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Abadie P, Roussel G, Dencausse B, Bonnet C, Bertocchi E, Louvet JM, Kremer A, Garnier-Géré P. Strength, diversity and plasticity of postmating reproductive barriers between two hybridizing oak species (Quercus robur L. and Quercus petraea (Matt) Liebl.). J Evol Biol 2011; 25:157-73. [PMID: 22092648 DOI: 10.1111/j.1420-9101.2011.02414.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Very little is known about the nature and strength of reproductive isolation (RI) in Quercus species, despite extensive research on the estimation and evolutionary significance of hybridization rates. We characterized postmating pre- and postzygotic RI between two hybridizing oak species, Quercus robur and Quercus petraea, using a large set of controlled crosses between different genotypes. Various traits potentially associated with reproductive barriers were quantified at several life history stages, from pollen-pistil interactions to seed set and progeny fitness-related traits. Results indicate strong intrinsic postmating prezygotic barriers, with significant barriers also at the postzygotic level, but relatively weaker extrinsic barriers on early hybrid fitness measures assessed in controlled conditions. Using general linear modelling of common garden data with clonal replicates, we showed that most traits exhibited important genotypic differences, as well as different levels of sensitivity to micro-environmental heterogeneity. These new findings suggest a large potential genetic diversity and plasticity of reproductive barriers and are confronted with hybridization evidence in these oak species.
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Affiliation(s)
- P Abadie
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France
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52
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Characterization and comparison of gene-based simple sequence repeats across Brassica species. Mol Genet Genomics 2011; 286:161-70. [PMID: 21766184 DOI: 10.1007/s00438-011-0636-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 07/04/2011] [Indexed: 01/21/2023]
Abstract
Simple sequence repeats (SSRs) are important components of eukaryotic genomes and may play an important role in regulating gene expression. However, the characteristics of genic SSRs and the effect of interspecific hybridization and polyploidization on genic SSRs seem not to have received desired attention in terms of scientific investigations. To determine the features of genic SSRs and elucidate their role in polyploidization process of the Brassica family, we identified SSRs in Plant Genome Database-assembled unique transcripts (PUTs) of Brassica species. A higher density of SSRs and a greater number of compound motif SSRs and mononucleotide motif types with large average number of repeats were detected in allotetraploid Brassica napus than in the diploid parental species (Brassica rapa and Brassica oleracea). In addition, a greater proportion of SSR-PUTs were found to be associated with the stress response and developmental processes in B. napus than in the parents. A negative correlation between the repeat number and the motif type and the total length, and a positive correlation between the repeat number and the total length of SSRs were observed. PUT-SSR might be generated from A/T-rich regions. The successful development of 123 pairs of SSR primers for Brassica PUTs showed that SSR-PUTs could be exploited as gene-based SSR functional markers for application in Brassica breeding. These results indicate that interspecific hybridization and polyploidization could trigger the amplification of SSRs, and long SSRs might become shorter to enable the plant to adapt to environmental and artificial selection.
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53
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Palma-Silva C, Wendt T, Pinheiro F, Barbará T, Fay MF, Cozzolino S, Lexer C. Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs. Mol Ecol 2011; 20:3185-201. [PMID: 21672064 DOI: 10.1111/j.1365-294x.2011.05143.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The roles of intra- and interspecific gene flow in speciation and species evolution are topics of great current interest in molecular ecology and evolutionary biology. Recent modelling studies call for new empirical data to test hypotheses arising from the recent shift from a 'whole-genome reproductive isolation' view to a 'genic' view of species and speciation. Particularly scarce (and thus of particular interest) are molecular genetic data on recently radiated, naturally hybridizing species in strongly structured and species-rich environments. Here, we studied four sympatric plant species (Pitcairnia spp.; Bromeliaceae) adapted to Neotropical inselbergs (isolated outcrops resembling habitat 'islands' in tropical rainforests) using nuclear and plastid DNA. Patterns of plastid DNA haplotype sharing and nuclear genomic admixture suggest the presence of both, incomplete lineage sorting and interspecific gene flow over extended periods of time. Integrity and cohesion of inselberg species of Pitcairnia are maintained despite introgression and in the face of extremely low within-species migration rates (N(e)m < 1 migrant per generation). Cross-evaluation of our genetic data against published pollination experiments indicate that species integrity is maintained by the simultaneous action of multiple prezygotic barriers, including flowering phenology, pollinator isolation and divergent mating systems. Postzygotic Bateson-Dobzhansky-Muller incompatibilities appear to contribute to isolation, as suggested by asymmetric introgression rates of single loci. Our results suggest that incomplete lineage sorting, hybridization and introgression form integral aspects of adaptive radiation in Neotropical inselberg 'archipelagos'. Inselbergs with multiple closely related co-occurring species should be of special interest to students of speciation in mountain systems, and to ongoing conservation programmes in the Atlantic Rainforest biodiversity hotspot.
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Affiliation(s)
- C Palma-Silva
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK.
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54
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Khimoun A, Burrus M, Andalo C, Liu ZL, Vicédo-Cazettes C, Thébaud C, Pujol B. Locally asymmetric introgressions between subspecies suggest circular range expansion at the Antirrhinum majus global scale. J Evol Biol 2011; 24:1433-41. [PMID: 21545420 DOI: 10.1111/j.1420-9101.2011.02276.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Assessing processes of geographic expansion in contact zones is a crucial step towards an accurate prediction of the evolution of species genetic diversity. The geographic distribution of cytonuclear discordance often reflects genetic introgression patterns across a species geographic range. Antirrhinum majus pseudomajus and A. m. striatum are two interfertile subspecies that occupy nonoverlapping areas but enter in contact in many locations at the margin of their geographic distribution. We found that genetic introgression between both subspecies was asymmetric at the local scale and geographically oriented in opposite directions at both ends of their contact zone perimeter in the Pyrenees. Our results suggest that the geographic expansion of A. majus subspecies was circular around the perimeter of their contact zone and pinpoint the need to integrate different spatial scales to unravel complex patterns of species geographic expansion.
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Affiliation(s)
- A Khimoun
- Université de Toulouse; UPS; EDB (Laboratoire Évolution et Diversité Biologique); UMR5174; Toulouse Cedex 9, France.
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55
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Yatabe Y, Yamamoto K, Tsutsumi C, Shinohara W, Murakami N, Kato M. Fertility and precocity of Osmunda x intermedia offspring in culture. JOURNAL OF PLANT RESEARCH 2011; 124:265-268. [PMID: 20839027 DOI: 10.1007/s10265-010-0374-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/17/2010] [Indexed: 05/27/2023]
Abstract
The feasibility of later-generation hybrid production in ferns has not been previously studied, although it is a significant factor in relation to reproductive isolation. Osmunda x intermedia, a hybrid between O. japonica and O. lancea, is semifertile and has moderate spore germination rates. Under the artificial conditions of this study, F2 and F3 offspring were formed. Some of the F2 offspring showed precocity, and some of the F3 offspring also showed precocity. This fertility suggests that introgressive hybridization might be ongoing in nature. This also indicates a currently unknown genetic control over the timing of fertile frond production in Osmunda.
