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Depecker J, Verleysen L, Asimonyio JA, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Bawin Y, Staelens A, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance. Heredity (Edinb) 2023; 130:145-153. [PMID: 36596880 PMCID: PMC9981769 DOI: 10.1038/s41437-022-00588-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18,894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. In addition, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.
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Affiliation(s)
- Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Meise Botanic Garden, Meise, Belgium.
- KU Leuven Plant Institute, Leuven, Belgium.
| | - Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium.
| | - Justin A Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ithe Mwanga Mwanga
- Centre de Recherche en Science Naturelles, Lwiro, Democratic Republic of the Congo
| | - Tshimi Ebele
- Institut National des Etudes et Recherches, Agronomique, Democratic Republic of the Congo
| | - Benoit Dhed'a
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Bawin
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Ariane Staelens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Filip Vandelook
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
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2
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Aavik T, Träger S, Zobel M, Honnay O, Van Geel M, Bueno CG, Koorem K. The joint effect of host plant genetic diversity and arbuscular mycorrhizal fungal communities on restoration success. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tsipe Aavik
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Sabrina Träger
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
- Institute of Biology/Geobotany and Botanical Garden Martin‐Luther‐University Halle‐Wittenberg Halle (Saale) Germany
| | - Martin Zobel
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Olivier Honnay
- Plant Conservation and Population Biology Biology Department University of Leuven Heverlee Belgium
| | - Maarten Van Geel
- Plant Conservation and Population Biology Biology Department University of Leuven Heverlee Belgium
| | - C. Guillermo Bueno
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Kadri Koorem
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
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Kaulfuß F, Reisch C. Restoration of species-rich grasslands by transfer of local plant material and its impact on species diversity and genetic variation-Findings of a practical restoration project in southeastern Germany. Ecol Evol 2021; 11:12816-12833. [PMID: 34594541 PMCID: PMC8462159 DOI: 10.1002/ece3.8029] [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: 11/17/2020] [Revised: 07/21/2021] [Accepted: 08/02/2021] [Indexed: 11/21/2022] Open
Abstract
Restoration of species-rich grasslands is a key issue of conservation. The transfer of seed-containing local plant material is a proven technique to restore species-rich grassland, since it potentially allows to establish genetically variable and locally adapted populations. In our study, we tested how the transfer of local plant material affected the species diversity and composition of restored grasslands and the genetic variation of the typical grassland plant species Knautia arvensis and Plantago lanceolata. For our study, we selected fifteen study sites in southeastern Germany. We analyzed species diversity and composition and used molecular markers to investigate genetic variation within and among populations of the study species from grasslands that served as source sites for restoration and grasslands, which were restored by transfer of green hay and threshed local plant material. The results revealed no significant differences in species diversity and composition between grasslands at source and restoration sites. Levels of genetic variation within populations of the study species Knautia arvensis and Plantago lanceolata were comparable at source and restoration sites and genetic variation among populations at source and their corresponding restoration sites were only marginal different. Our study suggests that the transfer of local plant material is a restoration approach highly suited to preserve the composition of species-rich grasslands and the natural genetic pattern of typical grassland plant species.
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Affiliation(s)
- Franziska Kaulfuß
- Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Christoph Reisch
- Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
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4
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Gene flow in a highly dynamic habitat and a single founder event: Proof from a plant population on a relocated river site. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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5
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Kotilínek M, Těšitelová T, Košnar J, Fibich P, Hemrová L, Koutecký P, Münzbergová Z, Jersáková J. Seed dispersal and realized gene flow of two forest orchids in a fragmented landscape. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:522-532. [PMID: 32056355 DOI: 10.1111/plb.13099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Species with vast production of dust-like windborne seeds, such as orchids, should not be limited by seed dispersal. This paradigm, however, does not fit recent studies showing that many sites suitable for orchids are unoccupied and most seeds land close to their maternal plant. To explore this issue, we studied seed dispersal and gene flow of two forest orchid species, Epipactis atrorubens and Cephalanthera rubra, growing in a fragmented landscape of forested limestone hills in southwest Bohemia, Czech Republic. We used a combination of seed trapping and plant genotyping methods (microsatellite DNA markers) to quantify short- and long-distance dispersal, respectively. In addition, seed production of both species was estimated. We found that most seeds landed very close to maternal plants (95% of captured seeds were within 7.2 m) in both species, and dispersal distance was influenced by forest type in E. atrorubens. In addition, C. rubra showed clonal reproduction (20% of plants were of clonal origin) and very low fruiting success (only 1.6% of plants were fruiting) in comparison with E. atrorubens (25.7%). Gene flow was frequent up to 2 km in C. rubra and up to 125 km in E. atrorubens, and we detected a relatively high dispersal rate among regions in both species. Although both species occupy similar habitats and have similar seed dispersal abilities, C. rubra is notably rarer in the study area. Considerably low fruiting success in this species likely limits its gene flow to longer distances and designates it more sensitive to habitat loss and fragmentation.
