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Masunungure C, Manyani A, Dalu MTB, Ngorima A, Dalu T. Decision support tools for invasive alien species management should better consider principles of robust decision making. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165606. [PMID: 37474055 DOI: 10.1016/j.scitotenv.2023.165606] [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: 04/27/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
Invasive alien species (IAS) pose global threat to economies and biodiversity. With rising number of species and limited resources, IAS management must be prioritised; yet agreed tools to assist decision-making and their application are currently inadequate. There is need for simple decision support tools (DST) that guide stakeholders to optimise investment based on objective and quantifiable criteria. This paper reviews DSTs for IAS management to assess their availability and application of principles of robust decision-making. The aim is to provide guidance towards adopting the principles of robust decision-making to improve applicability and practical use of DST. A literature search conducted to identify relevant studies that report on DST in biological invasion. Results indicate an increase in availability of DST; however, available studies are largely biased in geographical, habitat and taxonomic focus. The results also show challenges in practical use of existing tools as most of them do not apply principles of robust decision-making. Application of these principles has the potential to overcome weakness of the current decision-making process and as such, enable decision-makers to efficiently allocate resources towards IAS management. A call is made for more consideration and adoption of principles of robust decision-making when developing DST for IAS invasions.
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Affiliation(s)
- Current Masunungure
- Sustainability Research Unit, Nelson Mandela University, George Campus, South Africa.
| | - Amanda Manyani
- Centre for Sustainability Transitions, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Mwazvita T B Dalu
- School of Biology and Environmental Sciences, University of Mpumalanga, Nelspruit 1200, South Africa
| | | | - Tatenda Dalu
- School of Biology and Environmental Sciences, University of Mpumalanga, Nelspruit 1200, South Africa; Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa.
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Phylogeographic structure of common sage (Salvia officinalis L.) reveals microrefugia throughout the Balkans and colonizations of the Apennines. Sci Rep 2022; 12:15726. [PMID: 36130954 PMCID: PMC9492721 DOI: 10.1038/s41598-022-20055-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Studying the population-genetic and phylogeographic structures of a representative species of a particular geographical region can not only provide us with information regarding its evolutionary history, but also improve our understanding of the evolutionary processes underlying the patterns of species diversity in that area. By analysing eight highly polymorphic microsatellite loci and two chloroplast DNA regions, we have investigated the influence of Pleistocene climate fluctuations on the evolutionary history of Salvia officinalis L. (common sage). The populations with the highest genetic diversity were located in the central parts of the Balkan distribution range. A large group of closely related haplotypes was distributed throughout the Balkans and the central Apennines, while the private lineage occupied the southern Apennines. In addition, two highly differentiated lineages were scattered only over the Balkans. The results suggest that a single refugium of the studied species from the last glacial period was located in the central part of the range in the Balkans. Numerous microrefugia, probably spanning several glaciation cycles, were scattered across the Balkans, while colonisation of the Apennines from the Balkans occurred at least on two occasions.
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A Change in Conservation Status of Pachyphytum caesium (Crassulaceae), a Threatened Species from Central Mexico Based on Genetic Studies. BIOLOGY 2022; 11:biology11030379. [PMID: 35336753 PMCID: PMC8945335 DOI: 10.3390/biology11030379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Species decline has accelerated in recent decades, with rare species often being the first to go extinct, mainly due to low population sizes. This study worked with Pachyphytum cesium (Crassulaceae), an endemic species from central Mexico threatened by human activities and climate change. To increase our knowledge of the species, we analyze the diversity and genetic structure of all known populations of P. caesium to change their current genetic status and propose conservation strategies. The results indicate that this species presents low to moderate levels of genetic diversity and incipiently structured populations due to low genetic flow. We found that genetic parameters are essential to the conservation strategies and status vulnerability reclassification. Based on our results, we propose reclassifying the conservation status of the species in danger of extinction; hence a series of conservation strategies are provided to prevent its disappearance. Abstract Genetic studies in rare species are important to determine their patterns of genetic diversity among populations and implement conservation plans aimed to reduce extinction risks. Pachyphytum caesium is an endemic species with extremely small populations in central Mexico. This work analyzes the diversity and genetic structure of Pachyphytum cesium (Crassulaceae) to change the conservation status and propose conservation strategies. Twelve dominant ISSR markers were used to describe the genetic diversity of all known populations. Additionally, we carried out two simulations to explore how the loss of individuals or the local populations extinction affect the genetics parameters of the species. The average results indicated moderate levels of genetic diversity (number of alleles = 89.7 ± 3.9, expected heterozygosity = 0.212 ± 0.0, and percentage of polymorphic loci = 56.1 ± 3.9), parameters that decreased significantly when simulations were performed in P. caesium. Additionally, a genetic structure of the populations was found with low gene flow (Nm = 0.92). Genetic parameters are negatively affected by the loss of individuals and the local extinction of populations. Based on our results, we propose to reclassify the conservation status of the species in danger of extinction, hence a series of conservation strategies are provided to prevent its disappearance.
