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Abuelmaali SA, Mashlawi AM, Ishak IH, Wajidi MFF, Jaal Z, Avicor SW, Kassim NFA. Population genetic structure of Aedes aegypti subspecies in selected geographical locations in Sudan. Sci Rep 2024; 14:2978. [PMID: 38316804 PMCID: PMC10844603 DOI: 10.1038/s41598-024-52591-6] [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: 10/29/2023] [Accepted: 01/20/2024] [Indexed: 02/07/2024] Open
Abstract
Although knowledge of the composition and genetic diversity of disease vectors is important for their management, this is limiting in many instances. In this study, the population structure and phylogenetic relationship of the two Aedes aegypti subspecies namely Aedes aegypti aegypti (Aaa) and Aedes aegypti formosus (Aaf) in eight geographical areas in Sudan were analyzed using seven microsatellite markers. Hardy-Weinberg Equilibrium (HWE) for the two subspecies revealed that Aaa deviated from HWE among the seven microsatellite loci, while Aaf exhibited departure in five loci and no departure in two loci (A10 and M201). The Factorial Correspondence Analysis (FCA) plots revealed that the Aaa populations from Port Sudan, Tokar, and Kassala clustered together (which is consistent with the unrooted phylogenetic tree), Aaf from Fasher and Nyala populations clustered together, and Gezira, Kadugli, and Junaynah populations also clustered together. The Bayesian cluster analysis structured the populations into two groups suggesting two genetically distinct groups (subspecies). Isolation by distance test revealed a moderate to strong significant correlation between geographical distance and genetic variations (p = 0.003, r = 0.391). The migration network created using divMigrate demonstrated that migration and gene exchange between subspecies populations appear to occur based on their geographical proximity. The genetic structure of the Ae. aegypti subspecies population and the gene flow among them, which may be interpreted as the mosquito vector's capacity for dispersal, were revealed in this study. These findings will help in the improvement of dengue epidemiology research including information on the identity of the target vector/subspecies and the arboviruses vector surveillance program.
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Affiliation(s)
- Sara A Abuelmaali
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
- National Public Health Laboratory, Federal Ministry of Health, Khartoum, 11115, Sudan
| | - Abadi M Mashlawi
- Department of Biology, College of Science, Jazan University, P.O. Box. 114, Jazan, 45142, Kingdom of Saudi Arabia
| | - Intan Haslina Ishak
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | | | - Zairi Jaal
- Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Silas Wintuma Avicor
- Molecular Entomology Research Group, Universiti Sains Malaysia, 11800, Penang, Malaysia
- Entomology Division, Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
| | - Nur Faeza Abu Kassim
- 129 Medical Entomology Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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Mansour H, Alamer KH, Al-Hasawi ZM. Population Genetics, Genetic Structure, and Inbreeding of Commiphora gileadensis (L.) C. Chr Inferred from SSR Markers in Some Mountainous Sites of Makkah Province. PLANTS (BASEL, SWITZERLAND) 2023; 12:2506. [PMID: 37447067 DOI: 10.3390/plants12132506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Commiphora gileadensis (L.) C. Chr is a perennial plant existing mainly in the southern and western mountains of the Arabian Peninsula. In the Makkah province, the remaining populations are threatened by many factors such as overcutting, overgrazing, and urban developments. These dangers are expected to be aggravated by the progression of aridification factors arising from climate change. To overcome the decline in remaining populations of this valuable species, a timely evaluation of the population's genetic variables and genetic structure is vital for the conservation of existing C. gileadensis populations. In this study, we used 61 SSR primers to achieve this objective. Only 50 loci showed polymorphisms, which led to further analysis of the population genetics for 600 genotypes that were collected from 50 populations of C. gileadensis found in 10 different sites in the Makkah region: Gebel Al Muliesaa, Wadi Albathna, Wadi Houra, Wadi Albaidaa, Wadi Elebiedia, Gebel Kniethl, Wadi Sayaa, Wadi Elbarasa, Wadi Alfawara, and Wadi Alkharar. The results showed an obvious decrease in genetic diversity variables in all studied populations. The range of PPL was between 8 and 40; additionally, the low HT value of 0.804 and the high value of inbreeding, Fis = 0.238, reflected a severe lack of heterozygotes. High levels of FST and GST and low gene flow indicate considerable segregation among the C. gileadensis populations, which creates a barrier to gene migration. Our data suggest the need for conservation planning for C. gileadensis in order to avoid the species' forthcoming extinction. Efforts should be largely oriented around managing water consumption, prohibiting overcutting and overgrazing, and establishing appropriate seed banks.
