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Zimmer EA, Berg JA, Dudash MR. Genetic diversity and population structure among native, naturalized, and invasive populations of the common yellow monkeyflower, Mimulus guttatus (Phrymaceae). Ecol Evol 2023; 13:e9596. [PMID: 37038527 PMCID: PMC10082173 DOI: 10.1002/ece3.9596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/01/2022] [Accepted: 03/28/2022] [Indexed: 04/12/2023] Open
Abstract
An ongoing controversy in invasion biology is the prevalence of colonizing plant populations that are able to establish and spread, while maintaining limited amounts of genetic variation. Invasive populations can be established through several routes including from a single source or from multiple introductions. The aim of this study was to examine genetic diversity in populations of Mimulus guttatus in the United Kingdom, where the species is considered invasive, and compare this diversity to that in native populations on the west coast of North America. Additionally, we looked at diversity in non-native populations that have not yet become invasive (naturalized populations) in eastern North America. We investigated population structure among populations in these three regions and attempted to uncover the sources for populations that have established in the naturalized and invasive regions. We found that genetic diversity was, on average, relatively high in populations from the invasive UK region and comparable to native populations. Contrastingly, two naturalized M. guttatus populations were low in both genetic and genotypic diversity, indicating a history of asexual reproduction and self-fertilization. A third naturalized population was found to be a polyploid Mimulus hybrid of unknown origin. Our results demonstrate that M. guttatus has likely achieved colonization success outside of its native western North America distribution by a variety of establishment pathways, including those with genetic and demographic benefits resulting from multiple introductions in the UK, reproductive assurance through selfing, and asexual reproduction in eastern North America, and possible polyploidization in one Canadian population.
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Affiliation(s)
- Elizabeth A. Zimmer
- Department of Botany and Laboratories of Analytical Biology, National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of ColumbiaUSA
| | - Jason A. Berg
- Department of Biological SciencesUniversity of MarylandCollege ParkMarylandUSA
| | - Michele R. Dudash
- Department of Biological SciencesUniversity of MarylandCollege ParkMarylandUSA
- Department of Natural Resource ManagementSouth Dakota State UniversityBrookingsSouth DakotaUSA
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2
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The successful production of "sterbel" hybrids using beluga (Huso huso) cryopreserved sperm. Anim Reprod Sci 2023; 249:107197. [PMID: 36764190 DOI: 10.1016/j.anireprosci.2023.107197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/23/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
This is the first report of the production of viable "sterbel" hybrids using cryopreserved beluga (Huso huso) sperm. In the present study, beluga cryopreserved sperm were used for fertilization and activation of eggs collected from four females of sterlet (Acipenser ruthenus). Sperm were cryopreserved with the use of a glucose methanol extender with the application of an automatic freezer. The mean sperm concentration of beluga was 1.54 × 109 mL-1. Cryopreservation did not significantly change sperm velocity and trajectory parameters (VCL, VSL, VAP, LIN, STR, ALH, BCF). Cryopreservation affected only the values of percentage of motile sperm (MOT) and progressive motility (PRG). The frozen/thawed sperm were subsequently used for the fertilization of the sterlet ova. The fertilized and activated eggs from each female were incubated in separate experimental incubation cages in the RAS system (at 15 °C). This experiment resulted in the production of inter-generic hybrids that were incubated until hatching. Experimental hybridization was characterized by 20-35% hatching rates and normal development of "sterbel" larvae. Experimental hybrids were verified using molecular and cytogenetic analyses. All produced specimens were characterized by sterlet maternal and beluga paternal genomes and were diploids with 120 chromosomes. This study presents the procedure of hybridization of the sterlet with beluga cryopreserved sperm that can be applied in sturgeon aquaculture or research focused on the biology of sturgeon reproduction.
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Kinser TJ, Smith RD, Lawrence AH, Cooley AM, Vallejo-Marín M, Conradi Smith GD, Puzey JR. Endosperm-based incompatibilities in hybrid monkeyflowers. THE PLANT CELL 2021; 33:2235-2257. [PMID: 33895820 PMCID: PMC8364248 DOI: 10.1093/plcell/koab117] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/15/2021] [Indexed: 05/31/2023]
Abstract
Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.
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Affiliation(s)
- Taliesin J. Kinser
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
| | - Ronald D. Smith
- Department of Applied Science, College of William and Mary, Williamsburg, Virginia 23185
| | - Amelia H. Lawrence
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
| | | | - Mario Vallejo-Marín
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland FK9 4LA, UK
| | | | - Joshua R. Puzey
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185
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4
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Dutta A, Dutreux F, Schacherer J. Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds. eLife 2021; 10:70339. [PMID: 34159898 PMCID: PMC8245132 DOI: 10.7554/elife.70339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss of heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1% to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, that is, tracts extending to the end of the chromosome (n = 3168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.
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Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
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Simón-Porcar VI, Silva JL, Vallejo-Marín M. Rapid local adaptation in both sexual and asexual invasive populations of monkeyflowers (Mimulus spp.). ANNALS OF BOTANY 2021; 127:655-668. [PMID: 33604608 PMCID: PMC8052927 DOI: 10.1093/aob/mcab004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Traditionally, local adaptation has been seen as the outcome of a long evolutionary history, particularly with regard to sexual lineages. By contrast, phenotypic plasticity has been thought to be most important during the initial stages of population establishment and in asexual species. We evaluated the roles of adaptive evolution and phenotypic plasticity in the invasive success of two closely related species of invasive monkeyflowers (Mimulus) in the UK that have contrasting reproductive strategies: M. guttatus combines sexual (seeds) and asexual (clonal growth) reproduction while M. × robertsii is entirely asexual. METHODS We compared the clonality (number of stolons), floral and vegetative phenotype, and phenotypic plasticity of native (M. guttatus) and invasive (M. guttatus and M. × robertsii) populations grown in controlled environment chambers under the environmental conditions at each latitudinal extreme of the UK. The goal was to discern the roles of temperature and photoperiod on the expression of phenotypic traits. Next, we tested the existence of local adaptation in the two species within the invasive range with a reciprocal transplant experiment at two field sites in the latitudinal extremes of the UK, and analysed which phenotypic traits underlie potential local fitness advantages in each species. KEY RESULTS Populations of M. guttatus in the UK showed local adaptation through sexual function (fruit production), while M. × robertsii showed local adaptation via asexual function (stolon production). Phenotypic selection analyses revealed that different traits are associated with fitness in each species. Invasive and native populations of M. guttatus had similar phenotypic plasticity and clonality. M. × robertsii presents greater plasticity and clonality than native M. guttatus, but most populations have restricted clonality under the warm conditions of the south of the UK. CONCLUSIONS This study provides experimental evidence of local adaptation in a strictly asexual invasive species with high clonality and phenotypic plasticity. This indicates that even asexual taxa can rapidly (<200 years) adapt to novel environmental conditions in which alternative strategies may not ensure the persistence of populations.