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Sapkota S, Boggess SL, Trigiano RN, Klingeman WE, Hadziabdic D, Coyle DR, Olukolu BA, Kuster RD, Nowicki M. Microsatellite Loci Reveal Genetic Diversity of Asian Callery Pear ( Pyrus calleryana) in the Species Native Range and in the North American Cultivars. Life (Basel) 2021; 11:531. [PMID: 34200292 PMCID: PMC8226646 DOI: 10.3390/life11060531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/30/2021] [Accepted: 06/04/2021] [Indexed: 12/05/2022] Open
Abstract
Pyrus calleryana Decne. (Callery pear) includes cultivars that in the United States are popular ornamentals in commercial and residential landscapes. Last few decades, this species has increasingly naturalized across portions of the eastern and southern US. However, the mechanisms behind this plant's spread are not well understood. The genetic relationship of present-day P.calleryana trees with their Asian P. calleryana forebears (native trees from China, Japan, and Korea) and the original specimens of US cultivars are unknown. We developed and used 18 microsatellite markers to analyze 147 Pyrus source samples and to articulate the status of genetic diversity within Asian P. calleryana and US cultivars. We hypothesized that Asian P. calleryana specimens and US cultivars would be genetically diverse and would show genetic relatedness. Our data revealed high genetic diversity, high gene flow, and presence of population structure in P. calleryana, potentially relating to the highly invasive capability of this species. Strong evidence for genetic relatedness between Asian P. calleryana specimens and US cultivars was also demonstrated. Our data suggest the source for P. calleryana that have become naturalized in US was China. These results will help understand the genetic complexity of invasive P. calleryana when developing management for escaped populations: In follow-up studies, we use the gSSRs developed here to analyze P. calleryana escape populations from across US.
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Affiliation(s)
- Shiwani Sapkota
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (S.S.); (S.L.B.); (R.N.T.); (D.H.); (B.A.O.); (R.D.K.)
| | - Sarah L. Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (S.S.); (S.L.B.); (R.N.T.); (D.H.); (B.A.O.); (R.D.K.)
| | - Robert N. Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (S.S.); (S.L.B.); (R.N.T.); (D.H.); (B.A.O.); (R.D.K.)
| | - William E. Klingeman
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA;
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (S.S.); (S.L.B.); (R.N.T.); (D.H.); (B.A.O.); (R.D.K.)
| | - David R. Coyle
- Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC 29634, USA;
| | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (S.S.); (S.L.B.); (R.N.T.); (D.H.); (B.A.O.); (R.D.K.)
| | - Ryan D. Kuster
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (S.S.); (S.L.B.); (R.N.T.); (D.H.); (B.A.O.); (R.D.K.)
| | - Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (S.S.); (S.L.B.); (R.N.T.); (D.H.); (B.A.O.); (R.D.K.)
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Carress H, Lawson DJ, Elhaik E. Population genetic considerations for using biobanks as international resources in the pandemic era and beyond. BMC Genomics 2021; 22:351. [PMID: 34001009 PMCID: PMC8127217 DOI: 10.1186/s12864-021-07618-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/14/2021] [Indexed: 12/11/2022] Open
Abstract
The past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limits the global understanding of disease risk but also inhibits viable research into the genomic differences between carriers and patients. Whilst the community has agreed that more diverse samples are required, it is not enough to blindly increase diversity; the diversity must be quantified, compared and annotated to lead to insight. Genetic annotations from separate biobanks need to be comparable and computable and to operate without access to raw data due to privacy concerns. Comparability is key both for regular research and to allow international comparison in response to pandemics. Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner. The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally), increase the accuracy of association analyses and inform developmental efforts.
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Affiliation(s)
- Hannah Carress
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Daniel John Lawson
- School of Mathematics and Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK. .,Department of Biology, Lund University, Lund, Sweden.