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Affiliation(s)
- Hassan Mansour
- Biological Sciences Department, Faculty of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Khalid H Alamer
- Biological Sciences Department, Faculty of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Zaki M Al-Hasawi
- Biological Sciences Department, Faculty of Science and Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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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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Mansour H, Alsamadany H, Al-Hasawi ZM. Molecular Assessment of Genetic Diversity and Genetic Structure of Rhanterium epapposum Oliv. in Scarce Populations in Some Regions of Western Saudi Arabia. PLANTS 2022; 11:plants11121560. [PMID: 35736710 PMCID: PMC9230628 DOI: 10.3390/plants11121560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Rhanterium epapposum Oliv. is a perennial medicinal shrub growing mainly in desert habitats in the Arabian Peninsula. In western Saudi Arabia, the remaining few populations of this species are exposed to many threats, including overcutting, overgrazing, and recently, increasing human activities. These threats are predicted to be exacerbated by the advancement of aridification caused by climate change. The conservation and recovering of the diminished populations of R. epapposum necessitate measurement of their genetic diversity and genetic differentiation. To accomplish this objective, we tested 150 simple sequence repeat (SSR) primer pairs, with which 40 polymorphic loci were identified. These polymorphic loci were used to determine the population genetics of 540 plant accessions sampled from a total of 45 populations of R. epapposum located in 8 sites in western Saudi Arabia: Wadi Khurieba, Wadi Al Khamas, Gebel Al Twaal, Al Asaafer, Wadi ALHamda, Wadi Al Nassayeif, Wadi Qaraba, Wadi Kuliayah, and Wadi Dahban. Low levels of genetic diversity were found in all populations (the values of the PPL ranged between 52.5 and 15) along with a declined value of HT (0.123) and a considerable inbreeding value (F = 0.942), which confirmed a noticeable shortage of heterozygotes. High genetic differentiation among the populations and a low value of gene flow are indicative of high isolation among the R. epapposum populations, which has caused a severe deficiency in gene migration. The data obtained herein inspire several recommendations for conservation and retrieval of the existing populations, including seed banks, restoration of diminished populations, and monitoring and prevention of cutting and grazing activities at threatened sites. All of these measures are urgently required to avoid imminent extinction.
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Affiliation(s)
- Hassan Mansour
- Department of Biological Sciences, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia;
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: ; Tel.: +96-65-0674-1048
| | - Hameed Alsamadany
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Zaki M. Al-Hasawi
- Department of Biological Sciences, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia;
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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Mustafa MSEK, Jaal Z, Abu Kashawa S, Mohd Nor SA. Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan. Malar J 2021; 20:469. [PMID: 34923983 PMCID: PMC8684682 DOI: 10.1186/s12936-021-03994-7] [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: 12/14/2020] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Background Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis populations for developing control strategies. Methods Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published An. gambiae microsatellite loci primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant FST was observed between all pairwise analyses of An. arabiensis populations. The Kassala state population indicated high genetic differentiation (FST ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among the An. arabiensis populations investigated in Sudan, with the exception of Kassala state.