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Affiliation(s)
- Violeta I Simón-Porcar
- Departmento de Biología Vegetal y Ecología, Universidad de Sevilla, Apartado 1095, E-41080 Sevilla, Spain
| | - Jose L Silva
- Pyrenean Institute of Ecology (CSIC), Avenida Montañana 1005, 50059 Zaragoza, Spain
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland FK9 4LA, UK
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Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus. Commun Biol 2021; 4:327. [PMID: 33712659 PMCID: PMC7954805 DOI: 10.1038/s42003-021-01795-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/05/2021] [Indexed: 01/24/2023] Open
Abstract
Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments. Vallejo-Marín et al. combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. They found that M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range, and hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide.
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Meeus S, Šemberová K, De Storme N, Geelen D, Vallejo-Marín M. Effect of Whole-Genome Duplication on the Evolutionary Rescue of Sterile Hybrid Monkeyflowers. PLANT COMMUNICATIONS 2020; 1:100093. [PMID: 33367262 PMCID: PMC7747968 DOI: 10.1016/j.xplc.2020.100093] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/08/2020] [Accepted: 07/01/2020] [Indexed: 05/15/2023]
Abstract
Hybridization is a creative evolutionary force, increasing genomic diversity and facilitating adaptation and even speciation. Hybrids often face significant challenges to establishment, including reduced fertility that arises from genomic incompatibilities between their parents. Whole-genome duplication in hybrids (allopolyploidy) can restore fertility, cause immediate phenotypic changes, and generate reproductive isolation. Yet the survival of polyploid lineages is uncertain, and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions. Here, we use natural and synthetically produced hybrid and polyploid monkeyflowers (Mimulus spp.) to study how polyploidy contributes to the fertility, reproductive isolation, phenotype, and performance of hybrids in the field. We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents. The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication, in which plants have larger organs and are slower to flower. Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents, whereas natural hybrids have higher survival than all other taxa. We conclude that hybridization and polyploidy can act as sources of genomic novelty, but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.
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Affiliation(s)
- Sofie Meeus
- Department of Biological and Environmental Sciences. University of Stirling, Stirling FK9 4LA, UK
| | - Kristýna Šemberová
- Department of Botany, Charles University, 128 43 Prague 2, Czech Republic
| | - Nico De Storme
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Mario Vallejo-Marín
- Department of Biological and Environmental Sciences. University of Stirling, Stirling FK9 4LA, UK
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Butkuvienė J, Sinkevičienė Z, Naugžemys D, Žvingila D, Skridaila A, Bobrov AA. Genetic Diversity of Aquatic Ranunculus ( Batrachium, Ranunculaceae) in One River Basin Caused by Hybridization. PLANTS 2020; 9:plants9111455. [PMID: 33126633 PMCID: PMC7694053 DOI: 10.3390/plants9111455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/16/2022]
Abstract
Aquatic Ranunculus (sect. Batrachium) include homophyllous and heterophyllous plants. The development of floating leaves may be induced by genetic mechanisms or/and environmental conditions and this fact complicates the morphologically based identification of species. DNA-based studies provide the opportunity to expand the knowledge of this complicated group. We studied heterophyllous Ranunculus with well-developed capillary and intermediate leaves and visually homophyllous plants with capillary leaves from a single river basin, with the aim to evaluate their genetic polymorphism and taxonomic status-whether the plants with well-developed and weakly expressed intermediate leaves belong to different forms (taxa) or if they just express morphological variation of one or two taxa in a specific, very variable river environment. The studied heterophyllous and homophyllous plants from different rivers showed high genetic differentiation and a low level of genetic diversity within these groups. The molecular analysis did not reveal any inter simple sequence repeat (ISSR) polymorphism associated with the development of intermediate leaves. An analysis of nuclear ribosomal internal transcribed spacers ITS1-2 sequences revealed several ribotypes, which indicated the genetic heterogeneity of studied plants and indirectly confirmed the hybrid origin of some of them. Sterile plants originated from crossing of R. circinatus and R. penicillatus were discovered in the Skroblus River; however, identification of the parental species was impeded by the polymorphism detected. For this reason, cytological studies were performed and allowed confirmation of the hybrid origin of these plants.
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Affiliation(s)
- Jurgita Butkuvienė
- Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10222 Vilnius, Lithuania;
- Botanical Garden, Vilnius University, Kairėnų Str. 43, 01100 Vilnius, Lithuania; (D.N.); (A.S.)
- Correspondence: ; Tel.: +370-52398262
| | - Zofija Sinkevičienė
- Nature Research Centre, Institute of Botany, Žaliųjų Ežerų Str. 49, 12200 Vilnius, Lithuania;
| | - Donatas Naugžemys
- Botanical Garden, Vilnius University, Kairėnų Str. 43, 01100 Vilnius, Lithuania; (D.N.); (A.S.)
| | - Donatas Žvingila
- Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10222 Vilnius, Lithuania;
| | - Audrius Skridaila
- Botanical Garden, Vilnius University, Kairėnų Str. 43, 01100 Vilnius, Lithuania; (D.N.); (A.S.)
