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Gutiérrez J, Seguel M, Saenz-Agudelo P, Acosta-Jamett G, Verdugo C. Host genetic diversity and body condition influence parasite resistance and clearance in a wild marine mammal population. Biol Lett 2024; 20:20240302. [PMID: 39353568 PMCID: PMC11444764 DOI: 10.1098/rsbl.2024.0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/07/2024] [Accepted: 09/03/2024] [Indexed: 10/04/2024] Open
Abstract
Host genetic variability can modulate infection resistance, although its role in infection clearance remains unclear. Hookworm disease (Uncinaria sp.) is the leading cause of pup mortality in several otariid species, although the parasite can be cleared through immune-mediated processes. We evaluated the association of host genetic diversity, body condition and immune response with hookworm resistance and/or clearance in the South American fur seal (Arctocephalus australis). Uninfected pups had higher heterozygosity than parasitized individuals, indicating a negative relationship between heterozygosity and the chances of infection. Likewise, pups that died of hookworm infection had lower heterozygosity than those that died of non-infectious causes. Interestingly, once infected, pups that survived hookworm infection had heterozygosities similar to pups that died of hookworm disease. However, pups that cleared the infection had a higher body mass and parasite-specific immunoglobulin G levels than those that did not recover or died of hookworm disease. Thus, although heterozygosity predicted resistance to and mortality from hookworm infections, it did not affect parasite clearance, which was facilitated by better body condition and adaptive immune responses. This demonstrates that host genetic variability and host-environment interactions influence disease dynamics, acting at different, well-defined stages of infection.
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Affiliation(s)
- Josefina Gutiérrez
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Programa de Doctorado en Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Mauricio Seguel
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Gerardo Acosta-Jamett
- Instituto de Medicina Preventiva Veterinaria, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Center for Surveillance and Evolution of Infectious Diseases, Universidad Austral de Chile, Valdivia, Chile
| | - Claudio Verdugo
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
- Center for Surveillance and Evolution of Infectious Diseases, Universidad Austral de Chile, Valdivia, Chile
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Marrero P, Fregel R, Richardson DS. Inter and intra-island genetic structure and differentiation of the endemic Bolle's Laurel Pigeon (Columba bollii) in the Canary archipelago. ZOOLOGY 2024; 167:126209. [PMID: 39303381 DOI: 10.1016/j.zool.2024.126209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024]
Abstract
Islands provide excellent settings for studying the evolutionary history of species, since their geographic isolation and relatively small size limit gene flow between populations, and promote divergence and speciation. The endemic Bolle's Laurel Pigeon Columba bollii is an arboreal frugivorous bird species distributed on laurel forests in four islands of the Canary archipelago. To elucidate the population genetics, we genotyped ten microsatellite loci using DNA obtained from non-invasive samples collected across practically all laurel forest remnants, and subsequently grouped into eight sampling sites. Analyses including F-statistics, Bayesian clustering approaches, isolation by distance tests and population graph topologies, were used to infer the genetic diversity and the population differentiation within and among insular populations. Additionally, we evaluated the effect of null alleles on data analysis. Low genetic diversity was found in all populations of Bolle's Laurel Pigeon, with no significant differences in diversity among them. However, significant genetic differentiation was detected among all populations, with pigeons from La Palma and El Hierro exhibiting the closest affinity. Bayesian clustering supported population separation between islands, and also detected fine-scale structure within the Tenerife and La Gomera populations. Our results suggest that, despite columbids have a high movement ability, they can show signature of genetic divergence among populations, particularly on oceanic islands. Geological history of the islands and distribution range of habitats could have close influence on the evolutionary trajectories of these birds. This approach can provide practical tools to implement appropriate conservation measures for range-restricted species and their habitat.
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Affiliation(s)
- Patricia Marrero
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Island Ecology and Evolution Research Group, La Laguna, Tenerife, Canary Islands, Spain; School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Rosa Fregel
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Tenerife, Canary Islands, Spain.
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
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Albuja‐Quintana M, Rivas‐Torres G, Rojas López KE, Asadobay P, Palacios Cuenca W, Vinueza G, Torres MDL. Preliminary insights of the genetic diversity and invasion pathways of Cedrela odorata in the Galapagos Islands, Ecuador. Ecol Evol 2024; 14:e11723. [PMID: 38988340 PMCID: PMC11236438 DOI: 10.1002/ece3.11723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 06/19/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
Cedrela odorata is considered the second most invasive tree species of the Galapagos Islands. Although it is listed in CITES Appendix II and there are population losses in mainland Ecuador, in Galapagos it is paradoxically a species of concern due to its invasive potential. Genetic studies can shed light on the invasion history of introduced species causing effects on unique ecosystems like the Galapagos. We analyzed nine microsatellite markers in C. odorata individuals from Galapagos and mainland Ecuador to describe the genetic diversity and population structure of C. odorata in the Galapagos and to explore the origin and invasion history of this species. The genetic diversity found for C. odorata in Galapagos (H e = 0.55) was lower than reported in the mainland (H e = 0.81), but higher than other invasive insular plant species, which could indicate multiple introductions. Our results suggest that Ecuador's northern Coastal region is the most likely origin of the Galapagos C. odorata, although further genomic studies, like Whole Genome Sequencing, Rad-Seq, and/or Whole Genome SNP analyses, are needed to confirm this finding. Moreover, according to our proposed pathway scenarios, C. odorata was first introduced to San Cristobal and/or Santa Cruz from mainland Ecuador. After these initial introductions, C. odorata appears to have arrived to Isabela and Floreana from either San Cristobal or Santa Cruz. Here, we report the first genetic study of C. odorata in the Galapagos and the first attempt to unravel the invasion history of this species. The information obtained in this research could support management and control strategies to lessen the impact that C. odorata has on the islands' local flora and fauna.
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Affiliation(s)
- Martina Albuja‐Quintana
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito USFQQuitoEcuador
| | - Gonzalo Rivas‐Torres
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito USFQQuitoEcuador
- Galápagos Science CenterUniversidad San Francisco de QuitoSan CristobalEcuador
- University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito USFQQuitoEcuador
| | - Karla E. Rojas López
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito USFQQuitoEcuador
| | - Pacarina Asadobay
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito USFQQuitoEcuador
| | | | - Génesis Vinueza
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito USFQQuitoEcuador
| | - Maria de Lourdes Torres
- Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biotecnología VegetalUniversidad San Francisco de Quito (USFQ)QuitoEcuador
- Colegio de Ciencias Biológicas y AmbientalesUniversidad San Francisco de Quito USFQQuitoEcuador
- Galápagos Science CenterUniversidad San Francisco de QuitoSan CristobalEcuador
- University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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4
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Tang J, Fan X, Milne RI, Yang H, Tao W, Zhang X, Guo M, Li J, Mao K. Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen ( Populus rotundifolia) in the Hengduan Mountains. PLANT DIVERSITY 2024; 46:321-332. [PMID: 38798733 PMCID: PMC11119543 DOI: 10.1016/j.pld.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/31/2024] [Accepted: 03/31/2024] [Indexed: 05/29/2024]
Abstract
Biogeographical barriers to gene flow are central to plant phylogeography. In East Asia, plant distribution is greatly influenced by two phylogeographic breaks, the Mekong-Salween Divide and Tanaka-Kaiyong Line, however, few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both. Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia, a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China. Demographic and migration hypotheses were tested using coalescent-based approaches. Limited historical gene flow was observed between the western and eastern groups of P. rotundifolia, but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line, manifesting in clear admixture and high genetic diversity in the central group. Wind-borne pollen and seeds may have facilitated the dispersal of P. rotundifolia following prevalent northwest winds in the spring. We also found that the Hengduan Mountains, where multiple genetic barriers were detected, acted on the whole as a barrier between the western and eastern groups of P. rotundifolia. Ecological niche modeling suggested that P. rotundifolia has undergone range expansion since the last glacial maximum, and demographic reconstruction indicated an earlier population expansion around 600 Ka. The phylogeographic pattern of P. rotundifolia reflects the interplay of biological traits, wind patterns, barriers, niche differentiation, and Quaternary climate history. This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.
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Affiliation(s)
- Jieshi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xiaoyan Fan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Wenjing Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Xinran Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Mengyun Guo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, PR China
- School of Ecology and Environment, Tibet University, Lhasa 850000, PR China
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5
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Siziba VI, Scroeder MM, Wilson B, Sliwa A, Willows‐Munro S. A method for noninvasive individual genotyping of black-footed cat ( Felis nigripes). Ecol Evol 2024; 14:e11315. [PMID: 38660470 PMCID: PMC11040180 DOI: 10.1002/ece3.11315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 03/07/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
The black-footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black-footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black-footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives.
