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Guevara-Escudero M, Osorio AN, Cortés AJ. Integrative Pre-Breeding for Biotic Resistance in Forest Trees. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10102022. [PMID: 34685832 PMCID: PMC8541610 DOI: 10.3390/plants10102022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 05/18/2023]
Abstract
Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations' persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen-host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes.
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Affiliation(s)
- Melisa Guevara-Escudero
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Angy N. Osorio
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
| | - Andrés J. Cortés
- Department de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Sede Medellín, Medellín 050034, Colombia; (M.G.-E.); (A.N.O.)
- Main Address: Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Km 7 Vía Rionegro, Las Palmas, Rionegro 054048, Colombia
- Correspondence:
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Yan M, Liu R, Li Y, Hipp AL, Deng M, Xiong Y. Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages. BMC Evol Biol 2019; 19:202. [PMID: 31684859 PMCID: PMC6829957 DOI: 10.1186/s12862-019-1523-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/01/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Understanding the origin of genetic variation is the key to predict how species will respond to future climate change. The genus Quercus is a species-rich and ecologically diverse woody genus that dominates a wide range of forests and woodland communities of the Northern Hemisphere. Quercus thus offers a unique opportunity to investigate how adaptation to environmental changes has shaped the spatial genetic structure of closely related lineages. Furthermore, Quercus provides a deep insight into how tree species will respond to future climate change. This study investigated whether closely related Quercus lineages have similar spatial genetic structures and moreover, what roles have their geographic distribution, ecological tolerance, and historical environmental changes played in the similar or distinct genetic structures. RESULTS Despite their close relationships, the three main oak lineages (Quercus sections Cyclobalanopsis, Ilex, and Quercus) have different spatial genetic patterns and occupy different climatic niches. The lowest level and most homogeneous pattern of genetic diversity was found in section Cyclobalanopsis, which is restricted to warm and humid climates. The highest genetic diversity and strongest geographic genetic structure were found in section Ilex, which is due to their long-term isolation and strong local adaptation. The widespread section Quercus is distributed across the most heterogeneous range of environments; however, it exhibited moderate haplotype diversity. This is likely due to regional extinction during Quaternary climatic fluctuation in Europe and North America. CONCLUSIONS Genetic variations of sections Ilex and Quercus were significantly predicted by geographic and climate variations, while those of section Cyclobalanopsis were poorly predictable by geographic or climatic diversity. Apart from the different historical environmental changes experienced by different sections, variation of their ecological or climatic tolerances and physiological traits induced varying responses to similar environment changes, resulting in distinct spatial genetic patterns.
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Affiliation(s)
- Mengxiao Yan
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Ruibin Liu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ying Li
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- The Ecological Technique and Engineering College, Shanghai Institute of Technology, Shanghai, 201418, China
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA
| | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, 05282, Myanmar.
| | - Yanshi Xiong
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
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Ramsey AJ, McCauley DE, Mandel JR. Heteroplasmy and Patterns of Cytonuclear Linkage Disequilibrium in Wild Carrot. Integr Comp Biol 2019; 59:1005-1015. [DOI: 10.1093/icb/icz102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Abstract
Organellar genomes are considered to be strictly uniparentally-inherited. Uniparental inheritance allows for cytonuclear coevolution and the development of highly coordinated cytonuclear interactions. Yet, instances of biparental inheritance have been documented across eukaryotes. Biparental inheritance in otherwise uniparentally-inherited organelles is termed leakage (maternal or paternal) and allows for the presence of multiple variants of the same organellar genome within an individual, called heteroplasmy. It is unclear what, if any, evolutionary consequences are placed on nuclear and/or organellar genomes due to heteroplasmy. One way of accessing cytonuclear interactions and potential coevolution is through calculating cytonuclear linkage disequilibrium (cnLD), or the non-random association of alleles between nuclear and organellar genomes. Patterns of cnLD can indicate positive or negative cytonuclear selection, coevolution between the nuclear and organellar genomes, non-traditional organellar inheritance, or instances of ancestral heteroplasmy. In plants, cytonuclear interactions have been shown to play a role in cytoplasmic male sterility which occurs in gynodioecious species and is associated with leakage. We used the gynodioecious species, Daucus carota L. spp. carota, or wild carrot, to investigate cnLD. We genotyped a total of 265 individuals from two regions of the USA at 15 nuclear microsatellites, the mitochondrial genes cox1 and atp9, and an intergenic region between trnS and trnG (StoG) in the plastid genome to calculate nuclear–nuclear LD (nucLD), cnLD, and organellar LD (i.e., within the mtDNA and between mtDNA and ptDNA) within the two regions. We were further able to identify cox1 and StoG heteroplasmy and calculate some of the same LD measures within heteroplasmic and homoplasmic (non-heteroplasmic) datasets. We used a Z-transformation test to demonstrate that heteroplasmic individuals display significantly higher levels of cnLD within both regions. In spite of this, within and between organellar LD is low to moderate. Given these patterns of LD in two regions of the USA in which gene flow has been shown to occur between crop and wild carrot, we suggest that heteroplasmy is an evolutionary mechanism which permits the maintenance of cnLD while also acting to disrupt organellar LD.
