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Tomlin CM, Rajaraman S, Sebesta JT, Scheen AC, Bendiksby M, Low YW, Salojärvi J, Michael TP, Albert VA, Lindqvist C. Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat Commun 2024; 15:3109. [PMID: 38600100 PMCID: PMC11006916 DOI: 10.1038/s41467-024-47247-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai'i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploidy event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry and drift in small and fragmented populations, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms may have radiated on isolated island chains, settings that provided one of the principal natural laboratories for Darwin's thinking about the evolutionary process.
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Affiliation(s)
- Crystal M Tomlin
- Department of Biological Sciences, University at Buffalo, New York, USA
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - Mika Bendiksby
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Todd P Michael
- The Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, New York, USA.
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2
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Baldwin BG, Wood KR, Freyman WA. Directionally biased habitat shifts and biogeographically informative cytonuclear discordance in the Hawaiian silversword alliance (Compositae). AMERICAN JOURNAL OF BOTANY 2021; 108:2015-2037. [PMID: 34694624 DOI: 10.1002/ajb2.1757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Expanded phylogenetic analyses of the Hawaiian silversword alliance (Argyroxiphium, Dubautia, Wilkesia; Compositae) were undertaken to assess evolutionary and biogeographic informativeness of cytonuclear discordance and any biases in evolutionary directionality of ecological transitions within this prominent example of adaptive radiation. METHODS Samples spanning the geographic and ecological distributions of all recognized taxa were included in phylogenetic and biogeographic analyses of nuclear ribosomal DNA (nrDNA) and cpDNA sequences. Bayesian model testing approaches were used to model ecological evolution and the evolution of nuclear chromosomal arrangements while accounting for phylogenetic uncertainty. RESULTS Cytonuclear discordance detected previously appears to reflect chloroplast capture, at least in part, with nrDNA trees being largely congruent with nuclear chromosomal structural data and fine-scale taxonomy. Comparison of biogeographic histories estimated from the posterior distributions of nrDNA and cpDNA trees, including inferred chloroplast-capture events, provides additional resolution of dispersal history, including a back-dispersal to Maui Nui from Hawai'i. A newly resolved major nrDNA clade of endemic Kaua'i taxa that mostly were described as new-to-science since the 1980s strengthens the earlier hypothesis that diversification on Kaua'i has not waned since the island began to decline in area through subsidence and erosion. Bias in habitat shifts was estimated, with transitions from dry-to-mesic or -wet and from wet-to-mesic or -bog habitats dominating diversification of the silversword alliance from a dry-adapted tarweed ancestor. CONCLUSIONS The habitat-transition biases estimated here may indicate more limited pathways of ecological evolution than proposed previously for an adaptive radiation involving such major ecological shifts.
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Affiliation(s)
- Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California, 94720-2465, USA
| | - Kenneth R Wood
- National Tropical Botanical Garden, 3530 Papalina Road, Kalaheo, Hawaii, 96741, USA
| | - William A Freyman
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building #2465, University of California, Berkeley, California, 94720-2465, USA
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3
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Jones MR, Winkler DE, Massatti R. The demographic and ecological factors shaping diversification among rare
Astragalus
species. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Matthew R. Jones
- Southwest Biological Science Center U.S. Geological Survey Flagstaff AZ USA
| | - Daniel E. Winkler
- Southwest Biological Science Center U.S. Geological Survey Moab UT USA
| | - Rob Massatti
- Southwest Biological Science Center U.S. Geological Survey Flagstaff AZ USA
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4
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Zhang L, Sun PY, Xie HK, Zhang YH, Zhang YY, Peng XM, Yang Z. Characterization of γ-Radiation-Induced DNA Polymorphisms in the M1 Population of the Japonica Rice Variety Gaogengnuo by Whole-Genome Resequencing. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420060149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Hybridization increases population variation during adaptive radiation. Proc Natl Acad Sci U S A 2019; 116:23216-23224. [PMID: 31659024 DOI: 10.1073/pnas.1913534116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin's finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.