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Affiliation(s)
- Vimbai I. Siziba
- School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
| | | | - Beryl Wilson
- McGregor MuseumKimberleyNorthern CapeSouth Africa
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6
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Sommaro LV, Martínez JJ, Chiappero MB, Steinmann AR, Gardenal CN, Priotto JW. Relatedness dynamics and sex-biased dispersal in a seasonal cycle of corn mice from intensively managed agroecosystems. Curr Zool 2024; 70:1-12. [PMID: 38476139 PMCID: PMC10926262 DOI: 10.1093/cz/zoac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/17/2022] [Indexed: 03/14/2024] Open
Abstract
The sex-biased dispersal and kinship dynamics are important factors shaping the spatial distribution of individuals and are key parameters affecting a variety of ecological and evolutionary processes. Here, we studied the spatial distribution of related individuals within a population of corn mice Calomys musculinus in a seasonal cycle to infer dispersal patterns. The sampling was carried out from spring 2005 to winter 2006 in field borders of intensively managed agroecosystems. Genotyping data from 346 individuals with 9 microsatellites showed spatial genetic structure was weak for males, but not for females. The results indicate a complex spatial kinship dynamic of related females across all seasons. Which, contrary to our expectations, dispersal distances decrease with the increase of the population abundance. Meanwhile, male dispersal distances were greater when population abundance increased and thus the availability of active females. Males disperse greater distances to mate and sire offspring with distant females as a possible inbreeding avoidance mechanism. This study shows that C. musculinus is capable of much greater scattering distances than previously reported and that dispersal occurs fluidly and without barriers across the agroecosystem. The indirect benefit of dispersal on individual fitness could be related to relaxing the competition in the natal area and increasing the mating rate. Our study highlights the value of combining genetic relatedness, fieldwork observations, and behavioral data to estimate dispersal at a fine geographical scale.
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Affiliation(s)
- Lucia V Sommaro
- Laboratorio de Ecología Evolutiva y Biogeografía, Instituto de Ecorregiones Andinas (INECOA), Universidad Nacional de Jujuy - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Salvador de Jujuy, Jujuy, Argentina
| | - Juan J Martínez
- Laboratorio de Ecología Evolutiva y Biogeografía, Instituto de Ecorregiones Andinas (INECOA), Universidad Nacional de Jujuy - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Salvador de Jujuy, Jujuy, Argentina
| | - Marina B Chiappero
- Instituto de Diversidad y Ecología Animal (IDEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Universidad Nacional de Córdoba, Córdoba, Argentina
- Cátedra de Genética de Poblaciones y Evolución, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrea R Steinmann
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
| | - Cristina N Gardenal
- Instituto de Diversidad y Ecología Animal (IDEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Universidad Nacional de Córdoba, Córdoba, Argentina
- Cátedra de Genética de Poblaciones y Evolución, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - José W Priotto
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
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7
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Choquet M, Lizano AM, Le Moan A, Ravinet M, Dhanasiri AKS, Hoarau G. Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus. Mol Ecol 2023; 32:6854-6873. [PMID: 37902127 DOI: 10.1111/mec.17183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target-capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP-based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re-assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization.
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Affiliation(s)
- Marvin Choquet
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Apollo M Lizano
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Alan Le Moan
- CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Anusha K S Dhanasiri
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Sawai K, Arakawa A, Taniguchi M, Xiao B, Sawai M, Osaki M, Yamaguchi E, Hayama Y, Murato Y, Shimizu Y, Kondo S, Yamamoto T. Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan. Sci Rep 2023; 13:21186. [PMID: 38040788 PMCID: PMC10692317 DOI: 10.1038/s41598-023-48215-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023] Open
Abstract
Geographical wildlife patterns reflect historical range expansion and connectivity and provide insights into wildlife population management. In our large-scale phylogeographic population analysis of wild boars (Sus scrofa leucomystax) in Japan, we identified 15 clusters using 29 microsatellite markers, each structured within a range of approximately 200 km. This suggests that evolution was essentially driven by isolation by distance, and that the range of gene flow was limited. One cluster contained subpopulations located approximately 900 km apart, indicating the occurrence of past anthropogenic introductions. Moreover, we estimated effective migration to visualize the geographic genetic population diversity. This analysis identified six potential barriers, one of which involved large plains and mountainous areas in the Kanto region of eastern Japan. This barrier likely persisted in the two eastern clusters for an extended period, restricting migration to the neighboring areas. Overall, our study sheds light on the demographic history of wild boar in Japan, provides evidence of past anthropogenic introductions from distant areas, and highlights the importance of geographic barriers in shaping genetic diversity and population dynamics. This knowledge will be beneficial for forming informed wildlife management strategies toward the conservation of genetic integrity and ecological balance of wild boar populations in Japan.
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Affiliation(s)
- Kotaro Sawai
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Aisaku Arakawa
- Meat Animal Biosystems Group, Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan
| | - Masaaki Taniguchi
- Meat Animal Biosystems Group, Division of Meat Animal and Poultry Research, Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan
| | - Bo Xiao
- Virus Group, Division of Infectious Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Miwa Sawai
- Virus Group, Division of Infectious Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Makoto Osaki
- Division of Hygiene Management Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Emi Yamaguchi
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Yoko Hayama
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Yoshinori Murato
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Yumiko Shimizu
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Sonoko Kondo
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Takehisa Yamamoto
- Epidemiology and Arbovirus Group, Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan.
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9
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Unlusoy I. Determination of declined genetic diversity of Holstein stud bulls based on microsatellite markers. Anim Biotechnol 2023; 34:4627-4633. [PMID: 36847656 DOI: 10.1080/10495398.2023.2176866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Semen importing countries are trying to select the most suitable studs according to their breeding goals, while the globally widespread use of common genetic material has been turning the loss of genetic diversity into a possible danger. The aim of this study was to evaluate the genetic diversity of 304 high-yielding Holstein stud bulls whose semen were produced in Turkiye, Europe and the Americas. The values of allele frequencies, expected heterozygosity (He), observed heterozygosity (Ho), Hardy-Weinberg (HW) Equilibrium, the number of alleles per locus (Na), allelic richness (Rs), polymorphic information content (PIC) and F-statistics were calculated and compared the results with similar studies. It was observed that some indicator values of the genetic diversity were decreased compared to the values of the other studies in Holstein breed. Especially the decrease in some values of SPS115 locus was statistically significant. It is thought that this could be as a result of SPS115 to be close to possible QTL regions associated with traits which indicates overall potential of selection in stud bulls. Therefore, while applying a selection program to populations, national genetic resource management strategies that maintain genetic diversity should not be forgotten besides gaining high yield.
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Affiliation(s)
- Ilke Unlusoy
- Department of Animal Breeding and Genetics, International Center for Livestock Research and Training, Ankara, Turkiye
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10
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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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11
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Lai FY, Yin CY, Ding ST, Tu PA, Wang PH. Analysis of the population genetic structure using microsatellite markers in goat populations in Taiwan. Anim Biotechnol 2023; 34:3294-3305. [PMID: 36309814 DOI: 10.1080/10495398.2022.2138414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Due to the poor growth rate of the Taiwan black (TB) goat in Taiwan, many exotic breeds were brought into breeding schemes to improve TB goat. However, the excessive cross-breeding of alien species with TB goat has decreased its population numbers, genetic variation and biodiversity. Therefore, TB goat population considered an endemic species in Taiwan that needed to be conservation. The objective of the present study was to analyze the genetic structure and TB goat using genetic markers for genetic improvement and to sustain germplasm conservation and utilization. 15 microsatellite markers, divided into three sets, were used to analyze 690 goats sampled from 10 goat populations. The average number of alleles (Na) and effective alleles (Ne) was 11.87 ± 3.93 and 5.093 ± 1.768, respectively. The average expected heterozygosity (HE) and observed heterozygosity (HO) was 0.780 ± 0.084 and 0.602 ± 0.116, respectively. The average polymorphic information content (PIC) was 0.747 ± 0.103; FIS was 0.058 ± 0.075. All 15 microsatellite markers were highly polymorphic. The genetic distances between individuals were estimated to construct a phylogenetic tree. In present study, the 690 goat samples were divided into 8 clusters. The results indicated that these 15 microsatellite markers successfully clustered goat populations in Taiwan and could assist in the preservation of TB goats.
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Affiliation(s)
- Fang-Yu Lai
- Department of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Bioresources, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Chung-Ying Yin
- Department of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Bioresources, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Shih-Torng Ding
- Department of Animal Science and Technology, Laboratory of Molecular Genetic, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Po-An Tu
- Livestock Research Institute, Hsinchu Branch, Council of Agriculture, Hsinchu, Taiwan
| | - Pei-Hwa Wang
- Department of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Bioresources, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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12
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Kim S, Lee HJ, Kim YG, Kang KS. Spatial genetic structure and seed quality of a southernmost Abies nephrolepis population. Sci Rep 2023; 13:18419. [PMID: 37891234 PMCID: PMC10611809 DOI: 10.1038/s41598-023-45635-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Abies nephrolepis (Trautv. ex Maxim.) Maxim. has its southernmost populations in South Korea and they are expected to decline under climate change. To establish a strategic conservation plan, this study aimed to investigate the spatial genetic structure and seed characteristics of A. nephrolepis. We used nine microsatellite markers on 165 individuals of A. nephrolepis and sampled seeds in a southernmost population at Mt. Hambaeksan, South Korea. We observed a high level of heterozygosity, and a simulation study found that sampling 20 individuals was enough to secure sufficient genetic diversity on average. Spatial autocorrelation analysis revealed that individuals had a positive genetic relationship until 30 m. Bayesian clustering models, STRUCTURE and GENELAND, failed to achieve a consensus in the optimal number of population (K), estimating K = 1 and K = 2, respectively. Principal coordinate analysis supported the absence of genetic substructure within the study population. There was a large variance in seed production among mother trees. On average, seeds of A. nephrolepis from Mt. Hambaeksan had a purity of 70.4% and a germination percentage of 32.2%. We found that seed weight was the most effective indicator of seed quality. Mother trees at higher altitudes had poorer purity which is threatening to A. nephrolepis considering the upslope retreat of subalpine species under climate change. Our results provide insights into the interactions among spatial processes, genetic structure, and seed quality within a population of A. nephrolepis.