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Affiliation(s)
- Adam J Ramsey
- Department of Biological Sciences, The University of Memphis, 3700 Walker Avenue, Memphis, TN 38152, USA
| | - David E McCauley
- Department of Biological Sciences, Vanderbilt University, VU Station B, Nashville, TN Box 351634, USA
| | - Jennifer R Mandel
- Department of Biological Sciences, Vanderbilt University, VU Station B, Nashville, TN Box 351634, USA
- W. Harry Feinstone Center for Genomic Research, The University of Memphis, 3774 Walker Avenue, Memphis, TN 38152, USA
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Cardoso LW, Silva-Brandão KL, Duarte M. Adhemarius eurysthenes (Felder, 1874) (Lepidoptera, Sphingidae) in the Atlantic Rain Forest: A phylogeographic perspective. ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Genetic Diversity among Age Classes of a Pinus sylvestris (L.) Population from the Białowieża Primeval Forest, Poland. FORESTS 2017. [DOI: 10.3390/f8070227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Białowieża Primeval Forest (BPF) is Europe’s last primeval forest and an irreplaceable area for biodiversity conservation due to its size, protection status, and substantially undisturbed nature. There is no other forest in Europe with such a large surface representing highly-advanced natural succession. This article reports on the first analysis of the genetic variability and demographic structure of a self-renewed Pinus sylvestris population located in BPF, using both chloroplast and mitochondrial DNA markers. The analysis of molecular variance (AMOVA) for chloroplast simple sequence repeats (cpSSRs) revealed a significant genetic differentiation among age classes that accounted for about 2% of the total variance, comparable to those reported among different populations of Scots pine. None of the 117 detected chloroplast haplotypes were common to all age classes. Haplotype diversity ranged from 0.370 to 0.415 for cpSSRs and from 0.320 to 0.455 for mitochondrial markers. The genetic variation of the studied age classes—represented by mitochondrial markers—strongly depicts the maternal genetic structure, indicating limited seed dispersal. Temporal genetic substructuring is maintained within a self-renewed population of Scots pine from the BPF.
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Rau D, Rodriguez M, Rapposelli E, Murgia ML, Papa R, Brown AHD, Attene G. Spatial genetic structure in wild cardoon, the ancestor of cultivated globe artichoke: Limited gene flow, fragmentation and population history. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 253:194-205. [PMID: 27968988 DOI: 10.1016/j.plantsci.2016.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
Nuclear and chloroplast markers and phenotypic characters were integrated to analyse the population genetic structure of wild cardoon, Cynara cardunculus var. sylvestris, the ancestor of cultivated globe artichoke, Cynara cardunculus var. scolymus on the island of Sardinia, Italy. The spatial scale ranged from a few metres to ∼200km. Wild cardoon appears to be genetically fragmented, with significant genetic divergence at various scales, indicating that gene flow is insufficient to counterbalance the effects of genetic drift or founder effects. Divergence between populations was higher for chloroplast (40%) than for nuclear markers (15%), suggesting that gene flow via seed was lower than via pollen. Two main genetic groups were detected; these correlated with differences in flowering time, capitula size, glossiness, and anthocyanin pigmentation. A complex population structure of wild cardoon emerged over small spatial scales, likely resulting from the interplay between gene dispersal, colonisation history and selective forces. Indeed, Sardinia appears to be a 'hybrid zone' of different gene pools. The island has unique diverse germplasm that has originated from hybridisation among different gene pools. The sampling of seeds from a few plants but from many sites is suggested as the best strategy to harvest the genetic diversity of wild cardoon.
