MS, Mapelli FJ, Fameli A, Kittlein MJ. Influences of landscape characteristics and historical barriers on the population genetic structure in the endangered sand-dune subterranean rodent Ctenomys australis. Genetica 2020; 148:149-164. [PMID: 32451787 DOI: 10.1007/s10709-020-00096-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/20/2020] [Indexed: 11/29/2022]
Abstract
Understanding the processes and patterns of local adaptation and migration involves an exhaustive knowledge of how landscape features and population distances shape the genetic variation at the geographical level. Ctenomys australis is an endangered subterranean rodent characterized by having a restricted geographic range immerse in a highly fragmented sand dune landscape in the Southeast of Buenos Aires province, Argentina. We use 13 microsatellite loci in a total of 194 individuals from 13 sampling sites to assess the dispersal patterns and population structure in the complete geographic range of this endemic species. Our analyses show that populations are highly structured with low rates of gene flow among them. Genetic differentiation among sampling sites was consistent with an isolation by distance pattern, however, an important fraction of the population differentiation was explained by natural barriers such as rivers and streams. Although the individuals were sampled at locations distanced from each other, we also use some landscape genetics approaches to evaluate the effects of landscape configuration on the genetic connectivity among populations. These analyses showed that the sand dune habitat availability (the most suitable habitat for the occupation of the species), was one of the main factors that explained the differentiation patterns of the different sampling sites located on both sides of the Quequén Salado River. Finally, habitat availability was directly associated with the width of the sand dune landscape in the Southeast of Buenos Aires province, finding the greatest genetic differentiation among the populations of the Northeast, where this landscape is narrower.
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Affiliation(s)
- Ailin Austrich
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina.
| | - Matías S Mora
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina
| | - Fernando J Mapelli
- Grupo de Genética y Ecología Para la Conservación de la Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Alberto Fameli
- Grupo de Genética y Ecología Para la Conservación de la Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", CONICET, Ángel Gallardo 470, Buenos Aires, Argentina
| | - Marcelo J Kittlein
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET),, Universidad Nacional de Mar del Plata, Funes 3250, 3th Floor, 7600, Mar del Plata, Argentina
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14
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Barros J, Winkler FM, Velasco LA. Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: Effect of null alleles. Ecol Evol 2020; 10:3919-3931. [PMID: 32489620 PMCID: PMC7244797 DOI: 10.1002/ece3.6080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 11/15/2022] Open
Abstract
Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1,010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79, and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null allele frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity and indicate that null alleles were not the only cause of deviation from H-W equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlund effect.
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Affiliation(s)
- Judith Barros
- Laboratorio de Moluscos y MicroalgasUniversidad del MagdalenaSanta MartaColombia
| | - Federico M. Winkler
- Departamento de Biología MarinaFacultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
- Centro de Innovación Acuícola AquaPacíficoCoquimboChile
- Centro de Estudios Avanzados en Zona Áridas (CEAZA)CoquimboChile
| | - Luz Adriana Velasco
- Laboratorio de Moluscos y MicroalgasUniversidad del MagdalenaSanta MartaColombia
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15
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Aiello D, Ferradini N, Torelli L, Volpi C, Lambalk J, Russi L, Albertini E. Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare. PLANTS (BASEL, SWITZERLAND) 2020; 9:E175. [PMID: 32024130 PMCID: PMC7076658 DOI: 10.3390/plants9020175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/30/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites-also known as simple sequence repeats (SSRs)-are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.
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Affiliation(s)
- Domenico Aiello
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Nicoletta Ferradini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Lorenzo Torelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Chiara Volpi
- Enza Zaden Italia Research S.r.l. SS., 01016 Tarquinia, Italy;
| | - Joep Lambalk
- Enza Zaden, Research and Development B.V. P.O. Box 7, 1600AA Enkhuizen, The Netherlands;
| | - Luigi Russi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (D.A.); (N.F.); (L.T.); (L.R.)