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Affiliation(s)
- Sunjeong Kim
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hye-Jin Lee
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yang-Gil Kim
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyu-Suk Kang
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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13
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Shults P, Zhang X, Moran M, Cohnstaedt LW, Gerry AC, Vargo EL, Eyer PA. Immigration and seasonal bottlenecks: high inbreeding despite high genetic diversity in an oscillating population of Culicoides sonorensis (Diptera: Ceratopogonidae). JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:987-997. [PMID: 37417303 DOI: 10.1093/jme/tjad068] [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: 02/11/2023] [Revised: 05/01/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
Most population genetic studies concern spatial genetic differentiation, but far fewer aim at analyzing the temporal genetic changes that occur within populations. Vector species, including mosquitoes and biting midges, are often characterized by oscillating adult population densities, which may affect their dispersal, selection, and genetic diversity over time. Here, we used a population of Culicoides sonorensis from a single site in California to investigate short-term (intra-annual) and long-term (inter-annual) temporal variation in genetic diversity over a 3 yr period. This biting midge species is the primary vector of several viruses affecting both wildlife and livestock, thus a better understanding of the population dynamics of this species can help inform epidemiological studies. We found no significant genetic differentiation between months or years, and no correlation between adult populations and the inbreeding coefficient (FIS). However, we show that repeated periods of low adult abundance during cooler winter months resulted in recurring bottleneck events. Interestingly, we also found a high number of private and rare alleles, which suggests both a large, stable population, as well as a constant influx of migrants from nearby populations. Overall, we showed that the high number of migrants maintains a high level of genetic diversity by introducing new alleles, while this increased diversity is counterbalanced by recurrent bottleneck events potentially purging unfit alleles each year. These results highlight the temporal influences on population structure and genetic diversity in C. sonorensis and provide insight into factors effecting genetic variation that may occur in other vector species with fluctuating populations.
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Affiliation(s)
- Phillip Shults
- USDA-ARS, Foreign Arthropod-Borne Animal Diseases Research Unit (FABADRU), 1515 College Avenue, Manhattan, KS 66502, USA
| | - Xinmi Zhang
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA
| | - Megan Moran
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Lee W Cohnstaedt
- USDA-ARS, Foreign Arthropod-Borne Animal Diseases Research Unit (FABADRU), 1515 College Avenue, Manhattan, KS 66502, USA
| | - Alec C Gerry
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA
| | - Edward L Vargo
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Pierre-Andre Eyer
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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14
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Zhao M, Ran X, Bai Y, Ma Z, Gao J, Xing D, Li C, Guo X, Jian X, Liu W, Liao Y, Chen K, Zhang H, Zhao T. Genetic diversity of Aedes aegypti and Aedes albopictus from cohabiting fields in Hainan Island and the Leizhou Peninsula, China. Parasit Vectors 2023; 16:319. [PMID: 37684698 PMCID: PMC10486073 DOI: 10.1186/s13071-023-05936-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Aedes aegypti and Ae. albopictus are important human arbovirus vectors that can spread arboviral diseases such as yellow fever, dengue, chikungunya and Zika. These two mosquito species coexist on Hainan Island and the Leizhou Peninsula in China. Over the past 40 years, the distribution of Ae. albopictus in these areas has gradually expanded, while Ae. aegypti has declined sharply. Monitoring their genetic diversity and diffusion could help to explain the genetic influence behind this phenomenon and became key to controlling the epidemic of arboviruses. METHODS To better understand the genetic diversity and differentiation of these two mosquitoes, the possible cohabiting areas on Hainan Island and the Leizhou Peninsula were searched between July and October 2021, and five populations were collected. Respectively nine and 11 microsatellite loci were used for population genetic analysis of Ae. aegypti and Ae. albopictus. In addition, the mitochondrial coxI gene was also selected for analysis of both mosquito species. RESULTS The results showed that the mean diversity index (PIC and SI values) of Ae. albopictus (mean PIC = 0.754 and SI = 1.698) was higher than that of Ae. aegypti (mean PIC = 0.624 and SI = 1.264). The same results were also observed for the coxI gene: the genetic diversity of all populations of Ae. albopictus was higher than that of Ae. aegypti (total H = 45 and Hd = 0.89958 vs. total H = 23 and Hd = 0.76495, respectively). UPGMA dendrogram, DAPC and STRUCTURE analyses showed that Ae. aegypti populations were divided into three clusters and Ae. albopictus populations into two. The Mantel test indicated a significant positive correlation between genetic distance and geographic distance for the Ae. aegypti populations (R2 = 0.0611, P = 0.001), but the correlation was not significant for Ae. albopictus populations (R2 = 0.0011, P = 0.250). CONCLUSIONS The population genetic diversity of Ae. albopictus in Hainan Island and the Leizhou Peninsula was higher than that of Ae. aegypti. In terms of future vector control, the most important and effective measure was to control the spread of Ae. albopictus and monitor the population genetic dynamics of Ae. aegypti on Hainan Island and the Leizhou Peninsula, which could theoretically support the further elimination of Ae. aegypti in China.
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Affiliation(s)
- Minghui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Xin Ran
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, China
| | - Yu Bai
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Zu Ma
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jian Gao
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Dan Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chunxiao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoxia Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xianyi Jian
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wei Liu
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Yun Liao
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Kan Chen
- Jiangxi International Travel Healthcare Center, Nanchang, China
| | - Hengduan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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15
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Kabasakal A. Verification of pedigree information with paternity testing in Karacabey Merino sheep. Trop Anim Health Prod 2023; 55:271. [PMID: 37453999 DOI: 10.1007/s11250-023-03689-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Complex tests of DNA sequences, genetic research, and the use of specific DNA polymorphisms as genetic markers have all advanced rapidly in recent years. It is widely used in DNA-based parental testing. Therefore, it has replaced the blood types routinely used in pedigree tests. The study aimed to evaluate the 14 microsatellite loci in the study in terms of paternity test parameters and to investigate the usability of the relevant loci in determining the parentage of the Karacabey Merino breed. In this study, paternity testing was performed on 5 rams of the Karacabey Merino breed and their probable 98 offspring using 14 microsatellite loci. A total of 290 alleles were observed in the study. The observed heterozygosity ratio (Ho) based on loci was between 0.82 and 0.98, and the expected heterozygosity ratio (He) was between 0.87 and 0.93. Individual exclusion probability (PE) values for the loci were calculated to be between 0.596 and 0.761, with combined exclusion probability (CPE) values of 0.99999995. According to the results of the study, paternity tests using 14 microsatellite markers in Karacabey Merino sheep can be used with high accuracy.
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Affiliation(s)
- Adem Kabasakal
- Susurluk Vocational School, Bandırma Onyedi Eylül Üniversity, 10600, Balıkesir, Turkey.
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16
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Domínguez JC, Alda F, Calero-Riestra M, Olea PP, Martínez-Padilla J, Herranz J, Oñate JJ, Santamaría A, Viñuela J, García JT. Genetic footprints of a rapid and large-scale range expansion: the case of cyclic common vole in Spain. Heredity (Edinb) 2023; 130:381-393. [PMID: 36966202 PMCID: PMC10238521 DOI: 10.1038/s41437-023-00613-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
In the Anthropocene, many species are rapidly shifting their ranges in response to human-driven habitat modifications. Studying patterns and genetic signatures of range shifts helps to understand how species cope with environmental disturbances and predict future shifts in the face of global environmental change. We investigated the genetic signature of a contemporary wide-range expansion observed in the Iberian common vole Microtus arvalis asturianus shortly after a colonization event. We used mtDNA and microsatellite data to investigate patterns of genetic diversity, structure, demography, and gene flow across 57 localities covering the historical range of the species and the newly colonized area. The results showed a genetic footprint more compatible with a true range expansion (i.e. the colonization of previously unoccupied areas), than with a model of "colonization from within" (i.e. local expansions from small, unnoticed populations). Genetic diversity measures indicated that the source population was likely located at the NE of the historical range, with a declining gradient of genetic diversity towards the more recently invaded areas. At the expansion front, we observed the greatest gene flow and smallest pairwise differences between nearby localities. Both natural landscape features (rivers) and recent anthropogenic barriers (roads, railways) explained a large proportion of genetic variance among populations and had a significant impact on the colonization pathways used by voles.
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Affiliation(s)
- Julio C Domínguez
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain.
- IPE, Pyrenean Institute of Ecology (CSIC), 22700, Avda. Nuestra Señora de la Victoria 16, Jaca, Spain.