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Li H, Qu W, Obrycki JJ, Meng L, Zhou X, Chu D, Li B. Optimizing Sample Size for Population Genomic Study in a Global Invasive Lady Beetle, Harmonia Axyridis. INSECTS 2020; 11:E290. [PMID: 32397374 PMCID: PMC7291016 DOI: 10.3390/insects11050290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/30/2022]
Abstract
Finding optimal sample sizes is critical for the accurate estimation of genetic diversity of large invasive populations. Based on previous studies, we hypothesized that a minimal sample size of 3-8 individuals is sufficient to dissect the population architecture of the harlequin lady beetle, Harmonia axyridis, a biological control agent and an invasive alien species. Here, equipped with a type IIB endonuclease restriction site-associated (2b-RAD) DNA sequencing approach, we identified 13,766 and 13,929 single nucleotide polymorphisms (SNPs), respectively, among native and invasive H. axyridis populations. With this information we simulated populations using a randomly selected 3000 SNPs and a subset of individuals. From this simulation we finally determined that six individuals is the minimum sample size required for the accurate estimation of intra- and inter-population genetic diversity within and across H. axyridis populations. Our findings provide an empirical advantage for population genomic studies of H. axyridis in particular and suggest useful tactics for similar studies on multicellular organisms in general.
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Affiliation(s)
- Hongran Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (L.M.)
| | - Wanmei Qu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (W.Q.); (D.C.)
| | - John J. Obrycki
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA; (J.J.O.); (X.Z.)
| | - Ling Meng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (L.M.)
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY 40546, USA; (J.J.O.); (X.Z.)
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (W.Q.); (D.C.)
| | - Baoping Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (H.L.); (L.M.)
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Martínez-López V, García C, Zapata V, Robledano F, De la Rúa P. Intercontinental long-distance seed dispersal across the Mediterranean Basin explains population genetic structure of a bird-dispersed shrub. Mol Ecol 2020; 29:1408-1420. [PMID: 32168411 DOI: 10.1111/mec.15413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 01/04/2023]
Abstract
Long-distance dispersal (LDD) is a pivotal process for plants determining their range of distribution and promoting gene flow among distant populations. Most fleshy-fruited species rely on frugivorous vertebrates to disperse their seeds across the landscape. While LDD events are difficult to record, a few ecological studies have shown that birds move a sizeable number of ingested seeds across geographic barriers, such as sea straits. The foraging movements of migrant frugivores across distant populations, including those separated by geographic barriers, creates a constant flow of propagules that in turn shapes the spatial distributions of the genetic variation in populations. Here, we have analysed the genetic diversity and structure of 74 populations of Pistacia lentiscus, a fleshy-fruited shrub widely distributed in the Mediterranean Basin, to elucidate whether the Mediterranean Sea acts as a geographic barrier or alternatively whether migratory frugivorous birds promote gene flow among populations located on both sides of the sea. Our results show reduced genetic distances among populations, including intercontinental populations, and they show a significant genetic structure across an eastern-western axis. These findings are consistent with known bird migratory routes that connect the European and African continents following a north-southwards direction during the fruiting season of many fleshy-fruited plants. Further, approximate Bayesian analysis failed to explain the observed patterns as a result of historical population migrations at the end of Last Glacial Maximum. Therefore, anthropic and/or climatic changes that would disrupt the migratory routes of frugivorous birds might have genetic consequences for the plant species they feed upon.
