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Klimova A, Ruiz Mondragón KY, Aguirre-Planter E, Valiente A, Lira R, Eguiarte LE. Genomic analysis unveils reduced genetic variability but increased proportion of heterozygotic genotypes of the intensively managed mezcal agave, Agave angustifolia. AMERICAN JOURNAL OF BOTANY 2023; 110:e16216. [PMID: 37478873 DOI: 10.1002/ajb2.16216] [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: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/23/2023]
Abstract
PREMISE The central Oaxaca Basin has a century-long history of agave cultivation and is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics. METHODS Using restriction-site-associated DNA sequencing and over 8000 single-nucleotide polymorphisms, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations. RESULTS Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation. CONCLUSIONS The considerable heterozygosity found in espadín is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved.
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Affiliation(s)
- Anastasia Klimova
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Karen Y Ruiz Mondragón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alfonso Valiente
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rafael Lira
- Laboratorio de Recursos Naturales, Unidad de Biotecnología y Prototipos (UBIPRO), Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Jiang H, Zhang Y, Tu W, Sun G, Wu N, Zhang Y. The General Trends of Genetic Diversity Change in Alien Plants' Invasion. PLANTS (BASEL, SWITZERLAND) 2023; 12:2690. [PMID: 37514304 PMCID: PMC10385407 DOI: 10.3390/plants12142690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Genetic diversity is associated with invasion dynamics during establishment and expansion stages by affecting the viability and adaptive potential of exotics. There have been many reports on the comparison between the genetic diversity of invasive alien species (IAS) in and out of their native habitats, but the conclusions were usually inconsistent. In this work, a standard meta-analysis of the genetic diversity of 19 invasive plants based on 26 previous studies was carried out to investigate the general trend for the change of IASs' genetic diversity during their invasion process and its real correlation with the invasion fate. Those 26 studies were screened from a total of 3557 peer-reviewed publications from the ISI Web of Science database during the period of January 2000 to May 2022. Based on the selected studies in this work, a general reduction of IASs' genetic diversity was found in non-native populations compared to that in native ones, while the difference was not significant. This finding suggested that regardless of the change in genetic diversity, it had no substantial effect on the outcome of the invasion process. Therefore, genetic diversity might not serve as a reliable indicator for risk assessment and prediction of invasion dynamic prediction in the case of IASs.
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Affiliation(s)
- Han Jiang
- China-Croatia 'Belt and Road' Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhang
- China-Croatia 'Belt and Road' Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Wenqin Tu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Geng Sun
- China-Croatia 'Belt and Road' Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Ning Wu
- China-Croatia 'Belt and Road' Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yongmei Zhang
- China-Croatia 'Belt and Road' Joint Laboratory on Biodiversity and Ecosystem Services, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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3
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Gouvêa LP, Fragkopoulou E, Cavanaugh K, Serrão EA, Araújo MB, Costello MJ, Westergerling EHT, Assis J. Oceanographic connectivity explains the intra-specific diversity of mangrove forests at global scales. Proc Natl Acad Sci U S A 2023; 120:e2209637120. [PMID: 36996109 PMCID: PMC10083552 DOI: 10.1073/pnas.2209637120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 02/16/2023] [Indexed: 03/31/2023] Open
Abstract
The distribution of mangrove intra-specific biodiversity can be structured by historical demographic processes that enhance or limit effective population sizes. Oceanographic connectivity (OC) may further structure intra-specific biodiversity by preserving or diluting the genetic signatures of historical changes. Despite its relevance for biogeography and evolution, the role of oceanographic connectivity in structuring the distribution of mangrove's genetic diversity has not been addressed at global scale. Here we ask whether connectivity mediated by ocean currents explains the intra-specific diversity of mangroves. A comprehensive dataset of population genetic differentiation was compiled from the literature. Multigenerational connectivity and population centrality indices were estimated with biophysical modeling coupled with network analyses. The variability explained in genetic differentiation was tested with competitive regression models built upon classical isolation-by-distance (IBD) models considering geographic distance. We show that oceanographic connectivity can explain the genetic differentiation of mangrove populations regardless of the species, region, and genetic marker (significant regression models in 95% of cases, with an average R-square of 0.44 ± 0.23 and Person's correlation of 0.65 ± 0.17), systematically improving IBD models. Centrality indices, providing information on important stepping-stone sites between biogeographic regions, were also important in explaining differentiation (R-square improvement of 0.06 ± 0.07, up to 0.42). We further show that ocean currents produce skewed dispersal kernels for mangroves, highlighting the role of rare long-distance dispersal events responsible for historical settlements. Overall, we demonstrate the role of oceanographic connectivity in structuring mangrove intra-specific diversity. Our findings are critical for mangroves' biogeography and evolution, but also for management strategies considering climate change and genetic biodiversity conservation.
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Affiliation(s)
- Lidiane P. Gouvêa
- CCMAR–Center of Marine Sciences, University of the Algarve, 8005-139Faro, Portugal
| | - Eliza Fragkopoulou
- CCMAR–Center of Marine Sciences, University of the Algarve, 8005-139Faro, Portugal
| | - Kyle Cavanaugh
- Department of Geography, University of California, Los Angeles, CA90095
| | - Ester A. Serrão
- CCMAR–Center of Marine Sciences, University of the Algarve, 8005-139Faro, Portugal
| | - Miguel B. Araújo
- Department of Biogeography and Global Change, National Museum of Natural Sciences, CSIC-Spanish National Research Council,28806Madrid, Spain
- Rui Nabeiro Biodiversity Chair, MED–Mediterranean Institute for Agriculture, Environment and Development, University of Évora, 7000Évora, Portugal
| | - Mark John Costello
- Faculty of Bioscience and Aquaculture, Nord Universitet, 1490Bodø, Norway
| | - E. H. Taraneh Westergerling
- Department of Biological Sciences, University of Bergen,5020Bergen, Norway
- Institute of Marine Research, 5817Bergen, Norway
| | - Jorge Assis
- CCMAR–Center of Marine Sciences, University of the Algarve, 8005-139Faro, Portugal
- Faculty of Bioscience and Aquaculture, Nord Universitet, 1490Bodø, Norway
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Wu Z, Wang Z, Xie D, Wang H, Zhao A, Wang Y, Wang H, Xu X, Li T, Zhao J. Effects of highland environments on clonal diversity in aquatic plants: An interspecific comparison study on the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:1040282. [PMID: 36340384 PMCID: PMC9632175 DOI: 10.3389/fpls.2022.1040282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Clonal reproduction is one of the most distinctive characteristics of plants and is common and diverse in aquatic macrophytes. The balance between sexual and asexual reproduction is affected by various conditions, especially adverse environments. However, we know little about clonal diversity of aquatic plants under suboptimal conditions, such as at high altitudes, and having this information would help us understand how environmental gradients influence patterns of clonal and genetic variation in freshwater species. The microsatellite data of four aquatic taxa in our previous studies were revisited to estimate clonal and genetic diversity on the Qinghai-Tibetan Plateau. Clonal diversity among different genetic groups was compared. Local environmental features were surveyed. Beta regressions were used to identify the environmental factors that significantly explained clonal diversity for relative taxon. The level of clonal diversity from high to low was Stuckenia filiformis > Hippuris vulgaris > Myriophyllum species > Ranunculus section Batrachium species. A positive correlation between clonal and genetic diversity was identified for all taxa, except H. vulgaris. Clonal diversity was affected by climate in S. filiformis and by the local environment in H. vulgaris. For Myriophyllum spp., low elevation and high sediment nutrition were significant for sexual recruitment. The environmental effects on clonal diversity were not significant in R. sect. Batrachium spp. Clonal diversity of aquatic plants is moderate to high and varies greatly in highlands. The effects of breeding systems and environmental factors on the patterns of clonal variation were identified. Elevational gradients, climates and local conditions play different roles in clonal diversity among relative taxon. Our results highlight the importance of sexual recruitment in alpine aquatic plant populations and the influence of environmental factors on the genetic patterns in freshwater species at local and regional scales.
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Affiliation(s)
- Zhigang Wu
- The State Key Laboratory of Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhong Wang
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan, China
- School of Science, Tibet University, Lhasa, China
| | - Dong Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- The National Wetland Ecosystem Field Station of Taihu Lake, National Forestry Administration, Suzhou, China
| | - Huijun Wang
- The State Key Laboratory of Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Aiwen Zhao
- The State Key Laboratory of Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Science, Tibet University, Lhasa, China
| | - Yalin Wang
- The State Key Laboratory of Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hanling Wang
- Xi’an Jiaotong-Liverpool University, Suzhou, China
| | - Xinwei Xu
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Tao Li
- The State Key Laboratory of Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- The State Key Laboratory of Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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5
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da Cunha NL, Xue H, Wright SI, Barrett SCH. Genetic variation and clonal diversity in floating aquatic plants: Comparative genomic analysis of water hyacinth species in their native range. Mol Ecol 2022; 31:5307-5325. [PMID: 35984729 DOI: 10.1111/mec.16664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 07/24/2022] [Accepted: 08/10/2022] [Indexed: 12/15/2022]
Abstract
Many eukaryotic organisms reproduce by sexual and asexual reproduction. Genetic diversity in populations can be strongly dependent on the relative importance of these two reproductive modes. Here, we compare the amounts and patterns of genetic diversity in related water hyacinths that differ in their propensity for clonal propagation - highly clonal Eichhornia crassipes and moderately clonal E. azurea (Pontederiaceae). Our comparisons involved genotype-by-sequencing (GBS) of 137 E. crassipes ramets from 60 locations (193,495 nucleotide sites) and 118 E. azurea ramets from 53 locations (198,343 nucleotide sites) among six hydrological basins in central South America, the native range of both species. We predicted that because of more prolific clonal propagation, E. crassipes would exhibit lower clonal diversity than E. azurea. This prediction was supported by all measures of clonal diversity that we examined. Eichhornia crassipes also had a larger excess of heterozygotes at variant sites, another signature of clonality. However, genome-wide heterozygosity was not significantly different between the species. Eichhornia crassipes had weaker spatial genetic structure and lower levels of differentiation among hydrological basins than E. azurea, probably because of higher clonality and more extensive dispersal of its free-floating life form. Our findings for E. crassipes contrast with earlier studies from the invasive range which have reported very low levels of clonal diversity and extensive geographic areas of genetic uniformity.