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6
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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7
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Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y. The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha
(Myrtaceae). Mol Ecol 2017; 26:1515-1532. [DOI: 10.1111/mec.14016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Ayako Izuno
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kanehiro Kitayama
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yusuke Onoda
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yuki Tsujii
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Functional Genomics Center Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Atsushi J. Nagano
- Faculty of Agriculture; Ryukoku University; 1-5 Yokatani, Seta Ohe-cho Otsu Shiga 520-2194 Japan
- PRESTO, Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Mie N. Honjo
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
- Kihara Institute for Biological Research; Yokohama City University; 641-12 Maioka, Totsuka-ward Yokohama Kanagawa 244-0813 Japan
| | - Yuji Isagi
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
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8
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Kanapeckas KL, Vigueira CC, Ortiz A, Gettler KA, Burgos NR, Fischer AJ, Lawton-Rauh AL. Escape to Ferality: The Endoferal Origin of Weedy Rice from Crop Rice through De-Domestication. PLoS One 2016; 11:e0162676. [PMID: 27661982 PMCID: PMC5035073 DOI: 10.1371/journal.pone.0162676] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 08/26/2016] [Indexed: 11/30/2022] Open
Abstract
Domestication is the hallmark of evolution and civilization and harnesses biodiversity through selection for specific traits. In regions where domesticated lines are grown near wild relatives, congeneric sources of aggressive weedy genotypes cause major economic losses. Thus, the origins of weedy genotypes where no congeneric species occur raise questions regarding management effectiveness and evolutionary mechanisms responsible for weedy population success. Since eradication in the 1970s, California growers avoided weedy rice through continuous flood culture and zero-tolerance guidelines, preventing the import, presence, and movement of weedy seeds. In 2003, after decades of no reported presence in California, a weedy rice population was confirmed in dry-seeded fields. Our objectives were to identify the origins and establishment of this population and pinpoint possible phenotypes involved. We show that California weedy rice is derived from a different genetic source among a broad range of AA genome Oryzas and is most recently diverged from O. sativa temperate japonica cultivated in California. In contrast, other weedy rice ecotypes in North America (Southern US) originate from weedy genotypes from China near wild Oryza, and are derived through existing crop-wild relative crosses. Analyses of morphological data show that California weedy rice subgroups have phenotypes like medium-grain or gourmet cultivars, but have colored pericarp, seed shattering, and awns like wild relatives, suggesting that reversion to non-domestic or wild-like traits can occur following domestication, despite apparent fixation of domestication alleles. Additionally, these results indicate that preventive methods focused on incoming weed sources through contamination may miss burgeoning weedy genotypes that rapidly adapt, establish, and proliferate. Investigating the common and unique evolutionary mechanisms underlying global weed origins and subsequent interactions with crop relatives sheds light on how weeds evolve and addresses broader questions regarding the stability of selection during domestication and crop improvement.
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Affiliation(s)
- Kimberly L. Kanapeckas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, United States of America
| | - Cynthia C. Vigueira
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Department of Biology, High Point University, High Point, North Carolina, United States of America
| | - Aida Ortiz
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Kyle A. Gettler
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Nilda R. Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Albert J. Fischer
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Amy L. Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
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9
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Osborne OG, Chapman MA, Nevado B, Filatov DA. Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts. Genome Biol Evol 2016; 8:1038-47. [PMID: 26979797 PMCID: PMC4860686 DOI: 10.1093/gbe/evw053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 12/22/2022] Open
Abstract
The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.
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Affiliation(s)
- Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom
| | - Mark A Chapman
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Berkshire, United Kingdom Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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10
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Cheng Z, Lin J, Lin T, Xu M, Huang Z, Yang Z, Huang X, Zheng J. Genome-wide analysis of radiation-induced mutations in rice (Oryza sativa L. ssp. indica). MOLECULAR BIOSYSTEMS 2014; 10:795-805. [PMID: 24457353 DOI: 10.1039/c3mb70349e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Radiation has been efficiently used for rice germplasm innovation. However, the molecular mechanisms by which radiation induces mutations are still unclear. In this study, we performed whole genome sequencing to reveal the comprehensive mutations in rice treated with radiation. Red-1 (a rice rich in beneficial ingredients for human health) was derived from rice 9311 after γ-radiation. Solexa sequencing technology was applied to uncover the mutations. Compared with the 9311 genome, 9.19% of genome sequences were altered in the Red-1 genome. Among these alterations, there were 381,403 SNPs, 50,116 1-5 bp Indels, 1279 copy number variations, and 10,026 presence/absence variations. These alterations were located in 14,493 genes, the majority of which contained a kinase domain, leucine rich repeats, or Cyt_P450. Point mutations were the main type of variation in the Red-1 genome. Gene ontology clustering revealed that genes that are associated with cell components, binding function, catalytic activity and metabolic processes were susceptible to γ-radiation. It was also predicted that 8 mutated genes were involved in the biosynthetic pathways of beneficial products or pigment accumulation. We conclude that genome-wide analysis of mutations provides novel insights into the mechanisms by which radiation improves the beneficial ingredients in rice Red-1.