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16
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Fox G, Preziosi RF, Antwis RE, Benavides‐Serrato M, Combe FJ, Harris WE, Hartley IR, Kitchener AC, de Kort SR, Nekaris A, Rowntree JK. Multi-individual microsatellite identification: A multiple genome approach to microsatellite design (MiMi). Mol Ecol Resour 2019; 19:1672-1680. [PMID: 31339632 PMCID: PMC6900094 DOI: 10.1111/1755-0998.13065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 01/06/2023]
Abstract
Bespoke microsatellite marker panels are increasingly affordable and tractable to researchers and conservationists. The rate of microsatellite discovery is very high within a shotgun genomic data set, but extensive laboratory testing of markers is required for confirmation of amplification and polymorphism. By incorporating shotgun next-generation sequencing data sets from multiple individuals of the same species, we have developed a new method for the optimal design of microsatellite markers. This new tool allows us to increase the rate at which suitable candidate markers are selected by 58% in direct comparisons and facilitate an estimated 16% reduction in costs associated with producing a novel microsatellite panel. Our method enables the visualisation of each microsatellite locus in a multiple sequence alignment allowing several important quality checks to be made. Polymorphic loci can be identified and prioritised. Loci containing fragment-length-altering mutations in the flanking regions, which may invalidate assumptions regarding the model of evolution underlying variation at the microsatellite, can be avoided. Priming regions containing point mutations can be detected and avoided, helping to reduce sample-site-marker specificity arising from genetic isolation, and the likelihood of null alleles occurring. We demonstrate the utility of this new approach in two species: an echinoderm and a bird. Our method makes a valuable contribution towards minimising genotyping errors and reducing costs associated with developing a novel marker panel. The Python script to perform our method of multi-individual microsatellite identification (MiMi) is freely available from GitHub (https://github.com/graemefox/mimi).
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Affiliation(s)
- Graeme Fox
- Ecology and Environment Research Centre, Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | - Richard F. Preziosi
- Ecology and Environment Research Centre, Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | - Rachael E. Antwis
- School of Environment and Life SciencesUniversity of SalfordSalfordUK
| | - Milena Benavides‐Serrato
- Ecology and Environment Research Centre, Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
- Universidad Nacional de ColombiaPlaya SalgueroColombia
| | - Fraser J. Combe
- Ecology and Environment Research Centre, Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
- Division of BiologyKansas State UniversityManhattanKSUSA
| | - W. Edwin Harris
- Ecology and Environment Research Centre, Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
- Crop and Environment SciencesHarper Adams UniversityNewportUK
| | - Ian R. Hartley
- Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Selvino R. de Kort
- Ecology and Environment Research Centre, Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
| | - Anne‐Isola Nekaris
- Department of Social Sciences, Faculty of Humanities and Social SciencesOxford Brookes UniversityOxfordUK
| | - Jennifer K. Rowntree
- Ecology and Environment Research Centre, Department of Natural SciencesManchester Metropolitan UniversityManchesterUK
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17
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Macedo D, Caballero I, Mateos M, Leblois R, McCay S, Hurtado LA. Population genetics and historical demographic inferences of the blue crab Callinectes sapidus in the US based on microsatellites. PeerJ 2019; 7:e7780. [PMID: 31632846 PMCID: PMC6796965 DOI: 10.7717/peerj.7780] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/28/2019] [Indexed: 01/02/2023] Open
Abstract
The native range of the blue crab Callinectes sapidus spans Nova Scotia to northern Argentina. In the US, it constitutes a keystone species in estuarine habitats of the Atlantic coast and Gulf of Mexico (GOM), serving as both predator and prey to other species, and also has historically represented a multi-billion dollar fishery. Knowledge relevant to effective management and monitoring of this ecologically and economically important species, such as levels of population genetic differentiation and genetic diversity, is necessary. Although several population genetics studies have attempted to address these questions in one or more parts of its distribution, conflicting results and potential problems with the markers used, as well as other issues, have obscured our understanding on them. In this study, we examined large-scale genetic connectivity of the blue crab in the US, using 16 microsatellites, and genotyped individuals from Chesapeake Bay, in the US Atlantic, and from nine localities along the US GOM coast. Consistent with the high long-distance dispersal potential of this species, very low levels of genetic differentiation were detected for the blue crab among the ten US localities examined, suggesting it constitutes a large panmictic population within this region. Estimations of genetic diversity for the blue crab appear to be high in the US, and provide a baseline for monitoring temporal changes in this species. Demographic analyses indicate a recent range expansion of the US population, probably during the Holocene. In addition, capitalizing on published microsatellite data from southern Brazil, our analyses detected high genetic differentiation between localities in the US and Brazil. These results point to the need for examination of genetic diversity and differentiation along the area spanning the US to southern Brazil.