| | - Alexander A. Bobrov
- Papanin Institute for Biology of Inland Waters RAS, Borok, Nekouz distr., 152742 Yaroslavl reg., Russia;
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Beirinckx L, Vanschoenwinkel B, Triest L. Hidden Hybridization and Habitat Differentiation in a Mediterranean Macrophyte, the Euryhaline Genus Ruppia. FRONTIERS IN PLANT SCIENCE 2020; 11:830. [PMID: 32754168 PMCID: PMC7366321 DOI: 10.3389/fpls.2020.00830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
In many aquatic plant taxa, classification based on morphology has always been difficult. Molecular markers revealed that the complexity in several of these aquatic taxa could be addressed to recurrent hybridization events and cryptic species diversity. The submerged macrophyte genus Ruppia is one of these aquatic genera with a complex taxonomy due to the absence of clear distinguishable traits and several hybridization events. Two species co-exist throughout Europe, R. maritima and R. spiralis (previously known as R. cirrhosa), but recent molecular studies also found several indications of hybridization, introgression and chloroplast capture between these species. However, the full extent and frequency of hybridization and introgression in this genus has not been studied so far, nor is it clear how these hybrid lineages can co-exist locally with their parental species. In this paper, we wanted to detect whether a single coastal wetland where both species co-exist can act as a Ruppia hybrid zone. As a case study, we chose the Camargue, a Mediterranean coastal wetland that harbors a wide diversity in aquatic habitats, especially in terms of salinity and hydro-regime. We sampled several Ruppia populations within this wetland. To identify each sample and reconstruct the local genetic structure of the two parental species and their hybrids, we used both chloroplast and nuclear microsatellite markers. Afterward, we tested whether different species had different habitat preferences. Our results confirmed that R. maritima and R. spiralis are two strongly divergent species with different reproductive ecologies and different habitat preferences. This prevents frequent hybridization and consequently we could not detect any trace of a recent hybridization event. However, we found several populations of later-generation hybrids, including a population of R. maritima x hybrid backcrosses. The hybrid populations occupy a different habitat and are genetically distinct from their parental species, although they tend to be morphological similar to parental R. maritima. Although local hybridization and introgression in Ruppia is less frequent than we expected, the taxonomy of Ruppia is complicated due to ancient hybridizations and several back-crossings.
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Affiliation(s)
- Lise Beirinckx
- Ecology and Biodiversity Research Group, Plant Biology and Nature Management, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Bram Vanschoenwinkel
- Community Ecology Laboratory, Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Ludwig Triest
- Ecology and Biodiversity Research Group, Plant Biology and Nature Management, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Hollister JD, Greiner S, Johnson MTJ, Wright SI. Hybridization and a loss of sex shape genome-wide diversity and the origin of species in the evening primroses (Oenothera, Onagraceae). THE NEW PHYTOLOGIST 2019; 224:1372-1380. [PMID: 31309571 DOI: 10.1111/nph.16053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
Hybridization is thought to promote speciation in at least two ways - by fixation of heterozygosity from diploid progenitors in allopolyploids, and by generation of transgressive phenotypes and shifting fitness optima during homoploid hybrid speciation. While recent studies support a hybrid origin for a growing number of species, the extent to which hybrid origins shape patterns of diversity in asexual species remains underexplored. Here we employed transcriptome sequencing and population genomic analysis to describe patterns of genomic variation in the 13 species belonging to Oenothera subsection Oenothera. Eight of these species are functionally asexual and arose by hybrid speciation from parents spanning a range of phylogenetic divergence. We showed that genomic divergence between parents has been retained as heterozygosity in functionally asexual species, and that genome-wide levels of heterozygosity in these asexuals largely reflects the divergence of parental haplotypes coupled with a breakdown in recombination and segregation across the genome. These results show that divergence between parental species and loss of sex in hybrids shape patterns of whole-genome diversity and the origin of asexual species.
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Affiliation(s)
- Jesse D Hollister
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Stephan Greiner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 1A1, Canada
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12
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Stift M, Kolář F, Meirmans PG. STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations. Heredity (Edinb) 2019; 123:429-441. [PMID: 31285566 PMCID: PMC6781132 DOI: 10.1038/s41437-019-0247-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 01/19/2023] Open
Abstract
Analysis of population genetic structure has become a standard approach in population genetics. In polyploid complexes, clustering analyses can elucidate the origin of polyploid populations and patterns of admixture between different cytotypes. However, combining diploid and polyploid data can theoretically lead to biased inference with (artefactual) clustering by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) data to systematically compare the performance of k-means clustering and the model-based clustering methods implemented in STRUCTURE, ADMIXTURE, FASTSTRUCTURE and INSTRUCT under different scenarios of differentiation and with different marker types. Under scenarios of strong population differentiation, the tested applications performed equally well. However, when population differentiation was weak, STRUCTURE was the only method that allowed unbiased inference with markers with limited genotypic information (co-dominant markers with unknown dosage or dominant markers). Still, since STRUCTURE was comparatively slow, the much faster but less powerful FASTSTRUCTURE provides a reasonable alternative for large datasets. Finally, although bias makes k-means clustering unsuitable for markers with incomplete genotype information, for large numbers of loci (>1000) with known dosage k-means clustering was superior to FASTSTRUCTURE in terms of power and speed. We conclude that STRUCTURE is the most robust method for the analysis of genetic structure in mixed-ploidy populations, although alternative methods should be considered under some specific conditions.
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Affiliation(s)
- Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czechia.,Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
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13
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Pantoja PO, Paine CET, Vallejo-Marín M. Natural selection and outbreeding depression suggest adaptive differentiation in the invasive range of a clonal plant. Proc Biol Sci 2018; 285:20181091. [PMID: 30051824 PMCID: PMC6053932 DOI: 10.1098/rspb.2018.1091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/14/2018] [Indexed: 11/12/2022] Open
Abstract
Analyses of phenotypic selection and demography in field populations are powerful ways to establishing the potential role of natural selection in shaping evolution during biological invasions. Here we use experimental F2 crosses between native and introduced populations of Mimulus guttatus to estimate the pattern of natural selection in part of its introduced range, and to seek evidence of outbreeding depression of colonists. The F2s combined the genome of an introduced population with the genome of either native or introduced populations. We found that the introduced × introduced cross had the fastest population growth rate owing to increased winter survival, clonality and seed production. Our analysis also revealed that selection through sexual fitness favoured large floral displays, large vegetative and flower size, lateral spread and early flowering. Our results indicate a source-of-origin effect, consistent with outbreeding depression exposed by mating between introduced and native populations. Our findings suggest that well-established non-native populations may pay a high fitness cost during subsequent bouts of admixture with native populations, and reveal that processes such as local adaptation in the invasive range can mediate the fitness consequences of admixture.