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Affiliation(s)
- Zuxin Cheng
- Crop Quality Institute, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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11
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Sommer RJ, McGaughran A. The nematode Pristionchus pacificus as a model system for integrative studies in evolutionary biology. Mol Ecol 2013; 22:2380-93. [PMID: 23530614 DOI: 10.1111/mec.12286] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 01/06/2023]
Abstract
Comprehensive studies of evolution have historically been hampered by the division among disciplines. Now, as biology moves towards an '-omics' era, it is more important than ever to tackle the evolution of function and form by considering all those research areas involved in the regulation of phenotypes. Here, we review recent attempts to establish the nematode Pristionchus pacificus as a model organism that allows integrative studies of development and evo-devo, with ecology and population genetics. Originally developed for comparative study with the nematode Caenorhabditis elegans, P. pacificus provided insight into developmental pathways including dauer formation, vulva and gonad development, chemosensation, innate immunity and neurobiology. Its subsequent discovery across a wide geographic distribution in association with scarab beetles enabled its evaluation in a biogeographic context. Development of an evolutionary field station on La Réunion Island, where P. pacificus is present in high abundance across a number of widespread habitat types, allows examination of the microfacets of evolution - processes of natural selection, adaptation and drift among populations can now be examined in this island setting. The combination of laboratory-based functional studies with fieldwork in P. pacificus has the long-term prospective to provide both proximate (mechanistic) and ultimate (evolutionary and ecological) causation and might therefore help to overcome the long-term divide between major areas in biology.
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Affiliation(s)
- Ralf J Sommer
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Tübingen, Germany.
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12
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Signatures of demography and recombination at coding genes in naturally-distributed populations of Arabidopsis lyrata subsp. petraea. PLoS One 2013; 8:e58916. [PMID: 23554957 PMCID: PMC3595216 DOI: 10.1371/journal.pone.0058916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
Demography impacts the observed standing level of genetic diversity present in populations. Distinguishing the relative impacts of demography from selection requires a baseline of expressed gene variation in naturally occurring populations. Six nuclear genes were sequenced to estimate the patterns and levels of genetic diversity in natural Arabidopsis lyrata subsp. petraea populations that differ in demographic histories since the Pleistocene. As expected, northern European populations have genetic signatures of a strong population bottleneck likely due to glaciation during the Pleistocene. Levels of diversity in the northern populations are about half of that in central European populations. Bayesian estimates of historical population size changes indicate that central European populations also have signatures of population size change since the last glacial maxima, suggesting that these populations are not as stable as previously thought. Time since divergence amongst northern European populations is higher than amongst central European populations, suggesting that the northern European populations were established before the Pleistocene and survived glaciation in small separated refugia. Estimates of demography based on expressed genes are complementary to estimates based on microsatellites and transposable elements, elucidating temporal shifts in population dynamics and confirming the importance of marker selection for tests of demography.