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Affiliation(s)
- Nicolay Leme da Cunha
- Grupo de Ecología de la Polinización, INIBIOMA, CONICET-Universidad Nacional del Comahue, San Carlos de Bariloche, Rio Negro, Argentina.,Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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6
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Sofi IA, Rashid I, Lone JY, Tyagi S, Reshi ZA, Mir RR. Genetic diversity may help evolutionary rescue in a clonal endemic plant species of Western Himalaya. Sci Rep 2021; 11:19595. [PMID: 34599214 PMCID: PMC8486807 DOI: 10.1038/s41598-021-98648-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
Habitat loss due to climate change may cause the extinction of the clonal species with a limited distribution range. Thus, determining the genetic diversity required for adaptability by these species in sensitive ecosystems can help infer the chances of their survival and spread in changing climate. We studied the genetic diversity and population structure of Sambucus wightiana-a clonal endemic plant species of the Himalayan region for understanding its possible survival chances in anticipated climate change. Eight polymorphic microsatellite markers were used to study the allelic/genetic diversity and population structure. In addition, ITS1-ITS4 Sanger sequencing was used for phylogeny and SNP detection. A total number of 73 alleles were scored for 37 genotypes at 17 loci for 8 SSRs markers. The population structural analysis using the SSR marker data led to identifying two sub-populations in our collection of 37 S. wightiana genotypes, with 11 genotypes having mixed ancestry. The ITS sequence data show a specific allele in higher frequency in a particular sub-population, indicating variation in different S. wightiana accessions at the sequence level. The genotypic data of SSR markers and trait data of 11 traits of S. wightiana, when analyzed together, revealed five significant Marker-Trait Associations (MTAs) through Single Marker Analysis (SMA) or regression analysis. Most of the SSR markers were found to be associated with more than one trait, indicating the usefulness of these markers for working out marker-trait associations. Moderate to high genetic diversity observed in the present study may provide insurance against climate change to S. wightiana and help its further spread.
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Affiliation(s)
- Irshad Ahmad Sofi
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Irfan Rashid
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Javaid Yousuf Lone
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Sandhya Tyagi
- grid.418196.30000 0001 2172 0814Department of Plant Physiology, Indian Agricultural Research Institute, New Delhi, Delhi 110012 India
| | - Zafar A. Reshi
- grid.412997.00000 0001 2294 5433Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Reyazul Rouf Mir
- grid.444725.40000 0004 0500 6225Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura Campus, Sopore, Jammu and Kashmir 193201 India
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7
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Roberto T, de Carvalho J, Beale M, Hagen F, Fisher M, Hahn R, de Camargo Z, Rodrigues A. Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers. Stud Mycol 2021; 100:100131. [PMID: 34934463 PMCID: PMC8645518 DOI: 10.1016/j.simyco.2021.100131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation of Paracoccidioides propagules from the environment. The main agents include members of the P. brasiliensis complex (phylogenetically-defined species S1, PS2, PS3, and PS4) and P. lutzii. DNA-sequencing of protein-coding loci (e.g., GP43, ARF, and TUB1) is the reference method for recognizing Paracoccidioides species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity within Paracoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping Paracoccidioides species. The bioinformatic analysis generated 144 in silico AFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC/MseI-CT and #2 EcoRI-AT/MseI-CT). The combinations #1 and #2 were used in vitro to genotype 165 Paracoccidioides isolates recovered from across a vast area of South America. Considering the overall scored AFLP markers in vitro (67-87 fragments), the values of polymorphism information content (PIC = 0.3345-0.3456), marker index (MI = 0.0018), effective multiplex ratio (E = 44.6788-60.3818), resolving power (Rp = 22.3152-34.3152), discriminating power (D = 0.5183-0.5553), expected heterozygosity (H = 0.4247-0.4443), and mean heterozygosity (H avp = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciate Paracoccidioides and to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability among P. brasiliensis complex and P. lutzii (PhiPT = 0.651-0.658, P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for P. brasiliensis s. str. (χ2 = 1.025; P = 0.3113), P. venezuelensis (χ2 = 0.692; P = 0.4054), and P. lutzii (χ2 = 0.027; P = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for P. americana (χ2 = 8.909; P = 0.0028) and P. restrepiensis (χ2 = 4.571; P = 0.0325) with a preponderance of MAT1-1. Geographical distributions confirmed that P. americana, P. restrepiensis, and P. lutzii are more widespread than previously thought. P. brasiliensis s. str. is by far the most widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology of Paracoccidioides species, guiding disease-control strategies to mitigate PCM.
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Affiliation(s)
- T.N. Roberto
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - J.A. de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - M.A. Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - F. Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China
| | - M.C. Fisher
- MRC Center for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - R.C. Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá, 78060900, Brazil
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá, 78048902, Brazil
| | - Z.P. de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
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8
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Shum P, Palumbi SR. Testing small-scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding. Mol Ecol 2021; 30:3355-3373. [PMID: 33682164 DOI: 10.1111/mec.15851] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 01/27/2021] [Accepted: 02/10/2021] [Indexed: 12/25/2022]
Abstract
DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operational taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from 106 samples of benthic habitats in Monterey Bay. Using haplotypes as a unit we show fine-grained differences of abundance across locations for 15 species, and marked aggregation from sample to sample for most of the common species of plants and animals. Previous analyses could not distinguish these patterns from artefacts of amplification or sequence bias. Our haplotype data also reveal strong population genetic differentiation over small spatial scales for 48 species of red algae, sponges and Bryozoa. Last, phylogenetic analysis of mismatch frequencies among haplotypes show a wide variety of demographic histories from recent expansions to long, stable population sizes. These analyses show that abundant, small-bodied marine species that are often overlooked in ecological surveys can have strikingly different patterns of ecological and genetic structure leading to population, ecological and perhaps adaptive differences between habitats. MOTU diversity data from the same sequencing efforts that generate species-level analyses can greatly increase the scope and value of metabarcoding studies.
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Affiliation(s)
- Peter Shum
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
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9
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Stoeckel S, Porro B, Arnaud-Haond S. The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates. Mol Ecol Resour 2021; 21:1068-1084. [PMID: 33386695 DOI: 10.1111/1755-0998.13316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/05/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022]
Abstract
Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (FIS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.
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Affiliation(s)
- Solenn Stoeckel
- Institute for Genetics, Environment and Plant Protection, INRAE, Le Rheu, France
| | - Barbara Porro
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France.,MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
| | - Sophie Arnaud-Haond
- MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
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10
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Arnaud-Haond S, Stoeckel S, Bailleul D. New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations. Mol Ecol 2020; 29:3248-3260. [PMID: 32613610 DOI: 10.1111/mec.15532] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/30/2020] [Accepted: 06/11/2020] [Indexed: 01/23/2023]
Abstract
Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation and restoration strategies. However, poor knowledge of the effect of clonality on the population genetics of natural populations severely limits our understanding of the dynamics and connectivity of meadows. Recent modelling approaches have described the expected distributions of genotypic and genetic descriptors under increasing clonal rates, which may help us better understand and interpret population genetics data obtained for partial asexuals. Here, in the light of these recent theoretical developments, we revisited population genetics data for 165 meadows of four seagrass species. Contrasting shoot lifespan and rhizome turnover led to the prediction that the influence of asexual reproduction would increase along a gradient from Zostera noltii to Zostera marina, Cymodocea nodosa and Posidonia oceanica, with increasing departure from Hardy-Weinberg equilibrium (Fis ), mostly towards heterozygote excess, and decreasing genotypic richness (R). This meta-analysis provides a nested validation of this hypothesis at both the species and meadow scales through a significant relationship between Fis and R within each species. By empirically demonstrating the theoretical expectations derived from recent modelling approaches, this work calls for the use of Hardy-Weinberg equilibrium (Fis ) rather than only the strongly sampling-sensitive R to assess the importance of clonal reproduction (c), at least when the impact of selfing on Fis can be neglected. The results also emphasize the need to revise our appraisal of the extent of clonality and its influence on the dynamics, connectivity and evolutionary trajectory of partial asexuals in general, including in seagrass meadows, to develop the most accurate management strategies.