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Affiliation(s)
- Pauline O Pantoja
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - C E Timothy Paine
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
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14
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Genetic diversity of Spanish Prunus domestica L. germplasm reveals a complex genetic structure underlying. PLoS One 2018; 13:e0195591. [PMID: 29630655 PMCID: PMC5891032 DOI: 10.1371/journal.pone.0195591] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/25/2018] [Indexed: 12/17/2022] Open
Abstract
European plum (Prunus domestica L.) is an ancient domesticated species cultivated in temperate areas worldwide whose genetic structure has been scarcely analyzed to date. In this study, a broad representation of Spanish European plum germplasm collected in Northeastern Spain and a representative set of reference cultivars were compared using nuclear and chloroplast markers. The number of alleles per locus detected with the SSR markers ranged from 8 to 39, with an average of 23.4 alleles, and 8 haplotypes were identified. Bayesian model-based clustering, minimum spanning networks, and the analysis of molecular variance showed the existence of a hierarchical structure. At the first level, two genetic groups were found, one containing 'Reine Claude' type reference cultivars altogether with ca. 25% of local genotypes, and a second one much more diverse. This latter group split in two groups, one containing most (ca. 70%) local genotypes and some old Spanish and French reference cultivars, whereas the other included 24 reference cultivars and only six local genotypes. A third partition level allowed a significant finer delineation into five groups. As a whole, the genetic structure of European plum from Northeastern Spain was shown to be complex and conditioned by a geographical proximity factor. This study not only contributes to genetic conservation and breeding for this species at the national level, but also supports the relevance of undertaking similar tasks of collection and characterization in other unexplored areas. Moreover, this kind of research could lead to future coordinated actions for the examination of the whole European plum diversity, to define conservation strategies, and could be used to better understand the genetic control of traits of horticultural interest through association mapping.
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Viengkone M, Derocher AE, Richardson ES, Malenfant RM, Miller JM, Obbard ME, Dyck MG, Lunn NJ, Sahanatien V, Davis CS. Assessing polar bear ( Ursus maritimus) population structure in the Hudson Bay region using SNPs. Ecol Evol 2016; 6:8474-8484. [PMID: 28031799 PMCID: PMC5167041 DOI: 10.1002/ece3.2563] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 09/14/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Defining subpopulations using genetics has traditionally used data from microsatellite markers to investigate population structure; however, single‐nucleotide polymorphisms (SNPs) have emerged as a tool for detection of fine‐scale structure. In Hudson Bay, Canada, three polar bear (Ursus maritimus) subpopulations (Foxe Basin (FB), Southern Hudson Bay (SH), and Western Hudson Bay (WH)) have been delineated based on mark–recapture studies, radiotelemetry and satellite telemetry, return of marked animals in the subsistence harvest, and population genetics using microsatellites. We used SNPs to detect fine‐scale population structure in polar bears from the Hudson Bay region and compared our results to the current designations using 414 individuals genotyped at 2,603 SNPs. Analyses based on discriminant analysis of principal components (DAPC) and STRUCTURE support the presence of four genetic clusters: (i) Western—including individuals sampled in WH, SH (excluding Akimiski Island in James Bay), and southern FB (south of Southampton Island); (ii) Northern—individuals sampled in northern FB (Baffin Island) and Davis Strait (DS) (Labrador coast); (iii) Southeast—individuals from SH (Akimiski Island in James Bay); and (iv) Northeast—individuals from DS (Baffin Island). Population structure differed from microsatellite studies and current management designations demonstrating the value of using SNPs for fine‐scale population delineation in polar bears.
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Affiliation(s)
- Michelle Viengkone
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | | | - Evan Shaun Richardson
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada University of Alberta Edmonton AB Canada
| | - René Michael Malenfant
- Department of Biological Sciences University of Alberta Edmonton AB Canada; Department of Biology University of New Brunswick Fredericton NB Canada
| | - Joshua Moses Miller
- Department of Biological Sciences University of Alberta Edmonton AB Canada; Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Martyn E Obbard
- Wildlife Research and Monitoring Section Ontario Ministry of Natural Resources and Forestry Trent University Peterborough ON Canada
| | - Markus G Dyck
- Department of Environment Government of Nunavut Igloolik NU Canada
| | - Nick J Lunn
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada University of Alberta Edmonton AB Canada
| | - Vicki Sahanatien
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Corey S Davis
- Department of Biological Sciences University of Alberta Edmonton AB Canada
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Jones KE, Pérez-Espona S, Reyes-Betancort JA, Pattinson D, Caujapé-Castells J, Hiscock SJ, Carine MA. Why do different oceanic archipelagos harbour contrasting levels of species diversity? The macaronesian endemic genus Pericallis (Asteraceae) provides insight into explaining the 'Azores diversity Enigma'. BMC Evol Biol 2016; 16:202. [PMID: 27717307 PMCID: PMC5055660 DOI: 10.1186/s12862-016-0766-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/27/2016] [Indexed: 11/30/2022] Open
Abstract
Background Oceanic archipelagos typically harbour extensive radiations of flowering plants and a high proportion of endemics, many of which are restricted to a single island (Single Island Endemics; SIEs). The Azores represents an anomaly as overall levels of endemism are low; there are few SIEs and few documented cases of intra-archipelago radiations. The distinctiveness of the flora was first recognized by Darwin and has been referred to as the ‘Azores Diversity Enigma’ (ADE). Diversity patterns in the Macaronesian endemic genus Pericallis (Asteraceae) exemplify the ADE. In this study we used morphometric, Amplified Length Polymorphisms, and bioclimatic data for herbaceous Pericallis lineages endemic to the Azores and the Canaries, to test two key hypotheses proposed to explain the ADE: i) that it is a taxonomic artefact or Linnean shortfall, ie. the under description of taxa in the Azores or the over-splitting of taxa in the Canaries and (ii) that it reflects the greater ecological homogeneity of the Azores, which results in limited opportunity for ecological diversification compared to the Canaries. Results In both the Azores and the Canaries, morphological patterns were generally consistent with current taxonomic classifications. However, the AFLP data showed no genetic differentiation between the two currently recognized Azorean subspecies that are ecologically differentiated. Instead, genetic diversity in the Azores was structured geographically across the archipelago. In contrast, in the Canaries genetic differentiation was mostly consistent with morphology and current taxonomic treatments. Both Azorean and Canarian lineages exhibited ecological differentiation between currently recognized taxa. Conclusions Neither a Linnean shortfall nor the perceived ecological homogeneity of the Azores fully explained the ADE-like pattern observed in Pericallis. Whilst variation in genetic data and morphological data in the Canaries were largely congruent, this was not the case in the Azores, where genetic patterns reflected inter-island geographical isolation, and morphology reflected intra-island bioclimatic variation. The combined effects of differences in (i) the extent of geographical isolation, (ii) population sizes and (iii) geographical occupancy of bioclimatic niche space, coupled with the morphological plasticity of Pericallis, may all have contributed to generating the contrasting patterns observed in the archipelagos. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0766-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- K E Jones
- Botanischer Garten und Botanisches Museum Berlin-Dahlem, Dahlem Centre of Plant Sciences, Freie Universität Berlin, Königin-Luise Str. 6-8, Berlin, 14195, Germany.