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Affiliation(s)
| | - Zairi Jaal
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Sumia Abu Kashawa
- Faculty of Science, Department of Zoology, University of Khartoum, Khartoum, Sudan
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
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Ab Razak S, Ghazalli MN, Azman NHEN, Abd Majid AM, Ismail SN. RAD sequencing for the development of microsatellite markers for identification of Malaysian taro cultivars. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1969278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Shahril Ab Razak
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, MARDI Headquarters, Serdang, Selangor, Malaysia
| | - Mohd Norfaizal Ghazalli
- Resource Utilisation and Agrobiodiversity Conservation Programme, Agrobiodiversity and Environment Research Centre, MARDI Headquarters, Serdang, Selangor, Malaysia
| | - Nor Helwa Ezzah Nor Azman
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, MARDI Headquarters, Serdang, Selangor, Malaysia
| | - Alny Marlynni Abd Majid
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, MARDI Headquarters, Serdang, Selangor, Malaysia
| | - Siti Norhayati Ismail
- Agri-Omics and Bioinformatics Programme, Biotechnology and Nanotechnology Research Centre, MARDI Headquarters, Serdang, Selangor, Malaysia
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Sartori RQ, Lopes AG, Aires LPN, Bianchi RDC, de Mattos CCB, Morales AC, Castiglioni L. Identifying Priority Giant Anteater ( Myrmecophaga tridactyla) Populations for Conservation in São Paulo State, Brazil. Ecol Evol 2021; 11:700-713. [PMID: 33520159 PMCID: PMC7820152 DOI: 10.1002/ece3.6809] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 11/11/2022] Open
Abstract
Habitat loss is the main threat to biodiversity conservation worldwide. Some species may be particularly susceptible to the effects of fragmentation and the isolation of populations. The impacts of human activity on wild animal populations may be understood through relationships between individual genetic data and spatial landscape variables, particularly when considering local population dynamics influenced by fragmented habitats. Thus, the objective of this study was to analyze the population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla) using an individual sampling scheme (ISS) on a regional geographic scale. Data were collected from 41 specimens from twenty different locations in São Paulo State, Brazil, and six polymorphic microsatellite loci were genotyped. Our results indicate that barriers to gene flow exist and have segregated individuals of the farther away areas into two spatially structured clusters. The populations were also found to have high genetic diversity. The experimental sampling approach used herein enabled an analysis of the population dynamics of the giant anteater on a regional scale, as well as the identification of priority populations for genetic resource conservation for this species. The results reflect the need for adequate management plans. The efficacy of the sampling scheme may vary based on the study model used, but we argue that the use of an ISS combined with suitable molecular markers and statistical methods may serve as an important tool for initial analyses of threatened or vulnerable species, particularly in anthropized regions where populations are small or hard to characterize.
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Affiliation(s)
- Ricardo Quiterio Sartori
- School of Biosciences, Humanities, and Exact SciencesGraduate Program in BiosciencesSão Paulo State University (UNESP)São José do Rio PretoSão Paulo StateBrazil
| | - Alessandro Garcia Lopes
- School of Biosciences, Humanities, and Exact SciencesGraduate Program in BiosciencesSão Paulo State University (UNESP)São José do Rio PretoSão Paulo StateBrazil
| | | | - Rita de Cassia Bianchi
- School of Agricultural and Veterinary ScienceSão Paulo State University (UNESP)JaboticabalSão Paulo StateBrazil
| | | | - Adriana Coletto Morales
- School of Agricultural and Veterinary ScienceSão Paulo State University (UNESP)JaboticabalSão Paulo StateBrazil
| | - Lilian Castiglioni
- School of Biosciences, Humanities, and Exact SciencesGraduate Program in BiosciencesSão Paulo State University (UNESP)São José do Rio PretoSão Paulo StateBrazil
- São José do Rio Preto Medical School (FAMERP)São José do Rio PretoSão Paulo StateBrazil
- Rio Preto University Center (UNIRP)São José do Rio PretoSão Paulo StateBrazil
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Ab Razak S, Mad Radzuan S, Mohamed N, Nor Azman NHE, Abd Majid AM, Ismail SN, Mohd Yusof MF, Sarip J, Nasir KH. Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan ( Nephelium lappaceum L.) germplasm. Heliyon 2020; 6:e05077. [PMID: 33024864 PMCID: PMC7527576 DOI: 10.1016/j.heliyon.2020.e05077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/18/2020] [Accepted: 09/23/2020] [Indexed: 12/24/2022] Open
Abstract
The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.