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13
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Dkhar J, Kumaria S, Rao SR, Tandon P. New insights into character evolution, hybridization and diversity of IndianNymphaea(Nymphaeaceae): evidence from molecular and morphological data. SYST BIODIVERS 2013. [DOI: 10.1080/14772000.2013.773949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Andrew RL, Kane NC, Baute GJ, Grassa CJ, Rieseberg LH. Recent nonhybrid origin of sunflower ecotypes in a novel habitat. Mol Ecol 2012; 22:799-813. [DOI: 10.1111/mec.12038] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 02/04/2023]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Greg J. Baute
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
| | - Christopher J. Grassa
- Department of Botany; University of British Columbia; 3529-6270 University Blvd; Vancouver; BC; Canada; V6T 1Z4
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15
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Sambatti JB, Strasburg JL, Ortiz-Barrientos D, Baack EJ, Rieseberg LH. RECONCILING EXTREMELY STRONG BARRIERS WITH HIGH LEVELS OF GENE EXCHANGE IN ANNUAL SUNFLOWERS. Evolution 2012; 66:1459-73. [DOI: 10.1111/j.1558-5646.2011.01537.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Morgan K, McGaughran A, Villate L, Herrmann M, Witte H, Bartelmes G, Rochat J, Sommer RJ. Multi locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events and rare out-crossing. Mol Ecol 2011; 21:250-66. [PMID: 22126624 DOI: 10.1111/j.1365-294x.2011.05382.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pristionchus pacificus, recently established as a model organism in evolutionary biology, is a cosmopolitan nematode that has a necromenic association with scarab beetles. The diverse array of host beetle species and habitat types occupied by P. pacificus make it a good model for investigating local adaptation to novel environments. Presence of P. pacificus on La Réunion Island, a young volcanic island with a dynamic geological history and a wide variety of ecozones, facilitates such investigation in an island biogeographic setting. Microsatellite data from 20 markers and 223 strains and mitochondrial sequence data from 272 strains reveal rich genetic diversity among La Réunion P. pacificus isolates, shaped by differentially timed introductions from diverse sources and in association with different beetle species. Distinctions between volcanic zones and between arid western and wet eastern climatic zones have likely limited westward dispersal of recently colonized lineages and maintained a genetic distinction between eastern and western clades. The highly selfing lifestyle of P. pacificus contributes to the strong fine-scale population structure detected, with each beetle host harbouring strongly differentiated assemblages of strains. Periodic out-crossing generates admixture between genetically diverse lineages, creating a diverse array of allelic combinations likely to increase the evolutionary potential of the species and facilitate adaptation to local environments and beetle hosts.
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Affiliation(s)
- Katy Morgan
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spermannstr. 37, Tübingen, Germany
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Wachowiak W, Palmé AE, Savolainen O. Speciation history of three closely related pines Pinus mugo (T.), P. uliginosa (N.) and P. sylvestris (L.). Mol Ecol 2011; 20:1729-43. [PMID: 21375633 DOI: 10.1111/j.1365-294x.2011.05037.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleotide polymorphisms at genomic regions including 17 nuclear loci, two chloroplast and one mitochondrial DNA fragments were used to study the speciation history of three pine species: dwarf mountain pine (Pinus mugo), peat-bog pine (P. uliginosa) and Scots pine (P. sylvestris). We set out to investigate three specific speciation scenarios: (I) P. uliginosa is a homoploid hybrid between the other two, (II) the species have evolved without gene flow after divergence and (III) there has been substantial gene flow between the species since their divergence. Overall, the genetic data suggest that P. mugo and P. uliginosa share the same gene pool (average net divergence of 0.0001) and that the phenotypic differences (e.g. growth form) are most likely due to very limited areas of the genome. P. mugo and P. uliginosa are more diverged from P. sylvestris than from each other (average net divergence of 0.0027 and 0.0026, respectively). The nucleotide patterns can best be explained by the divergence with migration speciation scenario, although the hybrid speciation scenario with small genomic contribution from P. sylvestris cannot be completely ruled out. We suggest that the large amount of shared polymorphisms between the pine taxa and the lack of monophyly at all loci studied between P. sylvestris and P. mugo-P. uliginosa can largely be explained by relatively recent speciation history and large effective population sizes but also by interspecific gene flow. These closely related pine taxa form an excellent system for searching for loci involved in adaptive variation as they are differentiated in phenotype and ecology but have very similar genetic background.
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Affiliation(s)
- Witold Wachowiak
- Department of Biology, University of Oulu, 90014, Oulu, Finland.