| | - S Pérez-Espona
- Estación Biológica de Doñana, CSIC, C./ Américo Vespucio s/n, Sevilla, E-41092, Spain
| | - J A Reyes-Betancort
- Jardín de Aclimatación de La Oratava (ICIA), C/Retama 2, Puerto de la Cruz, Tenerife, 38400, Spain
| | - D Pattinson
- Natural History Museum, Cromwell Road, London, SE7 5ED, UK.,Present address: Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - J Caujapé-Castells
- Jardín Botánico Canario "Viera y Clavijo"-Unidad Asociada al CSIC (Cabildo de Gran Canaria), Camino del palmeral 15 (Tafira Alta), Las Palmas de Gran Canaria, 35017, Spain
| | - S J Hiscock
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - M A Carine
- Natural History Museum, Cromwell Road, London, SE7 5ED, UK
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Vallejo-Marín M, Hiscock SJ. Hybridization and hybrid speciation under global change. THE NEW PHYTOLOGIST 2016; 211:1170-87. [PMID: 27214560 DOI: 10.1111/nph.14004] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/07/2016] [Indexed: 05/24/2023]
Abstract
Contents 1170 I. 1170 II. 1172 III. 1175 IV. 1180 V. 1183 1184 References 1184 SUMMARY: An unintended consequence of global change is an increase in opportunities for hybridization among previously isolated lineages. Here we illustrate how global change can facilitate the breakdown of reproductive barriers and the formation of hybrids, drawing on the flora of the British Isles for insight. Although global change may ameliorate some of the barriers preventing hybrid establishment, for example by providing new ecological niches for hybrids, it will have limited effects on environment-independent post-zygotic barriers. For example, genic incompatibilities and differences in chromosome numbers and structure within hybrid genomes are unlikely to be affected by global change. We thus speculate that global change will have a larger effect on eroding pre-zygotic barriers (eco-geographical isolation and phenology) than post-zygotic barriers, shifting the relative importance of these two classes of reproductive barriers from what is usually seen in naturally produced hybrids where pre-zygotic barriers are the largest contributors to reproductive isolation. Although the long-term fate of neo-hybrids is still to be determined, the massive impact of global change on the dynamics and distribution of biodiversity generates an unprecedented opportunity to study large numbers of unpredicted, and often replicated, hybridization 'experiments', allowing us to peer into the birth and death of evolutionary lineages.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Simon J Hiscock
- University of Oxford Botanic Garden, Rose Lane, Oxford, OX1 4AZ, UK
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Liorzou M, Pernet A, Li S, Chastellier A, Thouroude T, Michel G, Malécot V, Gaillard S, Briée C, Foucher F, Oghina-Pavie C, Clotault J, Grapin A. Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4711-25. [PMID: 27406785 PMCID: PMC4973750 DOI: 10.1093/jxb/erw269] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Hybridization with introduced genetic resources is commonly practiced in ornamental plant breeding to introgress desired traits. The 19th century was a golden age for rose breeding in France. The objective here was to study the evolution of rose genetic diversity over this period, which included the introduction of Asian genotypes into Europe. A large sample of 1228 garden roses encompassing the conserved diversity cultivated during the 18th and 19th centuries was genotyped with 32 microsatellite primer pairs. Its genetic diversity and structure were clarified. Wide diversity structured in 16 genetic groups was observed. Genetic differentiation was detected between ancient European and Asian accessions, and a temporal shift from a European to an Asian genetic background was observed in cultivated European hybrids during the 19th century. Frequent crosses with Asian roses throughout the 19th century and/or selection for Asiatic traits may have induced this shift. In addition, the consistency of the results with respect to a horticultural classification is discussed. Some horticultural groups, defined according to phenotype and/or knowledge of their pedigree, seem to be genetically more consistent than others, highlighting the difficulty of classifying cultivated plants. Therefore, the horticultural classification is probably more appropriate for commercial purposes rather than genetic relatedness, especially to define preservation and breeding strategies.
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Affiliation(s)
- Mathilde Liorzou
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Alix Pernet
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Shubin Li
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Annie Chastellier
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Tatiana Thouroude
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Gilles Michel
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Sylvain Gaillard
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Céline Briée
- Université d'Angers, UMR CNRS 6258 CERHIO, Centre de recherches historiques de l'Ouest, 5 bis Bd Lavoisier 49045 Angers, France
| | - Fabrice Foucher
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Cristiana Oghina-Pavie
- Université d'Angers, UMR CNRS 6258 CERHIO, Centre de recherches historiques de l'Ouest, 5 bis Bd Lavoisier 49045 Angers, France
| | - Jérémy Clotault
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Agnès Grapin
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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Laport RG, Minckley RL, Ramsey J. Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex. AMERICAN JOURNAL OF BOTANY 2016; 103:1358-1374. [PMID: 27440793 DOI: 10.3732/ajb.1600105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Polyploidy is widely recognized as a mechanism of diversification. Contributions of polyploidy to specific pre- and postzygotic barriers-and classifications of polyploid speciation as "ecological" vs. "non-ecological"-are more contentious. Evaluation of these issues requires comprehensive studies that test ecological characteristics of cytotypes as well as the coincidence of genetic structure with cytotype distributions. METHODS We investigated a classical example of autopolyploid speciation, Larrea tridentata, at multiple areas of cytotype co-occurrence. Habitat and phenological differences were compared between diploid, tetraploid, and hexaploid populations on the basis of edaphic, community composition, and flowering time surveys. Frequency of hybridization between diploids and tetraploids was investigated using a diploid-specific chloroplast DNA (cpDNA) marker; genetic structure for all cytotypes was assessed using amplified fragment length polymorphisms (AFLPs). KEY RESULTS Across contact zones, we found cytotypes in habitats distinguished by soil and vegetation. We observed modest differences in timing and production of flowers, indicating a degree of assortative mating that was asymmetric between cytotypes. Nonetheless, cpDNA analyses in diploid-tetraploid contact zones suggested that ∼5% of tetraploid plants had hybrid origins involving unilateral sexual polyploidization. Genetic structure of AFLPs largely coincided with cytotype distributions in diploid-tetraploid contact zones. In contrast, there was little structure in areas of contact between tetraploids and hexaploids, suggesting intercytotype gene flow or recurrent hexaploid formation. CONCLUSIONS Diploid, tetraploid, and hexaploid cytotypes of L. tridentata are segregated by environmental distributions and flowering phenology in contact zones, with diploid and tetraploid populations having corresponding differences in genetic structure.