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Affiliation(s)
- Shahril Ab Razak
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Salehudin Mad Radzuan
- Horticulture Research Centre, MARDI Sintok, 06050, Bukit Kayu Hitam, Kedah, Malaysia
| | - Norkhairi Mohamed
- Department of Agriculture, Hulu Paka Agricultural Centre, 23300, Dungun, Terengganu, Malaysia
| | - Nor Helwa Ezzah Nor Azman
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Alny Marlynni Abd Majid
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Siti Norhayati Ismail
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | | | - Johari Sarip
- Horticulture Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Khairun Hisam Nasir
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
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Mansour H, Alsamadany H, Al-Hasawi ZM. Genetic diversity and genetic structure of Salvadora persica L., rare plant species in Rabigh province, Saudi Arabia: implications for conservation. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2020. [DOI: 10.1080/16583655.2020.1787640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Hassan Mansour
- Department of Biological Sciences, Rabigh-College of Science & Art, King Abdulaziz University, Rabigh, Saudi Arabia
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Hameed Alsamadany
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zaki M. Al-Hasawi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Rabigh-College of Science & Art, King Abdulaziz University, Rabigh, Saudi Arabia
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Watts AM, Hopkins GA, Goldstien SJ. Chimerism and population dieback alter genetic inference related to invasion pathways and connectivity of biofouling populations on artificial substrata. Ecol Evol 2019; 9:3089-3104. [PMID: 30962883 PMCID: PMC6434572 DOI: 10.1002/ece3.4817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/06/2018] [Accepted: 11/12/2018] [Indexed: 11/11/2022] Open
Abstract
Disentangling pathways by which nonindigenous species expand and spread regionally remains challenging. Molecular ecology tools are often employed to determine the origins and spread of introduced species, but the complexities of some organisms may be reducing the efficacy of these tools. Some colonial species exhibit complexities by way of chimerism and winter colony regression, which may alter the genetic diversity of populations and mask the connectivity occurring among them. This study uses nuclear microsatellite data and simple GIS-based modeling to investigate the influence of chimerism and winter regression on the genetic diversity and patterns of genetic population connectivity among colonies of Didemnum vexillum on artificial substrates. Colonies sampled in summer were shown to form a metapopulation, with high levels of admixture, extreme outcrossing, and some substructure. These patterns were consistent within the subsampled winter colonies and with the inclusion of chimeric data. However, allelic richness and diversity were significantly different between winter and summer samples, altering interpretations relating to population connectivity and pelagic larval duration. This study demonstrates the importance of including seasonal sampling and imperative life history traits in genetic studies for clear interpretations and the successful management of introduced species.
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Affiliation(s)
- Ashleigh Marie Watts
- School of Biological SciencesUniversity of CanterburyCanterburyNew Zealand
- Coastal and Freshwater GroupCawthron InstituteNelsonNew Zealand
- Present address:
Tonkin + Taylor International LtdChristchurchNew Zealand
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Hou X, Xu P, Lin Z, D'Urban-Jackson J, Dixon A, Bold B, Xu J, Zhan X. Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population. Integr Zool 2018; 13:553-568. [PMID: 29316314 DOI: 10.1111/1749-4877.12305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.
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Affiliation(s)
- Xian Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,School of Nature Conservation, Beijing Forestry University, Beijing, China
| | | | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Andrew Dixon
- Emirates Falconers' Club, Abu Dhabi, United Arab Emirates.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China
| | - Batbayar Bold
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Wildlife Science and Conservation Center, Ulaanbaatar, Mongolia
| | - Jiliang Xu
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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12
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Microsatellite Analysis for Identification of Individuals Using Bone from the Extinct Steller's Sea Cow (Hydrodamalis gigas). Methods Mol Biol 2017. [PMID: 28502003 DOI: 10.1007/978-1-4939-6990-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Microsatellite DNA can provide more detailed population genetic information than mitochondrial DNA which is normally used to research ancient bone. The methods detailed in this chapter can be utilized for any type of bone. However, for this example, four microsatellite loci were isolated from Steller's sea cow (Hydrodamalis gigas) using published primers for manatee and dugong microsatellites. The primers DduC05 (Broderick et al., Mol Ecol Notes 6:1275-1277, 2007), Tmakb60, TmaSC5 (Pause et al., Mol Ecol Notes 6: 1073-1076, 2007), and TmaE11 (Garcia-Rodriguez et al., Mol Ecol 12:2161-2163, 2000) all successfully amplified microsatellites from H. gigas. The DNA samples were from bone collected on Bering or St. Lawrence Islands. DNA was analyzed using primers with the fluorescent label FAM-6. Sequenced alleles were then used to indicate a difference in the number of repeats and thus a difference in individuals. This is the first time that H. gigas microsatellite loci have been isolated. These techniques for ancient bone microsatellite analysis allow an estimate of population size for a newly discovered St. Lawrence Island sea cow population.
