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Taraveau F, Bru D, Quembo CJ, Jourdan-Pineau H. Development of microsatellite markers for the soft tick Ornithodoros phacochoerus. Parasit Vectors 2024; 17:301. [PMID: 38992704 PMCID: PMC11238500 DOI: 10.1186/s13071-024-06382-7] [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: 01/23/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Soft ticks of the genus Ornithodoros are responsible for the maintenance and transmission of the African swine fever (ASF) virus in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of the Borrelia species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical Ornithodoros ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study is to design microsatellite markers that could be used for ticks of the Ornithodoros moubata complex, particularly Ornithodoros phacochoerus, to assess population structure and tick movements in ASF endemic areas. METHODS A total of 151 markers were designed using the O. moubata and O. porcinus genomes after elimination of repeated sequences in the genomes. All designed markers were tested on O. phacochoerus and O. porcinus DNA to select the best markers. RESULTS A total of 24 microsatellite markers were genotyped on two populations of O. phacochoerus and on individuals from four other Ornithodoros species. Nineteen markers were selected to be as robust as possible for population genetic studies on O. phacochoerus. CONCLUSIONS The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of O. phacochoerus.
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Affiliation(s)
- Florian Taraveau
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, 34398, Montpellier, France.
| | - David Bru
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, 34398, Montpellier, France
| | - Carlos João Quembo
- Central Region Office-Regional Veterinary Laboratory, Agricultural Research Institute of Mozambique, Chimoio, EN6.CP42, Mozambique
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Olah G, Waples RS, Stojanovic D. Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot. Ecol Evol 2024; 14:e11102. [PMID: 38524913 PMCID: PMC10961163 DOI: 10.1002/ece3.11102] [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: 08/01/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.
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Affiliation(s)
- George Olah
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Robin S. Waples
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Dejan Stojanovic
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
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Koontz AC, Schumacher EK, Spence ES, Hoban SM. Ex situ conservation of two rare oak species using microsatellite and SNP markers. Evol Appl 2024; 17:e13650. [PMID: 38524684 PMCID: PMC10960078 DOI: 10.1111/eva.13650] [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: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
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Affiliation(s)
| | | | - Emma S. Spence
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
- Cornell UniversityDepartment of Public and Ecosystem HealthIthacaNew YorkUSA
| | - Sean M. Hoban
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
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White SL, Rash JM, Kazyak DC. Is now the time? Review of genetic rescue as a conservation tool for brook trout. Ecol Evol 2023; 13:e10142. [PMID: 37250443 PMCID: PMC10213484 DOI: 10.1002/ece3.10142] [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: 02/24/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Brook trout populations have been declining throughout their native range in the east coast of the United States. Many populations are now distributed in small, isolated habitat patches where low genetic diversity and high rates of inbreeding reduce contemporary viability and long-term adaptive potential. Although human-assisted gene flow could theoretically improve conservation outcomes through genetic rescue, there is widespread hesitancy to use this tool to support brook trout conservation. Here, we review the major uncertainties that have limited genetic rescue from being considered as a viable conservation tool for isolated brook trout populations and compare the risks of genetic rescue with other management alternatives. Drawing on theoretical and empirical studies, we discuss methods for implementing genetic rescue in brook trout that could yield long-term evolutionary benefits while avoiding negative fitness effects associated with outbreeding depression and the spread of maladapted alleles. We also highlight the potential for future collaborative efforts to accelerate our understanding of genetic rescue as a viable tool for conservation. Ultimately, while we acknowledge that genetic rescue is not without risk, we emphasize the merits that this tool offers for protecting and propagating adaptive potential and improving species' resilience to rapid environmental change.
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Affiliation(s)
- Shannon L. White
- U.S. Geological Survey Eastern Ecological Science CenterKearneysvilleWest VirginiaUSA
| | - Jacob M. Rash
- North Carolina Wildlife Resources CommissionMarionNorth CarolinaUSA
| | - David C. Kazyak
- U.S. Geological Survey Eastern Ecological Science CenterKearneysvilleWest VirginiaUSA
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Pinzari CA, Bellinger MR, Price D, Bonaccorso FJ. Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, 'ōpe'ape'a, across the Hawaiian Islands. PeerJ 2023; 11:e14365. [PMID: 36718450 PMCID: PMC9884036 DOI: 10.7717/peerj.14365] [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: 01/17/2022] [Accepted: 10/19/2022] [Indexed: 01/26/2023] Open
Abstract
Island bat species are disproportionately at risk of extinction, and Hawai'i's only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as 'ōpe'ape'a, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988-2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawai'i, Maui, O'ahu, and Kaua'i. Genetic differentiation occurred between Hawai'i and Maui, both of which were differentiated from O'ahu and Kaua'i. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawai'i and Kaua'i. Contemporary genetic effective population sizes were smaller on O'ahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawai'i. Our study provides population-level estimates for the genetic diversity and geographic structure of 'ōpe'ape'a, that could be used by agencies tasked with wildlife conservation in Hawai'i.
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Affiliation(s)
- Corinna A. Pinzari
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,Hawaiʻi Cooperative Studies Unit, University of Hawaiʻi at Hilo, Hawaiʻi National Park, Hawaiʻi, United States of America
| | - M. Renee Bellinger
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,Hawaiʻi Cooperative Studies Unit, University of Hawaiʻi at Hilo, Hawaiʻi National Park, Hawaiʻi, United States of America,Pacific Island Ecosystems Research Center, U.S. Geological Survey, Hawaiʻi National Park, Hawaiʻi, United States of America
| | - Donald Price
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawaiʻi at Hilo, Hilo, Hawaiʻi, United States of America,School of Life Sciences, University of Nevada - Las Vegas, Las Vegas, NV, United States of America
| | - Frank J. Bonaccorso
- Pacific Island Ecosystems Research Center, U.S. Geological Survey, Hawaiʻi National Park, Hawaiʻi, United States of America
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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Galla SJ, Mittan-Moreau CS, Barbosa S. Capturing conservation in the post-genomics era: a book review of “Conservation and Genomics of Populations.”. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01481-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Genetic Structure of the Ca Rater Mallorquí Dog Breed Inferred by Microsatellite Markers. Animals (Basel) 2022; 12:ani12202733. [PMID: 36290119 PMCID: PMC9597762 DOI: 10.3390/ani12202733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/09/2022] Open
Abstract
Ca Rater Mallorquí is a dog breed from the Island of Mallorca (Spain) traditionally used as a hunting and ratting dog to prevent disease spread and economic losses related to rodent activities on farms. However, the census data shows a population decline that should be addressed by implementing a conservation program. The first step to implementing a conservation plan is knowing the genetic situation of the Ca Rater Mallorquí population. Therefore, we aimed to genetically characterise the breed in our study. We analysed 33 microsatellites recommended by the International Society of Animal Genetics (ISAG) in 77 samples. Data were obtained from 13 samples of Balearic, Spanish, and international dog breeds to study the genetic diversity among breeds. The population did not significantly deviate from the Hardy-Weinberg equilibrium with heterozygosity (Ho) of 0.655 and expected heterozygosity (He) of 0.685. The Wright's fixation indices, the Factorial Correspondence Analysis (FCA), a dendrogram representing Reynolds genetic distance between populations, and the pairwise FST values establish the Ca Rater Mallorquí as an independent breed distinct from the Balearic, Spanish, and international breeds.
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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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