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - María Calero-Riestra
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
- IPE, Pyrenean Institute of Ecology (CSIC), 22700, Avda. Nuestra Señora de la Victoria 16, Jaca, Spain
| | - Pedro P Olea
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Jesús Martínez-Padilla
- IPE, Pyrenean Institute of Ecology (CSIC), 22700, Avda. Nuestra Señora de la Victoria 16, Jaca, Spain
| | - Jesús Herranz
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Juan José Oñate
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Ana Santamaría
- Terrestrial Ecology Group (TEG)-Departamento de Ecología, and Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, c/ Darwin, 2, 28049, Madrid, Spain
| | - Javier Viñuela
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
| | - Jesús T García
- IREC, Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071, Ciudad Real, Spain
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17
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Papach A, Beaurepaire A, Yañez O, Huwiler M, Williams GR, Neumann P. Multiple mating by both sexes in an invasive insect species, Aethina tumida (Coleoptera: Nitidulidae). INSECT SCIENCE 2023; 30:517-529. [PMID: 36097706 DOI: 10.1111/1744-7917.13112] [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: 04/08/2022] [Revised: 07/11/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Multiple mating by both sexes is common among sexually reproducing animals. Small hive beetles (SHB), Aethina tumida, are parasites of bee nests endemic to sub-Saharan Africa and have become a widespread invasive species. Despite the considerable economic damages they can cause, their basic biology remains poorly understood. Here we show that male and female small hive beetles can mate multiple times, suggesting that costs for mating are low in this species. In an invasive A. tumida population in the United States, a combination of laboratory experiments for males and paternity analysis with eight polymorphic DNA microsatellite markers for field-caught females were used to estimate the number of mating by both sexes. The data show that females and males can mate multiple times-females mated with up to eight males, whereas males mated with at least seven females. The results also showed that A. tumida displayed a skewed paternity, although this was not consistent among the tested females. Thus, first or last male advantage seem to be unlikely in A. tumida. Our observations that individuals of both sexes of A. tumida can mate multiple times opens new research avenues for examining drivers of multiple mating and determining the role it may play in promoting biological invasions.
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Affiliation(s)
- Anna Papach
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Alexis Beaurepaire
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Meret Huwiler
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Geoffrey R Williams
- Department of Entomology & Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
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18
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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] [Key Words] [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)
| | | | | | | | | | | | | | | | | | | | | | - Hengduan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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19
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Amoutchi AI, Kersten P, Vogt A, Kohlmann K, Kouamelan EP, Mehner T. Population genetics of the African snakehead fish Parachanna obscura along West Africa's water networks: Implications for sustainable management and conservation. Ecol Evol 2023; 13:e9724. [PMID: 36694547 PMCID: PMC9842884 DOI: 10.1002/ece3.9724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023] Open
Abstract
An essential factor for aquatic conservation is genetic diversity or population divergence, which in natural populations reflects the interplay between geographical isolation with restricted gene flow and local evolution of populations. The long geological history of Africa may induce stronger among-population divergence and lower within-population divergence in fish populations of African watersheds. As an example, we studied population structure of the African snakehead fish Parachanna obscura. Our study aimed: (1) to develop a set of highly polymorphic microsatellite markers suitable for the analysis of genetic diversity among P. obscura and (2) to study the genetic diversity and structure of P. obscura populations from the West Africa region and mostly from Côte d'Ivoire, with respect to the effects of climate region and geographical distance on the genetic differentiation. A total of 259 specimens from 15 locations of P. obscura were collected over the West Africa region reflecting a high variability of pairwise geographical distances and variability of hydrological connectivity of the area. We developed a set of 21 polymorphic microsatellite markers for studying population genetics of the fish. The results showed relatively low intragenetic diversity for all the 15 locations, certainly attributable to confinement of fish in segregated catchments, resulting in limited gene flow. We also found evidence for local adaptation processes, suggested by five out of 21 microsatellite loci being under putative selection, according to BAYESCAN analysis. In turn, there was strong genetic differentiation (F ST > 0.5) among fish from most locations, reflecting the allopatric development in watersheds without hydraulic connectivity. Neighbor-joining dendrogram, Principal Coordinate Analysis, and analysis of ancestral groups by STRUCTURE suggested that the 15 locations can be divided into three clusters, mainly matching the dominant climate zones and the segregation of the watersheds in the region. The distinct genetic structure of the fish from the 15 locations obtained in this study suggests that conservation and sustainable management actions of this fish resource should avoid genetic mixing of potentially locally adapted populations.
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Affiliation(s)
- Amien Isaac Amoutchi
- West African Science Service Centre on Climate Change and Adapted Land Use (WASCAL) Graduate Research Program on Climate Change and BiodiversityUniversité Felix Houphouet‐BoignyAbidjanCôte d'Ivoire
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Petra Kersten
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Asja Vogt
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Klaus Kohlmann
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
| | - Essetchi Paul Kouamelan
- Laboratoire d'Hydrobiologie, UFR BiosciencesUniversité Felix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Thomas Mehner
- Leibniz‐Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
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Stanbridge D, O’Riain MJ, Dreyer C, le Roex N. Genetic restoration of black rhinoceroses in South Africa: conservation implications. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01486-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM. Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NEOBIOTA 2022. [DOI: 10.3897/neobiota.78.84986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Asian tiger mosquito (Aedes albopictus) arrived in the USA in the 1980’s and rapidly spread throughout eastern USA within a decade. The predicted northern edge of its overwintering distribution on the East Coast of the USA roughly falls across New York, Connecticut, and Massachusetts, where the species has been recorded as early as 2000. It is unclear whether Ae. albopictus populations have become established and survive the cold winters in these areas or are recolonized every year. We genotyped and analyzed populations of Ae. albopictus from the northeast USA using 15 microsatellite markers and compared them with other populations across the country and to representatives of the major global genetic clades to investigate their connectivity and stability. Founder effects or bottlenecks were rare at the northern range of the Ae. albopictus distribution in the northeastern USA, with populations displaying high levels of genetic diversity and connectivity along the East Coast. There is no evidence of population turnover in Connecticut during the course of three consecutive years, with consistent genetic structure throughout this period. Overall, these results support the presence of established populations of Ae. albopictus in New York, Connecticut, and Massachusetts, successfully overwintering and migrating in large numbers. Given the stability and interconnectedness of these populations, Ae. albopictus has the potential to continue to proliferate and expand its range northward under mean warming conditions of climate change. Efforts to control Ae. albopictus in these areas should thus focus on vector suppression rather than eradication strategies, as local populations have become firmly established and are expected to reemerge every summer.
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22
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Understanding Mendelian errors in SNP arrays data using a Gochu Asturcelta pig pedigree: genomic alterations, family size and calling errors. Sci Rep 2022; 12:19686. [PMID: 36385499 PMCID: PMC9668983 DOI: 10.1038/s41598-022-24340-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022] Open
Abstract
Up to 478 Gochu Asturcelta pig parents-offspring trios (61 different families) were genotyped using the Axiom_PigHDv1 Array to identify the causes of Mendelian errors (ME). Up to 545,364 SNPs were retained. Up to 40,540 SNPs gathering 292,297 allelic mismatches were identified and were overlapped with SINEs and LINEs (Sscrofa genome 11.1). Copy number variations (CNV) were called using PennCNV. ME were classified into eight different classes according to the trio member ("Trio" meaning no assignment) and the allele on which ME was identified: TrioA/B, FatherA/B, MotherA/B, OffspringA/B. Most ME occurred due to systematic causes: (a) those assigned to the Father, Mother or Offspring occurred by null or partial null alleles characterized by heterozygote deficiency, varied with family size, involved a low number of loci (6506), and gathered most mismatches (228,145); (b) TrioB errors varied with family size, covaried with SINEs, LINEs and CNV, and involved most ME loci (33,483) and mismatches (65,682); and (c) TrioA errors were non-systematic ME with no sampling bias involving 1.2% of mismatches only and a low number of loci (1939). The influence of TrioB errors on the overall genotyping quality may be low and, since CNV vary among populations, their removal should be considered in each particular dataset. ME assignable to the Father, Mother or Offspring may be consistent within technological platforms and may bias severely linkage or association studies. Most ME caused by null or partial null alleles can be removed using heterozygote deficiency without affecting the size of the datasets.
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Gloria-Soria A. Special Collection: Highlights of Medical, Urban and Veterinary Entomology. Highlights in Medical Entomology, 2021. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1853-1860. [PMID: 36197947 DOI: 10.1093/jme/tjac063] [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: 03/14/2022] [Indexed: 06/16/2023]
Abstract
Life remained far from normal as we completed the first year of the Covid-19 pandemic and entered a second year. Despite the challenges faced worldwide, together we continue to move the field of Medical Entomology forward. Here, I reflect on parallels between control of Covid-19 and vector-borne disease control, discuss the advantages and caveats of using new genotyping technologies for the study of invasive species, and proceed to highlight papers that were published between 2020 and 2021 with a focus on those related to mosquito surveillance and population genetics of mosquito vectors.