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Affiliation(s)
| | - Solenn Stoeckel
- IGEPP INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Diane Bailleul
- Université de Montpellier, Ifremer, CNRS, IRD, MARBEC, Sète, France
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11
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Millar MA, Byrne M. Variable clonality and genetic structure among disjunct populations of Banksia mimica. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01288-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Pringle JC, Wesolowski A, Berube S, Kobayashi T, Gebhardt ME, Mulenga M, Chaponda M, Bobanga T, Juliano JJ, Meshnick S, Moss WJ, Carpi G, Norris DE. High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo. Malar J 2019; 18:400. [PMID: 31801548 PMCID: PMC6894251 DOI: 10.1186/s12936-019-3023-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/21/2019] [Indexed: 01/25/2023] Open
Abstract
Background While the utility of parasite genotyping for malaria elimination has been extensively documented in low to moderate transmission settings, it has been less well-characterized in holoendemic regions. High malaria burden settings have received renewed attention acknowledging their critical role in malaria elimination. Defining the role for parasite genomics in driving these high burden settings towards elimination will enhance future control programme planning. Methods Amplicon deep sequencing was used to characterize parasite population genetic diversity at polymorphic Plasmodium falciparum loci, Pfama1 and Pfcsp, at two timepoints in June–July 2016 and January–March 2017 in a high transmission region along the international border between Luapula Province, Zambia and Haut-Katanga Province, the Democratic Republic of the Congo (DRC). Results High genetic diversity was observed across both seasons and in both countries. No evidence of population structure was observed between parasite populations on either side of the border, suggesting that this region may be one contiguous transmission zone. Despite a decline in parasite prevalence at the sampling locations in Haut-Katanga Province, no genetic signatures of a population bottleneck were detected, suggesting that larger declines in transmission may be required to reduce parasite genetic diversity. Analysing rare variants may be a suitable alternative approach for detecting epidemiologically important genetic signatures in highly diverse populations; however, the challenge is distinguishing true signals from potential artifacts introduced by small sample sizes. Conclusions Continuing to explore and document the utility of various parasite genotyping approaches for understanding malaria transmission in holoendemic settings will be valuable to future control and elimination programmes, empowering evidence-based selection of tools and methods to address pertinent questions, thus enabling more efficient resource allocation.
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Affiliation(s)
- Julia C Pringle
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Sophie Berube
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Mary E Gebhardt
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | | | - Thierry Bobanga
- Université Protestante au Congo and University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Steven Meshnick
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - William J Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Douglas E Norris
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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Schwarzer C, Joshi J. Ecotypic differentiation, hybridization and clonality facilitate the persistence of a cold-adapted sedge in European bogs. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Recent research has shown that many cold-adapted species survived the last glacial maximum (LGM) in northern refugia. Whether this evolutionary history has had consequences for their genetic diversity and adaptive potential remains unknown. We sampled 14 populations of Carex limosa, a sedge specialized to bog ecosystems, along a latitudinal gradient from its Scandinavian core to the southern lowland range-margin in Germany. Using microsatellite and experimental common-garden data, we evaluated the impacts of global climate change along this gradient and assessed the conservation status of the southern marginal populations. Microsatellite data revealed two highly distinct genetic groups and hybrid individuals. In our common-garden experiment, the two groups showed divergent responses to increased nitrogen/phosphorus (N/P) availability, suggesting ecotypic differentiation. Each group formed genetically uniform populations at both northern and southern sampling areas. Mixed populations occurred throughout our sampling area, an area that was entirely glaciated during the LGM. The fragmented distribution implies allopatric divergence at geographically separated refugia that putatively differed in N/P availability. Molecular data and an observed low hybrid fecundity indicate the importance of clonal reproduction for hybrid populations. At the southern range-margin, however, all populations showed effects of clonality, lowered fecundity and low competitiveness, suggesting abiotic and biotic constraints to population persistence.
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Affiliation(s)
- Christian Schwarzer
- University of Potsdam, Biodiversity Research/Systematic Botany, Maulbeerallee 1, 14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
| | - Jasmin Joshi
- University of Potsdam, Biodiversity Research/Systematic Botany, Maulbeerallee 1, 14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
- Hochschule für Technik HSR Rapperswil, Institute for Landscape and Open Space, Oberseestrasse 10, 8640 Rapperswil, Switzerland
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Lee SR, Park HS, Kim BY, Lee JH, Fan Q, Gaskin JF, Kim YD. An unexpected genetic diversity pattern and a complex demographic history of a rare medicinal herb, Chinese asparagus (Asparagus cochinchinensis) in Korea. Sci Rep 2019; 9:9757. [PMID: 31278330 PMCID: PMC6611897 DOI: 10.1038/s41598-019-46275-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 06/25/2019] [Indexed: 11/09/2022] Open
Abstract
Range-wide population studies of wide spread species are often associated with complex diversity patterns resulting from genetically divergent evolutionary significant units (ESUs). The compound evolutionary history creating such a pattern of diversity can be inferred through molecular analyses. Asparagus cochinchinensis, a medicinally important perennial herb, is in decline due to overharvesting in Korea. Eight A. cochinchinensis populations in Korea and three populations from neighboring countries (China, Japan and Taiwan) were examined using nine nuclear microsatellite loci and three chloroplast microsatellite loci to characterize molecular diversity patterns. The average within-population diversity was limited likely due to long-term bottlenecks observed in all eight populations. High pairwise FST values indicated that the populations have largely diverged, but the divergences were not correlated with geographic distances. Clustering analyses revealed a highly complex spatial structure pattern associated with two ESUs. Approximate Bayesian Computation (ABC) suggests that the two ESUs split about 21,000 BP were independently introduced to Korea approximately 1,800 years ago, and admixed in secondary contact zones. The two ESUs found in our study may have different habitat preferences and growth conditions, implying that the two genetically divergent groups should be considered not only for conservation and management but also for breeding programs in agricultural areas.
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Affiliation(s)
- Soo-Rang Lee
- Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, South Korea
| | - Han-Sol Park
- National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Bo-Yun Kim
- Multidisciplinary Genome Institute, Hallym University, Chuncheon, 24252, South Korea
| | - Jung-Hoon Lee
- Department of Life Sciences, Hallym University, Chuncheon, 24252, South Korea
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - John F Gaskin
- USDA-ARS, 1500 North Central Avenue, Sidney, Montana, 59270, USA
| | - Young-Dong Kim
- Department of Life Sciences, Hallym University, Chuncheon, 24252, South Korea.
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Rache L, Blondin L, Flores C, Trujillo C, Szurek B, Restrepo S, Koebnik R, Bernal A, Vernière C. An Optimized Microsatellite Scheme for Assessing Populations of Xanthomonas phaseoli pv. manihotis. PHYTOPATHOLOGY 2019; 109:859-869. [PMID: 30908143 DOI: 10.1094/phyto-06-18-0210-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Diverse molecular markers have been used to analyze the genetic diversity of plant pathogens. Compared with traditional fingerprinting methods, multiple loci variable number of tandem repeat analyses (MLVAs) have gained importance recently due to their reproducibility, high discriminatory power, ease of performance, low cost, and throughput potential. These characteristics are desirable for continuous pathogen monitoring, especially for pathogens with relatively low genetic diversity, and for disease epidemiology studies. Genetic diversity studies of Xanthomonas phaseoli pv. manihotis, which is the causal agent of cassava bacterial blight, have shown variability and changes in the bacterial population over time. Thus, an easy and fast method needs to be developed to type populations of this pathogen in different countries of the world, especially on small scales. In this study, we developed an MLVA scheme to analyze X. phaseoli pv. manihotis variability on a local scale. The MLVA-15 scheme comprises 15 variable number of tandem repeat loci grouped into four multiplex polymerase chain reaction pools. We showed that the MLVA-15 scheme had slightly higher discriminatory ability at the locality level when compared with amplified fragment length polymorphisms. The MLVA-15 scheme allowed for an accurate determination of the number of genotypes in the sample and showed reproducibility and portability. Additionally, this scheme could be used to analyze numerous strains in a reasonable timeframe. The MLVA-15 scheme was highly specific to X. phaseoli but up to eight tandem repeat loci could be amplified from other Xanthomonas spp. Finally, we assessed the utility of the scheme for analyses of X. phaseoli pv. manihotis genetic variability in the Colombian Caribbean region. MLVA-15 distinguished 88.9% of the haplotypes in our sample. Strains originating from the same field and isolated at the same time could be discriminated. In this study, the advantages of the MLVA-15 scheme targeting 6- or 7-bp repeats were demonstrated. Moreover, this scheme was a fast method that was appropriate for routine monitoring of X. phaseoli pv. manihotis populations on a local scale and, thus, was useful for addressing epidemiological questions.
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Affiliation(s)
- Leidy Rache
- 1 Laboratorio de Interacciones Moleculares de Microorganismos Agrícolas (LIMMA), Universidad de los Andes, Bogotá D.C., Colombia
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
| | | | - Carolina Flores
- 4 IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Cesar Trujillo
- 1 Laboratorio de Interacciones Moleculares de Microorganismos Agrícolas (LIMMA), Universidad de los Andes, Bogotá D.C., Colombia
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
- 5 Affiliated until 2015
| | - Boris Szurek
- 4 IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Silvia Restrepo
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
| | - Ralf Koebnik
- 4 IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Adriana Bernal
- 1 Laboratorio de Interacciones Moleculares de Microorganismos Agrícolas (LIMMA), Universidad de los Andes, Bogotá D.C., Colombia
- 2 Laboratorio de Micología y Fitopatología (LAMFU), Universidad de los Andes, Bogotá D.C., Colombia
| | - Christian Vernière
- 6 Cirad, UMR BGPI, F-34398 Montpellier, France; and
- 7 BGPI, Université de Montpellier, Cirad, INRA, Montpellier SupAgro, Montpellier, France
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Hamston TJ, de Vere N, King RA, Pellicer J, Fay MF, Cresswell JE, Stevens JR. Apomixis and Hybridization Drives Reticulate Evolution and Phyletic Differentiation in Sorbus L.: Implications for Conservation. FRONTIERS IN PLANT SCIENCE 2018; 9:1796. [PMID: 30619388 PMCID: PMC6300497 DOI: 10.3389/fpls.2018.01796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Hybridization and polyploidy are major forces in the evolution of plant diversity and the study of these processes is of particular interest to understand how novel taxa are formed and how they maintain genetic integrity. Sorbus is an example of a genus where active diversification and speciation are ongoing and, as such, represents an ideal model to investigate the roles of hybridization, polyploidy and apomixis in a reticulate evolutionary process. To elucidate breeding systems and evolutionary origins of a complex of closely related Sorbus taxa, we assessed genotypic diversity and population structure within and among taxa, combining data from nuclear DNA microsatellite markers and flow cytometry. Clonal analysis and low genotypic diversity within the polyploid taxa suggest apomixis is obligate. However, genetic variation has led to groups of 'clone-mates' within apomictic taxa that strongly suggest mutation is responsible for the genotypic diversity of these apomictic lineages. In addition, microsatellite profiles and site demographics suggest hybridization events among apomictic polyploid Sorbus may have contributed to the extant diversity of recognized taxa in this region. This research demonstrates that both macro- and micro-evolutionary processes are active within this reticulate Sorbus complex. Conservation measures should be aimed at maintaining this process and should therefore be prioritized for those areas of Sorbus species richness where the potential for interspecific gene flow is greatest.