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Affiliation(s)
- Yoko Yatabe
- Botanical Gardens, Graduate School of Science, The University of Tokyo, 3-7-1 Hakusan, Bunkyo-ku, Tokyo 112-0001, Japan.
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56
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Tranchida-Lombardo V, Cafasso D, Cristaudo A, Cozzolino S. Phylogeographic patterns, genetic affinities and morphological differentiation between Epipactis helleborine and related lineages in a Mediterranean glacial refugium. ANNALS OF BOTANY 2011; 107:427-36. [PMID: 21193482 PMCID: PMC3043932 DOI: 10.1093/aob/mcq256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS In the Mediterranean basin, the Italian peninsula has been suggested to be one of the most important glacial refugia for temperate tree species. The orchid genus Epipactis is widely represented in the Italian peninsula by widespread species and several endemic, localized taxa, including selfing and outcrossing taxa. Here the phylogenetic and phylogeographic relationships in a group of closely related taxa in Epipactis are investigated with the aim of understanding the role of this refugial area for cladogenesis and speciation in herbaceous species, such as terrestrial orchids. METHODS Ribosomal DNA (rDNA) was employed to assess phylogenetic relationships, and plastid sequence variation in the rbcL-accD spacer was used to reveal phylogeographic patterns among plastid haplotypes using a parsimony network. KEY RESULTS Low genetic variation and shared ribotypes were detected in rDNA, whereas high levels of sequence variation and a strong phylogeographic structure were found in the examined plastid region. The parsimony plastid haplotype network identified two main haplotype groups, one including E. atrorubens/microphylla/muelleri/leptochila and the other including all accessions of E. helleborine and several localized and endemic taxa, with a combination of widespread and rare haplotypes detected across the Italian peninsula. A greater genetic divergence separated the Italian and other European accessions of E. helleborine. CONCLUSIONS Phylogenetic and phylogeographic patterns support a working hypothesis in which the Italian peninsula has only recently been colonized by Epipactis, probably during the most recent phase of the Quaternary age and, nevertheless, it acted as a remarkable centre of diversification for this orchid lineage. Changes in pollination strategy and recurrent shifts in mating system (from allogamy to autogamy) could have represented the mechanism promoting this rapid diversification and the observed high taxonomic complexity detected in the E. helleborine species complex.
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Affiliation(s)
- Valentina Tranchida-Lombardo
- Sezione di Biologia ed Ecologia Vegetale DACPA, Università di Catania, via Vadisavoia 5, 95123, Catania, Italy
- Dipartimento di Biologia strutturale e funzionale, Università ‘Federico II’, complesso MSA, 80126 Napoli, Italy
| | - Donata Cafasso
- Dipartimento di Biologia strutturale e funzionale, Università ‘Federico II’, complesso MSA, 80126 Napoli, Italy
| | - Antonia Cristaudo
- Sezione di Biologia ed Ecologia Vegetale DACPA, Università di Catania, via Vadisavoia 5, 95123, Catania, Italy
| | - Salvatore Cozzolino
- Dipartimento di Biologia strutturale e funzionale, Università ‘Federico II’, complesso MSA, 80126 Napoli, Italy
- For correspondence. E-mail
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Moran EV, Clark JS. Estimating seed and pollen movement in a monoecious plant: a hierarchical Bayesian approach integrating genetic and ecological data. Mol Ecol 2011; 20:1248-62. [PMID: 21332584 DOI: 10.1111/j.1365-294x.2011.05019.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The scale of seed and pollen movement in plants has a critical influence on population dynamics and interspecific interactions, as well as on their capacity to respond to environmental change through migration or local adaptation. However, dispersal can be challenging to quantify. Here, we present a Bayesian model that integrates genetic and ecological data to simultaneously estimate effective seed and pollen dispersal parameters and the parentage of sampled seedlings. This model is the first developed for monoecious plants that accounts for genotyping error and treats dispersal from within and beyond a plot in a fully consistent manner. The flexible Bayesian framework allows the incorporation of a variety of ecological variables, including individual variation in seed production, as well as multiple sources of uncertainty. We illustrate the method using data from a mixed population of red oak (Quercus rubra, Q. velutina, Q. falcata) in the NC piedmont. For simulated test data sets, the model successfully recovered the simulated dispersal parameters and pedigrees. Pollen dispersal in the example population was extensive, with an average father-mother distance of 178 m. Estimated seed dispersal distances at the piedmont site were substantially longer than previous estimates based on seed-trap data (average 128 m vs. 9.3 m), suggesting that, under some circumstances, oaks may be less dispersal-limited than is commonly thought, with a greater potential for range shifts in response to climate change.
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Affiliation(s)
- Emily V Moran
- NIMBioS, University of Tennessee, Knoxville, TN 37996-1527, USA.
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58
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Zeng YF, Liao WJ, Petit RJ, Zhang DY. Exploring species limits in two closely related Chinese oaks. PLoS One 2010; 5:e15529. [PMID: 21152084 PMCID: PMC2994836 DOI: 10.1371/journal.pone.0015529] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/11/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The species status of two closely related Chinese oaks, Quercus liaotungensis and Q. mongolica, has been called into question. The objective of this study was to investigate the species status and to estimate the degree of introgression between the two taxa using different approaches. METHODOLOGY/PRINCIPAL FINDINGS Using SSR (simple sequence repeat) and AFLP (amplified fragment length polymorphism) markers, we found that interspecific genetic differentiation is significant and higher than the differentiation among populations within taxa. Bayesian clusters, principal coordinate analysis and population genetic distance trees all classified the oaks into two main groups consistent with the morphological differentiation of the two taxa rather than with geographic locations using both types of markers. Nevertheless, a few individuals in Northeast China and many individuals in North China have hybrid ancestry according to Bayesian assignment. One SSR locus and five AFLPs are significant outliers against neutral expectations in the interspecific FST simulation analysis, suggesting a role for divergent selection in differentiating species. MAIN CONCLUSIONS/SIGNIFICANCE All results based on SSRS and AFLPS reached the same conclusion: Q. liaotungensis and Q. mongolica maintain distinct gene pools in most areas of sympatry. They should therefore be considered as discrete taxonomic units. Yet, the degree of introgression varies between the two species in different contact zones, which might be caused by different population history or by local environmental factors.