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Affiliation(s)
- Robert G Laport
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska 68588 USA
| | - Robert L Minckley
- University of Rochester, Department of Biology, River Campus, Rochester, New York 14627 USA
| | - Justin Ramsey
- Black Hills State University, School of Natural Sciences, Spearfish, South Dakota 57799 USA
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20
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Vallejo-Marín M, Cooley AM, Lee MY, Folmer M, McKain MR, Puzey JR. Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor. AMERICAN JOURNAL OF BOTANY 2016; 103:1272-88. [PMID: 27221281 DOI: 10.3732/ajb.1500471] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/16/2016] [Indexed: 05/11/2023]
Abstract
PREMISE OF THE STUDY Hybridization between diploids and tetraploids can lead to new allopolyploid species, often via a triploid intermediate. Viable triploids are often produced asymmetrically, with greater success observed for "maternal-excess" crosses where the mother has a higher ploidy than the father. Here we investigated the evolutionary origins of Mimulus peregrinus, an allohexaploid recently derived from the triploid M. ×robertsii, to determine whether reproductive asymmetry has shaped the formation of this new species. METHODS We used reciprocal crosses between the diploid (M. guttatus) and tetraploid (M. luteus) progenitors to determine the viability of triploid M. ×robertsii hybrids resulting from paternal- vs. maternal-excess crosses. To investigate whether experimental results predict patterns seen in the field, we performed parentage analyses comparing natural populations of M. peregrinus to its diploid, tetraploid, and triploid progenitors. Organellar sequences obtained from pre-existing genomic data, supplemented with additional genotyping was used to establish the maternal ancestry of multiple M. peregrinus and M. ×robertsii populations. KEY RESULTS We found strong evidence for asymmetric origins of M. peregrinus, but opposite to the common pattern, with paternal-excess crosses significantly more successful than maternal-excess crosses. These results successfully predicted hybrid formation in nature: 111 of 114 M. ×robertsii individuals, and 27 of 27 M. peregrinus, had an M. guttatus maternal haplotype. CONCLUSION This study, which includes the first Mimulus chloroplast genome assembly, demonstrates the utility of parentage analysis through genome skimming. We highlight the benefits of complementing genomic analyses with experimental approaches to understand asymmetry in allopolyploid speciation.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Science, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA UK
| | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington 99362 USA
| | - Michelle Yuequi Lee
- Biological and Environmental Science, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA UK
| | - Madison Folmer
- Department of Biology, College of William and Mary, Williamsburg, Virginia 23185 USA
| | - Michael R McKain
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132 USA
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia 23185 USA
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Sakata Y, Itami J, Isagi Y, Ohgushi T. Multiple and mass introductions from limited origins: genetic diversity and structure of Solidago altissima in the native and invaded range. JOURNAL OF PLANT RESEARCH 2015; 128:909-921. [PMID: 26423999 DOI: 10.1007/s10265-015-0753-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/16/2015] [Indexed: 06/05/2023]
Abstract
Understanding the origins and diversity of invasive species can reveal introduction and invasion pathways, and inform an effective management of invasive species. Tall goldenrod, Solidago altissima, is a herbaceous perennial plant native to North America and it has become a widespread invasive weed in East Asian countries. We used microsatellite and chloroplast DNA markers to obtain information on neutral processes and on genetic diversity in native and invaded populations of S. altissima and to infer how it invaded and spread in Japan. We found that introduced (n = 12) and native (n = 20) populations had similar levels of genetic diversity at nuclear SSR loci. Genetic structure analysis indicated that at least two independent colonization events gave rise to current S. altissima populations in Japan. The majority (68%) of the Japanese S. altissima were genetically similar and likely shared a common origin from a single or a small number of populations from the southern USA populations, while the populations in Hokkaido were suggested to arise from a different source. Our results suggest that multiple and mass introductions have contributed to the persistence and rapid adaptation of S. altissima promoting its widespread establishment throughout Japan.
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Affiliation(s)
- Yuzu Sakata
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan.
| | - Joanne Itami
- Department of Biology, University of Minnesota Duluth, Duluth, MN, 55812, USA
| | - Yuji Isagi
- Laboratory of Forest Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Takayuki Ohgushi
- Center for Ecological Research, Kyoto University, Otsu, 520-2113, Japan
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Martínez-Garrido J, Serrão EA, Engelen AH, Cox CJ, García-Murillo P, González-Wangüemert M. Multilocus genetic analyses provide insight into speciation and hybridization in aquatic grasses, genusRuppia. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12666] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Jose Martínez-Garrido
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
- Departamento de Ciencias del Mar y Biología Aplicada; Universidad de Alicante (DCMBA, UA); PO Box 99 03080 Alicante Spain
| | - Ester A. Serrão
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
| | - Aschwin H. Engelen
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
| | - Cymon J. Cox
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Gambelas Faro 8005-139 Portugal
| | - Pablo García-Murillo
- Departamento de Biología Vegetal y Ecología; Universidad de Sevilla; C/Profesor García Gonzalez N°2 41012 Sevilla Spain
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23
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Preston CD, Pearman DA. Plant hybrids in the wild: evidence from biological recording. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12577] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Christopher D. Preston
- Biological Records Centre; Centre of Ecology and Hydrology; Maclean Building Benson Lane Crowmarsh Gifford Wallingford Oxfordshire OX10 8BB UK
| | - David A. Pearman
- Botanical Society of the Britain and Ireland; Alg4iers Feock Truro Cornwall TR3 6RA UK
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Vallejo-Marín M, Buggs RJA, Cooley AM, Puzey JR. Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus. Evolution 2015; 69:1487-1500. [PMID: 25929999 PMCID: PMC5033005 DOI: 10.1111/evo.12678] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Abstract
Whole genome duplication (polyploidization) is a mechanism of “instantaneous” species formation that has played a major role in the evolutionary history of plants. Much of what we know about the early evolution of polyploids is based upon studies of a handful of recently formed species. A new polyploid hybrid (allopolyploid) species Mimulus peregrinus, formed within the last 140 years, was recently discovered on the Scottish mainland and corroborated by chromosome counts. Here, using targeted, high‐depth sequencing of 1200 genic regions, we confirm the parental origins of this new species from M. x robertsii, a sterile triploid hybrid between the two introduced species M. guttatus and M. luteus that are naturalized and widespread in the United Kingdom. We also report a new population of M. peregrinus on the Orkney Islands and demonstrate that populations on the Scottish mainland and Orkney Islands arose independently via genome duplication from local populations of M. x robertsii. Our data raise the possibility that some alleles are already being lost in the evolving M. peregrinus genomes. The recent origins of a new species of the ecological model genus Mimulus via allopolyploidization provide a powerful opportunity to explore the early stages of hybridization and genome duplication in naturally evolved lineages.