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Affiliation(s)
- M Kotilínek
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - T Těšitelová
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - J Košnar
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - P Fibich
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - L Hemrová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - P Koutecký
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Z Münzbergová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - J Jersáková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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Dittberner H, Becker C, Jiao WB, Schneeberger K, Hölzel N, Tellier A, de Meaux J. Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species. Mol Ecol 2019; 28:3887-3901. [PMID: 31338892 DOI: 10.1111/mec.15194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/21/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022]
Abstract
Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious floodplain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay transfer on genetic diversity also depend on the genetic make-up of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay transfer for habitat restoration and emphasize the importance of prerestoration characterization of microgeographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, that is maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo- and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.
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Affiliation(s)
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Wen-Biao Jiao
- Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | | | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Aurélien Tellier
- Center of Life and Food Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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7
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Aavik T, Helm A. Restoration of plant species and genetic diversity depends on landscape-scale dispersal. Restor Ecol 2017. [DOI: 10.1111/rec.12634] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tsipe Aavik
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
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8
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Waud M, Brys R, Van Landuyt W, Lievens B, Jacquemyn H. Mycorrhizal specificity does not limit the distribution of an endangered orchid species. Mol Ecol 2017; 26:1687-1701. [DOI: 10.1111/mec.14014] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/08/2016] [Accepted: 01/11/2017] [Indexed: 01/26/2023]
Affiliation(s)
- Michael Waud
- Department of Biology, Plant Conservation and Population Biology; KU Leuven; B-3001 Leuven Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM); Department of Microbial and Molecular Systems (M2S); KU Leuven; Campus De Nayer B-2860 Sint-Katelijne-Waver Belgium
| | - Rein Brys
- Research Institute for Forest and Nature; B-1070 Brussels Belgium
| | | | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM); Department of Microbial and Molecular Systems (M2S); KU Leuven; Campus De Nayer B-2860 Sint-Katelijne-Waver Belgium
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology; KU Leuven; B-3001 Leuven Belgium
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9
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Mijangos JL, Pacioni C, Spencer PBS, Hillyer M, Craig MD. Characterizing the post-recolonization of Antechinus flavipes
and its genetic implications in a production forest landscape. Restor Ecol 2017. [DOI: 10.1111/rec.12493] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jose L. Mijangos
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Carlo Pacioni
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Peter B. S. Spencer
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
| | - Mia Hillyer
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
- Molecular Systematics Unit/Terrestrial Zoology; Western Australian Museum; Welshpool Western Australia 6106 Australia
| | - Michael D. Craig
- School of Veterinary and Life Sciences; Murdoch University; Murdoch Western Australia 6150 Australia
- Centre of Excellence for Environmental Decisions, School of Plant Biology; University of Western Australia; Crawley Western Australia 6009 Australia
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10
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Balao F, Tannhäuser M, Lorenzo MT, Hedrén M, Paun O. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex. Heredity (Edinb) 2016; 116:351-61. [PMID: 26604189 PMCID: PMC4787024 DOI: 10.1038/hdy.2015.98] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
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Affiliation(s)
- F Balao
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Tannhäuser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Hedrén
- Department of Biology, Lund University, Lund, Sweden
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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11
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Jaros U, Fischer GA, Pailler T, Comes HP. Spatial patterns of AFLP diversity in Bulbophyllum occultum (Orchidaceae) indicate long-term refugial isolation in Madagascar and long-distance colonization effects in La Réunion. Heredity (Edinb) 2016; 116:434-46. [PMID: 26883184 DOI: 10.1038/hdy.2016.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 10/21/2015] [Accepted: 12/15/2015] [Indexed: 01/30/2023] Open
Abstract
Bulbophyllum occultum, an epiphytic orchid mainly distributed in the rainforests of (north)eastern Madagascar and La Réunion, represents an interesting model case for testing the effects of anthropogenic vs historical (e.g., climate induced) habitat isolation and long-distance colonization on the genetic structure of plant species with disjunct distributions in the Madagascan region. To this aim, we surveyed amplified fragment length polymorphisms (AFLPs) across 13 populations in Madagascar and nine in La Réunion (206 individuals in total). We found overall high levels of population subdivision (Φ(PT)=0.387) and low within-population diversity (H(E), range: 0.026-0.124), indicating non-equilibrium conditions in a mainly selfing species. There was no impact of recent deforestation (Madagascar) or habitat disturbance (La Réunion) detectable on AFLP diversity. K-means clustering and BARRIER analyses identified multiple gene pools and several genetic breaks, both within and among islands. Inter-island levels of population genetic diversity and subdivision were similar, whereby inter-individual divergence in flower colour explained a significant part of gene pool divergence in La Réunion. Our results suggest that (i) B. occultum persisted across multiple isolated ('refugial') regions along the eastern rainforest corridor of Madagascar over recent climatic cycles and (ii) populations in La Réunion arose from either single or few independent introductions from Madagascar. High selfing rates and sufficient time for genetic drift likely promoted unexpectedly high population genetic and phenotypic (flower colour) differentiation in La Réunion. Overall, this study highlights a strong imprint of history on the genetic structure of a low-gene-dispersing epiphytic orchid from the Madagascan region.