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Affiliation(s)
- D Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy.
| | - M Rodriguez
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy; Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040 Alghero, Italy
| | - E Rapposelli
- AGRIS Sardegna, Servizio per la Ricerca in Arboricoltura, Via Mameli 126/D, Cagliari, Italy
| | - M L Murgia
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy
| | - R Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche (UNIVPM), Via Brecce Bianche, 60131 Ancona, Italy
| | - A H D Brown
- Bioversity International (Honorary Research Fellow), Via dei Tre Denari, 472/a, 00054 Maccarese, Fiumicino, Italy
| | - G Attene
- Dipartimento di Agraria, Università degli Studi di Sassari, Via E. De Nicola, 07100 Sassari, Italy; Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, Surigheddu, 07040 Alghero, Italy
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O’Donnell RP, Drost CA, Mock KE. Cryptic invasion of Northern Leopard Frogs (Rana pipiens) across phylogeographic boundaries and a dilemma for conservation of a declining amphibian. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1320-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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8
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Harrison E, Trexler JC, Collins TM, Vazquez-Domínguez E, Razo-Mendivil U, Matamoros WA, Barrientos C. Genetic evidence for multiple sources of the non-native fish Cichlasoma urophthalmus (Günther; Mayan Cichlids) in southern Florida. PLoS One 2014; 9:e104173. [PMID: 25184569 PMCID: PMC4153574 DOI: 10.1371/journal.pone.0104173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/09/2014] [Indexed: 02/03/2023] Open
Abstract
The number and diversity of source populations may influence the genetic diversity of newly introduced populations and affect the likelihood of their establishment and spread. We used the cytochrome b mitochondrial gene and nuclear microsatellite loci to identify the sources of a successful invader in southern Florida, USA, Cichlasoma urophthalmus (Mayan cichlid). Our cytochrome b data supported an introduction from Guatemala, while our microsatellite data suggested movement of Mayan Cichlids from the upper Yucatán Peninsula to Guatemala and introductions from Guatemala and Belize to Florida. The mismatch between mitochondrial and nuclear genomes suggests admixture of a female lineage from Guatemala, where all individuals were fixed for the mitochondrial haplotype found in the introduced population, and a more diverse but also relatively small number of individuals from Belize. The Florida cytochrome b haplotype appears to be absent from Belize (0 out of 136 fish screened from Belize had this haplotype). Genetic structure within the Florida population was minimal, indicating a panmictic population, while Mexican and Central American samples displayed more genetic subdivision. Individuals from the Upper Yucatán Peninsula and the Petén region of Guatemala were more genetically similar to each other than to fish from nearby sites and movement of Mayan Cichlids between these regions occurred thousands of generations ago, suggestive of pre-Columbian human transportation of Mayan Cichlids through this region. Mayan Cichlids present a rare example of cytonuclear disequilibrium and reduced genetic diversity in the introduced population that persists more than 30 years (at least 7-8 generations) after introduction. We suggest that hybridization occurred in ornamental fish farms in Florida and may contribute their establishment in the novel habitat. Hybridization prior to release may contribute to other successful invasions.
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Affiliation(s)
- Elizabeth Harrison
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
| | - Joel C. Trexler
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
| | - Timothy M. Collins
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
| | - Ella Vazquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Universidad Nacional Autónoma de México, México DF, México
| | | | - Wilfredo A. Matamoros
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Christian Barrientos
- Department of Fisheries and Aquatic Science, University of Florida, Gainesville, Florida, United States of America
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9
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Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SC, Graham SW. Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep? Mol Ecol 2014; 23:4737-56. [DOI: 10.1111/mec.12837] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 05/29/2014] [Accepted: 06/04/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Diana M. Percy
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - George W. Argus
- Canadian Museum of Nature; PO Box 3443 Stn “D” Ottawa ON Canada K1P 6P4
| | - Quentin C. Cronk
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - Aron J. Fazekas
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | | | - Kevin S. Burgess
- Department of Biology; Columbus State University; Columbus GA 31907-5645 USA
| | - Brian C. Husband
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Steven G. Newmaster
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Spencer C.H. Barrett
- Department of Ecology & Evolutionary Biology; University of Toronto; 25 Willcocks Street Toronto ON Canada M5S 3B2
| | - Sean W. Graham
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
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Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability. Heredity (Edinb) 2013; 112:99-104. [PMID: 24002238 DOI: 10.1038/hdy.2013.79] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 06/21/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022] Open
Abstract
Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D') between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005-0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system.