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Affiliation(s)
- Mario Vallejo-Marín
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Arielle M Cooley
- Biology Department, Whitman College, Walla Walla, Washington, 99362
| | - Joshua R Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, 23185
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Twyford AD, Streisfeld MA, Lowry DB, Friedman J. Genomic studies on the nature of species: adaptation and speciation inMimulus. Mol Ecol 2015; 24:2601-9. [DOI: 10.1111/mec.13190] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Alex D. Twyford
- Ashworth Laboratories; Institute of Evolutionary Biology; The University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | | | - David B. Lowry
- Plant Biology Laboratories; Department of Plant Biology; Michigan State University; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - Jannice Friedman
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
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Mason AS, Pires JC. Unreduced gametes: meiotic mishap or evolutionary mechanism? Trends Genet 2015; 31:5-10. [DOI: 10.1016/j.tig.2014.09.011] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
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Zozomová-Lihová J, Mandáková T, Kovaříková A, Mühlhausen A, Mummenhoff K, Lysak MA, Kovařík A. When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine × schulzii trigenomic allopolyploid. THE NEW PHYTOLOGIST 2014; 203:1096-1108. [PMID: 24916080 DOI: 10.1111/nph.12873] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/29/2014] [Indexed: 05/20/2023]
Abstract
Recently formed allopolyploids represent an excellent system to study the impacts of hybridization and genomic duplication on genome structure and evolution. Here we explored the 35SrRNA genes (rDNA) in the Cardamine × schulzii allohexaploid that was formed by two subsequent hybridization events within the past c. 150 yr. The rDNA loci were analyzed by cloning, next generation sequencing (NGS), RT-PCR and FISH methods. The primary C. × insueta triploid hybrid derived from C. rivularis (♀) and C. amara (♂) had gene ratios highly skewed towards maternal sequences. Similarly, C. × schulzii, originating from the secondary hybridization event involving C. × insueta (♀) and C. pratensis (♂), showed a reduction in paternal rDNA homeologs despite an excess of chromosomes inherited from C. pratensis. We also identified novel rDNA loci in C. × schulzii, suggesting that lost loci might be slowly reinstalled by translocation (but not recombination) of genes from partner genomes. Prevalent clonal propagation of allopolyploids, C. × insueta and C. × schulzii, indicates that concerted evolution of rDNA may occur in the absence of extensive meiotic cycles. Adoption of NGS in rDNA variant analysis is highly informative for deciphering the evolutionary histories of allopolyploid species with ongoing homogenization processes.
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Affiliation(s)
| | - Terezie Mandáková
- RG Plant Cytogenomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Alena Kovaříková
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | | | - Klaus Mummenhoff
- Department of Biology, University Osnabrueck, Osnabrueck, Germany
| | - Martin A Lysak
- RG Plant Cytogenomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Puzey J, Vallejo-Marín M. Genomics of invasion: diversity and selection in introduced populations of monkeyflowers (Mimulus guttatus). Mol Ecol 2014; 23:4472-85. [DOI: 10.1111/mec.12875] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/02/2014] [Accepted: 07/22/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Joshua Puzey
- Department of Biology; Duke University; Durham NC 27705 USA
- Department of Biology; College of William and Mary; Williamsburg VA 23185 USA
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences; University of Stirling; Stirling FK9 4LA UK
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Rouger R, Jump AS. A seascape genetic analysis reveals strong biogeographical structuring driven by contrasting processes in the polyploid saltmarsh species Puccinellia maritima and Triglochin maritima. Mol Ecol 2014; 23:3158-70. [PMID: 24862943 DOI: 10.1111/mec.12802] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/13/2014] [Accepted: 05/18/2014] [Indexed: 01/14/2023]
Abstract
Little is known about the processes shaping population structure in saltmarshes. It is expected that the sea should act as a powerful agent of dispersal. Yet, in contrast, import of external propagules into a saltmarsh is thought to be small. To determine the level of connectivity between saltmarsh ecosystems at a macro-geographical scale, we characterized and compared the population structure of two polyploid saltmarsh species, Puccinellia maritima and Triglochin maritima based on a seascape genetics approach. A discriminant analysis of principal components highlighted a genetic structure for both species arranged according to a regional pattern. Subsequent analysis based on isolation-by-distance and isolation-by-resistance frameworks indicated a strong role of coastal sediment transport processes in delimiting regional structure in P. maritima, while additional overland propagule dispersal was indicated for T. maritima. The identification and comparison of regional genetic structure and likely determining factors presented here allows us to understand the biogeographical units along the UK coast, between which barriers to connectivity occur not only at the species level but at the ecosystem scale. This information is valuable in plant conservation and community ecology and in the management and restoration of saltmarsh ecosystems.