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Affiliation(s)
- A Gloria-Soria
- Department of Environmental Sciences, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
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Sánchez-Velásquez JJ, Pinedo-Bernal PN, Reyes-Flores LE, Yzásiga-Barrera C, Zelada-Mázmela E. Genetic diversity and relatedness inferred from microsatellite loci as a tool for broodstock management of fine flounder Paralichthys adspersus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2021.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Null allele can bring to interpretative problems in a deficitary paternity case. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Pimid M, Krishnan KT, Ahmad AH, Mohd Naim D, Chambers GK, Mohd Nor SA, Ab Majid AH. Parentage Assignment Using Microsatellites Reveals Multiple Mating in Aedes aegypti (Diptera: Culicidae): Implications for Mating Dynamics. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1525-1533. [PMID: 35733165 DOI: 10.1093/jme/tjac081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Indexed: 06/15/2023]
Abstract
The mosquito Aedes aegypti is the primary vector of the dengue, yellow fever, and chikungunya viruses. Evidence shows that Ae. aegypti males are polyandrous whereas Ae. aegypti females are monandrous in mating. However, the degree to which Ae. aegypti males and females can mate with different partners has not been rigorously tested. Therefore, this study examined the rates of polyandry via parentage assignment in three sets of competitive mating experiments using wild-type male and female Ae. aegypti. Parentage assignment was monitored using nine microsatellite DNA markers. All Ae. aegypti offspring were successfully assigned to parents with 80% or 95% confidence using CERVUS software. The results showed that both male and female Ae. aegypti mated with up to 3-4 different partners. Adults contributed differentially to the emergent offspring, with reproductive outputs ranging from 1 to 25 viable progeny. This study demonstrates a new perspective on the capabilities of male and female Ae. aegypti in mating. These findings are significant because successful deployment of reproductive control methods using genetic modification or sterile Ae. aegypti must consider the following criteria regarding their mating fitness: 1) choosing Ae. aegypti males that can mate with many different females; 2) testing how transformed Ae. aegypti male perform with polyandrous females; and 3) prioritizing the selection of polyandrous males and/or females Ae. aegypti that have the most offspring.
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Affiliation(s)
- Marcela Pimid
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600 Kelantan, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Kumara Thevan Krishnan
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Jeli Campus, 17600 Kelantan, Malaysia
| | - Abu Hassan Ahmad
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Darlina Mohd Naim
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Geoffrey K Chambers
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, 6140 Wellington, New Zealand
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Terengganu, Malaysia
| | - Abdul Hafiz Ab Majid
- Household & Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
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A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder. Sci Rep 2022; 12:15480. [PMID: 36104480 PMCID: PMC9474449 DOI: 10.1038/s41598-022-19878-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 09/06/2022] [Indexed: 12/22/2022] Open
Abstract
The human SBF1 (SET binding factor 1) gene, alternatively known as MTMR5, is predominantly expressed in the brain, and its epigenetic dysregulation is linked to late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. This gene contains a (GCC)-repeat at the interval between + 1 and + 60 of the transcription start site (SBF1-202 ENST00000380817.8). We sequenced the SBF1 (GCC)-repeat in a sample of 542 Iranian individuals, consisting of late-onset NCDs (N = 260) and controls (N = 282). While multiple alleles were detected at this locus, the 8 and 9 repeats were predominantly abundant, forming > 95% of the allele pool across the two groups. Among a number of anomalies, the allele distribution was significantly different in the NCD group versus controls (Fisher’s exact p = 0.006), primarily as a result of enrichment of the 8-repeat in the former. The genotype distribution departed from the Hardy–Weinberg principle in both groups (p < 0.001), and was significantly different between the two groups (Fisher’s exact p = 0.001). We detected significantly low frequency of the 8/9 genotype in both groups, higher frequency of this genotype in the NCD group, and reverse order of 8/8 versus 9/9 genotypes in the NCD group versus controls. Biased heterozygous/heterozygous ratios were also detected for the 6/8 versus 6/9 genotypes (in favor of 6/8) across the human samples studied (Fisher’s exact p = 0.0001). Bioinformatics studies revealed that the number of (GCC)-repeats may change the RNA secondary structure and interaction sites at least across human exon 1. This STR was specifically expanded beyond 2-repeats in primates. In conclusion, we report indication of a novel biological phenomenon, in which there is selection against certain heterozygous genotypes at a STR locus in human. We also report different allele and genotype distribution at this STR locus in late-onset NCD versus controls. In view of the location of this STR in the 5′ untranslated region, RNA/RNA or RNA/DNA heterodimer formation of the involved genotypes and alternative RNA processing and/or translation should be considered.
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Genetic Diversity and Population Structure of Jubaea chilensis, an Endemic and Monotype Gender from Chile, Based on SNP Markers. PLANTS 2022; 11:plants11151959. [PMID: 35956437 PMCID: PMC9370131 DOI: 10.3390/plants11151959] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]
Abstract
Jubaea chilensis (Molina) Baill., also named Chilean palm, is an endemic species found in the coastal area of Mediterranean sclerophyllous forest in Chile. It has a highly restricted and fragmented distribution along the coast, being under intense exploitation and anthropogenic impact. Based on 1038 SNP markers, we evaluated the genetic diversity and population structure among six J. chilensis natural groups encompassing 96% of the species distribution. We observed low levels of genetic diversity, a deficit of heterozygotes (mean HE = 0.024; HO = 0.014), and high levels of inbreeding (mean FIS = 0.424). The fixation index (FST) and Nei’s genetic distance pairwise comparisons indicated low to moderate structuring among populations. There was no evidence of isolation by distance (r = −0.214, p = 0.799). In the cluster analysis, we observed a closer relationship among Culimo, Cocalán, and Candelaria populations. Migration rates among populations were low, except for some populations with moderate values. The K value that best represented the spatial distribution of genetic diversity was ∆K = 3. Habitat fragmentation, deterioration of the sclerophyllous forest, lack of long-distance dispersers, and a natural regeneration deficit may have driven inbreeding and low levels of genetic diversity in the palm groves of J. chilensis. Although extant populations are not at imminent risk of extinction, the rate of inbreeding could increase and migration could decrease if the effects of climate change and human impact become more acute.
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Pérez-Martínez AL, Eguiarte LE, Mercer KL, Martínez-Ainsworth NE, McHale L, van der Knaap E, Jardón-Barbolla L. Genetic diversity, gene flow, and differentiation among wild, semiwild, and landrace chile pepper (Capsicum annuum) populations in Oaxaca, Mexico. AMERICAN JOURNAL OF BOTANY 2022; 109:1157-1176. [PMID: 35694731 DOI: 10.1002/ajb2.16019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (>60 landraces) are common, and wild-resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role of elevation and domestication gradients in shaping the genetic diversity in C. annuum from the state of Oaxaca, Mexico. METHODS We collected samples of 341 individuals from 28 populations, corresponding to wild, semiwild (C. annuum var. glabriusculum) and cultivated C. annuum, and closely related species Capsicum frutescens and C. chinense. From the genetic variation of 10 simple sequence repeat (SSR) loci, we assessed the population genetic structure, inbreeding, and gene flow through variance distribution analyses, genetic clustering, and connectivity estimations. RESULTS Genetic diversity (HE ) did not differ across domestication levels. However, inbreeding coefficients were higher in semiwild and cultivated chiles than in wild populations. We found evidence for gene flow between wild populations and cultivated landraces along the coast. Genetic structure analysis revealed strong differentiation between most highland and lowland landraces. CONCLUSIONS Gene flow between wild and domesticated populations may be mediated by backyards and smallholder farms, while mating systems may facilitate gene flow between landraces and semiwild populations. Domestication and elevation may overlap in their influence on genetic differentiation. Lowland Gui'ña dani clustered with highland landraces perhaps due to the social history of the Zapotec peoples. In situ conservation may play an important role in preserving semiwild populations and private alleles found in landraces.
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Affiliation(s)
- Ana L Pérez-Martínez
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México; Circuito exterior s/n anexo al Jardín Botánico. C.P. 04510. Ciudad Universitaria, Ciudad de México, México
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - Natalia E Martínez-Ainsworth
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
| | - Leah McHale
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - Esther van der Knaap
- Department of Horticulture, Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Lev Jardón-Barbolla
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
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Promiscuity in the Greater Rhea: a genetic approach. Acta Ethol 2022. [DOI: 10.1007/s10211-022-00398-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sousa F, Costa J, Ribeiro C, Varandas M, Pina-Martins F, Simões F, Matos J, Glushkova M, Miguel C, Veloso MM, Oliveira M, Pinto Ricardo C, Batista D, Paulo OS. Population structure in Quercus suber L. revealed by nuclear microsatellite markers. PeerJ 2022; 10:e13565. [PMID: 35729909 PMCID: PMC9206845 DOI: 10.7717/peerj.13565] [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: 02/03/2022] [Accepted: 05/20/2022] [Indexed: 01/17/2023] Open
Abstract
Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean, a region that is considered highly vulnerable to increased temperatures and severe dry conditions due to environmental changes. Understanding the population structure and demographics of Q. suber is essential in order to anticipate whether populations at greater risk and the species as a whole have the genetic background and reproductive dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject to different studies using both chloroplast and nuclear data, but population structure patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13 nuclear microsatellite markers, and analysed 17 distinct locations across the entire range of the species. Structure analyses revealed that Q. suber may contain three major genetic clusters that likely result from isolation in refugia combined with posterior admixture and putative introgression from other Quercus species. Our results show a more complex structure scenario than previously inferred for Q. suber using nuclear markers and suggest that different southern populations contain high levels of genetic variation that may contribute to the resilience of Q. suber in a context of environmental change and adaptive pressure.