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McGlaughlin ME, Friar EA. Evolutionary diversification and geographical isolation in Dubautia laxa (Asteraceae), a widespread member of the Hawaiian silversword alliance. ANNALS OF BOTANY 2011; 107:357-70. [PMID: 21193480 PMCID: PMC3043929 DOI: 10.1093/aob/mcq252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The Hawaiian silversword alliance (Asteraceae) is one the best examples of a plant adaptive radiation, exhibiting extensive morphological and ecological diversity. No research within this group has addressed the role of geographical isolation, independent of ecological adaptation, in contributing to taxonomic diversity. The aims of this study were to examine genetic differentiation among subspecies of Dubautia laxa (Asteraceae) to determine if allopatric or sympatric populations and subspecies form distinct genetic clusters to understand better the role of geography in diversification within the alliance. METHODS Dubautia laxa is a widespread member of the Hawaiian silversword alliance, occurring on four of the five major islands of the Hawaiian archipelago, with four subspecies recognized on the basis of morphological, ecological and geographical variation. Nuclear microsatellites and plastid DNA sequence data were examined. Data were analysed using maximum-likelihood and Bayesian phylogenetic methodologies to identify unique evolutionary lineages. KEY RESULTS Plastid DNA sequence data resolved two highly divergent lineages, recognized as the Laxa and Hirsuta groups, that are more similar to other members of the Hawaiian silversword alliance than they are to each other. The Laxa group is basal to the young island species of Dubautia, whereas the Hirsuta group forms a clade with the old island lineages of Dubautia and with Argyroxiphium. The divergence between the plastid groups is supported by Bayesian microsatellite clustering analyses, but the degree of nuclear differentiation is not as great. Clear genetic differentiation is only observed between allopatric populations, both within and among islands. CONCLUSIONS These results indicate that geographical separation has aided diversification in D. laxa, whereas ecologically associated morphological differences are not associated with neutral genetic differentiation. This suggests that, despite the stunning ecological adaptation observed, geography has also played an important role in the Hawaiian silversword alliance plant adaptive radiation.
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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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20
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Cooper EA, Whittall JB, Hodges SA, Nordborg M. Genetic variation at nuclear loci fails to distinguish two morphologically distinct species of Aquilegia. PLoS One 2010; 5:e8655. [PMID: 20098727 PMCID: PMC2808223 DOI: 10.1371/journal.pone.0008655] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 12/11/2009] [Indexed: 11/18/2022] Open
Abstract
Aquilegia formosa and pubescens are two closely related species belonging to the columbine genus. Despite their morphological and ecological differences, previous studies have revealed a large degree of intercompatibility, as well as little sequence divergence between these two taxa. We compared the inter- and intraspecific patterns of variation for 9 nuclear loci, and found that the two species were practically indistinguishable at the level of DNA sequence polymorphism, indicating either very recent speciation or continued gene flow. As a comparison, we also analyzed variation at two loci across 30 other Aquilegia taxa; this revealed slightly more differentiation among taxa, which seemed best explained by geographic distance. By contrast, we found no evidence for isolation by distance on a more local geographic scale. We conclude that the extremely low levels of genetic differentiation between A. formosa and A. pubescens at neutral loci will facilitate future genome-wide scans for speciation genes.
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Affiliation(s)
- Elizabeth A Cooper
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States of America.
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21
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Strasburg JL, Rieseberg LH. How robust are "isolation with migration" analyses to violations of the im model? A simulation study. Mol Biol Evol 2009; 27:297-310. [PMID: 19793831 DOI: 10.1093/molbev/msp233] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Methods developed over the past decade have made it possible to estimate molecular demographic parameters such as effective population size, divergence time, and gene flow with unprecedented accuracy and precision. However, they make simplifying assumptions about certain aspects of the species' histories and the nature of the genetic data, and it is not clear how robust they are to violations of these assumptions. Here, we use simulated data sets to examine the effects of a number of violations of the "Isolation with Migration" (IM) model, including intralocus recombination, population structure, gene flow from an unsampled species, linkage among loci, and divergent selection, on demographic parameter estimates made using the program IMA. We also examine the effect of having data that fit a nucleotide substitution model other than the two relatively simple models available in IMA. We find that IMA estimates are generally quite robust to small to moderate violations of the IM model assumptions, comparable with what is often encountered in real-world scenarios. In particular, population structure within species, a condition encountered to some degree in virtually all species, has little effect on parameter estimates even for fairly high levels of structure. Likewise, most parameter estimates are robust to significant levels of recombination when data sets are pared down to apparently nonrecombining blocks, although substantial bias is introduced to several estimates when the entire data set with recombination is included. In contrast, a poor fit to the nucleotide substitution model can result in an increased error rate, in some cases due to a predictable bias and in other cases due to an increase in variance in parameter estimates among data sets simulated under the same conditions.