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Affiliation(s)
- Tracey J. Hamston
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Field Conservation and Research Department, Whitley Wildlife Conservation Trust, Paignton, United Kingdom
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthney, United Kingdom
- Faculty of Earth and Life Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - R. Andrew King
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - James E. Cresswell
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Jamie R. Stevens
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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17
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Santelices B, Gallegos Sánchez C, González AV. Intraorganismal genetic heterogeneity as a source of genetic variation in modular macroalgae. JOURNAL OF PHYCOLOGY 2018; 54:767-771. [PMID: 30206942 DOI: 10.1111/jpy.12784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Genetic diversity is considered a key factor of population survival and evolution, especially in changing environments. Genetic diversity arises from mutations in the DNA sequence of cell lines and from there it reaches the level of organisms, populations, and regions. However, many previous studies have not considered the organism architecture or pattern of thallus construction, ignoring the potential genetic complexities that intraorganismal genetic heterogeneity could generate in modular organisms. In seaweeds, modularity and clonality exist in many species. Modular organization has been related to advantages in terms of rapid construction and recovery after the loss of individual modules, which have their own demographic properties as they generate, mature, senesce, and die. Based on recent evidence from the literature, we suggest that modules also have their own genetic properties. Specifically, modular seaweeds have two possible sources of genetic diversity at the individual level: the heterozygosity of the genotypes composing the genet, and genetic heterogeneity among the modules within a genet (i.e., intraclonal genetic variability). Both sources of genetic diversity can have ecological and evolutionary consequences, and most of them must be considered in research on modular seaweeds. Linking intraorganismal genetic diversity with clonal architecture and propagation styles may help us to understand important ecological and evolutionary processes such as speciation modes, invasive capacities, or farming potential.
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Affiliation(s)
- Bernabé Santelices
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Alameda 340, Santiago, 8331150, Chile
| | - Cristóbal Gallegos Sánchez
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Casilla 114-D, Alameda 340, Santiago, 8331150, Chile
| | - Alejandra V González
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Casilla 653, Las Palmeras 3425, Ñuñoa, Santiago, 7800024, Chile
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18
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Bijak AL, van Dijk KJ, Waycott M. Population structure and gene flow of the tropical seagrass, Syringodium filiforme, in the Florida Keys and subtropical Atlantic region. PLoS One 2018; 13:e0203644. [PMID: 30183774 PMCID: PMC6124813 DOI: 10.1371/journal.pone.0203644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/26/2018] [Indexed: 11/28/2022] Open
Abstract
Evaluating genetic diversity of seagrasses provides insight into reproductive mode and adaptation potential, and is therefore integral to broader conservation strategies for coastal ecosystems. In this study, we assessed genetic diversity, population structure and gene flow in an opportunistic seagrass, Syringodium filiforme, in the Florida Keys and subtropical Atlantic region. We used microsatellite markers to analyze 20 populations throughout the Florida Keys, South Florida, Bermuda and the Bahamas primarily to understand how genetic diversity of S. filiforme partitions across the Florida Keys archipelago. We found low allelic diversity within populations, detecting 35–106 alleles across all populations, and in some instances moderately high clonal diversity (R = 0.04–0.62). There was significant genetic differentiation between Atlantic and Gulf of Mexico (Gulf) populations (FST = 0.109 ± 0.027, p-value = 0.001) and evidence of population structure based on cluster assignment, dividing the region into two major genetic demes. We observed asymmetric patterns in gene flow, with a few instances in which there was higher than expected gene flow from Atlantic to Gulf populations. In South Florida, clustering into Gulf and Atlantic groups indicate dispersal in S. filiforme may be limited by historical or contemporary geographic and hydrologic barriers, though genetic admixture between populations suggests exchange may occur between narrow channels in the Florida Keys, or has occurred through other mechanisms in recent evolutionary history, maintaining regional connectivity. The variable genotypic diversity, low genetic diversity and evidence of population structure observed in populations of S. filiforme resemble the population genetics expected for a colonizer species.
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Affiliation(s)
- Alexandra L. Bijak
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
| | - Kor-jent van Dijk
- School of Biological Sciences, Environment Institute, Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, South Australia, Australia
| | - Michelle Waycott
- School of Biological Sciences, Environment Institute, Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, South Australia, Australia
- State Herbarium of South Australia, Department of Environment, Water and Natural Resources, Adelaide, South Australia, Australia
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Lees LE, Krueger-Hadfield SA, Clark AJ, Duermit EA, Sotka EE, Murren CJ. Nonnative Gracilaria vermiculophylla tetrasporophytes are more difficult to debranch and are less nutritious than gametophytes. JOURNAL OF PHYCOLOGY 2018; 54:471-482. [PMID: 29676788 DOI: 10.1111/jpy.12746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 03/22/2018] [Indexed: 06/08/2023]
Abstract
Theory predicts that the maintenance of haplodiplontic life cycles requires ecological differences between the haploid gametophytes and diploid sporophytes, yet evidence of such differences remain scarce. The haplodiplontic red seaweed Gracilaria vermiculophylla has invaded the temperate estuaries of the Northern Hemisphere, where it commonly modifies detrital and trophic pathways. In native populations, abundant hard substratum enables spore settlement, and gametophyte:tetrasporophyte ratios are ~40:60. In contrast, many non-native populations persist in soft-sediment habitats without abundant hard substratum, and can be 90%-100% tetrasporophytic. To test for ecologically relevant phenotypic differences, we measured thallus morphology, protein content, organic content, "debranching resistance" (i.e., tensile force required to remove a branch from its main axis node), and material properties between male gametophytes, female gametophytes, and tetrasporophytes from a single, nonnative site in Charleston Harbor, South Carolina, USA in 2015 and 2016. Thallus length and surface area to volume ratio differed between years, but were not significantly different between ploidies. Tetrasporophytes had lower protein content than gametophytes, suggesting the latter may be more attractive to consumers. More force was required to pull a branch from the main axis of tetrasporophytes relative to gametophytes. A difference in debranching resistance may help to maintain tetrasporophyte thallus durability relative to gametophytes, providing a potential advantage in free-floating populations. These data may shed light on the invasion ecology of an important ecosystem engineer, and may advance our understanding of life cycle evolution and the maintenance of life cycle diversity.
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Affiliation(s)
- Lauren E Lees
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson Rd, Charleston, South Carolina, 29414, USA
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Stacy A Krueger-Hadfield
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson Rd, Charleston, South Carolina, 29414, USA
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, 35924, USA
| | - Andrew J Clark
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Elizabeth A Duermit
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson Rd, Charleston, South Carolina, 29414, USA
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Erik E Sotka
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson Rd, Charleston, South Carolina, 29414, USA
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
| | - Courtney J Murren
- Department of Biology, College of Charleston, 66 George Street, Charleston, South Carolina, 29424, USA
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Gallegos Sánchez CF, Beltrán J, Flores V, González AV, Santelices B. Testing the effects of heterozygosity on growth rate plasticity in the seaweed Gracilaria chilensis (Rhodophyta). Ecol Evol 2018; 8:5741-5751. [PMID: 29938089 PMCID: PMC6010757 DOI: 10.1002/ece3.4113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 02/09/2018] [Accepted: 03/29/2018] [Indexed: 11/11/2022] Open
Abstract
Heterozygosity has been positively associated with fitness and population survival. However, the relationship between heterozygosity and adaptive phenotypic plasticity (i.e., plasticity which results in fitness homeostasis or improvement in changing environments) is unclear and has been poorly explored in seaweeds. In this study, we explored this relationship in the clonal red seaweed, Gracilaria chilensis by conducting three growth rate plasticity experiments under contrasting salinity conditions and by measuring heterozygosity with five microsatellite DNA markers. Firstly, we compared growth rate plasticity between the haploid and diploid phases. Secondly, we compared growth rate plasticity between diploids with different numbers of heterozygous loci. Finally, we compared growth rate plasticity between diploid plants from two populations that are expected to exhibit significant differences in heterozygosity. We found that, (i) diploids displayed a higher growth rate and lower growth rate plasticity than haploids, (ii) diploids with a higher number of heterozygous loci displayed lower growth rate plasticity than those exhibiting less heterozygosity, and (iii) diploid sporophytes from the population with higher heterozygosity displayed lower growth rate plasticity than those with lower heterozygosity. Accordingly, this study suggests that heterozygosity is inversely related to growth rate plasticity in G. chilensis. However, better genetic tools in seaweeds are required for a more definitive conclusion on the relationship between heterozygosity and phenotypic plasticity.