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Affiliation(s)
- U Jaros
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
| | - G A Fischer
- Kadoorie Farm and Botanic Garden Corporation, Tai Po, N.T., Hong Kong, SAR
| | - T Pailler
- UMR CIRAD-université de La Réunion. Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Le Tampon, Réunion, France
| | - H P Comes
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
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12
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Cosentino BJ, Schooley RL, Bestelmeyer BT, McCarthy AJ, Sierzega K. Rapid genetic restoration of a keystone species exhibiting delayed demographic response. Mol Ecol 2015; 24:6120-33. [PMID: 26577599 DOI: 10.1111/mec.13469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 10/22/2022]
Abstract
Genetic founder effects are often expected when animals colonize restored habitat in fragmented landscapes, but empirical data on genetic responses to restoration are limited. We examined the genetic response of banner-tailed kangaroo rats (Dipodomys spectabilis) to landscape-scale grassland restoration in the Chihuahuan Desert of New Mexico, USA. Dipodomys spectabilis is a grassland specialist and keystone species. At sites treated with herbicide to remove shrubs, colonization by D. spectabilis is slow and populations persist at low density for ≥10 years (≥6 generations). Persistence at low density and low gene flow may cause strong founder effects. We compared genetic structure of D. spectabilis populations between treated sites and remnant grasslands, and we examined how the genetic response to restoration depended on treatment age, area, and connectivity to source populations. Allelic richness and heterozygosity were similar between treated sites and remnant grasslands. Allelic richness at treated sites was greatest early in the restoration trajectory, and genetic divergence did not differ between recently colonized and established populations. These results indicated that founder effects during colonization of treated sites were weak or absent. Moreover, our results suggested founder effects were not mitigated by treatment area or connectivity. Dispersal is negatively density-dependent in D. spectabilis, and we hypothesize that high gene flow may occur early in the restoration trajectory when density is low. Our study shows genetic diversity can be recovered more rapidly than demographic components of populations after habitat restoration and that founder effects are not inevitable for animals colonizing restored habitat in fragmented landscapes.
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Affiliation(s)
- Bradley J Cosentino
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, 14456, USA
| | - Robert L Schooley
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Brandon T Bestelmeyer
- USDA-ARS Jornada Experimental Range, New Mexico State University, MSC 3JER, Box 30003, Las Cruces, NM, 88003, USA
| | - Alison J McCarthy
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, 14456, USA
| | - Kevin Sierzega
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, 61801, USA
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13
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Mijangos JL, Pacioni C, Spencer PBS, Craig MD. Contribution of genetics to ecological restoration. Mol Ecol 2014; 24:22-37. [DOI: 10.1111/mec.12995] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/17/2014] [Accepted: 11/01/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Jose Luis Mijangos
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
| | - Carlo Pacioni
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
| | - Peter B. S. Spencer
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
| | - Michael D. Craig
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
- School of Plant Biology; University of Western Australia; Crawley WA 6009 Australia
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14
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Vanden Broeck A, Van Landuyt W, Cox K, De Bruyn L, Gyselings R, Oostermeijer G, Valentin B, Bozic G, Dolinar B, Illyés Z, Mergeay J. High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid. BMC Ecol 2014; 14:20. [PMID: 24998243 PMCID: PMC4099500 DOI: 10.1186/1472-6785-14-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/27/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. RESULTS We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) 'outlier' loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. CONCLUSIONS The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.