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Affiliation(s)
- Yan-Fei Zeng
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wan-Jin Liao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Rémy J. Petit
- INRA, UMR Biodiversity, Genes and Ecosystems, Cestas, France
- University of Bordeaux, UMR Biodiversity, Genes and Ecosystems, Cestas, France
| | - Da-Yong Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
- * E-mail:
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59
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Wang WK, Ho CW, Hung KH, Wang KH, Huang CC, Araki H, Hwang CC, Hsu TW, Osada N, Chiang TY. Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture. THE NEW PHYTOLOGIST 2010; 188:488-500. [PMID: 20673288 DOI: 10.1111/j.1469-8137.2010.03383.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
• Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. • Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. • High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis.
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Affiliation(s)
- Wei-Kuang Wang
- Department of Life Sciences, National Cheng-Kung University, Tainan, Taiwan
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60
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Species differentiation and gene flow in the Blackbutts (genus Eucalyptus subgenus Eucalyptus section Pseudophloius). CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0086-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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61
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Lepais O, Gerber S. Reproductive patterns shape introgression dynamics and species succession within the European white oak species complex. Evolution 2010; 65:156-70. [PMID: 20722727 DOI: 10.1111/j.1558-5646.2010.01101.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reproductive system of hybrids is an important factor shaping introgression dynamics within species complexes. We combined paternity and parentage analyses with previous species characterization by genetic assignment, to directly identify reproductive events that occurred within a stand comprising four European white oak species. Comparing species status of parent pairs provided a precise quantification of hybridization rate, backcrosses, and intraspecific matings in two life stages. The detailed mating system analysis revealed new findings on the dynamics of interspecific gene flow. First, hybrids acted successfully as both male and female during reproduction. They produced acorns and seedlings that were as viable as those sired by purebreds. Second, species maintenance could be due to a relatively low level of interspecific mating contrasting with a large proportion of intraspecific crosses and backcrosses. Despite a high proportion of hybrids and extensive interspecific gene flow, partial species integrity is maintained by genetically controlled pollen discrimination, ensuring preferential matings within purebreds and high parental species fidelity in hybrid reproduction, which impedes complete collapse into a continuous hybrid swarm. Finally, we showed that pollen from the different species had unequal contributions to reproduction suggesting that introgression processes could ultimately lead to extirpation or expansion of some species.
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Affiliation(s)
- Olivier Lepais
- INRA, UMR 1202 BIOGECO, 69 route d'Arcachon, F-33612 Cestas, France.
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62
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RYMER PAULD, MANNING JOHNC, GOLDBLATT PETER, POWELL MARTYNP, SAVOLAINEN VINCENT. Evidence of recent and continuous speciation in a biodiversity hotspot: a population genetic approach in southern African gladioli (
Gladiolus
; Iridaceae). Mol Ecol 2010; 19:4765-82. [PMID: 20735739 DOI: 10.1111/j.1365-294x.2010.04794.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- PAUL D. RYMER
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
| | - JOHN C. MANNING
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Cape Town, South Africa
| | - PETER GOLDBLATT
- Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166‐0299, USA
| | - MARTYN P. POWELL
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - VINCENT SAVOLAINEN
- Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
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63
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Piredda R, Simeone MC, Attimonelli M, Bellarosa R, Schirone B. Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity. Mol Ecol Resour 2010; 11:72-83. [PMID: 21429102 DOI: 10.1111/j.1755-0998.2010.02900.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA barcoding may be particularly important in influencing ecology, economic issues, and the fundamental crisis facing biodiversity as a standardized, species-level identification tool for taxonomy assessment. Trees play important roles in the conservation of many land ecosystems, the wood trade, and the definition of biogeographical processes; nevertheless, peculiar biological, evolutionary and taxonomical features will probably constitute an intriguing challenge to barcoders. We examined whether four marker regions (trnh-psba, rbcL, rpoc1, matK) proposed by the Consortium for the Barcode of Life (CBOL) matched species taxonomy in a preliminary tree biodiversity survey of Italian forested land. Our objective was to provide a test of future in situ applications of DNA barcodes by evaluating the efficacy of species discrimination under the criteria of uniformity of methods and natural co-occurrence of the species in the main forest ecosystems. Fifty-two species were included in a floristic study. We obtained 73% total discrimination success, with trnH-psbA as the best performing marker and oaks as the least responsive plants to the markers used. A further taxon-based study of Quercus (thirty specimens, 12 species) revealed that this genus is refractory to barcoding (0% discrimination success), a probable consequence of low variation rate at the plastid genome level, hybridization, and the incidence of biogeography. We conclude that some species-rich tree genera in small geographical regions may prove exceptionally difficult to barcode. Until more efficient markers are developed, we recommend that improved and diversified sampling (multiple locations of sympatric and co-occurring congenerics) be embraced as a timely and important goal for the precise assessment of haplotype specificity to facilitate the productive application of barcoding in practice.
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Affiliation(s)
- Roberta Piredda
- FOR-BOL, Dipartimento Ambiente e Foreste (D.A.F.), Università della Tuscia, 01100 Viterbo, Italy
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64
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McKinnon GE, Smith JJ, Potts BM. Recurrent nuclear DNA introgression accompanies chloroplast DNA exchange between two eucalypt species. Mol Ecol 2010; 19:1367-80. [PMID: 20298471 DOI: 10.1111/j.1365-294x.2010.04579.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Numerous studies within plant genera have found geographically structured sharing of chloroplast (cp) DNA among sympatric species, consistent with introgressive hybridization. Current research is aimed at understanding the extent, direction and significance of nuclear (nr) DNA exchange that accompanies putative cpDNA exchange. Eucalyptus is a complex tree genus for which cpDNA sharing has been established between multiple species. Prior phylogeographic analysis has indicated cpDNA introgression into the widespread forest species Eucalyptus globulus from its rare congener E. cordata. In this study, we use AFLP markers to characterize corresponding nrDNA introgression, on both a broad and fine spatial scale. Using 388 samples we examine (i) the fine-scale spatial structure of cp and nrDNA introgression from E. cordata into E. globulus at a site in natural forest and (ii) broad-scale patterns of AFLP marker introgression at six additional mixed populations. We show that while E. globulus and E. cordata retain strongly differentiated nuclear gene pools overall, leakage of nrDNA occurs at mixed populations, with some AFLP markers being transferred to E. globulus recurrently at different sites. On the fine scale, different AFLP fragments show varying distances of introgression into E. globulus, while introgression of cpDNA is extensive. The frequency of E. cordata markers in E. globulus is correlated with spatial proximity to E. cordata, but departs from expectations based on AFLP marker frequency in E. cordata, indicating that selection may be governing the persistence of introgressed fragments in E. globulus.
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Affiliation(s)
- G E McKinnon
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia.