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Pante E, Rohfritsch A, Becquet V, Belkhir K, Bierne N, Garcia P. SNP detection from de novo transcriptome sequencing in the bivalve Macoma balthica: marker development for evolutionary studies. PLoS One 2012; 7:e52302. [PMID: 23300636 PMCID: PMC3530552 DOI: 10.1371/journal.pone.0052302] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/16/2012] [Indexed: 11/28/2022] Open
Abstract
Hybrid zones are noteworthy systems for the study of environmental adaptation to fast-changing environments, as they constitute reservoirs of polymorphism and are key to the maintenance of biodiversity. They can move in relation to climate fluctuations, as temperature can affect both selection and migration, or remain trapped by environmental and physical barriers. There is therefore a very strong incentive to study the dynamics of hybrid zones subjected to climate variations. The infaunal bivalve Macoma balthica emerges as a noteworthy model species, as divergent lineages hybridize, and its native NE Atlantic range is currently contracting to the North. To investigate the dynamics and functioning of hybrid zones in M. balthica, we developed new molecular markers by sequencing the collective transcriptome of 30 individuals. Ten individuals were pooled for each of the three populations sampled at the margins of two hybrid zones. A single 454 run generated 277 Mb from which 17K SNPs were detected. SNP density averaged 1 polymorphic site every 14 to 19 bases, for mitochondrial and nuclear loci, respectively. An scan detected high genetic divergence among several hundred SNPs, some of them involved in energetic metabolism, cellular respiration and physiological stress. The high population differentiation, recorded for nuclear-encoded ATP synthase and NADH dehydrogenase as well as most mitochondrial loci, suggests cytonuclear genetic incompatibilities. Results from this study will help pave the way to a high-resolution study of hybrid zone dynamics in M. balthica, and the relative importance of endogenous and exogenous barriers to gene flow in this system.
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Affiliation(s)
- Eric Pante
- Littoral, Environnement et Sociétés Joint Research Unit 7266 Centre national de la recherche scientifique, Université de La Rochelle, La Rochelle, France.
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FREEDBERG STEVEN, MYERS ERINM. Cytonuclear equilibrium following interspecific introgression in a turtle lacking sex chromosomes. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01862.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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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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CASU MARCO, SANNA DARIA, COSSU PIERO, LAI TIZIANA, FRANCALACCI PAOLO, CURINI-GALLETTI MARCO. Molecular phylogeography of the microturbellarian Monocelis lineata (Platyhelminthes: Proseriata) in the North-East Atlantic. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01630.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Hu XS. F(ST) in the cytonuclear system. Theor Popul Biol 2009; 77:105-18. [PMID: 20005241 DOI: 10.1016/j.tpb.2009.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 11/25/2009] [Accepted: 12/07/2009] [Indexed: 10/20/2022]
Abstract
Selection on nuclear (or organelle) sites inevitably affects the spatial distribution of a neutral organelle (or nuclear) allele via transient cytonuclear disequilibrium. Here I examine this effect in terms of F(st) for a neutral allele by bringing together cytonuclear genomes with contrasting modes of inheritance. The relationships between cytonuclear disequilibrium and increment in F(st) are explored and confirmed through Monte Carlo simulations. Results show that the transient increment in F(st) for a neutral allele is not only related to the vectors of seed and pollen dispersal but also to the mode of its inheritance. Such increments can be substantial under certain conditions. Seed dispersal is more effective than pollen dispersal in changing the transient increment. The cumulative effects from multiple selective nuclear sites can amplify the transient increment in F(st) for a neutral paternal or maternal organelle allele. Selection on selective organelle sites facilitates the transient increment in F(st) for a neutral nuclear allele. Partial selfing can significantly reinforce the transient increment in F(st). These theoretical insights highlight the roles of transient cytonuclear disequilibrium as a biological factor in evolving population differentiation and refine our practical interpretations of F(st) with cytonuclear markers.
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Affiliation(s)
- Xin-Sheng Hu
- Department of Renewable Resources, 751 General Services Building, University of Alberta, Edmonton, AB T6G 2H1, Canada.
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16
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Affiliation(s)
- Xin-Sheng Hu
- Department of Renewable Resources, 751 General Services Building, University of Alberta, Edmonton, Alberta T6G 2H1, Canada.