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Affiliation(s)
- Vicente Martínez-López
- Department of Zoology and Physical Anthropology, University of Murcia, Murcia, Spain.,Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Cristina García
- Department of Evolution, Ecology, and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.,CIBIO/InBIO-Universidade do Porto, Vairão, Portugal
| | - Víctor Zapata
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | | | - Pilar De la Rúa
- Department of Zoology and Physical Anthropology, University of Murcia, Murcia, Spain
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Qu W, Liang N, Wu Z, Zhao Y, Chu D. Minimum sample sizes for invasion genomics: Empirical investigation in an invasive whitefly. Ecol Evol 2020; 10:38-49. [PMID: 31988715 PMCID: PMC6972819 DOI: 10.1002/ece3.5677] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/16/2019] [Accepted: 08/27/2019] [Indexed: 01/03/2023] Open
Abstract
Analysis of population genetics provides insights into the evolutionary processes, among which the sample size choice is per se a crucial issue in the analysis. Genome-wide high-throughput techniques based on RADseq have been increasingly used in studies on the population genomics of invasive species. However, there is little information available regarding optimal sample sizes for analyzing population genomics of invasive species. In this study, we first use type IIB endonucleases restriction site-associated DNA (2b-RAD) to mine thousands of single nucleotide polymorphisms (SNPs) for native and introduced populations in Q1 clade (SPB and 17JN) and Q2 clade (ISQ and UAS0601) of the whitefly, Bemisia tabaci (Gennadius) MED (also known as B. tabaci biotype Q). Then, we used resampling techniques to create simulated populations with a random subset of individuals and 3,000 SNPs to determine how many individuals should be sampled for accurate estimates of intra- and interpopulation genetic diversity. We calculated the intrapopulation genetic diversity parameters (unbiased expected heterozygosity, observed heterozygosity, and the number of effect alleles) and pairwise genetic differentiation F ST; finally, an ad hoc statistic, ΔK, was used to determine the optimal value. Our results showed that a sample size greater than four individuals (n ≥ 4) has little impact on estimates of genetic diversity within whitefly populations; moreover, precise estimate of F ST can be easily achieved at a very small simple size (n = 3 or 4). Our results will provide in-depth understanding of the optimization of sampling schemes in population genomics of invasive species.
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Affiliation(s)
- Wan‐Mei Qu
- Key Lab of Integrated Crop Pest Management of Shandong ProvinceCollege of Plant Health and MedicineQingdao Agricultural UniversityQingdaoChina
| | - Ni Liang
- Key Lab of Integrated Crop Pest Management of Shandong ProvinceCollege of Plant Health and MedicineQingdao Agricultural UniversityQingdaoChina
| | - Zi‐Ku Wu
- Science and Information CollegeQingdao Agricultural UniversityQingdaoChina
| | - You‐Gang Zhao
- Science and Information CollegeQingdao Agricultural UniversityQingdaoChina
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong ProvinceCollege of Plant Health and MedicineQingdao Agricultural UniversityQingdaoChina
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Gautier C, Esquibet M, Fournet S, Piriou C, Yvin JC, Nguema-Ona E, Grenier E, Montarry J. Microsatellite markers reveal two genetic groups in European populations of the carrot cyst nematode Heterodera carotae. INFECTION GENETICS AND EVOLUTION 2019; 73:81-92. [PMID: 31003010 DOI: 10.1016/j.meegid.2019.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022]
Abstract
The cyst nematode Heterodera carotae, which parasitizes carrot roots, has been recorded in many countries in Europe (Italy, The Netherlands, Switzerland, France, Denmark, …), in South Africa and in North America (Canada, USA). To date, there is a lack of knowledge about the genetic structure of the populations of this economically important nematode. The aim of this work was to study the structuration of the genetic diversity of the carrot cyst nematode at the European scale. We have developed a set of thirteen polymorphic microsatellite markers and used it to genotype seventeen European populations of H. carotae coming from France, Switzerland, Italy, Denmark and one non-European population from Canada. As previously showed for other cyst nematode species, the H. carotae populations were characterised by a strong heterozygote deficit. A Bayesian clustering analysis revealed two distinct genetic clusters, with one group located in the north of Europe and a second one located in the south of Europe. Moreover, our results highlighted rather limited gene flow at small spatial scale and some events of long distance migration. This first investigation of the genetic diversity of H. carotae populations would be useful to develop sustainable control strategies.
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Affiliation(s)
- Camille Gautier
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, 35650, Le Rheu, France; Centre Mondial de l'Innovation-Laboratoire de Nutrition Végétale Pôle Biocontrôle, Groupe Roullier, Saint Malo, France.
| | - Magali Esquibet
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Sylvain Fournet
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Christophe Piriou
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Jean-Claude Yvin
- Centre Mondial de l'Innovation-Laboratoire de Nutrition Végétale Pôle Biocontrôle, Groupe Roullier, Saint Malo, France
| | - Eric Nguema-Ona
- Centre Mondial de l'Innovation-Laboratoire de Nutrition Végétale Pôle Biocontrôle, Groupe Roullier, Saint Malo, France
| | - Eric Grenier
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, 35650, Le Rheu, France
| | - Josselin Montarry
- IGEPP, INRA, Agrocampus-Ouest, Université de Rennes 1, 35650, Le Rheu, France
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