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65
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Peñaloza-Ramírez JM, González-Rodríguez A, Mendoza-Cuenca L, Caron H, Kremer A, Oyama K. Interspecific gene flow in a multispecies oak hybrid zone in the Sierra Tarahumara of Mexico. ANNALS OF BOTANY 2010; 105:389-99. [PMID: 20056653 PMCID: PMC2826251 DOI: 10.1093/aob/mcp301] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Interspecific gene flow can occur in many combinations among species within the genus Quercus, but simultaneous hybridization among more than two species has been rarely analysed. The present study addresses the genetic structure and morphological variation in a triple hybrid zone formed by Q. hypoleucoides, Q. scytophylla and Q. sideroxyla in north-western Mexico. METHODS A total of 247 trees from ten reference and 13 presumed intermediate populations were characterized using leaf shape variation and geometric morphometrics, and seven nuclear microsatellites as genetic markers. Discriminant function analysis was performed for leaf shape variation, and estimates of genetic diversity and structure, and individual Bayesian genetic assignments were obtained. KEY RESULTS Reference populations formed three completely distinct groups according to discriminant function analysis based on the morphological data, and showed low, but significant, genetic differentiation. Populations from the zone of contact contained individuals morphologically intermediate between pairs of species in different combinations, or even among the three species. The Bayesian admixture analysis found that three main genetic clusters best fitted the data, with good correspondence of reference populations of each species to one of the genetic clusters, but various degrees of admixture evidenced in populations from the contact area. CONCLUSIONS The three oak species have formed a complex hybrid zone that is geographically structured as a mosaic, and comprising a wide range of genotypes, including hybrids between different species pairs, backcrosses and probable triple hybrids.
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Affiliation(s)
- Juan Manuel Peñaloza-Ramírez
- Centro de Investigaciones en Ecosistemas, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda la Huerta, 58190 Morelia, Mexico.
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66
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Muster C, Maddison WP, Uhlmann S, Berendonk TU, Vogler AP. Arctic-alpine distributions--metapopulations on a continental scale? Am Nat 2010; 173:313-26. [PMID: 19199524 DOI: 10.1086/596534] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cold-adapted species in the Northern Hemisphere frequently show arctic-alpine discontinuous ranges at high latitudes and on mountains farther south, but area connectivity through current and historical gene flow remains unclear. We used the coalescent-based program IMa (Isolation with Migration-analytic) to test for migration among disjunct European areas of arctic-alpine wolf spiders of the Pardosa saltuaria group. Mitochondrial (ND1) and nuclear (ITS1, 5.8S rDNA, ITS2) markers were analyzed simultaneously. Gene flow was unidirectional from Scandinavia to the Alps and the Carpathians, complex with respect to intermediate relict areas in central Europe, and very limited in outlying areas in the Balkans and Pyrenees. Population connectivity may have been greater during glacial events that might alternatively account for the inferred arctic-alpine links. A simulation study under various demographic histories (using a new module in the Mesquite package, which models episodic migration) showed that the empirical results are equally consistent with moderate levels of ongoing (continuous) migration or, alternatively, with strong migration bursts at the last glacial maximum but not at earlier times. Habitat connectivity was probably maximal during glacial events, illustrating the potential influence of ecology and life history on organismal responses to past climatic change.
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Affiliation(s)
- Christoph Muster
- Institute of Biology II, University of Leipzig, Leipzig, Germany.
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67
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Curtu AL, Gailing O, Finkeldey R. Patterns of contemporary hybridization inferred from paternity analysis in a four-oak-species forest. BMC Evol Biol 2009; 9:284. [PMID: 19968862 PMCID: PMC2795763 DOI: 10.1186/1471-2148-9-284] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 12/07/2009] [Indexed: 11/23/2022] Open
Abstract
Background Few studies address the issue of hybridization in a more than two-species context. The species-rich Quercus complex is one of the systems which can offer such an opportunity. To investigate the contemporary pattern of hybridization we sampled and genotyped 320 offspring from a natural mixed forest comprising four species of the European white oak complex: Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto. Results A total of 165 offspring were assigned unambiguously to one of the pollen donors within the study plot. The minimum amount of effective pollen originating from outside the plot varied markedly among the seed parents, ranging from 0.18 to 0.87. The majority of the successful matings (64.1%) occurred between conspecific individuals indicating the existence of reproductive barriers between oak species. However, the isolation was not complete since we found strong evidence for both first-generation (8.4%) and later-generation hybrids (27.5%). Only two out of eight seed parents, belonging to Q. petraea and Q. robur, showed a high propensity to hybridize with Q. pubescens and Q. petraea, respectively. Significant structure of the effective pollen pools (Φpt = 0.069, P = 0.01) was detected in our sample. However, no support was found for the isolation by distance hypothesis. The proportion of hybrids was much higher (79%) in the seed generation when compared to the adult tree generation. Conclusion First-generation hybrids were observed only between three out of six possible species combinations. Hybrids between one pair of species preferred to mate with one of their parental species. The observation of first and later-generation hybrids in higher frequency in acorns than in adults might be explained by selection against hybrid genotypes, the history of this uneven-aged forest or past introgression between species.
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Affiliation(s)
- Alexandru L Curtu
- Forest Genetics and Forest Tree Breeding, Büsgen-Institute, Georg-August University Göttingen, Büsgenweg 2, 37077, Germany.
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68
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Gailing O, Vornam B, Leinemann L, Finkeldey R. Genetic and genomic approaches to assess adaptive genetic variation in plants: forest trees as a model. PHYSIOLOGIA PLANTARUM 2009; 137:509-19. [PMID: 19627554 DOI: 10.1111/j.1399-3054.2009.01263.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the increasing availability of sequence information at putatively important genes or regulatory regions, the characterization of adaptive genetic diversity and their association with phenotypic trait variation becomes feasible for many non-model organisms such as forest trees. Especially in predominantly outcrossing forest tree populations with large effective size, a high genetic variation in relevant genes is maintained, that is the raw material for the adaptation to changing and variable environments, and likewise for plant breeding. Oaks (Quercus spp.) are excellent model species to study the adaptation of forest trees to changing environments. They show a wide geographic distribution in Europe as dominant tree species in many forests and grow under a wide range of climatic and edaphic conditions. With the availability of a growing amount of functional and expressional candidate genes, we are now able to test the functional importance of single nucleotide polymorphisms (SNPs) by associating nucleotide variation in these genes with phenotypic variation in adaptive traits in segregating or natural populations. Here, we report on quantitative trait locus (QTL), candidate gene and association mapping approaches that are applicable to characterize gene markers and SNPs associated with variation in adaptive traits, such as bud burst, drought resistance and other traits showing selective responses to environmental change and stress. Because genome-wide association mapping studies are not feasible because of the enormous amount of SNP markers required in outcrossing trees with high recombination rates, the success of such an approach depends largely on the reasonable selection of candidate genes.