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Walsh B, Redd AJ, Hammer MF. Joint match probabilities for Y chromosomal and autosomal markers. Forensic Sci Int 2007; 174:234-8. [PMID: 17449208 DOI: 10.1016/j.forsciint.2007.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 02/13/2007] [Accepted: 03/18/2007] [Indexed: 11/22/2022]
Abstract
Empirical tests of association between Y chromosome and autosomal markers are presented and a theoretical framework for determining a joint match probability is recommended. Statistical analyses of association were performed in 16 US populations between the autosomal genotypes from loci CSF1PO, FGA, THO1, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S512, D21S11 and Y chromosome haplotypes from loci DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. The sample populations include individuals of European-, African-, Hispanic-, Native-, and Asian-American ancestry. The results are consistent with independence of Y and autosomal markers, although small amounts of dependence would likely have escaped our tests. Given the data in hand, we suggest it is appropriate to compute joint match probabilities by multiplying the Y haplotype frequency with the appropriately corrected autosomal frequency. In addition to correcting for autosomal frequency differences between groups, a further correction may be required. Since two individuals sharing the same Y haplotype are likely to be more recently related than two randomly chosen individuals, the autosomal frequencies have to be adjusted to account for this, akin to the theta correction used to account for population substructure. The structure imposed on the autosomal frequencies conditioned in a Y match is a function of the number of markers scored and their mutation rate. However, in most settings theta<0.01. When population structure is already present in the autosomes, the additional effect due to conditioning on the Y is small. For example, if the amount of structure in the population is theta=0.01 or 0.03 (the NRCII range), then the effect of conditioning on the Y results in only a trivial increase in theta to 0.02-0.04, respectively.
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Affiliation(s)
- Bruce Walsh
- Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ 85721, USA
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Naydenov KD, Tremblay FM, Fenton NJ, Alexandrov A. Structure of Pinus nigra Arn. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: Provenance tests. BIOCHEM SYST ECOL 2006. [DOI: 10.1016/j.bse.2006.01.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Knowles LL, Richards CL. Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation. Mol Ecol 2006; 14:4023-32. [PMID: 16262856 DOI: 10.1111/j.1365-294x.2005.02711.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining what factors affect the structuring of genetic variation is key to deciphering the relative roles of different evolutionary processes in species differentiation. Such information is especially critical to understanding how the frequent shifts and fragmentation of species distributions during the Pleistocene translates into species differences, and why the effect of such rapid climate change on patterns of species diversity varies among taxa. Studies of mitochondrial DNA (mtDNA) have detected significant population structure in many species, including those directly impacted by the glacial cycles. Yet, understanding the ultimate consequence of such structure, as it relates to how species divergence occurs, requires demonstration that such patterns are also shared with genomic patterns of differentiation. Here we present analyses of amplified fragment length polymorphisms (AFLPs) in the montane grasshopper Melanoplus oregonensis to assess the evolutionary significance of past demographic events and associated drift-induced divergence as inferred from mtDNA. As an inhabitant of the sky islands of the northern Rocky Mountains, this species was subject to repeated and frequent shifts in species distribution in response to the many glacial cycles. Nevertheless, significant genetic structuring of M. oregonensis is evident at two different geographic and temporal scales: recent divergence associated with the recolonization of the montane meadows in individual sky islands, as well as older divergence associated with displacements into regional glacial refugia. The genomic analyses indicate that drift-induced divergence, despite the lack of long-standing geographic barriers, has significantly contributed to species divergence during the Pleistocene. Moreover, the finding that divergence associated with past demographic events involves the repartitioning of ancestral variation without significant reductions of genomic diversity has intriguing implications - namely, the further amplification of drift-induced divergence by selection.
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Affiliation(s)
- L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-1079, USA.