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Affiliation(s)
- R Rouger
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, FK94LA, UK
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30
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Berecha G, Aerts R, Vandepitte K, Van Glabeke S, Muys B, Roldán-Ruiz I, Honnay O. Effects of forest management on mating patterns, pollen flow and intergenerational transfer of genetic diversity in wild Arabica coffee (Coffea arabica L.) from Afromontane rainforests. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12274] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gezahegn Berecha
- Plant Conservation and Population Biology; University of Leuven; Kasteelpark Arenberg 31-2435 BE-3001 Leuven Belgium
- Department of Horticulture and Plant Science; Jimma University; PO Box 307 Jimma Ethiopia
| | - Raf Aerts
- Division Forest, Nature and Landscape; University of Leuven; Celestijnenlaan 200E-2411 BE-3001 Leuven Belgium
| | - Katrien Vandepitte
- Plant Conservation and Population Biology; University of Leuven; Kasteelpark Arenberg 31-2435 BE-3001 Leuven Belgium
| | - Sabine Van Glabeke
- Plant Sciences Unit - Growth and Development; Institute for Agricultural and Fisheries Research; Caritasstraat 21 9090 Melle Belgium
| | - Bart Muys
- Division Forest, Nature and Landscape; University of Leuven; Celestijnenlaan 200E-2411 BE-3001 Leuven Belgium
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit - Growth and Development; Institute for Agricultural and Fisheries Research; Caritasstraat 21 9090 Melle Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology; University of Leuven; Kasteelpark Arenberg 31-2435 BE-3001 Leuven Belgium
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Zozomová-Lihová J, Krak K, Mandáková T, Shimizu KK, Španiel S, Vít P, Lysak MA. Multiple hybridization events in Cardamine (Brassicaceae) during the last 150 years: revisiting a textbook example of neoallopolyploidy. ANNALS OF BOTANY 2014; 113:817-30. [PMID: 24577071 PMCID: PMC3962249 DOI: 10.1093/aob/mcu012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Recently formed allopolyploid species represent excellent subjects for exploring early stages of polyploid evolution. The hexaploid Cardamine schulzii was regarded as one of the few nascent allopolyploid species formed within the past ∼150 years that presumably arose by autopolyploidization of a triploid hybrid, C. × insueta; however, the most recent investigations have shown that it is a trigenomic hybrid. The aims of this study were to explore the efficiency of progenitor-specific microsatellite markers in detecting the hybrid origins and genome composition of these two allopolyploids, to estimate the frequency of polyploid formation events, and to outline their evolutionary potential for long-term persistence and speciation. METHODS Flow-cytometric ploidy-level screening and genotyping by progenitor-specific microsatellite markers (20 microsatellite loci) were carried out on samples focused on hybridizing populations at Urnerboden, Switzerland, but also including comparative material of the parental species from other sites in the Alps and more distant areas. KEY RESULTS It was confirmed that hybridization between the diploids C. amara and C. rivularis auct. gave rise to triploid C. × insueta, and it is inferred that this has occurred repeatedly. Evidence is provided that C. schulzii comprises three parental genomes and supports its origin from hybridization events between C. × insueta and the locally co-occurring hypotetraploid C. pratensis, leading to two cytotypes of C. schulzii: hypopentaploid and hypohexaploid. Each cytotype of C. schulzii is genetically uniform, suggesting their single origins. CONCLUSIONS Persistence of C. schulzii has presumably been achieved only by perennial growth and clonal reproduction. This contrasts with C. × insueta, in which multiple origins and occasional sexual reproduction have generated sufficient genetic variation for long-term survival and evolutionary success. This study illustrates a complex case of recurrent hybridization and polyploidization events, and highlights the role of triploids that promoted the origin of trigenomic hybrids.
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Affiliation(s)
- Judita Zozomová-Lihová
- Institute of Botany, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
- For correspondence. E-mail
| | - Karol Krak
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Switzerland
| | - Stanislav Španiel
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha, Czech Republic
| | - Petr Vít
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
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Lepais O, Muller SD, Ben Saad-Limam S, Benslama M, Rhazi L, Belouahem-Abed D, Daoud-Bouattour A, Gammar AM, Ghrabi-Gammar Z, Bacles CFE. High genetic diversity and distinctiveness of rear-edge climate relicts maintained by ancient tetraploidisation for Alnus glutinosa. PLoS One 2013; 8:e75029. [PMID: 24098677 PMCID: PMC3787099 DOI: 10.1371/journal.pone.0075029] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/08/2013] [Indexed: 11/19/2022] Open
Abstract
Populations located at the rear-edge of a species' distribution may have disproportionate ecological and evolutionary importance for biodiversity conservation in a changing global environment. Yet genetic studies of such populations remain rare. This study investigates the evolutionary history of North-African low latitude marginal populations of Alnus glutinosa Gaertn., a European tree species that plays a significant ecological role as a keystone of riparian ecosystems. We genotyped 551 adults from 19 populations located across North Africa at 12 microsatellite loci and applied a coalescent-based simulation approach to reconstruct the demographic and evolutionary history of these populations. Surprisingly, Moroccan trees were tetraploids demonstrating a strong distinctiveness of these populations within a species otherwise known as diploid. Best-fitting models of demographic reconstruction revealed the relict nature of Moroccan populations that were found to have withstood past climate change events and to be much older than Algerian and Tunisian populations. This study highlights the complex demographic history that can be encountered in rear-edge distribution margins that here consist of both old stable climate relict and more recent populations, distinctively diverse genetically both quantitatively and qualitatively. We emphasize the high evolutionary and conservation value of marginal rear-edge populations of a keystone riparian species in the context of on-going climate change in the Mediterranean region.
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Affiliation(s)
- Olivier Lepais
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, United Kingdom
- INRA, UMR 1224, Ecologie Comportementale et Biologie des Populations de Poissons, Saint Pée sur Nivelle, France
- Univ Pau & Pays Adour, UMR 1224, Ecologie Comportementale et Biologie des Populations de Poissons, Anglet, France
- * E-mail:
| | - Serge D. Muller
- Université Montpellier 2, CNRS, UMR 5554, Institut des Sciences de l’Evolution, Montpellier, France
| | - Samia Ben Saad-Limam
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Département de Biologie, Tunis, Tunisie
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
| | - Mohamed Benslama
- Laboratoire de Biologie Végétale et Environnement, Université Badji Mokhtar, Annaba, Algérie
| | - Laila Rhazi
- Université Hassan II Casablanca, Faculté des Sciences Aïn Chock, Laboratoire d’Ecologie Aquatique et Environnement, Casablanca, Maroc
| | | | - Amina Daoud-Bouattour
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Département de Biologie, Tunis, Tunisie
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
| | - Amor Mokhtar Gammar
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
| | - Zeineb Ghrabi-Gammar
- Université de Manouba, UR Biogéographie, Climatologie Appliquée et Dynamique Erosive, Faculté des Lettres des Arts et des Humanités de Manouba, Manouba, Tunisie
- Université de Carthage, Institut National Agronomique de Tunisie, Tunis, Tunisie
| | - Cécile Fanny Emilie Bacles
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, United Kingdom
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