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Affiliation(s)
- Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Germany.
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69
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Larson SR, Culumber CM, Schweigert RN, Chatterton NJ. Species delimitation tests of endemic Lepidium papilliferum and identification of other possible evolutionarily significant units in the Lepidium montanum complex (Brassicaceae) of western North America. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-0002-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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70
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Yatabe Y, Tsutsumi C, Hirayama Y, Mori K, Murakami N, Kato M. Genetic population structure of Osmunda japonica, rheophilous Osmunda lancea and their hybrids. JOURNAL OF PLANT RESEARCH 2009; 122:585-595. [PMID: 19636667 DOI: 10.1007/s10265-009-0254-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 06/19/2009] [Indexed: 05/27/2023]
Abstract
Rheophilous Osmunda lancea often hybridizes with a dryland ally, Osmunda japonica, to produce O. x intermedia, forming zonation in riverbanks and the adjacent dryland along flooding frequency clines. This study examined the genetic structure of populations consisting of O. x intermedia and the two parental species by analyzing ten nuclear DNA markers [six cleaved amplified polymorphic sequence (CAPS) markers and three simple sequence repeat (SSR) markers developed from an expressed sequence tag (EST) library, and the sequence of the glyceraldehyde-3-phosphate dehydrogenase gene GapCp] and chloroplast DNA sequences. The results suggest that the nuclear genes of O. japonica and O. lancea are genetically differentiated despite shared polymorphism in their chloroplast DNA sequences. This discrepancy may be attributable to natural selection and recent introgression, although it is not evident if introgression occurs between O. japonica and O. lancea in the examined populations. Our findings of putative F2 hybrids in O. x intermedia support its partial reproducibility, and also suggest that formation of later-generation hybrids generates morphological variation in O. x intermedia. O. lancea plants collected from geographically distant localities were genetically very similar, and it is suggested that O. lancea originated monotopically.
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Affiliation(s)
- Yoko Yatabe
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, 305-0005, Japan.
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71
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Salvini D, Bruschi P, Fineschi S, Grossoni P, Kjaer ED, Vendramin GG. Natural hybridisation between Quercus petraea (Matt.) Liebl. and Quercus pubescens Willd. within an Italian stand as revealed by microsatellite fingerprinting. PLANT BIOLOGY (STUTTGART, GERMANY) 2009; 11:758-765. [PMID: 19689784 DOI: 10.1111/j.1438-8677.2008.00158.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Interspecific gene flow is frequently reported in the genus Quercus. However, interfertile oak species often seem to remain distinct, even within areas of sympatry. This study employed molecular markers to verify, at a fine scale, the presence of interspecific gene flow in a natural population of Quercus petraea and Quercus pubescens. Within a delimited area of 6 ha, all adult trees belonging to the studied oak complex and seeds from a subsample of such trees were collected and analysed using molecular microsatellite markers. A low interspecific genetic differentiation and a high level of interspecific genetic admixture suggested past hybridisation. Paternity inference of seeds allowed the estimation of pollination frequencies from the three groups of pollen donors (Q. petraea, Q. pubescens, intermediate). We also assayed pollen viability and germinability of each species group. We observed natural hybridisation between Q. petraea and Q. pubescens, with a predominant component in the direction Q. petraea --> Q. pubescens: Q. pubescens displayed a higher level of heterospecific pollination by Q. petraea (25.8%) and intermediate morphotypes (14.7%), compared to Q. petraea acting as pollen receptor (with less than 5% heterospecific pollinations). Intermediate 'mother trees' were pollinated in similar proportions by Q. petraea (23.1%), Q. pubescens (37.8%) and intermediate morphotypes (39.1%). The asymmetrical introgression observed for the studied generation may be caused, among other factors, by the relative abundance of trees from each species group in the studied area.
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Affiliation(s)
- D Salvini
- Istituto per la Protezione delle Piante, Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Firenze, Italy
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72
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Liu SC, Lu CT, Wang JC. Reticulate hybridization of Alpinia (Zingiberaceae) in Taiwan. JOURNAL OF PLANT RESEARCH 2009; 122:305-316. [PMID: 19291357 DOI: 10.1007/s10265-009-0223-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 01/18/2009] [Indexed: 05/27/2023]
Abstract
Reticulate hybridization is a complicated and creative mechanism in plant evolution that can cause interference in phylogenetic studies. Based on observations of intermediate morphology, low pollen fertility, and overlapping distributions of putative parent species, Yang and Wang (Proceedings of the cross-strait symposium on floristic diversity and conservation. National Museum of Natural Science, Taichung, Taiwan, pp 183-197, 1998) first proposed reticulate hybridization of Alpinia in Taiwan. In the present study, molecular tools were used to explore relationships between four parental species and their homoploidy hybrids, and the impact of hybridization on phylogeny reconstruction. Based on DNA markers, maternal heritance of the chloroplast genome, and additivity of nuclear ribosomal internal transcribed spacer, the present results provide strong support for the hybridization hypothesis. Co-existence of parental ribotypes within hybrids revealed that these hybridization events were current, while reciprocal and introgressive hybridization were inferred from chloroplast DNA data. Furthermore, iterative hybridizations involving more than two parental species may occur in notorious hybrid zones. Ecological, phenological, and physiological evidence provides insight into why such frequent hybridization occurs in Taiwanese Alpinia. In the phylogenetic tree of the Zerumbet clade reconstructed in this study, the chloroplast sequences from one hybrid species were not grouped into a subclade, implying instability caused by hybridization. Failure to find morphological apomorphies and biogeographical patterns in this clade was likely partially due to reticulate hybridization.
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Affiliation(s)
- Shu-Chuan Liu
- Department of Life Science, National Taiwan Normal University, No. 88, Ting-Chow Rd., Sect. 4, Taipei 11677, Taiwan
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73
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Lepais O, Petit RJ, Guichoux E, Lavabre JE, Alberto F, Kremer A, Gerber S. Species relative abundance and direction of introgression in oaks. Mol Ecol 2009; 18:2228-42. [PMID: 19302359 DOI: 10.1111/j.1365-294x.2009.04137.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Successful hybridisation and subsequent introgression lead to the transfer of genetic material across species boundaries. In this process, species relative abundance can play a significant role. If one species is less abundant than the other, its females will receive many heterospecific gametes, increasing mate-recognition errors and thus hybridisation rate. Moreover, first-generation hybrids will also more likely mate with the more abundant species, leading to asymmetric introgression. These predictions have important fundamental consequences, especially during biological invasions or when a rare species threatened by extinction is surrounded by individuals from a related species. However, experimental tests in nature of the importance of the relative abundance of each species on hybridisation dynamics remain scarce. We assess here the impact of species relative abundance on hybridisation dynamics among four species from the European white oak species complex. A total of 2107 oak trees were genotyped at 10 microsatellite markers and Bayesian clustering methods were used to identify reference trees of each species. We then used these reference trees to simulate purebred and hybrid genotypes to determine optimal threshold for genetic assignment. With this approach, we found widespread evidence of hybridisation between all studied oak species, with high occurrence of hybrids, varying from 11% to 31% according to stand and sampling strategies. This finding suggests that hybridisation is a common phenomenon that plays a significant role in evolution of this oak species complex. In addition, we demonstrate a strong impact of species abundance on both hybridisation rate and introgression directionality.