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20
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Johannesen J, Johannesen B, Griebeler EM, Baran I, Tunç MR, Kiefer A, Veith M. Distortion of symmetrical introgression in a hybrid zone: evidence for locus-specific selection and uni-directional range expansion. J Evol Biol 2006; 19:705-16. [PMID: 16674567 DOI: 10.1111/j.1420-9101.2005.01064.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The fate of species integrity upon natural hybridization depends on the interaction between selection and dispersal. The relative significance of these processes may be studied in the initial phase of contact before selection and gene flow reach equilibrium. Here we study a hybrid zone of two salamander species, Lyciasalamandra antalyana and Lyciasalamandra billae, at the initial phase of hybridization. We quantify the degree and mode of introgression using nuclear and mtDNA markers. The hybrid zone can be characterized as an abrupt transition zone, the central hybrid zone being only c. 400 m, but introgressed genes were traced up to 3 km. Introgression was traced in both sexes but gene flow may be slightly male-biased. Indirect evidence suggests that hybrid males are less viable than females. Introgression occurred at two levels: (1) locus-specific selection led to different allelic introgression patterns independent of species, while (2) asymmetrical species-level introgression occurred predominately from L. antalyana to L. billae due to range expansion of the former. This indicates that foreign genes can be incorporated into novel genomic environments, which in turn may contribute to the great diversity of morphological variants in Lyciasalamandra.
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Affiliation(s)
- J Johannesen
- Institut für Zoologie, Abt. V Okologie, Universität Mainz, Mainz, Germany.
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21
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Abstract
The taxonomy of fire ants has been plagued by difficulties in recognizing species on the basis of morphological characters. We surveyed allozyme markers and sequences of the mtDNA COI gene in several closely related nominal species from two areas of sympatry in the native ranges to learn whether the morphology-based delimitation of these species is supported by genetic data. We found that Solenopsis invicta and Solenopsis richteri, pest species whose distinctiveness has been debated, appear to be fully reproductively isolated at both study sites. This isolation contrasts with the extensive hybridization occurring between them in the USA, where both have been introduced. We also found strong genetic differentiation consistent with barriers to gene flow between Solenopsis quinquecuspis and the other two species. However, several lines of evidence suggest that nuclear and mitochondrial genes of S. invicta and S. richteri are introgressing into S. quinquecuspis. The latter apparently is a recently derived member of the clade that includes all three species, suggesting that there has been insufficient time for its full development of intrinsic isolating mechanisms. Finally, our discovery of genetically distinct populations within both S. invicta and S. richteri suggests the presence of previously unrecognized (cryptic) species. Their existence, together with the difficulties in developing diagnostic morphological characters for described species, imply that the group is actively radiating species and that morphological divergence generally does not keep pace with the development of reproductive isolation and neutral genetic divergence in this process.
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Affiliation(s)
- Kenneth G Ross
- Department of Entomology, University of Georgia, Athens, GA 30602-2603, USA.
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22
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Naydenov KD, Tremblay FM, Alexandrov A, Fenton NJ. Structure of Pinus sylvestris L. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: Provenance tests. BIOCHEM SYST ECOL 2005. [DOI: 10.1016/j.bse.2005.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Double MC, Peakall R, Beck NR, Cockburn A. DISPERSAL, PHILOPATRY, AND INFIDELITY: DISSECTING LOCAL GENETIC SWTRUCTURE IN SUPERB FAIRY-WRENS (MALURS CYANEUS). Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb01021.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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24
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Dissimilar patterns of Pinus heldreichii Christ. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis. BIOCHEM SYST ECOL 2005. [DOI: 10.1016/j.bse.2004.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Double MC, Peakall R, Beck NR, Cockburn A. DISPERSAL, PHILOPATRY, AND INFIDELITY: DISSECTING LOCAL GENETIC STRUCTURE IN SUPERB FAIRY-WRENS (MALURUS CYANEUS). Evolution 2005. [DOI: 10.1554/04-166] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Korpelainen H. The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes. Naturwissenschaften 2004; 91:505-18. [PMID: 15452701 DOI: 10.1007/s00114-004-0571-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. It is emphasized that varying inheritance patterns and copy numbers among different types of genomes, and the potential advantage achieved through the transfer of many cytoplasmic genes to the nucleus, have important implications for the evolution of nuclear, mitochondrial and chloroplast genomes. Cytoplasmic genes transferred to the nucleus have joined the more strictly controlled genetic system of the nuclear genome, including also sexual recombination, while genes retained within the cytoplasmic organelles can be involved in selection and drift processes both within and among individuals. Within-individual processes can be either intra- or intercellular. In the case of heteroplasmy, which is attributed to mutations or biparental inheritance, within-individual selection on cytoplasmic DNA may provide a mechanism by which the organism can adapt rapidly. The inheritance of cytoplasmic genomes is not universally maternal. The presence of a range of inheritance patterns indicates that different strategies have been adopted by different organisms. On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution.