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22
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Wallace LE, Weller SG, Wagner WL, Sakai AK, Nepokroeff M. Phylogeographic patterns and demographic history of Schiedea globosa (Caryophyllaceae) on the Hawaiian Islands. AMERICAN JOURNAL OF BOTANY 2009; 96:958-967. [PMID: 21628248 DOI: 10.3732/ajb.0800243] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Geomorphological changes have been demonstrated to have had profound impacts on biodiversity, often leading to demographic expansions and contractions and allopatric divergence of taxa. We examined DNA sequence variation at two nuclear and one maternally inherited plastid locus among 10 populations of Schiedea globosa on the Hawaiian Islands to assess the primary factors shaping genetic structure, phylogeographic patterns, and the importance of geographic isolation to population divergence. Schiedea globosa has characteristics that may promote gene flow, including wind pollination and rafting of plants in ocean currents. However, we detected significant differentiation among populations on all islands except Hawaii, with the maternally inherited plastid locus having the greatest genetic structure (F(ST) = 0.81). Migration rates across all loci are less than one migrant per generation. We found evidence of growth in several populations and on the islands of Molokai and Maui, which supports population expansion associated with the formation of Maui Nui during the last glacial maximum. Similar to data for many other Hawaiian taxa, these data suggest S. globosa originated on Oahu and subsequently colonized Molokai, Maui, and Hawaii in progression. Given the high level of genetic structure, allopatric divergence will likely contribute to further divergence of populations.
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Affiliation(s)
- Lisa E Wallace
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762 USA
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23
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Geraldes A, Basset P, Gibson B, Smith KL, Harr B, Yu HT, Bulatova N, Ziv Y, Nachman MW. Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol Ecol 2009; 17:5349-63. [PMID: 19121002 DOI: 10.1111/j.1365-294x.2008.04005.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Patterns of genetic differentiation among taxa at early stages of divergence provide an opportunity to make inferences about the history of speciation. Here, we conduct a survey of DNA-sequence polymorphism and divergence at loci on the autosomes, X chromosome, Y chromosome and mitochondrial DNA in samples of Mus domesticus, M. musculus and M. castaneus. We analyzed our data under a divergence with gene flow model and estimate that the effective population size of M. castaneus is 200,000-400,000, of M. domesticus is 100,000-200,000 and of M. musculus is 60,000-120,000. These data also suggest that these species started to diverge approximately 500,000 years ago. Consistent with this recent divergence, we observed considerable variation in the genealogical patterns among loci. For some loci, all alleles within each species formed a monophyletic group, while at other loci, species were intermingled on the phylogeny of alleles. This intermingling probably reflects both incomplete lineage sorting and gene flow after divergence. Likelihood ratio tests rejected a strict allopatric model with no gene flow in comparisons between each pair of species. Gene flow was asymmetric: no gene flow was detected into M. domesticus, while significant gene flow was detected into both M. castaneus and M. musculus. Finally, most of the gene flow occurred at autosomal loci, resulting in a significantly higher ratio of fixed differences to polymorphisms at the X and Y chromosomes relative to autosomes in some comparisons, or just the X chromosome in others, emphasizing the important role of the sex chromosomes in general and the X chromosome in particular in speciation.
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Affiliation(s)
- Armando Geraldes
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
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Cantone C, Sica M, Gaudio L, Aceto S. The OrcPI locus: genomic organization, expression pattern, and noncoding regions variability in Orchis italica (Orchidaceae) and related species. Gene 2008; 434:9-15. [PMID: 19162144 DOI: 10.1016/j.gene.2008.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 11/11/2008] [Accepted: 12/11/2008] [Indexed: 11/19/2022]
Abstract
OrcPI is a class B MADS-box gene of Orchis italica (Orchidaceae), homologous of the PISTILLATA/GLOBOSA gene isolated in Arabidopsis and Antirrhinum. Its role in determining petals and stamens is conserved in orchids, where it seems to be involved also in other functions, such as flower longevity and ovary development. The present study reports the genomic characterization of the OrcPI locus in O. italica including coding and noncoding regions (introns, 5'- and 3' untranslated regions, and putative promoter). Nucleotide polymorphism distribution confirmed that this gene is subjected to different evolutionary forces, phylogenetic and distance analyses demonstrated that OrcPI is a useful nuclear marker at low taxonomic level in orchids. The expression pattern analysis showed that OrcPI transcripts are present in all the floral structures, undetected in the vegetative tissues, and decreased in the natural senescent flower. Finally, micro-RNAs putative target sites were identified within the OrcPI gene, conserved among orchids.