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Affiliation(s)
- Danielle Macedo
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Isabel Caballero
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Raphael Leblois
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Shelby McCay
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Luis A Hurtado
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
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18
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Lack of genetic structuring, low effective population sizes and major bottlenecks characterise common and German wasps in New Zealand. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02039-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Fernández-Pérez J, Nantón A, Méndez J. Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae). BMC Genet 2018; 19:97. [PMID: 30367592 PMCID: PMC6204057 DOI: 10.1186/s12863-018-0684-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/11/2018] [Indexed: 01/04/2023] Open
Abstract
Background The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated. Results The length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170–210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies. Conclusions This is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources. Electronic supplementary material The online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain.
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
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Lukindu M, Bergey CM, Wiltshire RM, Small ST, Bourke BP, Kayondo JK, Besansky NJ. Spatio-temporal genetic structure of Anopheles gambiae in the Northwestern Lake Victoria Basin, Uganda: implications for genetic control trials in malaria endemic regions. Parasit Vectors 2018; 11:246. [PMID: 29661226 PMCID: PMC5902950 DOI: 10.1186/s13071-018-2826-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/28/2018] [Indexed: 11/30/2022] Open
Abstract
Background Understanding population genetic structure in the malaria vector Anopheles gambiae (s.s.) is crucial to inform genetic control and manage insecticide resistance. Unfortunately, species characteristics such as high nucleotide diversity, large effective population size, recent range expansion, and high dispersal ability complicate the inference of genetic structure across its range in sub-Saharan Africa. The ocean, along with the Great Rift Valley, is one of the few recognized barriers to gene flow in this species, but the effect of inland lakes, which could be useful sites for initial testing of genetic control strategies, is relatively understudied. Here we examine Lake Victoria as a barrier between the Ugandan mainland and the Ssese Islands, which lie up to 60 km offshore. We use mitochondrial DNA (mtDNA) from populations sampled in 2002, 2012 and 2015, and perform Bayesian cluster analysis on mtDNA combined with microsatellite data previously generated from the same 2002 mosquito DNA samples. Results Hierarchical analysis of molecular variance and Bayesian clustering support significant differentiation between the mainland and lacustrine islands. In an mtDNA haplotype network constructed from this and previous data, haplotypes are shared even between localities separated by the Rift Valley, a result that more likely reflects retention of shared ancestral polymorphism than contemporary gene flow. Conclusions The relative genetic isolation of An. gambiae on the Ssese Islands, their small size, level terrain and ease of access from the mainland, the relative simplicity of the vectorial system, and the prevalence of malaria, are all attributes that recommend these islands as possible sites for the testing of genetic control strategies.
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Affiliation(s)
- Martin Lukindu
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Christina M Bergey
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Rachel M Wiltshire
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Scott T Small
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Brian P Bourke
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jonathan K Kayondo
- Department of Entomology, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Nora J Besansky
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
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Development of microsatellite markers using next-generation sequencing for the fish Colossoma macropomum. Mol Biol Rep 2017; 45:9-18. [DOI: 10.1007/s11033-017-4134-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 12/11/2017] [Indexed: 02/07/2023]
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