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Affiliation(s)
- O Lepais
- INRA, UMR 1202 BIOGECO, Cestas, France
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74
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Mir C, Jarne P, Sarda V, Bonin A, Lumaret R. Contrasting nuclear and cytoplasmic exchanges between phylogenetically distant oak species (Quercus suber L. and Q. ilex L.) in Southern France: inferring crosses and dynamics. PLANT BIOLOGY (STUTTGART, GERMANY) 2009; 11:213-26. [PMID: 19228328 DOI: 10.1111/j.1438-8677.2008.00106.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Gene flow is particularly frequent in the genus Quercus (oaks), especially between closely related species. We focus here on Quercus ilex and the cork-producing Quercus suber, which occasionally hybridize although they are phylogenetically markedly separated. Morphological observations were combined with both allozymic and chloroplastic diagnostic markers to characterize hybridization and introgression and to infer their dynamics in two French regions (French Catalonia and Provence), which are separated by several hundred kilometres. Some hybrids were found in both regions, indicating recent hybridization events. As expected from previous studies, most hybrids resulted from female symbol Q. ilex x male symbol Q. suber crosses, but our data showed that the reciprocal cross is also possible. Partial independence between nuclear and chloroplastic introgression was observed in the two species. Nuclear introgression was limited in both species and both regions, with no preferred direction. In Provence, chloroplastic introgression was very rare in both species. Conversely, all Q. suber individuals from French Catalonia were introgressed by Q. ilex chlorotypes. This might be explained by introgression in the Iberian Peninsula antedating the first occurrence of the two species in French Catalonia. We also observed a new chlorotype that was created locally, and was exchanged between the two species. However, the two species still remain genetically differentiated. The dynamics and complexity of exchanges and the factors determining them (including human management of Q. suber) are discussed.
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Affiliation(s)
- C Mir
- UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive, Centre National de la Recherche Scientifique, Montpellier, France.
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75
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Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex). Heredity (Edinb) 2009; 102:442-52. [PMID: 19240752 DOI: 10.1038/hdy.2009.8] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Powerful and accurate detection of first-generation (F1) hybrids and backcrosses in nature is needed to achieve a better understanding of the function and dynamics of introgression. To document the frequency of ongoing interspecific gene exchange between two Mediterranean evergreen oaks, the cork oak (Quercus suber) and the holm oak (Q. ilex), we analyzed 1487 individuals originating from across the range of the two species using eight microsatellite loci and two Bayesian clustering approaches (implemented in the programs STRUCTURE and NEWHYBRIDS). Simulated data were used to assess the differences between the two clustering methods and to back up the choice of the threshold value for the posterior probability to discriminate admixed from pure individuals. We found that the use of STRUCTURE resulted in the highest power to detect hybrids, whereas NEWHYBRIDS provided the highest accuracy. Irrespective of the approach, the two species were clearly distinguished as independent genetic entities without any prior information. In contrast with previous reports, we found no evidence for unidirectional introgression. The overall hybridization rate was very low (<2% of introgressed individuals). Only two individuals were identified as F1 hybrids and five as early backcrosses. This work shows that the combined application of the two complementary Bayesian approaches and their systematic validation with simulations, fit for the case at hand, helps gain resolution in the identification of admixed individuals.
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76
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EDWARDS CE, SOLTIS DE, SOLTIS PS. Using patterns of genetic structure based on microsatellite loci to test hypotheses of current hybridization, ancient hybridization and incomplete lineage sorting inConradina(Lamiaceae). Mol Ecol 2008; 17:5157-74. [DOI: 10.1111/j.1365-294x.2008.03985.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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77
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Gugerli F, Brodbeck S, Holderegger R. Utility of multilocus genotypes for taxon assignment in stands of closely related European white oaks from Switzerland. ANNALS OF BOTANY 2008; 102:855-63. [PMID: 18775969 PMCID: PMC2712387 DOI: 10.1093/aob/mcn164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS European white oaks (Quercus petraea, Q. pubescens, Q. robur) have long puzzled plant biologists owing to disputed species differentiation. Extensive hybridization or shared ancestry have been proposed as alternative hypotheses to explain why genetic differentiation between these oak species is low. Species delimitation is usually weak and often shows gradual transitions in leaf morphology. Hence, individual identification may be difficult, but remains a critical step for both scientific work and practical management. METHODS Multilocus genotype data (five nuclear microsatellites) were used from ten Swiss oak stands for taxon identification without a priori grouping of individuals or populations, using model-based Bayesian assignment tests. KEY RESULTS Three groups best structured the data, indicating that the taxonomical signal was stronger than the spatial signal. Most individuals showed high posterior probabilities for either of three genetic groups that were best circumscribed as taxonomical units. The assignment of a subset of trees, whose taxonomic status had been previously characterized in detail, supported this classification scheme. CONCLUSIONS Molecular-genetic assignment tests are useful in the identification of species status in critical taxon complexes such as the European white oaks. Such an approach is of practical importance for forest management, e.g. for stand certification or in seed trade to trace the origin of forest products.
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Affiliation(s)
- Felix Gugerli
- WSL Swiss Federal Research Institute, Ecological Genetics and Evolution, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.
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78
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Sampson JF, Byrne M. Outcrossing between an agroforestry plantation and remnant native populations of Eucalyptus loxophleba. Mol Ecol 2008; 17:2769-81. [PMID: 18444981 DOI: 10.1111/j.1365-294x.2008.03779.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Gene dispersal among populations of a species is an important force influencing their genetic structure. Dispersal may also occur between taxa that would normally be isolated when nonendemic, domesticated or transgenic species are planted within the natural range of interfertile taxa. Such a mosaic of populations is typical of many agricultural landscapes, and investigations are needed to assess the risks of genetic contamination of the endemic populations but a combination of approaches may be necessary because of the limitations of research in this landscape. This study used microsatellite markers and a range of analyses (mating system, paternity exclusion, Bayesian assignment) to examine gene dispersal between remnants of the endemic Eucalyptus loxophleba ssp. supralaevis and a plantation of a nonendemic subspecies. Our results indicate that remnant populations are connected by significant dispersal to pollen sources up to 1.94 km away including the plantation. The combined analyses showed that the pollen pool and outcrossing rates of individuals within remnants varied significantly probably because of asynchronous flowering and that the likelihood of paternity was not correlated with spatial proximity. More than half of all progeny had male parents from outside their stand with the largest proportions estimated to come from the plantation by exclusion (42.4%) or Bayesian analyses (18.8-76%). Fragmentation may not be associated with decreased gene dispersal between populations of tree species, natural or planted, so that the distances required to buffer endemic trees in fragmented rural landscapes are likely to be large.