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Affiliation(s)
| | - Jessica Beltrán
- Departamento de EcologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Verónica Flores
- Departamento de EcologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
| | - Alejandra V. González
- Departamento de Ciencias EcológicasFacultad de CienciasUniversidad de ChileSantiagoChile
| | - Bernabé Santelices
- Departamento de EcologíaFacultad de Ciencias BiológicasPontificia Universidad Católica de ChileSantiagoChile
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Doležálková-Kaštánková M, Pruvost NBM, Plötner J, Reyer HU, Janko K, Choleva L. All-male hybrids of a tetrapod Pelophylax esculentus share its origin and genetics of maintenance. Biol Sex Differ 2018; 9:13. [PMID: 29609661 PMCID: PMC5880063 DOI: 10.1186/s13293-018-0172-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/15/2018] [Indexed: 02/07/2023] Open
Abstract
Background Sexual parasites offer unique insights into the reproduction of unisexual and sexual populations. Because unisexuality is almost exclusively linked to the female sex, most studies addressed host-parasite dynamics in populations where sperm-dependent females dominate. Pelophylax water frogs from Central Europe include hybrids of both sexes, collectively named P. esculentus. They live syntopically with their parental species P. lessonae and/or P. ridibundus. Some hybrid lineages consist of all males providing a chance to understand the origin and perpetuation of a host-parasite (egg-dependent) system compared to sperm-dependent parthenogenesis. Methods We focused on P. ridibundus-P. esculentus populations where P. ridibundus of both sexes lives together with only diploid P. esculentus males. Based on 17 microsatellite markers and six allozyme loci, we analyzed (i) the variability of individual genomes, (ii) the reproductive mode(s) of all-male hybrids, and (iii) the genealogical relationships between the hybrid and parental genomes. Results Our microsatellite data revealed that P. esculentus males bear Mendelian-inherited ridibundus genomes while the lessonae genome represents a single clone. Our data indicate that this clone did not recently originate from adjacent P. lessonae populations, suggesting an older in situ or ex situ origin. Conclusions Our results confirm that also males can perpetuate over many generations as the unisexual lineage and successfully compete with P. ridibundus males for eggs provided by P. ridibundus females. Natural persistence of such sex-specific hybrid populations allows to studying the similarities and differences between male and female reproductive parasitism in many biological settings. Electronic supplementary material The online version of this article (10.1186/s13293-018-0172-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marie Doležálková-Kaštánková
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 277 21, Liběchov, Czech Republic. .,Department of Zoology, Faculty of Science, Charles University in Prague, 128 43, Praha 2, Czech Republic.
| | - Nicolas B M Pruvost
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jörg Plötner
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115, Berlin, Germany
| | - Heinz-Ulrich Reyer
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 277 21, Liběchov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 277 21, Liběchov, Czech Republic. .,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic.
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Wang X, Jia Y, Wamishe Y, Jia MH, Valent B. Dynamic Changes in the Rice Blast Population in the United States Over Six Decades. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:803-812. [PMID: 28677493 DOI: 10.1094/mpmi-04-17-0101-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice blast disease caused by Magnaporthe oryzae is one of the most destructive diseases of rice. Field isolates of M. oryzae rapidly adapt to their hosts and climate. Tracking the genetic and pathogenic variability of field isolates is essential to understand how M. oryzae interacts with hosts and environments. In this study, a total of 1,022 United States field isolates collected from 1959 to 2015 were analyzed for pathogenicity toward eight international rice differentials. A subset of 457 isolates was genotyped with 10 polymorphic simple sequence repeat (SSR) markers. The average polymorphism information content value of markers was 0.55, suggesting that the SSR markers were highly informative to capture the population variances. Six genetic clusters were identified by both STRUCTURE and discriminant analysis of principal components methods. Overall, Nei's diversity of M. oryzae in the United States was 0.53, which is higher than previously reported in a world rice blast collection (0.19). The observed subdivision was associated with collection time periods but not with geographic origin of the isolates. Races such as IC-17, IE-1, and IB-49 have been identified across almost all collection periods and all clusters; races such as IA-1, IB-17, and IH-1 have a much higher frequency in certain periods and clusters. Both genomic and pathogenicity changes of United States blast isolates were associated with collection year, suggesting that hosts are a driving force for the genomic variability of rice blast fungus.
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Affiliation(s)
- Xueyan Wang
- 1 Rice Research and Extension Center, University of Arkansas, Stuttgart, AR 72160, U.S.A
- 2 Dale Bumper National Rice Research Center, USDA, ARS, Stuttgart, AR 72160, U.S.A.; and
| | - Yulin Jia
- 2 Dale Bumper National Rice Research Center, USDA, ARS, Stuttgart, AR 72160, U.S.A.; and
| | - Yeshi Wamishe
- 1 Rice Research and Extension Center, University of Arkansas, Stuttgart, AR 72160, U.S.A
| | - Melissa H Jia
- 2 Dale Bumper National Rice Research Center, USDA, ARS, Stuttgart, AR 72160, U.S.A.; and
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Dowling ME, Schnabel G, Boatwright HG, Everhart SE. Novel gene-sequence markers for isolate tracking within Monilinia fructicola lesions. PEST MANAGEMENT SCIENCE 2017; 73:1822-1829. [PMID: 28160377 DOI: 10.1002/ps.4544] [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: 10/05/2016] [Revised: 12/19/2016] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Monilinia fructicola is a diverse pathogen of pome and stone fruits that causes severe economic losses each year. However, little is known about inoculum flow within or between orchards and pathogen establishment in an orchard, because few methods exist for detecting diversity or tracking isolates over time. SSR loci are an effective option, but may be confounded by a high degree of mutability and potential sensitivity to abiotic stress. RESULTS Through transcriptome analysis, we identified novel markers mrr1, DHFR and MfCYP01 and validated stability of these markers under fungicide stress in natural infection sites. Nucleotide variation within mrr1, DHFR and MfCYP01 sequences differentiated isolates at all spatial scales: within the same infection site, between trees and between two farms. Sequenced regions were also effective for matching isolates collected from blossoms at the beginning of the season to progeny in cankers obtained at the end of the season. CONCLUSIONS Collectively, results show that mrr1, DHFR and MfCYP01 are able to accurately differentiate M. fructicola isolates at the population level, can be used to track isolates over time, and are more stable than SSRs under external stresses. Either by themselves or combined with SSR markers, these gene-encoding regions are a much-needed tool for better understanding M. fructicola population dynamics. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Madeline E Dowling
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Guido Schnabel
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Harriet G Boatwright
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Sydney E Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
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24
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Wu Z, Wu J, Wang Y, Hou H. Development of EST-derived microsatellite markers in the aquatic macrophyte Ranunculus bungei (Ranunculaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700022. [PMID: 28791205 PMCID: PMC5546165 DOI: 10.3732/apps.1700022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Microsatellite or simple sequence repeat (SSR) markers were developed to investigate the influence of ecological factors on gene flow and spatial genetic structuring of the submerged plant Ranunculus bungei (Ranunculaceae), which is regarded as an important species for understanding how plants adapt to an aquatic environment. METHODS AND RESULTS Twenty-two microsatellite loci were identified from an expressed sequence tag (EST) library. The number of alleles per locus ranged from one to five, and the expected heterozygosity varied from 0.0 to 0.5 in four Chinese populations of R. bungei. Fourteen loci were polymorphic and significantly deviated from Hardy-Weinberg equilibrium. All of the loci were found to be amplifiable in two other species of Ranunculus section Batrachium, and cross-amplification in six riparian and aquatic species of Ranunculaceae was also partially successful. CONCLUSIONS These novel EST-SSR markers will be useful for ecological and evolutionary studies of R. bungei as well as related species.
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Affiliation(s)
- Zhigang Wu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People’s Republic of China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People’s Republic of China
| | - Jinwei Wu
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Yalin Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People’s Republic of China
| | - Hongwei Hou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People’s Republic of China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People’s Republic of China
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Arnaud-Haond S, Aires T, Candeias R, Teixeira SJL, Duarte CM, Valero M, Serrão EA. Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia. Mol Ecol 2017; 26:2379-2391. [PMID: 28133884 DOI: 10.1111/mec.14030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 11/08/2016] [Accepted: 11/29/2016] [Indexed: 11/30/2022]
Abstract
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and β diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.