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Affiliation(s)
- An Vanden Broeck
- Research Institute for Nature and Forest (INBO), Gaverstraat 4, Geraardsbergen B-9500, Belgium
| | - Wouter Van Landuyt
- Research Institute for Nature and Forest (INBO), Kliniekstraat 25, Brussels B-1070, Belgium
| | - Karen Cox
- Research Institute for Nature and Forest (INBO), Gaverstraat 4, Geraardsbergen B-9500, Belgium
| | - Luc De Bruyn
- Research Institute for Nature and Forest (INBO), Kliniekstraat 25, Brussels B-1070, Belgium
- Evolutionary Ecology, University of Antwerp, Groenenborgerlaan 171, Antwerpen 2020, Belgium
| | - Ralf Gyselings
- Research Institute for Nature and Forest (INBO), Kliniekstraat 25, Brussels B-1070, Belgium
| | - Gerard Oostermeijer
- Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam, Postbus 94248, Amsterdam 1090 GE, The Netherlands
| | - Bertille Valentin
- Conservatoire Botanique National de Bailleul, Hameau de Haendries, Bailleul F- 59 270, France
| | - Gregor Bozic
- Slovenian Forestry Institute, Vecna pot 2, Ljubljana SI-1000, Slovenia
| | - Branko Dolinar
- Botanical Society of Slovenia, Izanska cesta 15, Ljubljana SI-1000, Slovenia
| | | | - Joachim Mergeay
- Research Institute for Nature and Forest (INBO), Gaverstraat 4, Geraardsbergen B-9500, Belgium
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15
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Qian X, Wang CX, Tian M. Genetic diversity and population differentiation of Calanthe tsoongiana, a rare and endemic orchid in China. Int J Mol Sci 2013; 14:20399-413. [PMID: 24129175 PMCID: PMC3821621 DOI: 10.3390/ijms141020399] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/24/2013] [Accepted: 09/25/2013] [Indexed: 11/16/2022] Open
Abstract
Calanthe tsoongiana is a rare terrestrial orchid endemic to China, and this species has experienced severe habitat loss and fragmentation. Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and differentiation of six populations of C. tsoongiana. Based on 124 discernible fragments yielded by eleven selected primers, high genetic diversity was revealed at the species level; however, genetic diversity at the population level was relatively low. High-level genetic differentiation among populations was detected based on analysis of molecular variance (AMOVA), indicating potential limited gene flow. No significant relationship was observed between genetic and geographic distances among the sampled populations. These results suggested that restricted gene flow might be due to habitat fragmentation and reduced population size as a result of human activities. Based on the findings, several conservation strategies were proposed for the preservation of this threatened species.
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Affiliation(s)
- Xin Qian
- Research Institution of Subtropical Forestry, Chinese Academy of Forestry, 73, Daqiao Road, Fuyang 311400, Zhejiang, China.
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16
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Helsen K, Jacquemyn H, Hermy M, Vandepitte K, Honnay O. Rapid Buildup of Genetic Diversity in Founder Populations of the Gynodioecious Plant Species Origanum vulgare after Semi-Natural Grassland Restoration. PLoS One 2013; 8:e67255. [PMID: 23840642 PMCID: PMC3686717 DOI: 10.1371/journal.pone.0067255] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/15/2013] [Indexed: 11/18/2022] Open
Abstract
In most landscapes the success of habitat restoration is largely dependent on spontaneous colonization of plant species. This colonization process, and the outcome of restoration practices, can only be considered successful if the genetic makeup of founding populations is not eroded through founder effects and subsequent genetic drift. Here we used 10 microsatellite markers to investigate the genetic effects of recent colonization of the long-lived gynodioecious species Origanum vulgare in restored semi-natural grassland patches. We compared the genetic diversity and differentiation of fourteen recent populations with that of thirteen old, putative source populations, and we evaluated the effects of spatial configuration of the populations on colonization patterns. We did not observe decreased genetic diversity in recent populations, or inflated genetic differentiation among them. Nevertheless, a significantly higher inbreeding coefficient was observed in recent populations, although this was not associated with negative fitness effects. Overall population genetic differentiation was low (FST = 0.040). Individuals of restored populations were assigned to on average 6.1 different source populations (likely following the 'migrant pool' model). Gene flow was, however, affected by the spatial configuration of the grasslands, with gene flow into the recent populations mainly originating from nearby source populations. This study demonstrates how spontaneous colonization after habitat restoration can lead to viable populations in a relatively short time, overcoming pronounced founder effects, when several source populations are nearby. Restored populations can therefore rapidly act as stepping stones and sources of genetic diversity, likely increasing overall metapopulation viability of the study species.
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Affiliation(s)
- Kenny Helsen
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
- * E-mail:
| | - Hans Jacquemyn
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
| | - Martin Hermy
- Division Forest, Nature and Landscape Research, Department of Earth and Environmental Sciences, University of Leuven, Leuven, Belgium
| | - Katrien Vandepitte
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Leuven, Belgium
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17
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Vandepitte K, Gristina AS, De Raedt R, Roldán-Ruiz I, Marcenò C, Sciandrello S, Honnay O. Conservation genetics of an endemic from the Mediterranean Basin: high genetic differentiation but no genetic diversity loss from the last populations of the Sicilian Grape Hyacinth Leopoldia gussonei. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0487-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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