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Affiliation(s)
- Jane F Sampson
- Science Division, Department of Environment and Conservation, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983, Australia.
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79
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Curtu AL, Gailing O, Finkeldey R. Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community. BMC Evol Biol 2007; 7:218. [PMID: 17996115 PMCID: PMC2244923 DOI: 10.1186/1471-2148-7-218] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Accepted: 11/10/2007] [Indexed: 11/10/2022] Open
Abstract
Background Analysis of interspecific gene flow is crucial for the understanding of speciation processes and maintenance of species integrity. Oaks (genus Quercus, Fagaceae) are among the model species for the study of hybridization. Natural co-occurrence of four closely related oak species is a very rare case in the temperate forests of Europe. We used both morphological characters and genetic markers to characterize hybridization in a natural community situated in west-central Romania and which consists of Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto, respectively. Results On the basis of pubescence and leaf morphological characters ~94% of the sampled individuals were assigned to pure species. Only 16 (~6%) individual trees exhibited intermediate morphologies or a combination of characters of different species. Four chloroplast DNA haplotypes were identified in the study area. The distribution of haplotypes within the white oak complex showed substantial differences among species. However, the most common haplotypes were present in all four species. Furthermore, based on a set of 7 isozyme and 6 microsatellite markers and using a Bayesian admixture analysis without any a priori information on morphology we found that four genetic clusters best fit the data. There was a very good correspondence of each species with one of the inferred genetic clusters. The estimated introgression level varied markedly between pairs of species ranging from 1.7% between Q. robur and Q. frainetto to 16.2% between Q. pubescens and Q. frainetto. Only nine individuals (3.4%) appeared to be first-generation hybrids. Conclusion Our data indicate that natural hybridization has occurred at relatively low rates. The different levels of gene flow among species might be explained by differences in flowering time and spatial position within the stand. In addition, a partial congruence between phenotypically and genetically intermediate individuals was found, suggesting that intermediate appearance does not necessarily mean hybridization. However, it appears that natural hybridization did not seriously affect the species identity in this area of sympatry.
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Affiliation(s)
- Alexandru L Curtu
- Department of Forest Genetics and Forest Tree Breeding, Büsgen-Institute Georg - August University Göttingen, Büsgenweg 2, Göttingen 37077, Germany.
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80
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Baack EJ, Rieseberg LH. A genomic view of introgression and hybrid speciation. Curr Opin Genet Dev 2007; 17:513-8. [PMID: 17933508 DOI: 10.1016/j.gde.2007.09.001] [Citation(s) in RCA: 251] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 08/29/2007] [Accepted: 09/02/2007] [Indexed: 12/31/2022]
Abstract
Hybridization in plants and animals is more common and has more complex outcomes than previously realized. Genome-wide analyses of introgression in organisms ranging from oaks to sunflowers to fruit flies show that a substantial fraction of their genomes are permeable to alleles from related species. Hybridization can lead to rapid genomic changes, including chromosomal rearrangements, genome expansion, differential gene expression, and gene silencing, some of which are mediated by transposable elements. These genomic changes may lead to beneficial new phenotypes, and selection for fertility and ecological traits may in turn alter genome structure. Dramatic increases in the availability of genomic tools will produce a new understanding of the genetic nature of species and will resolve a century-old debate over the basis of hybrid vigor, while the natural recombinants found in hybrid zones will permit genetic mapping of species differences and reproductive barriers in nonmodel organisms.
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Affiliation(s)
- Eric J Baack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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81
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Sapir Y, Moody ML, Brouillette LC, Donovan LA, Rieseberg LH. Patterns of genetic diversity and candidate genes for ecological divergence in a homoploid hybrid sunflower, Helianthus anomalus. Mol Ecol 2007; 16:5017-29. [PMID: 17944850 DOI: 10.1111/j.1365-294x.2007.03557.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Natural hybridization accompanied by a shift in niche preference by hybrid genotypes can lead to hybrid speciation. Natural selection may cause the fixation of advantageous alleles in the ecologically diverged hybrids, and the loci experiencing selection should exhibit a reduction in allelic diversity relative to neutral loci. Here, we analyzed patterns of genetic diversity at 59 microsatellite loci associated with expressed sequence tags (ESTs) in a homoploid hybrid sunflower species, Helianthus anomalus. We used two indices, ln RV and ln RH, to compare variation and heterozygosity (respectively) at each locus between the hybrid species and its two parental species, H. annuus and H. petiolaris. Mean values of ln RV and ln RH were significantly lower than zero, which implies that H. anomalus experienced a population bottleneck during its recent evolutionary history. After correcting for the apparent bottleneck, we found six loci with a significant reduction in variation or with heterozygosity in the hybrid species, compared to one or both of the parental species. These loci should be viewed as a ranked list of candidate loci, pending further sequencing and functional analyses. Sequence data were generated for two of the candidate loci, but population genetics tests failed to detect deviations from neutral evolution at either locus. Nonetheless, a greater than eight-fold excess of nonsynonymous substitutions was found near a putative N-myristoylation motif at the second locus (HT998), and likelihood-based models indicated that the protein has been under selection in H. anomalus in the past and, perhaps, in one or both parental species. Finally, our data suggest that selective sweeps may have united populations of H. anomalus isolated by a mountain range, indicating that even low gene-flow species may be held together by the spread of advantageous alleles.