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Affiliation(s)
- S Arnaud-Haond
- IFREMER, Station de Sète, UMR MARBEC, Avenue Jean Monnet, CS 30171, 34203, Sète Cedex, France.,OREME - Station Marine, Université Montpellier, 2 rue des Chantiers - CC 99009, 34200, Sète, France.,CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - T Aires
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - R Candeias
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - S J L Teixeira
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - C M Duarte
- RSRC (Red Sea Research Center), King Abdullah University of Science and Technology (KAUST), Building 2, Level 3, Room 3219, Thuwal, 23955-6900, Saudi Arabia
| | - M Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, UPMC, PUCCh, UACH, Station Biologique de Roscoff, Sorbonne Universités, CS 90074, Place Georges Teissier, 29688, Roscoff Cedex, France
| | - E A Serrão
- CCMAR-CIMAR, MAREE, Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
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Nakajima Y, Matsuki Y, Arriesgado DM, Campos WL, Nadaoka K, Lian C. Population genetics information for the regional conservation of a tropical seagrass, Enhalus acoroides, around the Guimaras Strait, Philippines. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0927-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Alors D, Grande FD, Cubas P, Crespo A, Schmitt I, Molina MC, Divakar PK. Panmixia and dispersal from the Mediterranean Basin to Macaronesian Islands of a macrolichen species. Sci Rep 2017; 7:40879. [PMID: 28102303 PMCID: PMC5244402 DOI: 10.1038/srep40879] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/12/2016] [Indexed: 02/04/2023] Open
Abstract
The Mediterranean region, comprising the Mediterranean Basin and the Macaronesian Islands, represents a center of diversification for many organisms. The genetic structure and connectivity of mainland and island microbial populations has been poorly explored, in particular in the case of symbiotic fungi. Here we investigated genetic diversity and spatial structure of the obligate outcrossing lichen-forming fungus Parmelina carporrhizans in the Mediterranean region. Using eight microsatellite and mating-type markers we showed that fungal populations are highly diverse but lack spatial structure. This is likely due to high connectivity and long distance dispersal of fungal spores. Consistent with low levels of linkage disequilibrium and lack of clonality, we detected both mating-type idiomorphs in all populations. Furthermore we showed that the Macaronesian Islands are the result of colonization from the Mediterranean Basin. The unidirectional gene flow, though, seemed not to be sufficient to counterbalance the effects of drift, resulting in comparatively allelic poor peripheral populations. Our study is the first to shed light on the high connectivity and lack of population structure in natural populations of a strictly sexual lichen fungus. Our data further support the view of the Macaronesian Islands as the end of the colonization road for this symbiotic ascomycete.
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Affiliation(s)
- David Alors
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Paloma Cubas
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe Universität, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany
| | - M. Carmen Molina
- Departamento de Biología y Geología, Física y Química Inorgánica (Área de Biodiversidad y Conservación), ESCET, Universidad Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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Fant JB, Price AL, Larkin DJ. The influence of habitat disturbance on genetic structure and reproductive strategies within stands of native and non-native Phragmites australis
(common reed). DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Jeremie B. Fant
- Plant Science and Conservation; Chicago Botanic Garden; 1000 Lake Cook Road Glencoe IL 60022 USA
- Plant Biology and Conservation; Northwestern University; Evanston IL 60208 USA
| | - Amy L. Price
- Plant Science and Conservation; Chicago Botanic Garden; 1000 Lake Cook Road Glencoe IL 60022 USA
- Plant Biology and Conservation; Northwestern University; Evanston IL 60208 USA
| | - Daniel J. Larkin
- Plant Science and Conservation; Chicago Botanic Garden; 1000 Lake Cook Road Glencoe IL 60022 USA
- Department of Fisheries, Wildlife, and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; St. Paul MN 55108 USA
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30
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Persistence of the gypsophile Lepidospartum burgessii (Asteraceae) through clonal growth and limited gene flow. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0855-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Krueger‐Hadfield SA, Kollars NM, Byers JE, Greig TW, Hammann M, Murray DC, Murren CJ, Strand AE, Terada R, Weinberger F, Sotka EE. Invasion of novel habitats uncouples haplo‐diplontic life cycles. Mol Ecol 2016; 25:3801-16. [DOI: 10.1111/mec.13718] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/23/2016] [Accepted: 05/20/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Stacy A. Krueger‐Hadfield
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - Nicole M. Kollars
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - James E. Byers
- Odum School of Ecology University of Georgia 130 E. Green St. Athens GA 30602 USA
| | - Thomas W. Greig
- NOAA/National Ocean Service Center for Coastal Environmental Health and Biomolecular Research 219 Fort Johnson Rd Charleston SC 29312 USA
| | - Mareike Hammann
- GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 20 D‐23105 Kiel Germany
| | - David C. Murray
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
| | - Courtney J. Murren
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - Allan E. Strand
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - Ryuta Terada
- Department of Fisheries Kagoshima University Shimoarata 3‐50‐20 Kagoshima City 890‐0056 Japan
| | - Florian Weinberger
- GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 20 D‐23105 Kiel Germany
| | - Erik E. Sotka
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
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Chaïr H, Traore RE, Duval MF, Rivallan R, Mukherjee A, Aboagye LM, Van Rensburg WJ, Andrianavalona V, Pinheiro de Carvalho MAA, Saborio F, Sri Prana M, Komolong B, Lawac F, Lebot V. Genetic Diversification and Dispersal of Taro (Colocasia esculenta (L.) Schott). PLoS One 2016; 11:e0157712. [PMID: 27314588 PMCID: PMC4912093 DOI: 10.1371/journal.pone.0157712] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 06/05/2016] [Indexed: 11/18/2022] Open
Abstract
Taro (Colocasia esculenta (L.) Schott) is widely distributed in tropical and sub-tropical areas. However, its origin, diversification and dispersal remain unclear. While taro genetic diversity has been documented at the country and regional levels in Asia and the Pacific, few reports are available from Americas and Africa where it has been introduced through human migrations. We used eleven microsatellite markers to investigate the diversity and diversification of taro accessions from nineteen countries in Asia, the Pacific, Africa and America. The highest genetic diversity and number of private alleles were observed in Asian accessions, mainly from India. While taro has been diversified in Asia and the Pacific mostly via sexual reproduction, clonal reproduction with mutation appeared predominant in African and American countries investigated. Bayesian clustering revealed a first genetic group of diploids from the Asia-Pacific region and to a second diploid-triploid group mainly from India. Admixed cultivars between the two genetic pools were also found. In West Africa, most cultivars were found to have originated from India. Only one multi-locus lineage was assigned to the Asian pool, while cultivars in Madagascar originated from India and Indonesia. The South African cultivars shared lineages with Japan. The Caribbean Islands cultivars were found to have originated from the Pacific, while in Costa Rica they were from India or admixed between Indian and Asian groups. Taro dispersal in the different areas of Africa and America is thus discussed in the light of available records of voyages and settlements.
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Affiliation(s)
- H. Chaïr
- CIRAD, UMR AGAP, Montpellier, France
- * E-mail:
| | - R. E. Traore
- Université de Ouagadougou, UFR-SVT, Ouagadougou, Burkina Faso
| | | | | | | | | | | | | | | | - F. Saborio
- Universidad de Costa Rica, San Jose, Costa Rica
| | | | - B. Komolong
- NARI, LAE, Morobe Province, Papua New Guinea
| | | | - V. Lebot
- CIRAD, UMR AGAP, Port Vila, Vanuatu
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Ravelomanantsoa S, Robène I, Chiroleu F, Guérin F, Poussier S, Pruvost O, Prior P. A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of the Ralstonia solanacearum species complex. PeerJ 2016; 4:e1949. [PMID: 27168969 PMCID: PMC4860299 DOI: 10.7717/peerj.1949] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022] Open
Abstract
Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC phylotype III.
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Affiliation(s)
- Santatra Ravelomanantsoa
- BIOS UMR PVBMT, CIRAD, Saint-Pierre, La Réunion, France
- UMR PVBMT, Université de la Reunion, Saint-Denis, La Réunion, France
- Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | | | | | - Fabien Guérin
- UMR PVBMT, Université de la Reunion, Saint-Denis, La Réunion, France
| | - Stéphane Poussier
- UMR PVBMT, Université de la Reunion, Saint-Pierre La Réunion, France
| | | | - Philippe Prior
- BIOS UMR PVBMT, CIRAD, Saint-Pierre, La Réunion, France
- Department of Plant Health and Environment, INRA, Paris, France
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Burrell AM, Pepper AE, Hodnett G, Goolsby JA, Overholt WA, Racelis AE, Diaz R, Klein PE. Exploring origins, invasion history and genetic diversity ofImperata cylindrica(L.) P. Beauv. (Cogongrass) in the United States using genotyping by sequencing. Mol Ecol 2015; 24:2177-93. [DOI: 10.1111/mec.13167] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 12/31/2022]
Affiliation(s)
- A. Millie Burrell
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
| | - Alan E. Pepper
- Department of Biology; Texas A&M University; College Station TX 77843-3258 USA
| | - George Hodnett
- Department of Soil and Crop Sciences; Texas A&M University; College Station TX 77843-2474 USA
| | - John A. Goolsby
- Cattle Fever Tick Research Laboratory; USDA-ARS; Moore Air Base Building 6419 Edinburg TX 78541 USA
| | - William A. Overholt
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Alexis E. Racelis
- Department of Biology; University of Texas Pan American; 1201 West University Drive Edinburg TX 78539 USA
| | - Rodrigo Diaz
- Biological Control and Containment Laboratory; University of Florida; 2199 South Rock Road Fort Pierce FL 34945-3138 USA
| | - Patricia E. Klein
- Institute for Plant Genomics and Biotechnology; Department of Horticultural Sciences; Texas A&M University; College Station TX 77843-2123 USA
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Tedder A, Helling M, Pannell JR, Shimizu-Inatsugi R, Kawagoe T, van Campen J, Sese J, Shimizu KK. Female sterility associated with increased clonal propagation suggests a unique combination of androdioecy and asexual reproduction in populations of Cardamine amara (Brassicaceae). ANNALS OF BOTANY 2015; 115:763-76. [PMID: 25776435 PMCID: PMC4373288 DOI: 10.1093/aob/mcv006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 09/29/2014] [Accepted: 12/23/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The coexistence of hermaphrodites and female-sterile individuals, or androdioecy, has been documented in only a handful of plants and animals. This study reports its existence in the plant species Cardamine amara (Brassicaceae), in which female-sterile individuals have shorter pistils than seed-producing hermaphrodites. METHODS Morphological analysis, in situ manual pollination, microsatellite genotyping and differential gene expression analysis using Arabidopsis microarrays were used to delimit variation between female-sterile individuals and hermaphrodites. KEY RESULTS Female sterility in C. amara appears to be caused by disrupted ovule development. It was associated with a 2.4- to 2.9-fold increase in clonal propagation. This made the pollen number of female-sterile genets more than double that of hermaphrodite genets, which fulfils a condition of co-existence predicted by simple androdioecy theories. When female-sterile individuals were observed in wild androdioecious populations, their ramet frequencies ranged from 5 to 54 %; however, their genet frequencies ranged from 11 to 29 %, which is consistent with the theoretically predicted upper limit of 50 %. CONCLUSIONS The results suggest that a combination of sexual reproduction and increased asexual proliferation by female-sterile individuals probably explains the invasion and maintenance of female sterility in otherwise hermaphroditic populations. To our knowledge, this is the first report of the coexistence of female sterility and hermaphrodites in the Brassicaceae.