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Affiliation(s)
- Carmela Cantone
- Department of Biological Sciences, Section of Genetics and Molecular Biology, University of Naples Federico II, 80134 Napoli, Italy
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25
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Strasburg JL, Rieseberg LH. Molecular demographic history of the annual sunflowers Helianthus annuus and H. petiolaris--large effective population sizes and rates of long-term gene flow. Evolution 2008; 62:1936-50. [PMID: 18462213 DOI: 10.1111/j.1558-5646.2008.00415.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hybridization between distinct species may lead to introgression of genes across species boundaries, and this pattern can potentially persist for extended periods as long as selection at some loci or genomic regions prevents thorough mixing of gene pools. However, very few reliable estimates of long-term levels of effective migration are available between hybridizing species throughout their history. Accurate estimates of divergence dates and levels of gene flow require data from multiple unlinked loci as well as an analytical framework that can distinguish between lineage sorting and gene flow and incorporate the effects of demographic changes within each species. Here we use sequence data from 18 anonymous nuclear loci in two broadly sympatric sunflower species, Helianthus annuus and H. petiolaris, analyzed within an "isolation with migration" framework to make genome-wide estimates of the ages of these two species, long-term rates of gene flow between them, and effective population sizes and historical patterns of population growth. Our results indicate that H. annuus and H. petiolaris are approximately one million years old and have exchanged genes at a surprisingly high rate (long-term N(ef)m estimates of approximately 0.5 in each direction), with somewhat higher rates of introgression from H. annuus into H. petiolaris than vice versa. In addition, each species has undergone dramatic population expansion since divergence, and both species have among the highest levels of genetic diversity reported for flowering plants. Our results provide the most comprehensive estimate to date of long-term patterns of gene flow and historical demography in a nonmodel plant system, and they indicate that species integrity can be maintained even in the face of extensive gene flow over a prolonged period.
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Affiliation(s)
- Jared L Strasburg
- Department of Biology, Indiana University, 915 E. 3rd Street #150, Bloomington, Indiana 47405, USA.
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Salazar C, Jiggins CD, Taylor JE, Kronforst MR, Linares M. Gene flow and the genealogical history of Heliconius heurippa. BMC Evol Biol 2008; 8:132. [PMID: 18454858 PMCID: PMC2391162 DOI: 10.1186/1471-2148-8-132] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 05/02/2008] [Indexed: 12/05/2022] Open
Abstract
Background The neotropical butterfly Heliconius heurippa has a hybrid colour pattern, which also contributes to reproductive isolation, making it a likely example of hybrid speciation. Here we used phylogenetic and coalescent-based analyses of multilocus sequence data to investigate the origin of H. heurippa. Results We sequenced a mitochondrial region (CoI and CoII), a sex-linked locus (Tpi) and two autosomal loci (w and sd) from H. heurippa and the putative parental species, H. cydno and H. melpomene. These were analysed in combination with data from two previously sequenced autosomal loci, Dll and Inv. H. heurippa was monophyletic at mtDNA and Tpi, but showed a shared distribution of alleles derived from both parental lineages at all four autosomal loci. Estimates of genetic differentiation showed that H. heurippa is closer to H. cydno at mtDNA and three autosomal loci, intermediate at Tpi, and closer to H. melpomene at Dll. Using coalescent simulations with the Isolation-Migration model (IM), we attempted to establish the incidence of gene flow in the origin of H. heurippa. This analysis suggested that ongoing introgression is frequent between all three species and variable in extent between loci. Conclusion Introgression, which is a necessary precursor of hybrid speciation, seems to have also blurred the coalescent history of these species. The origin of Heliconius heurippa may have been restricted to introgression of few colour pattern genes from H. melpomene into the H. cydno genome, with little evidence of genomic mosaicism.
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Affiliation(s)
- Camilo Salazar
- Instituto de Genética, Departamento de Ciencias Biologicas, Universidad de los Andes, P.O. Box 4976, Bogotá, Colombia.