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Affiliation(s)
- Filipe Sousa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Joana Costa
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,RAIZ, Herdade de Espirra, Pegões, Portugal
| | - Carla Ribeiro
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
| | - Marta Varandas
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Francisco Pina-Martins
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Polytechnic Institute of Setúbal, ESTBarreiro, Setúbal, Portugal
| | - Fernanda Simões
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - José Matos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Maria Glushkova
- Forest Research Institute of B.A.S., Department of Forest Genetics, Physiology and Plantations, Sofia, Bulgaria
| | - Célia Miguel
- Faculdade de Ciências, Universidade de Lisboa, Biosystems & Integrative Sciences Institute, Lisboa, Portugal,iBET, Oeiras, Portugal
| | - Maria Manuela Veloso
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Unidade de Investigação de Biotecnologia e Recursos Genéticos, Oeiras, Portugal
| | - Margarida Oliveira
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Cândido Pinto Ricardo
- Universidade Nova de Lisboa (ITQB-NOVA), Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
| | - Dora Batista
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal,Instituto Superior de Agronomia, Universidade de Lisboa, LEAF—Linking Landscape, Environment, Agriculture and Food (LEAF), Lisboa, Portugal
| | - Octávio S. Paulo
- Faculdade de Ciências, Universidade de Lisboa, cE3c—Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal
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Development of the First Microsatellite Multiplex PCR Panel for Meagre (Argyrosomus regius), a Commercial Aquaculture Species. FISHES 2022. [DOI: 10.3390/fishes7030117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this study, a microsatellite-based multiplex PCR panel for meagre (Argyrosomus regius) was developed as a useful and single tool in parental assignment and population studies. Twenty-one specific and interspecific microsatellites from different aquaculture species of meagre (Argyrosomus regius), Japanese meagre (A. japonicus), red drum (Sciaenops ocellatus) and yellow meagre (Acoupa weakfish) were assessed for genetic variability, allelic range and genotype reliability. Finally, a SuperMultiplex for Argyrosomus regius (SMAr) was designed with only the best eight microsatellite markers. The panel assessment was performed using a batch of brood stock from one company and a sample of 616 offspring. It was possible to assign 95% of the offspring to a single pair of parents using the exclusion method. It is therefore considered an easy procedure, and a powerful and low-cost tool for parental assignment to support companies’ breeding programs and to exchange information between research groups.
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Driskill M, Pardee K, Hummer KE, Zurn JD, Amundsen K, Wiles A, Wiedow C, Patzak J, Henning JA, Bassil NV. Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers. PLoS One 2022; 17:e0257746. [PMID: 35421090 PMCID: PMC9009645 DOI: 10.1371/journal.pone.0257746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/06/2022] [Indexed: 11/18/2022] Open
Abstract
Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used to genotype 629 hop accessions from the US Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR), the USDA Forage Seed and Cereal Research (FSCR), and the University of Nebraska-Lincoln (UNL) collections. The SSR set identified unique genotypes except for 89 sets of synonymous samples. These synonyms included: cultivars with different designations, the same cultivars from different sources, heat-treated clones, and clonal variants. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Diversity was slightly higher in the cultivated samples due to larger sample size. Parentage and sib-ship analyses were used to identify true-to-type cultivars. The HI-AGA7 marker generated two male- and nine female-specific alleles among the cultivated and WNA samples. The SSR and KASP fingerprinting sets were compared in 190 samples consisting of cultivated and WNA accession for their ability to confirm identity and assess diversity and population structure. The SSR fingerprinting set distinguished cultivars, selections and WNA accessions while the KASP assays were unable to distinguish the WNA samples and had lower diversity estimates than the SSR set. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop for different purposes. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (<96) while the KASP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96).
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Affiliation(s)
- Mandie Driskill
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Katie Pardee
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Kim E. Hummer
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Jason D. Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Keenan Amundsen
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Annette Wiles
- Midwest Hops Producers, Plattsmouth, Nebraska, United States of America
| | - Claudia Wiedow
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Josef Patzak
- Hop Research Institute, Co, Ltd., Žatec, Czech Republic
| | - John A. Henning
- USDA-ARS, Forage Seed and Cereal Research Unit, Corvallis, Oregon, United States of America
| | - Nahla V. Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
- * E-mail:
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Labiros DA, Catalig AMP, Ymbong RRJ, Sakuntabhai A, Lluisma AO, Edillo FE. Novel and Broadly Applicable Microsatellite Markers in Identified Chromosomes of the Philippine Dengue Mosquitoes, Aedes aegypti (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:545-553. [PMID: 35134978 PMCID: PMC8924974 DOI: 10.1093/jme/tjab194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 05/12/2023]
Abstract
Dengue is the leading arboviral infection in the Philippines. Its endemicity in the country is due to the presence of its primary mosquito vector, Aedes aegypti (L.). This species has limited microsatellite markers. This study characterized microsatellite markers screened in silico from intergenic regions of the updated reference genome of Ae. aegypti from Liverpool, U.K. Criteria for good markers are: polymorphic, inherited in a Mendelian codominant manner, no null alleles, selectively neutral, randomly associated, and broadly applicable across different regions. Genotypes were scored using ABI Peak Scanner and were screened for the presence of null alleles. Hardy-Weinberg equilibrium, linkage disequilibrium, and robustness of the markers were determined by GENEPOP using Ae. aegypti samples from selected highland and lowland sites (n = 30 each) in the Philippines and outgroups (Thailand and Vietnam). Mendelian codominant inheritance was examined using F1 offspring of Ae. aegypti family (n = 30 each) derived from samples collected from Cebu city highlands and Maramag, Bukidnon. From the 63 randomly selected markers, nine were polymorphic. Two markers (Aaeg1-3D of chromosome 1 and Aaeg3-4C of chromosome 3) satisfied all criteria, hence, are good broadly useful microsatellite markers. Two other markers (Aaeg2-2E of chromosome 2 and Aaeg3-2A of chromosome 3) met all criteria but deviated from Mendelian codominant inheritance. These new markers of the Philippine Ae. aegypti with their chromosomal locations relative to the other published markers are presented, and will ultimately be useful in a variety of population genetic studies of Ae. aegypti to protect the public health.
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Affiliation(s)
- Dinesse A Labiros
- Department of Biology, University of San Carlos—Talamban Campus, Talamban, Cebu city, 6000, Philippines
| | - Antonio Mari P Catalig
- Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon city, Philippines
| | - Rhoniel Ryan J Ymbong
- Department of Biology, University of San Carlos—Talamban Campus, Talamban, Cebu city, 6000, Philippines
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Rue de Docteur Roux, 75015, Paris, France
- Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Arturo O Lluisma
- Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon city, Philippines
| | - Frances E Edillo
- Department of Biology, University of San Carlos—Talamban Campus, Talamban, Cebu city, 6000, Philippines
- Corresponding author, e-mail:
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Huang CJ, Chu FH, Huang YS, Tu YC, Hung YM, Tseng YH, Pu CE, Hsu CT, Chao CH, Chou YS, Liu SC, You YT, Hsu SY, Hsieh HC, Wang CT, Chen CT. SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis. Sci Rep 2022; 12:4126. [PMID: 35260700 PMCID: PMC8904461 DOI: 10.1038/s41598-022-07870-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 02/03/2022] [Indexed: 12/25/2022] Open
Abstract
Chamaecyparis formosensis is an endemic species of Taiwan, threatened from intensive use and illegal felling. An individual identification system for C. formosensis is required to provide scientific evidence for court use and deter illegal felling. In this study, 36 polymorphic simple sequence repeat markers were developed. By applying up to 28 non-linked of the developed markers, it is calculated that the cumulative random probability of identity (CPI) is as low as 1.652 × 10–12, and the identifiable population size is up to 60 million, which is greater than the known C. formosensis population size in Taiwan. Biogeographical analysis data show that C. formosensis from four geographic areas belong to the same genetic population, which can be further divided into three clusters: SY (Eastern Taiwan), HV and GW (Northwestern Taiwan), and MM (Southwestern Taiwan). The developed system was applied to assess the provenance of samples with 88.44% accuracy rate and therefore can serve as a prescreening tool to reduce the range required for comparison. The system developed in this study is a potential crime-fighting tool against illegal felling.
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Affiliation(s)
- Chiun-Jr Huang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan. .,Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan.
| | - Fang-Hua Chu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Yi-Shiang Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Ching Tu
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Yu-Mei Hung
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Yu-Hsin Tseng
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chang-En Pu
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Cheng Te Hsu
- Hualien Forest District Office, Forestry Bureau, Council of Agriculture, Hualien, 97051, Taiwan
| | - Chi-Hsiang Chao
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Yu-Shyang Chou
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan
| | - Shau-Chian Liu
- Department of Applied Science, National Taitung University, Taitung, 95092, Taiwan
| | - Ya Ting You
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Shuo-Yu Hsu
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsiang-Chih Hsieh
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chieh-Ting Wang
- The Experimental Forest, National Taiwan University, No. 12, Sec. 1, Qianshan Rd., Nantou County, 55750, Taiwan
| | - Chi-Tsong Chen
- Department of Forensic Science, Investigation Bureau, Ministry of Justice, New Taipei City, 23149, Taiwan.