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Affiliation(s)
- Andrew Tedder
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
| | - Matthias Helling
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
| | - John R Pannell
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
| | - Rie Shimizu-Inatsugi
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
| | - Tetsuhiro Kawagoe
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
| | - Julia van Campen
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
| | - Jun Sese
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
| | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, CH-8057, Switzerland, Department of Ecology and Evolution, University of Lausanne, Lausanne CH-1015, Switzerland, Center for Ecological Research (CER), Kyoto University, 2-509-3, Hirano, Otsu, Shiga 520-2113, Japan and Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku, Tokyo, 135-0064, Japan
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Hmeljevski KV, dos Reis MS, Forzza RC. Patterns of gene flow in Encholirium horridum L.B.Sm., a monocarpic species of Bromeliaceae from Brazil. J Hered 2014; 106:93-101. [PMID: 25472982 DOI: 10.1093/jhered/esu067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Encholirium horridum is a bromeliad that occurs exclusively on inselbergs in the Atlantic Forest biome of Brazil. These rock outcrops form natural islands that isolate populations from each other. We investigated gene flow by pollen through paternity analyses of a bromeliad population in an area of approximately 2 ha in Espírito Santo State, Brazil. To that end, seed rosettes and seedlings were genotyped using nuclear microsatellite loci. A plot was also established from the same population and specimens were genotyped to evaluate their fine-scale spatial genetic structure (SGS) through analyses of spatial autocorrelation and clonal growth. Paternity analysis indicated that 80% of the attributed progenitors of the genotyped seedlings were from inside the study area. The pollen dispersal distances within the area were restricted (mean distance of 45.5 m, varying from 3 to 156 m) and fine-scale SGS was weak (F(ij) = 0.0122, P < 0.001; Sp = 0.009). Clonal growth was found to be a rare event, supporting the monocarpy of this species.
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Affiliation(s)
- Karina Vanessa Hmeljevski
- From the Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil (Hmeljevski); Federal University of Santa Catarina, PO Box 476, Florianópolis 88040-900, SC, Brazil (Reis); and the Rio de Janeiro Botanical Garden, Rio de Janeiro 22460-030, RJ, Brazil (Forzza).
| | - Maurício Sedrez dos Reis
- From the Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil (Hmeljevski); Federal University of Santa Catarina, PO Box 476, Florianópolis 88040-900, SC, Brazil (Reis); and the Rio de Janeiro Botanical Garden, Rio de Janeiro 22460-030, RJ, Brazil (Forzza)
| | - Rafaela Campostrini Forzza
- From the Federal University of Rio de Janeiro, Rio de Janeiro 21941-617, RJ, Brazil (Hmeljevski); Federal University of Santa Catarina, PO Box 476, Florianópolis 88040-900, SC, Brazil (Reis); and the Rio de Janeiro Botanical Garden, Rio de Janeiro 22460-030, RJ, Brazil (Forzza)
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Leme da Cunha N, Fischer E, Lorenz-Lemke AP, Barrett SCH. Floral variation and environmental heterogeneity in a tristylous clonal aquatic of the Pantanal wetlands of Brazil. ANNALS OF BOTANY 2014; 114:1637-49. [PMID: 25180289 PMCID: PMC4416129 DOI: 10.1093/aob/mcu181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/28/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS The balance between stochastic forces and frequency-dependent mating largely governs style morph frequencies in heterostylous populations. In clonal species, deviations from equal morph ratios often result from founder events and unfavourable conditions for sexual reproduction. The aim of this study was to investigate whether different flooding regimes, because of their influence on sexual vs. clonal reproduction, are associated with regional variation in morph frequencies and floral trait differentiation in populations of the clonal, tristylous, aquatic Eichhornia azurea (Pontederiaceae) in the Pantanal wetlands of Brazil. METHODS Style morph frequencies were sampled from 73 populations distributed across four flooding regimes differing in depth and duration. Measurements of flower size, sex-organ dimension, pollen size and pollen production were made in selected populations, and pollinator assemblages and their functional traits were recorded. KEY RESULTS Most populations of E. azurea were tristylous (78 %), but the majority exhibited uneven morph ratios. The frequency of the mid-styled morph was significantly lower than that of the long- and short-styled morphs. Morph evenness was positively associated with population size but not with flooding regime. There were significant phenotypic differences among flooding regimes for all floral traits, including populations with reduced flower size, sex-organ length and smaller pollen. Pollinator assemblages varied with flood duration. CONCLUSIONS The similar morph structure and evenness of populations, regardless of flooding regime, suggest that sexual reproduction and clonal dispersal are sufficiently common to prevent the signature of founder events from dominating in a region. However, the pervasive occurrence of biased morph ratios in most populations suggests that many are in a non-equilibrium state. The reduced frequency of the mid-styled morph in trimorphic and dimorphic populations may be associated with the weak self-incompatibility of this morph resulting in selfing and inbreeding depression. Clonality in E. azurea and the weak self-incompatibility of the mid-styled morph may make it more vulnerable to geitonogamous selfing.
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Affiliation(s)
- Nicolay Leme da Cunha
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, Mato Grosso do Sul, Brazil
| | - Erich Fischer
- Centro de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, Mato Grosso do Sul, Brazil
| | - Aline P Lorenz-Lemke
- Centro de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso do Sul, 79070-900 Campo Grande, Mato Grosso do Sul, Brazil
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
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Nakajima Y, Matsuki Y, Lian C, Fortes MD, Uy WH, Campos WL, Nakaoka M, Nadaoka K. The Kuroshio current influences genetic diversity and population genetic structure of a tropical seagrass, Enhalus acoroides. Mol Ecol 2014; 23:6029-44. [PMID: 25384848 DOI: 10.1111/mec.12996] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 11/30/2022]
Abstract
Information on genetic diversity and differentiation of seagrass populations is essential for the conservation of coastal ecosystems. However, little is known about the seagrasses in the Indo-West Pacific Ocean, where the world's highest diversity of seagrasses occurs. The influence of sea currents on these populations is also unknown. We estimated the genetic diversity and population genetic structure and identified reproductive features in Enhalus acoroides populations from the Yaeyama Islands, Hainan Island and the Philippines. The Philippines are situated at the centre of the E. acoroides range, Yaeyama and Hainan are peripheral populations, and the Yaeyama population is at the northern limit of the species range. The powerful Kuroshio Current flows from the Philippines to Yaeyama. Genetic analyses using nine microsatellite markers indicated that reproduction of E. acoroides is mostly sexual. Clonal diversity does not decrease in northern populations, although genetic diversity does. However, the genetic diversity of the Yaeyama populations is greater than that of the Hainan populations. Significant genetic differentiation among most populations was evident; however, the Yaeyama and north-east Philippines populations were genetically similar, despite being separated by ~1100 km. An assignment test suggested that recruitment occurs from the north-east Philippines to Yaeyama. The strong current in this region is probably responsible for the extant genetic diversity and recruitment patterns.
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Affiliation(s)
- Yuichi Nakajima
- Asian Natural Environmental Science Center, The University of Tokyo, 1-1-8 Midori-cho, Nishitokyo, Tokyo, 188-0002, Japan
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Kim ES, Zaya DN, Fant JB, Ashley MV. Genetic factors accelerate demographic decline in rare Asclepias species. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0663-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Bijak AL, van Dijk KJ, Waycott M. Development of microsatellite markers for a tropical seagrass, Syringodium filiforme (Cymodoceaceae). APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1400082. [PMID: 25309842 PMCID: PMC4189501 DOI: 10.3732/apps.1400082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 09/11/2014] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY A total of 17 polymorphic microsatellite markers were developed for the tropical Atlantic seagrass Syringodium filiforme (Cymodoceaceae), enabling analysis of population genetic structure in this species for the first time. • METHODS AND RESULTS The 17 primers amplified di- and trinucleotide repeats revealing two to eight alleles per locus among the South Florida populations tested. In the analysis of two populations from the Florida Keys (Florida, USA), observed heterozygosity ranged from 0.063 to 0.905, although sampling was from relatively closely located populations so heterozygosity is expected to be higher across larger spatial scales. Multiplex PCRs consisting of two 6-plex and one 5-plex reactions were developed to maximize genotyping efficiency. • CONCLUSIONS We present here 17 polymorphic markers that will be useful for the study of clonality and population structure of S. filiforme, a marine plant that forms extensive habitat throughout the tropical Atlantic and Caribbean.