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Affiliation(s)
- Yuval Sapir
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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82
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Yatabe Y, Kane NC, Scotti-Saintagne C, Rieseberg LH. Rampant gene exchange across a strong reproductive barrier between the annual sunflowers, Helianthus annuus and H. petiolaris. Genetics 2007; 175:1883-93. [PMID: 17277373 PMCID: PMC1855124 DOI: 10.1534/genetics.106.064469] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant species may remain morphologically distinct despite gene exchange with congeners, yet little is known about the genomewide pattern of introgression among species. Here we analyze the effects of persistent gene flow on genomic differentiation between the sympatric sunflower species Helianthus annuus and H. petiolaris. While the species are strongly isolated in testcrosses, genetic distances at 108 microsatellite loci and 14 sequenced genes are highly variable and much lower (on average) than for more closely related but historically allopatric congeners. Our analyses failed to detect a positive association between levels of genetic differentiation and chromosomal rearrangements (as reported in a prior publication) or proximity to QTL for morphological differences or hybrid sterility. However, a significant increase in differentiation was observed for markers within 5 cM of chromosomal breakpoints. Together, these results suggest that islands of differentiation between these two species are small, except in areas of low recombination. Furthermore, only microsatellites associated with ESTs were identified as outlier loci in tests for selection, which might indicate that the ESTs themselves are the targets of selection rather than linked genes (or that coding regions are not randomly distributed). In general, these results indicate that even strong and genetically complex reproductive barriers cannot prevent widespread introgression.
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Affiliation(s)
- Yoko Yatabe
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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Curtu AL, Gailing O, Leinemann L, Finkeldey R. Genetic variation and differentiation within a natural community of five oak species (Quercus spp.). PLANT BIOLOGY (STUTTGART, GERMANY) 2007; 9:116-26. [PMID: 17048143 DOI: 10.1055/s-2006-924542] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Chloroplast DNA and two categories of nuclear markers - isozymes and microsatellites - were used to examine a very rich natural community of oaks (Quercus spp.) situated in west-central Romania. The community consists of five oak species: Q. robur, Q. petraea, Q. pubescens, and Q. frainetto - that are closely related -, and Q. cerris. A total of five chloroplast haplotypes was identified. Q. cerris was fixed for a single haplotype. The other four species shared the two most common haplotypes. One haplotype was confined to Q. robur and a very rare one was restricted to Q. petraea. Both types of nuclear markers revealed a larger genetic variation for Q. pubescens and Q. petraea than for Q. frainetto and Q. robur, although the differences between species are in most cases not significant. At the nuclear level, Q. cerris could be clearly separated from the other four oak species confirming the taxonomic classification. Regardless of the estimate used, the levels of polymorphism revealed by microsatellites were much higher than those based on isozymes. For the four closely related species the overall genetic differentiation was significant at both categories of nuclear markers. Several loci, such as Acp-C for isozymes, and ssrQpZAG36 and ssrQrZAG96 for microsatellites were very useful to discriminate among species. However, the level of differentiation varied markedly between pairs of species. The genetic affinities among the species may reflect different phylogenetic distances and/or different rates of recurrent gene flow at this site.
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Affiliation(s)
- A L Curtu
- Institute of Forest Genetics and Forest Tree Breeding, Georg August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
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84
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Grillo V, Jackson F, Cabaret J, Gilleard JS. Population genetic analysis of the ovine parasitic nematode Teladorsagia circumcincta and evidence for a cryptic species. Int J Parasitol 2006; 37:435-47. [PMID: 17234192 DOI: 10.1016/j.ijpara.2006.11.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/20/2006] [Accepted: 11/27/2006] [Indexed: 11/23/2022]
Abstract
An understanding of genetic variation in parasite populations, and how it is partitioned, is required to underpin many areas of basic and applied research. Population genetic studies on parasitic nematode populations are still in their infancy and have been dominated by the use of single locus markers. We have used a panel of five microsatellite markers to undertake a genetic study of a number of field and laboratory populations of Teladorsagia circumcincta. High levels of polymorphism were seen in all the populations examined with the majority of diversity being within rather than between populations. There was no detectable genetic differentiation between the UK populations examined although they included both laboratory passaged and field isolates derived from different geographical regions and host species. This broadly supports previous mtDNA sequence diversity studies of this parasite in the UK and USA. However, some between-population genetic differentiation was apparent when several populations from French goats and a laboratory population from New Zealand were examined. Most notably, a population from a French goat farm, which has previously been suggested to contain a cryptic species, showed very high levels of genetic differentiation from all the other populations. Analysis of multi-locus genotypes suggested the presence of two sympatric parasite populations on this farm with little or no gene flow between them. This supports the hypothesis that parasites currently defined as T. circumcincta by routine morphological criteria comprise more than a single species.
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Affiliation(s)
- Victoria Grillo
- Division of Infection and Immunity, Institute of Comparative Medicine, Faculty of Veterinary Medicine, Bearsden Rd, University of Glasgow, G61 1QH, UK
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85
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Gerard PR, Fernandez-Manjarres JF, Frascaria-Lacoste N. Temporal cline in a hybrid zone population between Fraxinus excelsior L. and Fraxinus angustifolia Vahl. Mol Ecol 2006; 15:3655-67. [PMID: 17032264 DOI: 10.1111/j.1365-294x.2006.03032.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The two closely related ash species Fraxinus excelsior L. (common ash) and Fraxinus angustifolia Vahl (narrow-leaved ash) have a broad contact zone in France where they hybridize. However, little is known about the local structure of hybrid zone populations and the isolation mechanisms. We assessed the potential effect of floral phenology on the structure of a riparian ash hybrid zone population in central France. The distribution of flowering times was unimodal and lay between the flowering periods of the two species. Using microsatellite markers, we detected isolation by time, which has possibly originated from assortative mating. Multivariate analyses indicated that morphological variation is not distributed at random with respect to flowering times. Spatial autocorrelation analyses showed that temporal and spatial patterns were tightly linked. Interestingly, despite the fact that the population shows isolation by time, neighbourhood size and historical dispersal variance (sigma = 63 m) are similar to those detected in pure stands of F. excelsior where individuals flower rather synchronously and hermaphrodites are not the most frequent sexual type. Trees flowering at intermediate dates, which comprised the majority of the population, produced on average more flowers and fruits. We detected no significant differences in floral parasite infections relative to reproductive timing, although there was a tendency for late flowering trees to suffer from more gall attack. We discuss the impact of temporal variation in fitness traits and their possible role in the maintenance of the hybrid zone.
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Affiliation(s)
- Pierre R Gerard
- Ecologie, Systématique, Evolution, UMR CNRS-UPXI-ENGREF 8079, Bât. 360, Université Paris-Sud, 91405 Orsay cedex, France.
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86
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Muir G, Schlötterer C. Moving beyond single-locus studies to characterize hybridization between oaks (Quercus spp.). Mol Ecol 2006; 15:2301-4. [PMID: 16780442 DOI: 10.1111/j.1365-294x.2006.02912.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Graham Muir
- School of Biosciences, University of Birmingham, Birmingham, BI5 2TT, UK
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87
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Lexer C, Kremer A, Petit RJ. Shared alleles in sympatric oaks: recurrent gene flow is a more parsimonious explanation than ancestral polymorphism. Mol Ecol 2006; 15:2007-12. [PMID: 16689915 DOI: 10.1111/j.1365-294x.2006.02896.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- C Lexer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
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