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A genome survey sequence (GSS) analysis and microsatellite marker development for Indian mackerel, Rastrelliger kanagurta , using Ion Torrent technology. Meta Gene 2016. [DOI: 10.1016/j.mgene.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Mansour H, Bryngelsson T, Garkava-Gustavsson L. Development, characterization and transferability of 10 novel microsatellite markers in Cotoneaster orbicularis Schltdl. (Rosaceae). J Genet 2016; 95:e9-e12. [PMID: 27659209 DOI: 10.1007/s12041-016-0687-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Hassan Mansour
- Faculty of Science, Department of Botany, Suez Canal University, 41522 Ismailia, Egypt.
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Kulibaba RA, Liashenko YV. Influence of the PCR artifacts on the genotyping efficiency by the microsatellite loci using native polyacrylamide gel electrophoresis. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716030087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Tan MP, Jamsari AFJ, Siti Azizah MN. Genotyping of microsatellite markers to study genetic structure of the wild striped snakehead Channa striata in Malaysia. JOURNAL OF FISH BIOLOGY 2016; 88:1932-1948. [PMID: 27027270 DOI: 10.1111/jfb.12956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
Genetic variability and differences in wild striped snakehead Channa striata from Malaysia were analysed by genotyping nine novel nuclear microsatellite loci. Analysis revealed moderate-to-high genetic diversity in most of the populations, indicative of large effective population sizes. The highly diversified populations are admixed populations and, therefore, can be recommended as potential candidates for selective breeding and conservation since they each contain most of the alleles found in their particular region. Three homogenous groups of the wild populations were identified, apparently separated by effective barriers, in accordance with contemporary drainage patterns. The highest population pairwise FST found between members of the same group reflects the ancient population connectivity; yet prolonged geographical isolation resulted in adaptation of alleles to local contemporary environmental change. A significant relationship between genetic distance and geographical isolation was observed (r = 0·644, P < 0·01). Anthropogenic perturbations indicated apparent genetic proximity between distant populations.
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Affiliation(s)
- M P Tan
- School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
- Institut Akuakultur Tropika (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - A F J Jamsari
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - M N Siti Azizah
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
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Valdivia C, Carvajal CA, Campino C, Allende F, Martinez-Aguayo A, Baudrand R, Vecchiola A, Lagos CF, Tapia-Castillo A, Fuentes CA, Aglony M, Solari S, Kalergis AM, García H, Owen GI, Fardella CE. Citosine-Adenine-Repeat Microsatellite of 11β-hydroxysteroid dehydrogenase 2 Gene in Hypertensive Children. Am J Hypertens 2016; 29:25-32. [PMID: 25907225 DOI: 10.1093/ajh/hpv052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/17/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The impairment of 11β-hydroxysteroid dehydrogenase type 2 enzyme (11βHSD2) results in an inefficient conversion of cortisol to cortisone, which triggers hypertension. Cytosine-adenine repeat (CA repeat) microsatellite has been associated with low HSD11B2 gene expression. AIM To determine whether the CA-repeat length in intron 1 affect the serum cortisol to cortisone (F/E) ratio and/or blood pressure (BP) levels in pediatric subjects. SUBJECTS AND METHODS Eighty-one hypertensive (HT) and 117 normotensive (NT) subjects participated in this study. We measured BP levels, as well as the F and E and F/E ratio in morning sera and 12-hour urine samples. The length of CA repeats was determined through fragment analysis. We compared the allele distribution between the HT and NT groups, and the patients were dichotomized into groups with short alleles (S) (<21 CA repeats) or long alleles (L), and also in groups according genotype (allele combination: S/S and S/L + L/L). RESULTS We found no differences in the distribution of CA-repeat allelic length between the NT and HT groups (P = 0.7807), and there was no correlation between the CA-repeat allelic length and BP (P = 0.1151) levels or the serum F/E ratio (P = 0.6778). However, the serum F/E ratio was higher in the HT group than in the NT group (P = 0.0251). The serum F/E ratio was associated with systolic BP index independent of body mass index only in HT group. CONCLUSIONS The CA-repeat length did not influence BP levels or serum F/E ratios in pediatric subjects. However, the serum F/E ratio was associated with BP, suggesting a role of 11βHSD2 in mineralocorticoid hypertension.