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Affiliation(s)
- Alexandra L. Bijak
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia 22904 USA
| | - Kor-jent van Dijk
- School of Earth and Environmental Sciences, Environment Institute, Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, South Australia 5001, Australia
| | - Michelle Waycott
- School of Earth and Environmental Sciences, Environment Institute, Australian Centre for Evolutionary Biology and Biodiversity, University of Adelaide, Adelaide, South Australia 5001, Australia
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Jiang K, Xu NN, Tsang PKE, Chen XY. Genetic variation in populations of the threatened seagrass Halophila beccarii (Hydrocharitaceae). BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2013.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Arnaud-Haond S, Moalic Y, Hernandez-Garcia E, Eguiluz VM, Alberto F, Serrao EA, Duarte CM. Disentangling the Influence of Mutation and Migration in Clonal Seagrasses Using the Genetic Diversity Spectrum for Microsatellites. J Hered 2014; 105:532-541. [DOI: 10.1093/jhered/esu015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/23/2014] [Indexed: 11/13/2022] Open
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Saleh D, Milazzo J, Adreit H, Fournier E, Tharreau D. South-East Asia is the center of origin, diversity and dispersion of the rice blast fungus, Magnaporthe oryzae. THE NEW PHYTOLOGIST 2014; 201:1440-1456. [PMID: 24320224 PMCID: PMC4265293 DOI: 10.1111/nph.12627] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/23/2013] [Indexed: 05/11/2023]
Abstract
• Inferring invasion routes and identifying reservoirs of diversity of plant pathogens are essential in proposing new strategies for their control. Magnaporthe oryzae, the fungus responsible for rice blast disease, has invaded all rice growing areas. Virulent genotypes regularly (re)emerge, causing rapid resistance breakdowns. However, the world-wide genetic subdivision of M. oryzae populations on rice and its past history of invasion have never been elucidated. • In order to investigate the centers of diversity, origin and migration of M. oryzae on rice, we analyzed the genetic diversity of 55 populations from 15 countries. • Three genetic clusters were identified world-wide. Asia was the center of diversity and the origin of most migrations to other continents. In Asia, two centers of diversity were revealed in the Himalayan foothills: South China-Laos-North Thailand, and western Nepal. Sexual reproduction persisted only in the South China-Laos-North Thailand region, which was identified as the putative center of origin of all M. oryzae populations on rice. • Our results suggest a scenario of early evolution of M. oryzae on rice that matches the past history of rice domestication. This study confirms that crop domestication may have considerable influence on the pestification process of natural enemies.
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Affiliation(s)
- Dounia Saleh
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
- INRA, UMR BGPITA A54/K, F 34398, Montpellier, France
| | | | - Henri Adreit
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
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Berrebi P, Retif X, Bouhbouh S. Genetic evidence of unisexual reproduction in the Moroccan hexaploid barbelLabeobarbus fritschi. FOLIA ZOOLOGICA 2013. [DOI: 10.25225/fozo.v62.i4.a2.2013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Patrick Berrebi
- Institut des Sciences de l'Evolution, UMR 5554 UM2-CNRS-IRD, Université Montpellier II, CC 065, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Xavier Retif
- Institut des Sciences de l'Evolution, UMR 5554 UM2-CNRS-IRD, Université Montpellier II, CC 065, Place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Saadia Bouhbouh
- Université Sidi Mohamed Ben Abdellah, Faculté des Sciences Dhar El Mehraz, Fès, Morocco
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Chong C, Edwards W, Pearson R, Waycott M. Sprouting and genetic structure vary with flood disturbance in the tropical riverine paperbark tree, Melaleuca leucadendra (Myrtaceae). AMERICAN JOURNAL OF BOTANY 2013; 100:2250-2260. [PMID: 24186959 DOI: 10.3732/ajb.1200614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Sprouting in woody plants promotes persistence in the face of disturbance, ultimately influencing population structure. Different disturbance regimes drive variable population responses, but there have been few direct tests of the relative differences in population structure to specific drivers. We measured population structure as genotypic diversity (clonality) as a function of hydrological regime for a riverine tree, Melaleuca leucadendra, a major structural component in flood landscapes in the Australian dry tropics. METHODS We estimated clonality, genotypic richness, and population allelic diversity. The relationship among disturbance, genetic estimates of clonality, and population distinctiveness was compared with flood regime, characterized by return frequencies and hydrological stress at individual river reaches. KEY RESULTS Two contrasting patterns of genotypic structure were detected and corresponded to order-of-magnitude differences in flood regime between sites. At mainstem locations characterized by greatest flood intensity, sprouting generated clonal structure to 17 m (30% ramets clonal). By contrast, clonality was atypical at lower-disturbance tributaries (0% clonal). Population allelic distributions showed extensive genetic exchange among mainstem locations, but strong genetic differentiation between mainstem and tributaries. CONCLUSIONS Population structure and distinctiveness in riverine Melaleuca are determined by differences in sprouting and recruitment responses that depend on localized hydrological regime. Sprouting contributes to population persistence via localized clonal growth. Resprouting following disturbance in M. leucadendra may help explain its numerical dominance in tropical river systems. This study, although preliminary, suggests that flood ecosystems may represent excellent experimental systems to develop a better understanding of whole-organism responses to environmental drivers.
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Affiliation(s)
- Caroline Chong
- School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia
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MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms. INFECTION GENETICS AND EVOLUTION 2013; 20:188-96. [PMID: 24025589 DOI: 10.1016/j.meegid.2013.08.029] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/29/2013] [Accepted: 08/31/2013] [Indexed: 11/22/2022]
Abstract
Multi-locus sequence typing (MLST) is a frequently used genotyping method whose goal is the unambiguous assignment of microorganisms to genetic clusters. MLST typically involves analysis of DNA sequence results generated from several house-keeping gene loci. MLST remains the gold standard for molecular typing of many bacterial pathogens. Eukaryotic pathogens have also been the subject of MLST, however, few tools are available to deal with diploid sequence data. Here we present novel software for MLST data analysis tailored towards diploid Eukaryotes: MLSTest. This software meets various methods used in MLST and introduces some novel methodologies for the evaluation of the data set. In addition to construction of allelic profiles and basic clustering analysis, the MLSTest looks for network structures that suggest genetic exchange in BURST graphs. Additionally, it uses several simple methods for tree construction with the advantage of managing heterozygous or three-state sites. Additionally, the software analyses whether concatenation of fragments from different genes is suitable for the data set using different tests (bionj-incongruence length difference test, Templeton test). It evaluates how the incongruence is distributed across the tree using a variation of the localized incongruence length difference test based on a modified neighbour joining algorithm. We tested the last method in simulated datasets. We showed that is conservative (adequate type I error rate) and moderately to highly powerful as well as useful to localize incongruences in two bacterial and two eukaryotic MLST datasets. MLSTest was also designed for developing MLST schemes. It thus has tools to optimize locus combinations and to reduce the number of targets required for typing. MLSTest also analyses whether the discriminatory power of the typing scheme is increased by including more loci. We evaluated the software over simulated and real datasets from bacterial and eukaryotic microorganisms. The software is freely available at http://www.ipe.unsa.edu.ar/software.
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Cidade FW, Vigna BBZ, de Souza FHD, Valls JFM, Dall’Agnol M, Zucchi MI, de Souza-Chies TT, Souza AP. Genetic variation in polyploid forage grass: assessing the molecular genetic variability in the Paspalum genus. BMC Genet 2013; 14:50. [PMID: 23759066 PMCID: PMC3682885 DOI: 10.1186/1471-2156-14-50] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 05/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. RESULTS Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). CONCLUSIONS The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a valuable tool for species identification in the initial assessment of germplasm as well as for characterization, conservation and successful species hybridization.
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Affiliation(s)
- Fernanda W Cidade
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), CP 6010, Campinas, SP CEP 13083-875, Brazil
| | - Bianca BZ Vigna
- Brazilian Agricultural Research Corporation (Embrapa) Southeast Livestock, CP 339, São Carlos, SP CEP 13560-970, Brazil
| | - Francisco HD de Souza
- Brazilian Agricultural Research Corporation (Embrapa) Southeast Livestock, CP 339, São Carlos, SP CEP 13560-970, Brazil
| | - José Francisco M Valls
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica - PqEB, CP 02372, Brasília, DF CEP 70770-917, Brasil
| | - Miguel Dall’Agnol
- Faculty of Agronomy, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 7712 Agronomia, Porto Alegre, Rio Grande do Sul CEP 91501-970, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios/APTA, Km 30, CP 28, Pólo Regional Centro Sul, Rodovia SP127, Piracicaba, SP CEP13400-970, Brazil
| | - Tatiana T de Souza-Chies
- Department of Botany, Prédio 43433, Federal University of Rio Grande do Sul, Av. Bento Gonçalves, 9500 Agronomia, Porto Alegre, Rio Grande do Sul, CEP 91501-970, Brazil
| | - Anete P Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), CP 6010, Campinas, SP CEP 13083-875, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), CP 6109 Campinas, SP, CEP 13083-875, Brazil
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How clonal are Trypanosoma and Leishmania? Trends Parasitol 2013; 29:264-9. [DOI: 10.1016/j.pt.2013.03.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 11/20/2022]
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Meloni M, Reid A, Caujapé-Castells J, Marrero A, Fernández-Palacios JM, Mesa-Coelo RA, Conti E. Effects of clonality on the genetic variability of rare, insular species: the case of Ruta microcarpa from the Canary Islands. Ecol Evol 2013; 3:1569-79. [PMID: 23789068 PMCID: PMC3686192 DOI: 10.1002/ece3.571] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 11/08/2022] Open
Abstract
Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short-lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long-term viability.
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Affiliation(s)
- M Meloni
- Institute of Systematic Botany, University of Zurich Zollikerstrase 107, Zurich, 8008, Switzerland
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