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Wang H, Gao S, Liu Y, Wang P, Zhang Z, Chen D. A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi-sample genomic data. Ecol Evol 2022; 12:e8705. [PMID: 35342577 PMCID: PMC8928897 DOI: 10.1002/ece3.8705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 01/24/2023] Open
Abstract
Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next-generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi-sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared-pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high-quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.
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Affiliation(s)
- Hui Wang
- MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Shenghan Gao
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yu Liu
- MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
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Fopp-Bayat D, Chandra G, Nitkiewicz A. How Cold Shock Affects Ploidy Level and Early Ontogenetic Development of the Sterlet, A. ruthenus L. Int J Mol Sci 2022; 23:ijms23010494. [PMID: 35008920 PMCID: PMC8745760 DOI: 10.3390/ijms23010494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 02/04/2023] Open
Abstract
The objective of the present research was to study the effect of cold shock (3 °C and 6 °C) on fertilized eggs of the sterlet, Acipenser ruthenus L. Cold shock was applied for various durations (30, 60 and 90 min) and the ploidy levels, survival, and genotypes of the treated embryos/larvae were recorded. Analysis of ploidy levels confirmed the presence of diploid, triploid, and mosaic (1n/2n, 2n/3n, and 1n/2n/3n) genotypes in experimental groups, while it was strictly diploid in control groups. Microsatellite genotyping confirmed both the incidence of polyspermy and retention of the 2nd polar body in experimental groups. However, patterns of inheritance in all diploid offspring in experimental and control groups revealed classical Mendelian disomic inheritance. Interestingly, the observed mosaic sterlets had normal morphology and were alive. However, some larvae had abnormal morphology which may be due to haploid syndrome. In all treatment groups (treatments: 3 °C-30 min; 3 °C-60 min; 3 °C-90 min; 6 °C-60 min), where the percentage of polyploid/mosaic larvae were high, the mortality was also high. Whereas, in the control groups (where there were only diploid (2n) larvae), the mortality was relatively low.
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Melo PZ, Antunes AM, Fernandes JG, Targueta CP, Guimarães RA, Boaventura-Novaes CRD, Soares TN. Development of microsatellite markers in Pterodon pubescens and transferability to Pterodon emarginatus, two Brazilian plant species with medicinal potential. RODRIGUÉSIA 2022. [DOI: 10.1590/2175-7860202273091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Abstract Pterodon pubescens and P. emarginatus (Leguminosae) are native medicinal plants of Brazil. Extractivism due to its therapeutic properties threatens populations of both species. Studies of genetic diversity is a way to reason the use and promote conservation. We developed microsatellite markers for P. pubescens and transferred them to P. emarginatus to further genetic diversity investigation of these species. From genomic sequences of P. pubescens, obtained via the Illumina MiSeq platform, it was possible to identify 6,514 microsatellite regions, to design 5,419 primer pairs, and to test 30 markers amplification. We provide 26 polymorphic microsatellite markers, 10 of which were genotyped in 48 individuals per species. The number of alleles per locus range from 3 to 16, with high average genetic diversity ( P. pubescens HE = 0.753; P. emarginatus HE = 0.691). The genotyped markers have a high paternity exclusion probability (Q values greater than 0.99) and low probability of identity, indicating that set of loci is capable of individual discriminating in P. pubescens and P. emarginatus. Microsatellite markers provided in this study are a tool for population genetics studies and conservation of the two species and can be applied to closely related non-model species.
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Affiliation(s)
- Priscila Zei Melo
- Universidade Federal de Goiás, Brazil; Universidade Federal de Goiás, Brazil
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Sánchez-Velásquez JJ, Reyes-Flores LE, Yzásiga-Barrera C, Zelada-Mázmela E. Performance comparison of gel and capillary electrophoresis-based microsatellite genotyping strategies in a population research and kinship testing framework. BMC Res Notes 2021; 14:444. [PMID: 34876205 PMCID: PMC8650532 DOI: 10.1186/s13104-021-05861-9] [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: 06/17/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The advancement of molecular techniques in an era in which high-throughput sequencing has revolutionized biology renders old-fashioned alternatives to high-throughput methods obsolete. Such advanced molecular techniques, however, are not yet accessible to economically disadvantaged region-based laboratories that still obtain DNA profiles using gel-based techniques. To explore whether cost-efficient techniques can produce results that are as robust as those obtained using high-throughput methods, we compared the performance of polyacrylamide gel electrophoresis (PAGE)- and capillary electrophoresis (CE)-derived genomic data in estimating genetic diversity and inferring relatedness using 70 individuals of fine flounder (Paralichthys adspersus) selected from a hatchery population and genotyped for five microsatellite loci. RESULTS Here, we show that PAGE- and CE-derived genomic datasets yield comparable genetic diversity levels regarding allelic diversity measures and heterozygosity. However, relatedness inferred from each dataset showed that the categorization of dyads in the different relationship categories strongly differed. This suggests that while scientists can reliably use PAGE-derived genomic data to estimate genetic diversity, they cannot use the same for parentage testing. The findings could help laboratories committed to population research not be discouraged from using the PAGE system if high-throughput technologies are unavailable and the method is adequate to address the biological question.
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Affiliation(s)
- Julissa J Sánchez-Velásquez
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru
| | - Lorenzo E Reyes-Flores
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru
| | - Carmen Yzásiga-Barrera
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru
| | - Eliana Zelada-Mázmela
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru.
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Bairu MW, Amelework AB, Coetzer WG. Genetic diversity and population structure of six South African Acacia mearnsii breeding populations based on SSR markers. JOURNAL OF PLANT RESEARCH 2021; 134:1243-1252. [PMID: 34302570 DOI: 10.1007/s10265-021-01331-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Black wattle (Acacia mearnsii) has great economic value as a commercial source of tannins, timber and a source of firewood for local and international markets. It has been suggested that to maximize the genetic gain of A. mearnsii plantations in South Africa, the gene pool that exist within ICFR needs to be broadened via introduction of new genotypes with diverse traits. In this work, 282 A. mearnsii samples sourced from the ICFR breeding program were genotyped using 11 cross-species SSR markers. Our results showed low to moderate genetic differentiation (FST) among the six breeding subpopulations, with positive inbreeding (FIS) values that could be attributed to an historical inbreeding event. Low levels of relatedness could however indicate some mechanism of inbreeding avoidance. The effects from a recent supplementation of genetic material from two native Australian populations were observed through genetic structuring analyses. Analysis of molecular variance (AMOVA) revealed that significant genetic variation was mainly distributed within populations (75%) and among individuals (23%). The results provide significant information on A. mearnsii population genetic diversity and structure, which can be used for conservation of the current subpopulations and future tree improvement programs.
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Affiliation(s)
- Michael W Bairu
- Institute for Commercial Forestry Research (ICFR), P. O. Box 100281, Scottsville, 3209, South Africa
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria, 0001, South Africa
| | - Assefa B Amelework
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria, 0001, South Africa
| | - Willem G Coetzer
- Institute for Commercial Forestry Research (ICFR), P. O. Box 100281, Scottsville, 3209, South Africa.
- Department of Genetics, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa.
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Abd Hamid FN, Wan Ahmad WJ, Mohamad Ismail S, Ratnam W. High Genetic Diversity of Shorea acuminata Dyer in the Rehabilitated Area of a Degraded Lowland Dipterocarp Tropical Rainforest. FORESTS 2021; 12:1344. [DOI: 10.3390/f12101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The United Nation’s Decade on Ecosystem Restoration 2021–2030 aims to halt ecosystem degradation to achieve Sustainable Development Goals (SDGs) by 2030. In Malaysia, the concept of sustainable forest management (SFM) has been practiced since 1901. In this study, we evaluated the genetic diversity of the native dipterocarp timber tree Shorea acuminata in a rehabilitated area at Kenaboi Forest Reserve (Kenaboi FR). The rehabilitated area was formerly a degraded forest managed with the taungya restoration system for 50 years. All trees with diameter at breast height (DBH) of 5 cm and over were measured, tagged and identified in a one-hectare study plot. A total of 132 inner bark samples were collected for DNA extraction. Four SSR markers (Sle280, Sle392, Sle475 and Sle566) and two EST-SSR markers (SleE07 and SleE16) were used to analyse 95 good-quality DNA samples. Genetic diversity parameters including maternal contribution were determined for 75 samples. The genetic diversity of big trees (He = 0.656 ± 0.19) and small trees (He = 0.652 ± 0.17) were high and both were in genetic equilibrium, with Fis values of the big trees being 0.035 and small trees being 0.164. Clustering analysis based on Jaccard’s similarity values (at 95% confidence level) confirmed that big trees in the Kenaboi FR rehabilitated area had originated from genetically diverse seed trees of the Sungai Menyala Forest Reserve which were used as the planting stock for the taungya restoration system. Maternal contribution showed that the allele contribution of the small trees came from the planted S. acuminata trees within the study area. The high genetic diversity of small trees in this study provides strong evidence that the existing big trees would be suitable for a genetically diverse seed collection to rehabilitate other degraded forests. Sustainable forest management must emphasise genetic diversity in order to ensure the resilience of rehabilitated forest ecosystems.