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Affiliation(s)
- Carolina Valdivia
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristian A Carvajal
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Carmen Campino
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Fidel Allende
- Departamento de Laboratorios Clínicos, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandro Martinez-Aguayo
- Unidad de Endocrinología, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rene Baudrand
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrea Vecchiola
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Carlos F Lagos
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile; Facultad de Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Alejandra Tapia-Castillo
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristobal A Fuentes
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Marlene Aglony
- Unidad de Endocrinología, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sandra Solari
- Departamento de Laboratorios Clínicos, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M Kalergis
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile; Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile
| | - Hernan García
- Unidad de Endocrinología, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gareth I Owen
- Departamento de Fisiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos E Fardella
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute on Immunology and Immunotherapy, Santiago, Chile;
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Nazia AK, Siti Azizah MN. Isolation of microsatellites in the bighead catfish, Clarias macrocephalus and cross-amplification in selected Clarias species. Mol Biol Rep 2014; 41:1207-13. [PMID: 24381108 DOI: 10.1007/s11033-013-2965-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 12/23/2013] [Indexed: 11/30/2022]
Abstract
The present study documents the isolation of eight polymorphic microsatellite markers from the bighead catfish, Clarias macrocephalus and cross-amplification in two other catfish species. The number of alleles per locus in C. macrocephalus ranged from 2 to 21. The most polymorphic locus was NCm-G12 with 21 alleles while the least polymorphic locus was NCm-H2 with only two alleles. Locus NCm-F8 significantly deviated from Hardy-Weinberg equilibrium (P value <0.05) after Bonferroni correction. Linkage disequilibrium was non-significant in all loci comparisons. The observed and expected heterozygosities varied from 0.033 to 0.967 and from 0.033 to 0.942, respectively. Mean polymorphic information content for the eight loci was 0.765. Cross-amplification was successfully performed with two other catfish species, C. batrachus and C. meladerma for all eight loci. Locus NCm-D8 was monomorphic in both species while NCm-F8 was monomorphic only in C. batrachus. These newly developed markers would be useful for better management and conservation of the economically important C. macrocephalus species.
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Affiliation(s)
- A K Nazia
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia,
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Mansour H, Jiménez A, Keller B, Nowak MD, Conti E. Development of 13 microsatellite markers in the endangered Sinai primrose (Primula boveana, Primulaceae). APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1200515. [PMID: 25202556 PMCID: PMC4105029 DOI: 10.3732/apps.1200515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 11/16/2012] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY We developed microsatellite markers for the endangered plant Primula boveana, the Sinai primrose, and assessed the cross-transferability of these markers to six related taxa. • METHODS AND RESULTS DNA sequences containing microsatellites were isolated from a microsatellite-enriched library. We obtained successful amplification of 13 microsatellite primer pairs, seven of which were polymorphic in P. boveana. Eleven of these primers successfully cross-amplified to related taxa. • CONCLUSIONS The markers reported herein will be useful to characterize the genetic diversity of the endangered P. boveana and to evaluate its mating system, and have the potential to be useful for similar studies in close relatives.
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Affiliation(s)
- Hassan Mansour
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; and
| | - Ares Jiménez
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich 8008, Switzerland
| | - Barbara Keller
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich 8008, Switzerland
| | - Michael D. Nowak
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich 8008, Switzerland
| | - Elena Conti
- Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, Zurich 8008, Switzerland
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Liu J, Sun ZX, Chen YT, Jiang JM. Isolation and characterization of microsatellite loci from an endangered tree species, Toona ciliata var. pubescens. GENETICS AND MOLECULAR RESEARCH 2012; 11:4411-7. [DOI: 10.4238/2012.september.19.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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