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Lawton-Rauh A. Demographic processes shaping genetic variation. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:103-109. [PMID: 18353707 DOI: 10.1016/j.pbi.2008.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2008] [Revised: 02/14/2008] [Accepted: 02/15/2008] [Indexed: 05/26/2023]
Abstract
Demographic processes modulate genome-wide levels and patterns of genetic variation via impacting effective population size independently of natural selection. Such processes include the perturbation of population distributions from external events shaping habitat landscape and internal factors shaping the probability of contemporaneous alleles in a population (coalescence). Several patterns have recently emerged: spatial and temporal heterogeneity in population structure have different influences on the persistence of new mutations and genetic variation, multi-locus analyses indicate that gene flow continues to occur during speciation and the incorporation of demographic processes into models of molecular evolution and association genetics approaches has improved statistical power to detect deviations from neutral-equilibrium expectations and decreased false positive rates.
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Affiliation(s)
- Amy Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, 100 Jordan Hall, Clemson, SC 29634-0318, USA.
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Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon). Genetics 2008; 178:339-50. [PMID: 18202377 DOI: 10.1534/genetics.107.081810] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a multilocus sequencing study to assess patterns of polymorphism and divergence in the closely related wild tomato species, Solanum peruvianum and S. chilense (Solanum section Lycopersicon, Solanaceae). The data set comprises seven mapped nuclear loci (approximately 9.3 kb of analyzed sequence across loci) and four local population samples per species that cover much of the species' range (between 80 and 88 sequenced alleles across both species). We employ the analytical framework of divergence population genetics (DPG) in evaluating the utility of the "isolation" model of speciation to explain observed patterns of polymorphism and divergence. Whereas the isolation model is not rejected by goodness-of-fit criteria established via coalescent simulations, patterns of intragenic linkage disequilibrium provide evidence for postdivergence gene flow at two of the seven loci. These results suggest that speciation occurred under residual gene flow, implying that natural selection is one of the evolutionary forces driving the divergence of these tomato species. This inference is fully consistent with their recent divergence, conservatively estimated to be <or=0.55 million years. We discuss possible biases in the demographic parameter estimates due to the current restriction of DPG algorithms to panmictic species.
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Friar EA, Cruse-Sanders JM, McGlaughlin ME. Gene flow in Dubautia arborea and D. ciliolata: the roles of ecology and isolation by distance in maintaining species boundaries despite ongoing hybridization. Mol Ecol 2008; 16:4028-38. [PMID: 17894757 DOI: 10.1111/j.1365-294x.2007.03423.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The relative roles of gene flow and natural selection in maintaining species differentiation have been a subject of debate for some time. The traditional view is that gene flow constrains adaptive divergence and maintains species cohesiveness. Alternatively, ecological speciation posits that the reverse is true: that adaptive ecological differentiation constrains gene flow. In this study, we examine gene flow and population differentiation among populations of two species of the Hawaiian silversword alliance, Dubautia arborea and D. ciliolata. We compare divergence in putatively neutral microsatellite markers with divergence in leaf morphometric traits, which may be selectively important or physiologically linked to selectively important traits. Gene flow between populations was found to be significant in only one of the two species, D. arborea. Leaf morphometric differentiation between species was significant, though not among populations within species. No evidence of effective genetic introgression was observed between apparently 'pure' populations of these species. Gene flow as measured by microsatellites was not correlated with geographic distance between populations, but was correlated with the linear placement of the widest part of the leaf. Because these two species are interfertile, as demonstrated by the presence of active hybrid zone, the lack of genetic introgression and the maintenance of species boundaries may be associated with natural selection on differential habitat.
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Affiliation(s)
- E A Friar
- Rancho Santa Ana Botanic Garden, 1500 N. College Ave. Claremont, CA 91711, USA.
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31
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Lawton-Rauh A, Friar EA, Remington DL. Collective evolution processes and the tempo of lineage divergence in the Hawaiian silversword alliance adaptive radiation (Heliantheae, Asteraceae). Mol Ecol 2007; 16:3993-4. [PMID: 17868289 DOI: 10.1111/j.1365-294x.2007.03521.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- A Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, 101 Jordan Hall, Clemson, SC 29634-0318, USA.
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