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Evaluation of novel genomic markers for pedigree construction in an isolated population of Weddell Seals (Leptonychotes weddellii) at White Island, Antarctica. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01237-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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de Deus ARS, Silva GR, Sena LS, Britto FB, de Carvalho DA, de Freitas JVG, Sarmento JLR. Comparison of kinship estimates in Santa Inês sheep using microsatellite and genome-wide SNP markers. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Fopp-Bayat D, Nitkiewicz A, Chandra G. First report on embryonic and larval development of 2n/3n mosaic sterlet. Animal 2021; 15:100317. [PMID: 34340140 DOI: 10.1016/j.animal.2021.100317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/25/2022] Open
Abstract
Mosaicism is frequently observed in aquaculture practices, and it adversely affects the production as well as the restoration programme of the sturgeon. The purpose of the present study was the induction of 2n/3n mosaic in sterlet, Acipenser ruthenus L., and compare their embryonic and larval development with diploid control sterlet. Microsatellite DNA loci genotyping was conducted for the identification of the genotypes and parentage analysis. Embryonic development was monitored in experimental groups at every 24 h interval. Identification of individual stages of embryonic development was recorded based on a 36-degree scale of development. Additionally, the BW and body length (LT) of experimental fishes were taken during 110 days of the rearing period. The Fulton's condition coefficient (F), length-weight parameters, and specific growth rate (SGR) coefficient were calculated. The analysis of embryonic development of the 2n/3n mosaic and the diploid control group did not show differences. However, higher mortality (88%) was observed in 2n/3n mosaic groups in comparison to the diploid control groups (55%). BW and body length of 2n/3n mosaic sterlet were slightly lower than the diploid control sterlet, but the differences were not statistically significant. F analysis did not confirm a lower growth performance of the fishes in the 2n/3n mosaic group. Microsatellite DNA loci genotyping confirmed both the incidence of polyspermy and retention of the second polar body. This paper presents the first report on embryonic development and growth performance of 2n/3n mosaic sturgeons.
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Affiliation(s)
- D Fopp-Bayat
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, Poland.
| | - A Nitkiewicz
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, Poland
| | - G Chandra
- Department of Ichthyology and Aquaculture, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-718 Olsztyn, Poland
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Beketov SV, Piskunov AK, Voronkova VN, Petrov SN, Kharzinova VR, Dotsev AV, Zinovieva NA, Selionova MI, Stolpovsky YA. Genetic Diversity and Phylogeny of Fleece-Bearing Goats of Central and Middle Asia. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421070036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Podbielska A, Piórkowska K, Szmatoła T. Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland. Animals (Basel) 2021; 11:ani11082193. [PMID: 34438651 PMCID: PMC8388510 DOI: 10.3390/ani11082193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022] Open
Abstract
This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.
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Affiliation(s)
- Angelika Podbielska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
- Correspondence:
| | - Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland
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47
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Gutiérrez J, Seguel M, Saenz‐Agudelo P, Acosta‐Jamett G, Verdugo C. Genetic diversity and kinship relationships in one of the largest South American fur seal (
Arctocephalus australis
) populations of the Pacific Ocean. Ecol Evol 2021. [DOI: 10.1002/ece3.7683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Josefina Gutiérrez
- Instituto de Patología Animal Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
- Programa de Investigación Aplicada a la Fauna Silvestre Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
| | - Mauricio Seguel
- Department of Pathobiology Ontario Veterinary College University of Guelph ON Canada
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y Evolutivas Facultad de Ciencias Universidad Austral de Chile Valdivia Chile
| | - Gerardo Acosta‐Jamett
- Programa de Investigación Aplicada a la Fauna Silvestre Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
- Instituto de Medicina Preventiva Veterinaria Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
| | - Claudio Verdugo
- Instituto de Patología Animal Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
- Programa de Investigación Aplicada a la Fauna Silvestre Facultad de Ciencias Veterinarias Universidad Austral de Chile Valdivia Chile
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48
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Rahimi O, Ohana‐Levi N, Brauner H, Inbar N, Hübner S, Drori E. Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range. Ecol Evol 2021; 11:6657-6671. [PMID: 34141248 PMCID: PMC8207413 DOI: 10.1002/ece3.7519] [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] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.
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Affiliation(s)
- Oshrit Rahimi
- Department of Chemical EngineeringAriel UniversityArielIsrael
| | | | - Hodaya Brauner
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
| | - Nimrod Inbar
- Department of Civil EngineeringAriel UniversityArielIsrael
- The Department of Geophysics and Space ScienceEastern Regional R&D CenterArielIsrael
| | - Sariel Hübner
- Galilee Research Institute (Migal)Tel‐Hai Academic CollegeUpper GalileeIsrael
| | - Elyashiv Drori
- Department of Chemical EngineeringAriel UniversityArielIsrael
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
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49
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Liotta MN, Abbott JK, Morris MR, Rios‐Cardenas O. Antagonistic selection on body size and sword length in a wild population of the swordtail fish, Xiphophorus multilineatus: Potential for intralocus tactical conflict. Ecol Evol 2021; 11:3941-3955. [PMID: 33976786 PMCID: PMC8093718 DOI: 10.1002/ece3.7288] [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: 12/15/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 11/06/2022] Open
Abstract
Alternative reproductive tactics (ARTs) have provided valuable insights into how sexual selection and life history trade-offs can lead to variation within a sex. However, the possibility that tactics may constrain evolution through intralocus tactical conflict (IATC) is rarely considered. In addition, when IATC has been considered, the focus has often been on the genetic correlations between the ARTs, while evidence that the ARTs have different optima for associated traits and that at least one of the tactics is not at its optimum is often missing. Here, we investigate selection on three traits associated with the ARTs in the swordtail fish Xiphophorus multilineatus; body size, body shape, and the sexually selected trait for which these fishes were named, sword length (elongation of the caudal fin). All three traits are tactically dimorphic, with courter males being larger, deeper bodied and having longer swords, and the sneaker males being smaller, more fusiform and having shorter swords. Using measures of reproductive success in a wild population we calculated selection differentials, as well as linear and quadratic gradients. We demonstrated that the tactics have different optima and at least one of the tactics is not at its optimum for body size and sword length. Our results provide the first evidence of selection in the wild on the sword, an iconic trait for sexual selection. In addition, given the high probability that these traits are genetically correlated to some extent between the two tactics, our study suggests that IATC is constraining both body size and the sword from reaching their phenotypic optima. We discuss the importance of considering the role of IATC in the evolution of tactical dimorphism, how this conflict can be present despite tactical dimorphism, and how it is important to consider this conflict when explaining not only variation within a species but differences across species as well.
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Affiliation(s)
- Melissa N. Liotta
- Department of Biological SciencesThe Ohio Center for Ecological and Evolutionary StudiesOhio UniversityAthensOHUSA
| | | | - Molly R. Morris
- Department of Biological SciencesThe Ohio Center for Ecological and Evolutionary StudiesOhio UniversityAthensOHUSA
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Jeon JY, Jung JH, Suk HY, Lee H, Min MS. The Asian plethodontid salamander preserves historical genetic imprints of recent northern expansion. Sci Rep 2021; 11:9193. [PMID: 33911092 PMCID: PMC8080585 DOI: 10.1038/s41598-021-88238-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
The Korean Peninsula, located at the southern tip of Northeast Asia, has never been covered by ice sheets and was a temperate refugium during the Pleistocene. Karsenia koreana, the sole Asian plethodontid salamander species, occurs only on the southern half of the Korean Peninsula and is thought to have found various climatic refugia. Despite its phylogenetic and biogeographic importance, no population-level genetic analysis has been performed on this species. Here we study the population genetic structure of K. koreana using mitochondrial and microsatellite loci to understand the recent historical dispersion process that shaped its current distribution. Overall, the genetic distance between populations correlated well with the spatial distance, and the genetic structure among populations showed signs of a unilateral northward expansion from a southernmost refugium population. Given the distinct genetic structure formed among the populations, the level of historical gene flow among populations appears to have been very low. As the estimated effective population size of K. koreana was also small, these results suggest that the small, restricted populations of K. koreana are extremely vulnerable to environmental changes that may require high levels of genetic diversity to cope with. Thus, special management strategies are needed to preserve these remnant populations.
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Affiliation(s)
- Jong Yoon Jeon
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
| | - Ji-hwa Jung
- grid.31501.360000 0004 0470 5905Department of Forest Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Ho Young Suk
- grid.413028.c0000 0001 0674 4447Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 38541 South Korea
| | - Hang Lee
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
| | - Mi-Sook Min
- grid.31501.360000 0004 0470 5905Research Institute for Veterinary Science and Conservation Genome Resource Bank for Korean Wildlife, College of Veterinary Medicine, Seoul National University, Seoul, 08826 South Korea
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