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Affiliation(s)
- Helena Korpelainen
- Department of Applied Biology, University of Helsinki, PO Box 27, 00014, Helsinki, Finland.
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27
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Heuertz M, Vekemans X, Hausman JF, Palada M, Hardy OJ. Estimating seed vs. pollen dispersal from spatial genetic structure in the common ash. Mol Ecol 2003; 12:2483-95. [PMID: 12919486 DOI: 10.1046/j.1365-294x.2003.01923.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Spatial genetic structure was analysed with five highly polymorphic microsatellite loci in a Romanian population of common ash (Fraxinus excelsior L.), a wind-pollinated and wind-dispersed tree species occurring in mixed deciduous forests over almost all of Europe. Contributions of seed and pollen dispersal to total gene flow were investigated by analysing the pattern of decrease in kinship coefficients among pairs of individuals with geographical distance and comparing it with simulation results. Plots of kinship against the logarithm of distance were decomposed into a slope and a shape component. Simulations showed that the slope is informative about the global level of gene flow, in agreement with theoretical expectations, whereas the shape component was correlated with the relative importance of seed vs. pollen dispersal. Hence, our results indicate that insights into the relative contributions of seed and pollen dispersal to overall gene flow can be gained from details of the pattern of spatial genetic structure at biparentally inherited loci. In common ash, the slope provided an estimate of total gene dispersal in terms of Wright's neighbourhood size of Nb = 519 individuals. No precise estimate of seed vs. pollen flow could be obtained from the shape because of the stochasticity inherent to the data, but the parameter combinations that best fitted the data indicated restricted seed flow, sigmas pound 14 m, and moderate pollen flow, 70 m pound sigmap pound 140 m.
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Affiliation(s)
- M Heuertz
- Centre de Recherche Public-Gabriel Lippmann, CREBS Research Unit, avenue de la Faïencerie 162a, L-1511 Luxembourg, Luxembourg.
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Johansen AD, Latta RG. Mitochondrial haplotype distribution, seed dispersal and patterns of postglacial expansion of ponderosa pine. Mol Ecol 2003; 12:293-8. [PMID: 12492897 DOI: 10.1046/j.1365-294x.2003.01723.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Maternally inherited mtDNA in a secondary contact zone of ponderosa pine revealed a cline less than 10 km wide - much narrower than previously described. A survey of 76 populations gave no evidence either of intermixing or of a mosaic contact zone. Such sharp contact zones are consistent with diffusive range expansion, rather than long distance colonization. However, evidence for long distance seed dispersal events was found in two populations where haplotypes were observed far from their main area of occurrence. The results suggest a small number of long distance colonists with diffusive dispersal from these centres.
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Affiliation(s)
- A D Johansen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada.
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Hamilton MB, Miller JR. Comparing relative rates of pollen and seed gene flow in the island model using nuclear and organelle measures of population structure. Genetics 2002; 162:1897-909. [PMID: 12524358 PMCID: PMC1462371 DOI: 10.1093/genetics/162.4.1897] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a method for comparing nuclear and organelle population differentiation (F(ST)) in seed plants to test the hypothesis that pollen and seed gene flow rates are equal. Wright's infinite island model is used, with arbitrary levels of self-fertilization and biparental organelle inheritance. The comparison can also be applied to gene flow in animals. Since effective population sizes are smaller for organelle genomes than for nuclear genomes and organelles are often uniparentally inherited, organelle F(ST) is expected to be higher at equilibrium than nuclear F(ST) even if pollen and seed gene flow rates are equal. To reject the null hypothesis of equal seed and pollen gene flow rates, nuclear and organelle F(ST)'s must differ significantly from their expected values under this hypothesis. Finite island model simulations indicate that infinite island model expectations are not greatly biased by finite numbers of populations (>/=100 subpopulations). The power to distinguish dissimilar rates of pollen and seed gene flow depends on confidence intervals for fixation index estimates, which shrink as more subpopulations and loci are sampled. Using data from the tropical tree Corythophora alta, we rejected the null hypothesis that seed and pollen gene flow rates are equal but cannot reject the alternative hypothesis that pollen gene flow is 200 times greater than seed gene flow.
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Affiliation(s)
- Matthew B Hamilton
- Department of Biology, Georgetown University, Washington, DC 20057, USA.
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